Psyllid ID: psy7959

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-
Protein Sequence
MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQVPSP
Secondary Structure (PSIPRED)
ccccEEEEEEEccccccccccccEEEEEcccccccHHHHHHcccccccccccEEEEEEccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEEEEEccccccccEEEEEEEccccccEEEEEEccccccccccccEEEEEcHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
MRGEINVITATisfgmgidrqNVRFVVhwgmpssipayyqesgragrdgLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQVPSP
Flexible Loop (DISEMBL)
MRGEINVITatisfgmgidRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHsehskksleyvIKTDTSTKREQLELKFKNYLSMLEYCEQVPSP
Low Complexity Region (SEG)
MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQVPSP
Disordered region (IsUnstruct)
****INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDT****EQLELKFKNYLSMLEYC******
Disordered Region (DISOPRED)
*RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLE********************YLSMLEYCEQV***
Disordered Region (DISEMBL)
MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQVPSP
Disordered Region (DISPRO)
*RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQVP**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQVPSP
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	101	2.2.26 [Sep-21-2011]
P54132	1417	Bloom syndrome protein OS	no	N/A	0.910	0.064	0.467	8e-20
O18017	988	Bloom syndrome protein ho	no	N/A	0.930	0.095	0.463	1e-19
Q9DEY9	1364	Bloom syndrome protein ho	N/A	N/A	0.960	0.071	0.432	1e-19
O94762	991	ATP-dependent DNA helicas	no	N/A	0.970	0.098	0.403	2e-19
P35187	1447	ATP-dependent helicase SG	yes	N/A	0.940	0.065	0.442	5e-19
O88700	1416	Bloom syndrome protein ho	no	N/A	0.910	0.064	0.456	2e-18
Q9I920	1142	Bloom syndrome protein ho	no	N/A	0.910	0.080	0.445	1e-17
Q9VGI8	1487	Bloom syndrome protein ho	no	N/A	0.970	0.065	0.377	1e-16
A8WK63	618	Putative ATP-dependent DN	N/A	N/A	0.554	0.090	0.642	1e-16
Q9FT70	1150	ATP-dependent DNA helicas	yes	N/A	0.950	0.083	0.385	3e-16

>sp|P54132|BLM_HUMAN Bloom syndrome protein OS=Homo sapiens GN=BLM PE=1 SV=1

 Score = 95.5 bits (236), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 43/92 (46%), Positives = 59/92 (64%)

Query: 7    VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
            VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  S+C ++++ H    L
Sbjct: 942  VICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCLLFYTYHDVTRL 1001

Query: 67   EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
            + +I  +        E  F N  SM+ YCE +
Sbjct: 1002 KRLIMMEKDGNHHTRETHFNNLYSMVHYCENI 1033

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|O18017|BLM_CAEEL Bloom syndrome protein homolog OS=Caenorhabditis elegans GN=him-6 PE=2 SV=2

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 44/95 (46%), Positives = 63/95 (66%), Gaps = 1/95 (1%)

Query: 4   EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK 63
           + +VI ATI+FGMGID+ +VRFV+H+ +P SI  YYQE+GRAGRDG+ SYC + +S H  
Sbjct: 519 KFDVICATIAFGMGIDKPDVRFVIHYSLPKSIEGYYQETGRAGRDGMPSYCLMLYSYHDS 578

Query: 64  KSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
             L  +I+   +T   +  +   N L ++ YCE V
Sbjct: 579 IRLRRMIEEGNTTTGVR-SMHLNNVLQVVAYCENV 612

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9DEY9|BLM_XENLA Bloom syndrome protein homolog OS=Xenopus laevis GN=blm PE=2 SV=1

 Score = 95.1 bits (235), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 42/97 (43%), Positives = 61/97 (62%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH 61
           + +  VI ATI+FGMGID+ +VR+V+H  +P S+  YYQESGRAGRDG  S+C +++S H
Sbjct: 889 QDDCQVICATIAFGMGIDKPDVRYVIHASLPKSVEGYYQESGRAGRDGETSHCLLFYSYH 948

Query: 62  SKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
               +  +I+ +        +  F N  SM+ YCE V
Sbjct: 949 DVTRIRRLIQMEKDGNSHTKQTHFNNLYSMVHYCENV 985

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O94762|RECQ5_HUMAN ATP-dependent DNA helicase Q5 OS=Homo sapiens GN=RECQL5 PE=1 SV=2

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/104 (40%), Positives = 69/104 (66%), Gaps = 6/104 (5%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG  S+CR+Y+S 
Sbjct: 306 MEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSR 365

Query: 61  HSKKSLEYVIKTDTSTKREQLELKFKN------YLSMLEYCEQV 98
           + +  + ++I+ + +  +E+   K  +      + +++ +CE++
Sbjct: 366 NDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEEL 409

May have an important role in DNA metabolism.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P35187|SGS1_YEAST ATP-dependent helicase SGS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SGS1 PE=1 SV=1

 Score = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 42/95 (44%), Positives = 61/95 (64%)

Query: 4    EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK 63
            EI VI AT++FGMGID+ +VRFV H+ +P ++  YYQE+GRAGRDG  SYC  Y S    
Sbjct: 950  EIQVICATVAFGMGIDKPDVRFVYHFTVPRTLEGYYQETGRAGRDGNYSYCITYFSFRDI 1009

Query: 64   KSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
            ++++ +I+ D +  RE  E        ++ YC+ V
Sbjct: 1010 RTMQTMIQKDKNLDRENKEKHLNKLQQVMAYCDNV 1044

Interacts with topoisomerases II and TOP3. Could create a deleterious topological substrate that TOP3 preferentially resolves. The TOP3-SGS1 protein complex may function as a eukaryotic reverse gyrase introducing positive supercoils into extrachromosomal ribosomal DNA rings. Together with topoisomerase II has a role in chromosomal segregation. Maintains rDNA structure where it has a role in re-starting stalled replication forks.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|O88700|BLM_MOUSE Bloom syndrome protein homolog OS=Mus musculus GN=Blm PE=1 SV=1

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/92 (45%), Positives = 58/92 (63%)

Query: 7    VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
            VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  S+C ++++ H    L
Sbjct: 950  VICATIAFGMGIDKPDVRFVIHASLPKSMEGYYQESGRAGRDGEISHCVLFYTYHDVTRL 1009

Query: 67   EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
            + +I  +        E    N  SM+ YCE +
Sbjct: 1010 KRLIMMEKDGNYHTKETHVNNLYSMVHYCENI 1041

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9I920|BLM_CHICK Bloom syndrome protein homolog (Fragment) OS=Gallus gallus GN=BLM PE=2 SV=1

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/92 (44%), Positives = 56/92 (60%)

Query: 7   VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
           VI ATI+FGMGID+ +VR+V+H  +P S+  YY ESGRAGRDG  S+C +++S      L
Sbjct: 672 VICATIAFGMGIDKPDVRYVIHASLPKSVEGYYHESGRAGRDGEMSHCLLFYSYSDVTRL 731

Query: 67  EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
             +I  +        +  F N  SM+ YCE V
Sbjct: 732 RRLILMEKDGNSHTRQTHFNNLYSMVHYCENV 763

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9VGI8|BLM_DROME Bloom syndrome protein homolog OS=Drosophila melanogaster GN=mus309 PE=1 SV=1

 Score = 85.1 bits (209), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/98 (37%), Positives = 64/98 (65%)

Query: 1    MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
            + G++ VI AT++FGMGID+ +VRFV+H+ +P SI  YYQE+GRAGRDG  + C +Y++ 
Sbjct: 1005 LTGKMRVICATVAFGMGIDKPDVRFVLHYSLPKSIEGYYQEAGRAGRDGDVADCILYYNY 1064

Query: 61   HSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
                 ++ ++ +D + +    ++   N   ++ YCE +
Sbjct: 1065 SDMLRIKKMLDSDKALQYNVKKIHVDNLYRIVGYCENL 1102

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|A8WK63|RECQ1_CAEBR Putative ATP-dependent DNA helicase Q1 OS=Caenorhabditis briggsae GN=CBG24191 PE=3 SV=1

 Score = 85.1 bits (209), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 36/56 (64%), Positives = 45/56 (80%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH 58
           GEI VI AT++FGMGID+ +VRFV+H  +P SI  YYQESGRAGRDGL + C +Y+
Sbjct: 358 GEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQESGRAGRDGLPATCILYY 413

DNA helicase that may play a role in the repair of DNA that is damaged by ultraviolet light or other mutagens. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.

Caenorhabditis briggsae (taxid: 6238)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9FT70|RQL4B_ARATH ATP-dependent DNA helicase Q-like 4B OS=Arabidopsis thaliana GN=RECQL4B PE=2 SV=1

 Score = 83.6 bits (205), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 42/109 (38%), Positives = 63/109 (57%), Gaps = 13/109 (11%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH 61
           + EIN+I AT++FGMGI++ +VRFV+H  +P SI  Y+QE GRAGRDG +S C +Y+S  
Sbjct: 737 KDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYT 796

Query: 62  SKKSLEYVIKTD-------------TSTKREQLELKFKNYLSMLEYCEQ 97
               ++++I                 ++    LE   +N L M+ YCE 
Sbjct: 797 DYIRVKHMISQGGLGQGQMKMGYNCKASSGRMLETNTENLLRMVSYCEN 845

3'-5' DNA helicase that may play a role in the repair of DNA (By similarity). Required to promote but not to suppress crossovers.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	101
328713283	1075	PREDICTED: ATP-dependent DNA helicase Q5	0.970	0.091	0.553	1e-28
242008765	853	DNA helicase recq5, putative [Pediculus	0.970	0.114	0.553	2e-26
427788647	924	Putative atp-dependent dna helicase [Rhi	0.940	0.102	0.56	5e-25
321476989	997	DNA helicase RecQ5 [Daphnia pulex]	0.950	0.096	0.514	6e-24
312373020	1482	hypothetical protein AND_18377 [Anophele	0.970	0.066	0.504	1e-23
157110525	846	DNA helicase recq5 [Aedes aegypti] gi|10	0.950	0.113	0.495	2e-23
347965591	1523	AGAP001255-PA [Anopheles gambiae str. PE	0.950	0.063	0.495	3e-23
170039315	859	ATP-dependent DNA helicase recQ [Culex q	0.950	0.111	0.457	4e-23
340377955	906	PREDICTED: ATP-dependent DNA helicase Q5	0.970	0.108	0.463	6e-23
198433869	1114	PREDICTED: similar to RecQ protein-like	0.930	0.084	0.471	3e-22

>gi|328713283|ref|XP_001944776.2| PREDICTED: ATP-dependent DNA helicase Q5-like [Acyrthosiphon pisum]

 Score =  130 bits (326), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 57/103 (55%), Positives = 78/103 (75%), Gaps = 5/103 (4%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G I VITAT+SFGMGID+  VRFV+HWG+PSSIPAYYQESGRAGRDG  + CRIYHS+
Sbjct: 320 MSGHIQVITATVSFGMGIDKATVRFVIHWGIPSSIPAYYQESGRAGRDGKLARCRIYHSK 379

Query: 61  HSKKSLEYVIKT-----DTSTKREQLELKFKNYLSMLEYCEQV 98
            +K SL++++K+      T  K+++ +  +  +L M+++CE V
Sbjct: 380 QAKNSLDFILKSAITQAKTQDKQKKAKGSYSMFLKMIQFCESV 422

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242008765|ref|XP_002425170.1| DNA helicase recq5, putative [Pediculus humanus corporis] gi|212508872|gb|EEB12432.1| DNA helicase recq5, putative [Pediculus humanus corporis]

 Score =  123 bits (308), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 57/103 (55%), Positives = 77/103 (74%), Gaps = 5/103 (4%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G+  VI+AT+SFGMGID+  VRFVVHWGMP S+ AYYQESGRAGRDGL S CRIY+S+
Sbjct: 298 MSGKCPVISATVSFGMGIDKAAVRFVVHWGMPQSVAAYYQESGRAGRDGLPSLCRIYYSK 357

Query: 61  HSKKSLEYVIKTD-----TSTKREQLELKFKNYLSMLEYCEQV 98
             +  +++++KT+     T  K E+ +L +K+Y  M+ YCE+V
Sbjct: 358 IERDRVDFILKTEARKAKTEDKVEKAKLAYKSYERMVRYCEEV 400

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427788647|gb|JAA59775.1| Putative atp-dependent dna helicase [Rhipicephalus pulchellus]

 Score =  118 bits (295), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 56/100 (56%), Positives = 71/100 (71%), Gaps = 5/100 (5%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH 61
           RG++ +I AT+SFGMG+DR  VRFV HW +P SIPAYYQESGRAGRDG  SYCRIY+S  
Sbjct: 321 RGQVPIIAATVSFGMGVDRAMVRFVAHWSVPQSIPAYYQESGRAGRDGRPSYCRIYYSRK 380

Query: 62  SKKSLEYVIKTD---TSTKREQL--ELKFKNYLSMLEYCE 96
            +KS+ Y++K D     TKR ++  E+  K +  M  YCE
Sbjct: 381 DRKSITYLLKRDEQGAKTKRAKIVAEMATKAFEKMASYCE 420

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321476989|gb|EFX87948.1| DNA helicase RecQ5 [Daphnia pulex]

 Score =  114 bits (286), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 53/103 (51%), Positives = 71/103 (68%), Gaps = 7/103 (6%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G+I VITATISFGMG+D+ +VRFV HW MP S+  YYQESGRAGRDG  S CRI++S 
Sbjct: 303 MTGKIPVITATISFGMGVDKASVRFVAHWCMPQSVAGYYQESGRAGRDGQPSGCRIFYSR 362

Query: 61  HSKKSLEYVIKTDTSTK-------REQLELKFKNYLSMLEYCE 96
             + ++E+++K D S K        +Q +   K+Y +M+ YCE
Sbjct: 363 KERNAVEFLLKQDVSKKTKKGAKYEKQAKQMMKSYEAMVRYCE 405

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312373020|gb|EFR20851.1| hypothetical protein AND_18377 [Anopheles darlingi]

 Score =  113 bits (282), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 69/103 (66%), Gaps = 5/103 (4%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G+   I ATISFGMG+D+ +VRFVVHW  P ++ AYYQESGRAGRDG +SYCRIYH  
Sbjct: 446 MEGKYVAIAATISFGMGVDKGSVRFVVHWDNPQNVAAYYQESGRAGRDGKKSYCRIYHCR 505

Query: 61  HSKKSLEYVIKTD-----TSTKREQLELKFKNYLSMLEYCEQV 98
              KS+++++K D      + K    +   KN+  M+E+CE V
Sbjct: 506 DQCKSIDFLLKQDLQKSKDTGKEAAAKQAIKNFEKMIEFCETV 548

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157110525|ref|XP_001651140.1| DNA helicase recq5 [Aedes aegypti] gi|108878672|gb|EAT42897.1| AAEL005597-PA [Aedes aegypti]

 Score =  113 bits (282), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 50/101 (49%), Positives = 73/101 (72%), Gaps = 5/101 (4%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G+   I+ATISFGMG+D+ +VRFV+HW +P S+ +YYQESGRAGRDG +S+CR+YH  
Sbjct: 532 MDGKYAAISATISFGMGVDKGSVRFVIHWDIPQSVASYYQESGRAGRDGKKSFCRVYHCR 591

Query: 61  HSKKSLEYVI-----KTDTSTKREQLELKFKNYLSMLEYCE 96
              KS+++++     KT  S K E+ +L  KN+  +++YCE
Sbjct: 592 DQCKSIDFLLQQDLQKTKGSAKEEKAKLAVKNFEKIVQYCE 632

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347965591|ref|XP_001238556.3| AGAP001255-PA [Anopheles gambiae str. PEST] gi|333470440|gb|EAU75726.3| AGAP001255-PA [Anopheles gambiae str. PEST]

 Score =  112 bits (280), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 50/101 (49%), Positives = 69/101 (68%), Gaps = 5/101 (4%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G+   I ATISFGMG+D+ +VRFV+HW  P ++ AYYQESGRAGRDG +S+CRIYH  
Sbjct: 471 MEGKYVAIAATISFGMGVDKGSVRFVIHWDNPQNVAAYYQESGRAGRDGKKSFCRIYHCR 530

Query: 61  HSKKSLEYVIKTD-----TSTKREQLELKFKNYLSMLEYCE 96
              KS+E++++ D      + K E  +   KN+  M+E+CE
Sbjct: 531 DGCKSIEFLLRQDLQKSKDTPKEESAKQAVKNFEKMVEFCE 571

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170039315|ref|XP_001847485.1| ATP-dependent DNA helicase recQ [Culex quinquefasciatus] gi|167862886|gb|EDS26269.1| ATP-dependent DNA helicase recQ [Culex quinquefasciatus]

 Score =  111 bits (278), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 48/105 (45%), Positives = 73/105 (69%), Gaps = 9/105 (8%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M G+  VI+ATISFGMG+D+ +VRFV+HW +P ++ +YYQESGRAGRDG +SYCRIYH  
Sbjct: 536 MDGKYPVISATISFGMGVDKGSVRFVIHWDIPQNVASYYQESGRAGRDGKKSYCRIYHCR 595

Query: 61  HSKKSLEYVIKTD---------TSTKREQLELKFKNYLSMLEYCE 96
              KS++++++ D            K ++ +L  KN+  ++++CE
Sbjct: 596 EQCKSIDFLLRQDLGKSKDKDGKEDKHDKAKLAVKNFEKIVDFCE 640

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340377955|ref|XP_003387494.1| PREDICTED: ATP-dependent DNA helicase Q5-like [Amphimedon queenslandica]

 Score =  111 bits (277), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 51/110 (46%), Positives = 76/110 (69%), Gaps = 12/110 (10%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           M+G + +I ATISFGMG+D+ NVRFVVHW +P  I AYYQESGRAGRDGL++YCRIY+S 
Sbjct: 299 MKGVVPIIVATISFGMGVDKANVRFVVHWTLPKGIEAYYQESGRAGRDGLKAYCRIYYSR 358

Query: 61  HSKKSLEYVIKTDTS---TKREQLELKF---------KNYLSMLEYCEQV 98
             +  L ++++ + S   TK+ + + K          K++ ++++YCE+ 
Sbjct: 359 FDRDQLLFLLQKEISEKETKKGKSQFKSASRSKEATEKSFETLVKYCEEA 408

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|198433869|ref|XP_002126337.1| PREDICTED: similar to RecQ protein-like 5 [Ciona intestinalis]

 Score =  108 bits (271), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 49/104 (47%), Positives = 70/104 (67%), Gaps = 10/104 (9%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS 62
           G++ +I AT+SFGMG+D+ NVRFV HW +P S+  YYQESGRAGRDG QS CR+Y+S   
Sbjct: 306 GKVPIIVATVSFGMGVDKSNVRFVAHWTIPKSMAGYYQESGRAGRDGEQSLCRLYYSRTD 365

Query: 63  KKSLEYVIKTDTSTKR--EQLELKFK--------NYLSMLEYCE 96
           + ++ ++I+ D   KR   + E +FK        N+ S++ YCE
Sbjct: 366 RNNINFLIRKDFDRKRAKSKSETQFKKHVQAITENFSSLVNYCE 409

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

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	101
FB|FBgn0027375	1058	RecQ5 "homolog of RecQ" [Droso	0.960	0.091	0.475	3.4e-21
UNIPROTKB|I3LFW3	432	RECQL5 "Uncharacterized protei	0.792	0.185	0.5	2.4e-19
UNIPROTKB|F1NT69	451	F1NT69 "Uncharacterized protei	0.970	0.217	0.438	1.3e-18
WB|WBGene00004322	809	rcq-5 [Caenorhabditis elegans	0.950	0.118	0.427	2.2e-18
UNIPROTKB|J3KTQ2	480	RECQL5 "ATP-dependent DNA heli	0.792	0.166	0.487	2.6e-18
UNIPROTKB|E2RS76	1407	BLM "Uncharacterized protein"	0.910	0.065	0.478	3.8e-18
UNIPROTKB|J9PB86	1420	BLM "Uncharacterized protein"	0.910	0.064	0.478	3.9e-18
WB|WBGene00001865	988	him-6 [Caenorhabditis elegans	0.930	0.095	0.463	5e-18
UNIPROTKB|E1BQ04	1417	BLM "Uncharacterized protein"	0.910	0.064	0.478	5e-18
UNIPROTKB|F1RMJ2	511	BLM "Uncharacterized protein"	0.910	0.180	0.467	5.1e-18

FB|FBgn0027375 RecQ5 "homolog of RecQ" [Drosophila melanogaster (taxid:7227)]

 Score = 261 (96.9 bits), Expect = 3.4e-21, P = 3.4e-21
 Identities = 49/103 (47%), Positives = 70/103 (67%)

Query:     1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             MRG+  +I AT SFGMG+D+ +VRFV+HW +P ++ AYYQESGRAGRDGLQSYCR+Y+  
Sbjct:   303 MRGDQPIICATNSFGMGVDKPSVRFVIHWDVPQNVAAYYQESGRAGRDGLQSYCRLYYGR 362

Query:    61 HSKKSLEYVIKTDTSTKR-----EQL-ELKFKNYLSMLEYCEQ 97
                +S+ ++++ D    R     E L E   K +  + E+CE+
Sbjct:   363 EDVRSIRFLLQNDAHRARGRGDKELLTERAIKQFEKITEFCER 405

GO:0004003 "ATP-dependent DNA helicase activity" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0003678 "DNA helicase activity" evidence=ISS

GO:0004386 "helicase activity" evidence=ISS

GO:0017116 "single-stranded DNA-dependent ATP-dependent DNA helicase activity" evidence=IDA

GO:0003924 "GTPase activity" evidence=IDA

GO:0005525 "GTP binding" evidence=IDA

GO:0006310 "DNA recombination" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IDA;IMP

GO:0045930 "negative regulation of mitotic cell cycle" evidence=IMP

GO:0010165 "response to X-ray" evidence=IDA

GO:0045002 "double-strand break repair via single-strand annealing" evidence=IMP

GO:0090007 "regulation of mitotic anaphase" evidence=IDA

UNIPROTKB|I3LFW3 RECQL5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 236 (88.1 bits), Expect = 2.4e-19, P = 2.4e-19
 Identities = 40/80 (50%), Positives = 59/80 (73%)

Query:     1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             M G++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG  S+CR+Y+S 
Sbjct:   302 MEGKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGRPSWCRLYYSR 361

Query:    61 HSKKSLEYVIKTDTSTKREQ 80
             + +  + ++I+ + +  +E+
Sbjct:   362 NDRDQVSFLIRKEVAKLQEK 381

GO:0031965 "nuclear membrane" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NT69 F1NT69 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 230 (86.0 bits), Expect = 1.3e-18, P = 1.3e-18
 Identities = 46/105 (43%), Positives = 70/105 (66%)

Query:     1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             M  +I VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG  S CR+Y+S 
Sbjct:   312 MEEKIPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSCCRLYYSR 371

Query:    61 HSKKSLEYVIKTDTSTKREQ---LELKFKNYLS----MLEYCEQV 98
             + +  + ++IK + S  +E+   L+   K+ ++    ++ +CE++
Sbjct:   372 NDRDQVSFLIKKELSKIQEKKGTLKESDKSVMTAFDAIVSFCEEL 416

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

WB|WBGene00004322 rcq-5 [Caenorhabditis elegans (taxid:6239)]

 Score = 233 (87.1 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 47/110 (42%), Positives = 70/110 (63%)

Query:     1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             M  EI V+ AT++FGMGID+ +VR V+HW    ++  YYQE+GRAGRDG +SYCRIY+S+
Sbjct:   461 MNNEIPVVAATVAFGMGIDKPDVRAVIHWSPSQNLAGYYQEAGRAGRDGKRSYCRIYYSK 520

Query:    61 HSKKSLEYVIKTDTSTKREQL----------ELKFKNYLS----MLEYCE 96
               K +L +++  + +  RE+           E++ K+  +    MLEYCE
Sbjct:   521 QDKNALNFLVSGELAKLREKAKKNNAEGEKAEMQIKSIQTGLAKMLEYCE 570

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0006974 "response to DNA damage stimulus" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

UNIPROTKB|J3KTQ2 RECQL5 "ATP-dependent DNA helicase Q5" [Homo sapiens (taxid:9606)]

 Score = 228 (85.3 bits), Expect = 2.6e-18, P = 2.6e-18
 Identities = 39/80 (48%), Positives = 58/80 (72%)

Query:     1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             M  ++ VI ATISFGMG+D+ NVRFV HW +  S+  YYQESGRAGRDG  S+CR+Y+S 
Sbjct:   306 MEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSR 365

Query:    61 HSKKSLEYVIKTDTSTKREQ 80
             + +  + ++I+ + +  +E+
Sbjct:   366 NDRDQVSFLIRKEVAKLQEK 385

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E2RS76 BLM "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 234 (87.4 bits), Expect = 3.8e-18, P = 3.8e-18
 Identities = 44/92 (47%), Positives = 60/92 (65%)

Query:     7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
             VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  S+C ++++ H    L
Sbjct:   931 VICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCLLFYTYHDVTRL 990

Query:    67 EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
             + +I  +    R   E  F N  SM+ YCE +
Sbjct:   991 KRLILMEKDGNRHTRETHFNNLYSMVHYCENI 1022

GO:0051880 "G-quadruplex DNA binding" evidence=IEA

GO:0051782 "negative regulation of cell division" evidence=IEA

GO:0051259 "protein oligomerization" evidence=IEA

GO:0051098 "regulation of binding" evidence=IEA

GO:0046641 "positive regulation of alpha-beta T cell proliferation" evidence=IEA

GO:0046632 "alpha-beta T cell differentiation" evidence=IEA

GO:0045950 "negative regulation of mitotic recombination" evidence=IEA

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

GO:0045120 "pronucleus" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005657 "replication fork" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0000800 "lateral element" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000729 "DNA double-strand break processing" evidence=IEA

GO:0000723 "telomere maintenance" evidence=IEA

GO:0000405 "bubble DNA binding" evidence=IEA

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

UNIPROTKB|J9PB86 BLM "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 234 (87.4 bits), Expect = 3.9e-18, P = 3.9e-18
 Identities = 44/92 (47%), Positives = 60/92 (65%)

Query:     7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
             VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  S+C ++++ H    L
Sbjct:   944 VICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCLLFYTYHDVTRL 1003

Query:    67 EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
             + +I  +    R   E  F N  SM+ YCE +
Sbjct:  1004 KRLILMEKDGNRHTRETHFNNLYSMVHYCENI 1035

GO:0005524 "ATP binding" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

WB|WBGene00001865 him-6 [Caenorhabditis elegans (taxid:6239)]

 Score = 231 (86.4 bits), Expect = 5.0e-18, P = 5.0e-18
 Identities = 44/95 (46%), Positives = 63/95 (66%)

Query:     4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK 63
             + +VI ATI+FGMGID+ +VRFV+H+ +P SI  YYQE+GRAGRDG+ SYC + +S H  
Sbjct:   519 KFDVICATIAFGMGIDKPDVRFVIHYSLPKSIEGYYQETGRAGRDGMPSYCLMLYSYHDS 578

Query:    64 KSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
               L  +I+   +T   +  +   N L ++ YCE V
Sbjct:   579 IRLRRMIEEGNTTTGVR-SMHLNNVLQVVAYCENV 612

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0051307 "meiotic chromosome separation" evidence=IMP

GO:0051276 "chromosome organization" evidence=IGI

GO:0007059 "chromosome segregation" evidence=IGI

GO:0007126 "meiosis" evidence=IGI

GO:0007067 "mitosis" evidence=IGI

GO:0007131 "reciprocal meiotic recombination" evidence=IMP

GO:0000077 "DNA damage checkpoint" evidence=IMP

GO:0010165 "response to X-ray" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0019899 "enzyme binding" evidence=IPI

UNIPROTKB|E1BQ04 BLM "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 233 (87.1 bits), Expect = 5.0e-18, P = 5.0e-18
 Identities = 44/92 (47%), Positives = 60/92 (65%)

Query:     7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
             VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  S+C ++++ H    L
Sbjct:   942 VICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISHCILFYTYHDVTRL 1001

Query:    67 EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
             + +I  +    R   E  F N  SM+ YCE +
Sbjct:  1002 KRLILMEKDGNRHTRETHFNNLYSMVHYCENI 1033

GO:0051880 "G-quadruplex DNA binding" evidence=IEA

GO:0051782 "negative regulation of cell division" evidence=IEA

GO:0051259 "protein oligomerization" evidence=IEA

GO:0051098 "regulation of binding" evidence=IEA

GO:0046641 "positive regulation of alpha-beta T cell proliferation" evidence=IEA

GO:0046632 "alpha-beta T cell differentiation" evidence=IEA

GO:0045950 "negative regulation of mitotic recombination" evidence=IEA

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

GO:0045120 "pronucleus" evidence=IEA

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0016363 "nuclear matrix" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005657 "replication fork" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0001673 "male germ cell nucleus" evidence=IEA

GO:0000800 "lateral element" evidence=IEA

GO:0000781 "chromosome, telomeric region" evidence=IEA

GO:0000729 "DNA double-strand break processing" evidence=IEA

GO:0000723 "telomere maintenance" evidence=IEA

GO:0000405 "bubble DNA binding" evidence=IEA

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

UNIPROTKB|F1RMJ2 BLM "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 226 (84.6 bits), Expect = 5.1e-18, P = 5.1e-18
 Identities = 43/92 (46%), Positives = 58/92 (63%)

Query:     7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL 66
             VI ATI+FGMGID+ +VRFV+H  +P S+  YYQESGRAGRDG  S C ++++ H    L
Sbjct:    39 VICATIAFGMGIDKPDVRFVIHASLPKSVEGYYQESGRAGRDGEISQCLLFYTYHDVTRL 98

Query:    67 EYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
             + +I  +        E  F N  SM+ YCE +
Sbjct:    99 KRLILMEKDGNHHTKETHFNNLYSMVHYCENI 130

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P40724	RECQ_SALTY	3, ., 6, ., 4, ., 1, 2	0.5087	0.5643	0.0935	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	101
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	3e-28
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	5e-28
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	4e-25
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	3e-22
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	3e-20
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	5e-13
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	6e-13
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	8e-13
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	5e-06
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	7e-06
COG1205	851	COG1205, COG1205, Distinct helicase family with a	6e-04
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	7e-04
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	8e-04
PRK09751	1490	PRK09751, PRK09751, putative ATP-dependent helicas	0.003
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	0.003
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.004

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

 Score =  105 bits (265), Expect = 3e-28
 Identities = 40/100 (40%), Positives = 61/100 (61%), Gaps = 9/100 (9%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           +  EI V+ AT +FGMGID+ +VRFV+H+ +P SI +YYQE+GRAGRDGL +   + +S 
Sbjct: 277 LNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSP 336

Query: 61  HSKKSLEYVIKT----DTSTKREQLELKFKNYLSMLEYCE 96
              +   Y+I+     +   + E  +L+      M+ YCE
Sbjct: 337 EDIRWQRYLIEQSKPDEEQKQIELAKLR-----QMIAYCE 371

Length = 590

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

 Score =  104 bits (262), Expect = 5e-28
 Identities = 40/96 (41%), Positives = 62/96 (64%), Gaps = 3/96 (3%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
            R EI V+ AT++FGMGI++ +VRFV+H+ +P S+ +YYQESGRAGRDGL S C ++++ 
Sbjct: 273 QRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332

Query: 61  HSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 96
                L  ++  +   ++   +LK      M+EYC 
Sbjct: 333 ADINRLRRLLMEEPDGQQRTYKLKL---YEMMEYCL 365

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|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score = 97.1 bits (242), Expect = 4e-25
 Identities = 38/97 (39%), Positives = 61/97 (62%), Gaps = 3/97 (3%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
           +  ++ V+ AT +FGMGID+ NVRFV+H+ MP ++ +YYQE+GRAGRDGL +   + +S 
Sbjct: 271 LYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSP 330

Query: 61  HSKKSLEYVIKTDTST-KREQLELKFKNYLSMLEYCE 96
                L+  I+   +    +Q+E +     +M+ YCE
Sbjct: 331 ADIALLKRRIEQSEADDDYKQIEREKLR--AMIAYCE 365

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

 Score = 89.2 bits (221), Expect = 3e-22
 Identities = 44/107 (41%), Positives = 63/107 (58%), Gaps = 15/107 (14%)

Query: 4   EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK 63
           EIN+I AT++FGMGI++ +VRFV+H  +P SI  Y+QE GRAGRDG +S C +Y+S    
Sbjct: 730 EINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDY 789

Query: 64  KSLEYVI--------------KTDTSTKREQLELKFKNYLSMLEYCE 96
             ++++I                  S+ R  LE   +N L M+ YCE
Sbjct: 790 IRVKHMISQGGVEQSPMAMGYNRMASSGR-ILETNTENLLRMVSYCE 835

Length = 1195

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

 Score = 83.6 bits (207), Expect = 3e-20
 Identities = 29/49 (59%), Positives = 42/49 (85%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL 50
           R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL
Sbjct: 284 RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGL 332

Length = 607

>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 = 59.9 bits (146), Expect = 5e-13
 Identities = 22/56 (39%), Positives = 30/56 (53%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIY 57
            GEI V+ AT     GID  NV  V+++ +P S  +Y Q  GRAGR G +    + 
Sbjct: 76  EGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

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

 Score = 58.3 bits (142), Expect = 6e-13
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 2  RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           G+  V+ AT   G GID  +V  V+++ +P +  +Y Q  GRAGR G
Sbjct: 31 NGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRAGRAG 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 = 58.0 bits (141), Expect = 8e-13
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 2  RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           G+I V+ AT     G+D   V  V+ + +P S  +Y Q  GRAGR G
Sbjct: 35 NGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 42.9 bits (101), Expect = 5e-06
 Identities = 21/47 (44%), Positives = 28/47 (59%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           GE+ VI AT   G G+D   VR V+ + MP++I  Y  + GRA R G
Sbjct: 417 GEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMG 463

Length = 518

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

 Score = 42.5 bits (100), Expect = 7e-06
 Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYC-RIYHS 59
             GE+ V+ AT     G+D  +V  V+++ +P     Y    GR GR G +         
Sbjct: 320 KDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTE 379

Query: 60  EHSKKSLEYVIKT 72
           E   K L+ + K 
Sbjct: 380 EEEVKKLKRIEKR 392

Length = 513

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

 Score = 37.0 bits (86), Expect = 6e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSY-CRIYHS 59
            GE+  + AT +  +GID  ++  V+ +G P  S+ ++ Q +GRAGR G +S    +  S
Sbjct: 362 EGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRS 421

Query: 60  EH 61
           + 
Sbjct: 422 DP 423

Length = 851

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 16/48 (33%), Positives = 27/48 (56%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
            GE+  +  T +  +G+D   +  VV  G P +  + +Q++GRAGR G
Sbjct: 327 DGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG 374

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. Length = 742

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

 Score = 36.5 bits (85), Expect = 8e-04
 Identities = 17/46 (36%), Positives = 25/46 (54%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 47
            GE+  + AT S  +GID  ++  V+  G P S+  + Q  GRAG 
Sbjct: 302 EGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347

Length = 814

>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr; Provisional

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 17/44 (38%), Positives = 23/44 (52%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG 46
           GE+  + AT S  +GID   V  V+    P S+ +  Q  GRAG
Sbjct: 326 GELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAG 369

Length = 1490

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

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           G   V+  T     GID Q V  V+++ +P+S   Y    GR+GR G
Sbjct: 316 GSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362

Length = 401

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

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 19/47 (40%), Positives = 25/47 (53%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           G +NV+ AT     GID  +V  V+++ MP S   Y    GR GR G
Sbjct: 294 GRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG 340

Length = 434

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	101
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.87
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.85
KOG0330|consensus	476		99.84
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.84
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.84
KOG0331|consensus	519		99.83
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.83
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.82
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.82
KOG0336|consensus	629		99.81
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.8
PTZ00110	545	helicase; Provisional	99.79
KOG0352|consensus	641		99.79
KOG0333|consensus	673		99.79
KOG0340|consensus	442		99.79
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.78
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.78
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.78
KOG0328|consensus	400		99.77
PTZ00424	401	helicase 45; Provisional	99.77
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.77
KOG0342|consensus	543		99.76
KOG0350|consensus	620		99.76
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.76
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.75
KOG0335|consensus	482		99.75
KOG0326|consensus	459		99.75
KOG0338|consensus	691		99.75
KOG0345|consensus	567		99.74
KOG0351|consensus	941		99.74
KOG0344|consensus	593		99.74
KOG0332|consensus	477		99.72
KOG0341|consensus	610		99.72
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.71
KOG0348|consensus	708		99.68
KOG0343|consensus	758		99.67
KOG0347|consensus	731		99.67
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.59
PHA02653	675	RNA helicase NPH-II; Provisional	99.58
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.56
KOG0327|consensus	397		99.56
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.53
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.51
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.51
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.51
PRK13767	876	ATP-dependent helicase; Provisional	99.5
KOG0346|consensus	569		99.49
KOG0353|consensus	695		99.48
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.48
KOG4284|consensus	980		99.47
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.47
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.47
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.45
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.44
PRK04914	956	ATP-dependent helicase HepA; Validated	99.44
KOG0334|consensus	997		99.43
PRK13766	773	Hef nuclease; Provisional	99.41
PRK02362	737	ski2-like helicase; Provisional	99.4
KOG0329|consensus	387		99.4
KOG0948|consensus	1041		99.4
KOG0339|consensus	731		99.39
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.39
PRK10689	1147	transcription-repair coupling factor; Provisional	99.38
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.38
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.37
KOG0354|consensus	746		99.37
PRK05298	652	excinuclease ABC subunit B; Provisional	99.34
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.33
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.32
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.32
PRK00254	720	ski2-like helicase; Provisional	99.3
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.29
KOG0337|consensus	529		99.27
KOG0349|consensus	725		99.25
PRK05580	679	primosome assembly protein PriA; Validated	99.23
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.23
PRK01172	674	ski2-like helicase; Provisional	99.23
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.23
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.21
PHA02558	501	uvsW UvsW helicase; Provisional	99.19
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.11
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.11
KOG0947|consensus	1248		99.11
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.1
KOG0953|consensus	700		99.07
KOG4150|consensus	1034		99.06
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.02
PRK14701	1638	reverse gyrase; Provisional	98.95
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.82
KOG0922|consensus	674		98.77
KOG0924|consensus	1042		98.77
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.76
KOG0923|consensus	902		98.75
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.75
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.71
COG1205	851	Distinct helicase family with a unique C-terminal	98.67
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.67
PRK09401	1176	reverse gyrase; Reviewed	98.59
COG1204	766	Superfamily II helicase [General function predicti	98.55
KOG0926|consensus	1172		98.54
KOG0949|consensus	1330		98.53
KOG0950|consensus	1008		98.51
PRK09694	878	helicase Cas3; Provisional	98.44
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.39
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.39
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.35
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.3
KOG0920|consensus	924		98.23
KOG0925|consensus	699		98.14
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.13
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.06
KOG0952|consensus	1230		98.0
PRK12904	830	preprotein translocase subunit SecA; Reviewed	97.98
KOG0951|consensus	1674		97.97
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	97.86
COG1202	830	Superfamily II helicase, archaea-specific [General	97.85
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.58
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.48
PRK13107	908	preprotein translocase subunit SecA; Reviewed	97.47
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	97.38
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.26
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.23
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.13
PF13871	278	Helicase_C_4: Helicase_C-like	96.42
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	96.27
PRK14873	665	primosome assembly protein PriA; Provisional	96.16
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	96.06
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	95.89
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	95.73
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	95.72
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	95.62
KOG0390|consensus	776		95.58
CHL00122	870	secA preprotein translocase subunit SecA; Validate	95.24
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	95.1
KOG0387|consensus	923		95.02
COG4889	1518	Predicted helicase [General function prediction on	94.8
KOG0385|consensus	971		94.72
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	94.47
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	94.46
KOG1015|consensus	1567		94.3
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	93.87
COG4096	875	HsdR Type I site-specific restriction-modification	93.83
KOG0384|consensus	1373		93.72
KOG1513|consensus	1300		93.23
KOG0388|consensus	1185		92.8
KOG0701|consensus	1606		92.19
KOG0921|consensus	1282		91.62
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	91.24
KOG0389|consensus	941		91.23
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	90.98
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	90.94
KOG1000|consensus	689		90.84
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	90.01
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	89.61
KOG0391|consensus	1958		88.48
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	88.34
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	87.94
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	86.01
KOG0386|consensus	1157		84.45

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

Probab=99.87  E-value=2.1e-22  Score=161.96  Aligned_cols=97  Identities=43%  Similarity=0.743  Sum_probs=84.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchh----
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTK----   77 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~----   77 (101)
                      +|+++|||||++++||||+|+|++|||||+|.+++.|+||+|||||.|..+.|++|+...|...+..++.....+.    
T Consensus       728 ~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~~~~~~~s~~~  807 (1195)
T PLN03137        728 KDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMA  807 (1195)
T ss_pred             cCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHhccccccchhh
Confidence            6899999999999999999999999999999999999999999999999999999999999988888886532211    


Q ss_pred             ---------HHHHHHHHHHHHHHHHHHhcC
Q psy7959          78 ---------REQLELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        78 ---------~~~~~~~~~~l~~m~~~~e~~   98 (101)
                               ....+...+++.+|+.||++.
T Consensus       808 ~~~~r~~~s~~~~e~~~~~L~~m~~yce~~  837 (1195)
T PLN03137        808 MGYNRMASSGRILETNTENLLRMVSYCENE  837 (1195)
T ss_pred             hhhcccchhHHHHHHHHHHHHHHHHHHhCh
Confidence                     112345678899999999974

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

Probab=99.85  E-value=1.5e-21  Score=149.30  Aligned_cols=97  Identities=41%  Similarity=0.766  Sum_probs=88.0

Q ss_pred             CCCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHH
Q psy7959           1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ   80 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (101)
                      +.++++|+|||.+++||||.|||++|||+|+|.++++|+|.+|||||+|..+.|++++.+.|.....+++....+ ....
T Consensus       277 ~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~~~~-~~~~  355 (590)
T COG0514         277 LNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQSKP-DEEQ  355 (590)
T ss_pred             hcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHhhcc-hHHH
Confidence            468899999999999999999999999999999999999999999999999999999999999999898888665 3335


Q ss_pred             HHHHHHHHHHHHHHHhcC
Q psy7959          81 LELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        81 ~~~~~~~l~~m~~~~e~~   98 (101)
                      ......+++.|..||++.
T Consensus       356 ~~~~~~kl~~~~~~~e~~  373 (590)
T COG0514         356 KQIELAKLRQMIAYCETQ  373 (590)
T ss_pred             HHHHHHHHHHHHHhcccc
Confidence            666778899999999976

>KOG0330|consensus

Probab=99.84  E-value=9.9e-22  Score=143.60  Aligned_cols=70  Identities=19%  Similarity=0.317  Sum_probs=64.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|..+||||||+++||+|+|+|++|||||+|.+..+|+||+||+||.|.+|.+|++++..|.+.++.+-.
T Consensus       348 ~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~  417 (476)
T KOG0330|consen  348 AGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEH  417 (476)
T ss_pred             ccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHH
Confidence            4778999999999999999999999999999999999999999999999999999999988876655443

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.84  E-value=3.9e-21  Score=148.51  Aligned_cols=95  Identities=34%  Similarity=0.668  Sum_probs=82.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQL   81 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (101)
                      +|+++|||||+++++|+|+|+|++|||+|+|.+.++|+||+||+||.|..+.+++++++.|...++.++........  .
T Consensus       284 ~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~~~~~~~~~~--~  361 (607)
T PRK11057        284 RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQ--Q  361 (607)
T ss_pred             CCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHHHhcCCcHHH--H
Confidence            58899999999999999999999999999999999999999999999999999999999999888888877654432  2


Q ss_pred             HHHHHHHHHHHHHHhcC
Q psy7959          82 ELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        82 ~~~~~~l~~m~~~~e~~   98 (101)
                      ......+..|..||++.
T Consensus       362 ~~~~~~l~~~~~~~~~~  378 (607)
T PRK11057        362 DIERHKLNAMGAFAEAQ  378 (607)
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            33445778889998854

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.84  E-value=7.4e-21  Score=143.10  Aligned_cols=76  Identities=45%  Similarity=0.884  Sum_probs=70.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchh
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTK   77 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~   77 (101)
                      +|+++|||||+++++|+|+|+|++||++++|.+.+.|+||+||+||.|..+.|++++.+.|...++.++.......
T Consensus       274 ~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~~~~~~~  349 (470)
T TIGR00614       274 RDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQ  349 (470)
T ss_pred             cCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHhcCCchh
Confidence            5889999999999999999999999999999999999999999999999999999999999998888887655443

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

>KOG0331|consensus

Probab=99.83  E-value=2.9e-21  Score=145.83  Aligned_cols=72  Identities=25%  Similarity=0.438  Sum_probs=66.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD   73 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~   73 (101)
                      +|+.+||||||+++||||+|+|++|||||+|.+.++|+||+||+||+|+.|.+++|+...+......+++-.
T Consensus       389 eG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l  460 (519)
T KOG0331|consen  389 EGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVL  460 (519)
T ss_pred             cCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999999999999999999999988887666655543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.83  E-value=1.5e-20  Score=144.63  Aligned_cols=97  Identities=37%  Similarity=0.681  Sum_probs=83.9

Q ss_pred             CCCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHH
Q psy7959           1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ   80 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (101)
                      ++|+++|||||+++++|+|+|+|++||++++|.+..+|+|++||+||.|..+.|++++...+....+.++........ .
T Consensus       271 ~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i~~~~~~~~-~  349 (591)
T TIGR01389       271 LYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQSEADDD-Y  349 (591)
T ss_pred             HcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHHHhccCCcHH-H
Confidence            368899999999999999999999999999999999999999999999999999999999999998888877554433 2


Q ss_pred             HHHHHHHHHHHHHHHhcC
Q psy7959          81 LELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        81 ~~~~~~~l~~m~~~~e~~   98 (101)
                      .......+.+|..||++.
T Consensus       350 ~~~~~~~l~~~~~~~~~~  367 (591)
T TIGR01389       350 KQIEREKLRAMIAYCETQ  367 (591)
T ss_pred             HHHHHHHHHHHHHHHccc
Confidence            333466788888998863

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.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.82  E-value=1.4e-20  Score=139.74  Aligned_cols=68  Identities=24%  Similarity=0.409  Sum_probs=63.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|+++||||||++++|+|+|+|++||+||+|.+..+|+||+||+||.|+.|.+++|+.+.+...+..+
T Consensus       303 ~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i  370 (423)
T PRK04837        303 RGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAI  370 (423)
T ss_pred             cCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999998876655544

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

Probab=99.82  E-value=1.2e-20  Score=143.60  Aligned_cols=71  Identities=28%  Similarity=0.461  Sum_probs=63.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcc-cHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH-SKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~-~~~~~~~~~~~   72 (101)
                      +|+.+||||||+++||||+|+|++|||||+|.+++.|+||+||+||+|..|.+++|+.+. +...+..+.+.
T Consensus       321 ~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~  392 (513)
T COG0513         321 DGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKR  392 (513)
T ss_pred             cCCCCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999999999999999999999975 66555444433

>KOG0336|consensus

Probab=99.81  E-value=2.2e-20  Score=137.90  Aligned_cols=71  Identities=24%  Similarity=0.424  Sum_probs=66.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|+++||||||+++||+|+++|++|+|||+|.+++.|+||+||+||.|+.|.++.|+...|+.....++.-
T Consensus       513 sG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~I  583 (629)
T KOG0336|consen  513 SGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQI  583 (629)
T ss_pred             cCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999998877666554

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

Probab=99.80  E-value=3.6e-20  Score=140.93  Aligned_cols=69  Identities=32%  Similarity=0.526  Sum_probs=63.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+++|||||+++++|+|+|+|++||+||+|.+..+|+||+||+||.|..|.+++|++..+...+..+.
T Consensus       416 ~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~  484 (518)
T PLN00206        416 VGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELV  484 (518)
T ss_pred             CCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHH
Confidence            588999999999999999999999999999999999999999999999999999999988766554443

>PTZ00110 helicase; Provisional

Probab=99.79  E-value=6.7e-20  Score=140.25  Aligned_cols=71  Identities=23%  Similarity=0.462  Sum_probs=65.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|+.+|||||+++++|+|+|+|++|||||+|.+..+|+||+||+||.|+.|.+++|+++.+...+..+.+.
T Consensus       425 ~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~  495 (545)
T PTZ00110        425 TGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKV  495 (545)
T ss_pred             cCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHH
Confidence            58899999999999999999999999999999999999999999999999999999999887766555443

>KOG0352|consensus

Probab=99.79  E-value=1.5e-19  Score=134.11  Aligned_cols=98  Identities=48%  Similarity=0.947  Sum_probs=90.2

Q ss_pred             CCCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHH-
Q psy7959           1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKRE-   79 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-   79 (101)
                      |+|++.|++||..++||+|-|+|++||||++|.+.+-|+|.+|||||.|..+.|-++|..+|...+..++.++...+.+ 
T Consensus       302 M~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~~i~FLi~~e~aklrek  381 (641)
T KOG0352|consen  302 MNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRDGKRSYCRLYYSRQDKNALNFLVSGELAKLREK  381 (641)
T ss_pred             hcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhccccccCCCccceeeeecccchHHHHHHHhhHHHHHHHh
Confidence            7899999999999999999999999999999999999999999999999999999999999999999998887766554 


Q ss_pred             -----HHHHHHHHHHHHHHHHhcC
Q psy7959          80 -----QLELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        80 -----~~~~~~~~l~~m~~~~e~~   98 (101)
                           ..+.....+++|++|||..
T Consensus       382 ~~ke~~~k~~I~~F~k~~eFCE~~  405 (641)
T KOG0352|consen  382 AKKEMQIKSIITGFAKMLEFCESA  405 (641)
T ss_pred             cchhhhHHHHHHHHHHHHHHHHHc
Confidence                 4567778899999999975

>KOG0333|consensus

Probab=99.79  E-value=4.3e-20  Score=139.07  Aligned_cols=63  Identities=30%  Similarity=0.470  Sum_probs=59.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      .|...||||||+++||+|+|+|.+|||||++++...|.||+||+||+|+.|.+++|+++.+..
T Consensus       565 ~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~  627 (673)
T KOG0333|consen  565 EGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTA  627 (673)
T ss_pred             hcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhH
Confidence            367889999999999999999999999999999999999999999999999999999998854

>KOG0340|consensus

Probab=99.79  E-value=7.7e-20  Score=132.61  Aligned_cols=68  Identities=21%  Similarity=0.325  Sum_probs=63.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      ++.++||+|||+++||+|+|.|++|||+|+|.++..|+||+||++|+|+.|.+|.+++..|.+.++.+
T Consensus       302 s~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~ai  369 (442)
T KOG0340|consen  302 SNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAI  369 (442)
T ss_pred             hcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999998888766544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.78  E-value=1.7e-19  Score=135.25  Aligned_cols=70  Identities=26%  Similarity=0.360  Sum_probs=64.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+++|||||+++++|+|+|+|++|||||+|.++.+|+||+||+||.|..|.+++++...+...++.+.+
T Consensus       293 ~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~  362 (456)
T PRK10590        293 SGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEK  362 (456)
T ss_pred             cCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHH
Confidence            5889999999999999999999999999999999999999999999999999999999888766555443

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.78  E-value=2.4e-19  Score=133.28  Aligned_cols=69  Identities=30%  Similarity=0.454  Sum_probs=63.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+++||||||++++|+|+|++++|||||+|.+...|+||+||+||.|..|.+++++...|...+..+.
T Consensus       293 ~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~  361 (434)
T PRK11192        293 DGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIE  361 (434)
T ss_pred             CCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999999999988876665543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.78  E-value=2.7e-19  Score=133.99  Aligned_cols=70  Identities=16%  Similarity=0.221  Sum_probs=64.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|.+..+|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus       290 ~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~  359 (460)
T PRK11776        290 NRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIED  359 (460)
T ss_pred             cCCCcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHH
Confidence            5889999999999999999999999999999999999999999999999999999999888766555443

>KOG0328|consensus

Probab=99.77  E-value=2.5e-19  Score=127.26  Aligned_cols=70  Identities=24%  Similarity=0.418  Sum_probs=65.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+||++||+.+||+|+|+|++|||||+|.+.+.|+||+||+||.|+.|.+|.|+...|.+.+..+-+
T Consensus       314 sg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq  383 (400)
T KOG0328|consen  314 SGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQ  383 (400)
T ss_pred             cCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999999887765544

>PTZ00424 helicase 45; Provisional

Probab=99.77  E-value=2.8e-19  Score=131.20  Aligned_cols=70  Identities=26%  Similarity=0.432  Sum_probs=64.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+++|||||+++++|+|+|++++||++|+|.+..+|+||+||+||.|..|.++.++++.+.+.+..+.+
T Consensus       315 ~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~  384 (401)
T PTZ00424        315 SGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER  384 (401)
T ss_pred             cCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999999888776665544

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.77  E-value=3.9e-19  Score=133.74  Aligned_cols=68  Identities=26%  Similarity=0.450  Sum_probs=62.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|+++|||||+++++|+|++++++||++|+|.+..+|+||+||+||.|..|.+++++.+.|...+..+
T Consensus       383 ~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~  450 (475)
T PRK01297        383 EGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEI  450 (475)
T ss_pred             CCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999987765544433

>KOG0342|consensus

Probab=99.76  E-value=5e-19  Score=132.12  Aligned_cols=72  Identities=24%  Similarity=0.359  Sum_probs=66.1

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccc
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTS   75 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~   75 (101)
                      +.=||||||+++||+|+|+|++||++|.|.++.+|+||+||+||.|..|.+++++.+++...++++.+-...
T Consensus       380 esgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK~lpl~  451 (543)
T KOG0342|consen  380 ESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLKKLPLE  451 (543)
T ss_pred             ccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHhhCCCc
Confidence            345899999999999999999999999999999999999999999999999999999999988888754443

>KOG0350|consensus

Probab=99.76  E-value=1.9e-18  Score=129.59  Aligned_cols=74  Identities=27%  Similarity=0.507  Sum_probs=69.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTS   75 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~   75 (101)
                      +|++++|||||+++||+|+.+|+.|||||+|.+..+|+||+||++|+|+.|.|+++....+...+.++++....
T Consensus       481 ~g~i~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~~  554 (620)
T KOG0350|consen  481 KGDINVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTNL  554 (620)
T ss_pred             cCCceEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhcc
Confidence            58999999999999999999999999999999999999999999999999999999999999888888876544

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.76  E-value=6.9e-19  Score=135.36  Aligned_cols=69  Identities=22%  Similarity=0.380  Sum_probs=63.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+++||||||++++|+|+|+|++|||||+|.++.+|+||+||+||.|..|.+++|+.+.+...+..+.
T Consensus       305 ~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~  373 (572)
T PRK04537        305 KGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIE  373 (572)
T ss_pred             cCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHH
Confidence            588999999999999999999999999999999999999999999999999999999987766555443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.75  E-value=8.8e-19  Score=135.99  Aligned_cols=70  Identities=21%  Similarity=0.480  Sum_probs=64.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+++||||||++++|+|+|+|++|||||+|.++.+|+||+||+||.|+.|.+++++.+.+...++.+.+
T Consensus       293 ~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~  362 (629)
T PRK11634        293 DGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIER  362 (629)
T ss_pred             CCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHH
Confidence            5889999999999999999999999999999999999999999999999999999999887666655543

>KOG0335|consensus

Probab=99.75  E-value=1e-18  Score=130.73  Aligned_cols=65  Identities=29%  Similarity=0.497  Sum_probs=60.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL   66 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~   66 (101)
                      +|.+.+||||++++||+|+|+|++||+||+|.+..+|+||+||+||.|+.|.++.|++..+....
T Consensus       385 ~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~  449 (482)
T KOG0335|consen  385 NGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIA  449 (482)
T ss_pred             cCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhH
Confidence            58899999999999999999999999999999999999999999999999999999996554433

>KOG0326|consensus

Probab=99.75  E-value=8.7e-19  Score=126.23  Aligned_cols=71  Identities=24%  Similarity=0.348  Sum_probs=65.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|.++.|||||.+-||+|+++|++|||||+|+++++|.||+||+||.|.-|.+|.+++..|...+..+..+
T Consensus       370 ~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~e  440 (459)
T KOG0326|consen  370 NGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQE  440 (459)
T ss_pred             ccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999998887766555443

>KOG0338|consensus

Probab=99.75  E-value=2e-18  Score=129.96  Aligned_cols=72  Identities=31%  Similarity=0.488  Sum_probs=68.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD   73 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~   73 (101)
                      +++++||||||+++||+|++.|..||||++|.+...|+||+||+.|+|+.|.+|+|+...+...++.++++.
T Consensus       474 ~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~  545 (691)
T KOG0338|consen  474 KEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSS  545 (691)
T ss_pred             hccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhh
Confidence            467999999999999999999999999999999999999999999999999999999999999999888883

>KOG0345|consensus

Probab=99.74  E-value=1.9e-18  Score=128.81  Aligned_cols=65  Identities=18%  Similarity=0.382  Sum_probs=59.1

Q ss_pred             eEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           6 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      -+|+|||+++||+|+|+|++||+||.|.++++|+||+||+||.|+.|.+|+|+.+.+......+-
T Consensus       309 ~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~aYveFl~  373 (567)
T KOG0345|consen  309 GVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEAYVEFLR  373 (567)
T ss_pred             ceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHHHHHHHH
Confidence            48999999999999999999999999999999999999999999999999999997665544433

>KOG0351|consensus

Probab=99.74  E-value=2.4e-18  Score=137.47  Aligned_cols=97  Identities=38%  Similarity=0.728  Sum_probs=86.4

Q ss_pred             CCCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHH
Q psy7959           1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQ   80 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~   80 (101)
                      |.++++|+|||-++++|+|.|+|++||||.+|++.+.|+|.+|||||.|..+.|++|+...|...++.++.... .....
T Consensus       532 ~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~ll~s~~-~~~~~  610 (941)
T KOG0351|consen  532 MSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRRLLTSGN-RLSGV  610 (941)
T ss_pred             hcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHHHHHccc-cccch
Confidence            57889999999999999999999999999999999999999999999999999999999999999999998882 22222


Q ss_pred             HH-HHHHHHHHHHHHHhcC
Q psy7959          81 LE-LKFKNYLSMLEYCEQV   98 (101)
Q Consensus        81 ~~-~~~~~l~~m~~~~e~~   98 (101)
                      .. ....++.+++.||++.
T Consensus       611 ~~~~~~~~l~~~~~yCen~  629 (941)
T KOG0351|consen  611 KKFTRLLELVQVVTYCENE  629 (941)
T ss_pred             hhccchhhHHHHHHhhcCc
Confidence            22 5678899999999975

>KOG0344|consensus

Probab=99.74  E-value=1.7e-18  Score=131.13  Aligned_cols=67  Identities=25%  Similarity=0.427  Sum_probs=63.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEY   68 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~   68 (101)
                      .|+++||+||++++||+|+.+++.|||||+|.+..+|+||+||+||+|+.|.+++||++.+.+.++.
T Consensus       436 ~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~  502 (593)
T KOG0344|consen  436 IGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRS  502 (593)
T ss_pred             ccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhh
Confidence            5899999999999999999999999999999999999999999999999999999999988775543

>KOG0332|consensus

Probab=99.72  E-value=2.8e-18  Score=125.31  Aligned_cols=61  Identities=26%  Similarity=0.435  Sum_probs=57.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCC------CCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMP------SSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p------~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      .|+.+|||+|++++||+|++.|++|||||+|      .+++.|+||+||+||+|+.|.++.++...+
T Consensus       378 ~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~  444 (477)
T KOG0332|consen  378 EGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKD  444 (477)
T ss_pred             cCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccC
Confidence            5889999999999999999999999999999      468899999999999999999999998764

>KOG0341|consensus

Probab=99.72  E-value=1.3e-18  Score=127.99  Aligned_cols=61  Identities=26%  Similarity=0.523  Sum_probs=58.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      .|+.+||||||++++|+|+|++.+|||||+|..+++|+||+||+||.|+.|.+.+|.+...
T Consensus       469 ~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~  529 (610)
T KOG0341|consen  469 AGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQ  529 (610)
T ss_pred             cCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccc
Confidence            4789999999999999999999999999999999999999999999999999999999764

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

Probab=99.71  E-value=5.4e-18  Score=133.61  Aligned_cols=60  Identities=27%  Similarity=0.480  Sum_probs=57.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|++++|||||++++|+|++++++||++|+|.+.++|+||+||+||.|+.|.++++....
T Consensus       327 ~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~  386 (742)
T TIGR03817       327 DGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDD  386 (742)
T ss_pred             cCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCC
Confidence            689999999999999999999999999999999999999999999999999999998744

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.

>KOG0348|consensus

Probab=99.68  E-value=2e-17  Score=125.10  Aligned_cols=68  Identities=24%  Similarity=0.369  Sum_probs=62.5

Q ss_pred             eEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcc
Q psy7959           6 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD   73 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~   73 (101)
                      -||+|||+++||+|+|+|++||+||.|.++.+|+||+||++|.|..|.+++|+.+.|.+.+..+.+..
T Consensus       499 ~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey~~~l~~~~  566 (708)
T KOG0348|consen  499 AVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEYVNYLKKHH  566 (708)
T ss_pred             eEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHHHHHHHhhc
Confidence            49999999999999999999999999999999999999999999999999999999988665554443

>KOG0343|consensus

Probab=99.67  E-value=7.6e-17  Score=122.42  Aligned_cols=70  Identities=19%  Similarity=0.252  Sum_probs=62.0

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH-HHHHHHHccc
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK-SLEYVIKTDT   74 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~-~~~~~~~~~~   74 (101)
                      .-||+|||+++||+|+|.|++||++|+|.++.+|+||+||++|....|.+++++.+.+.+ .+..+-+..+
T Consensus       366 ~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~~Lq~k~I  436 (758)
T KOG0343|consen  366 AVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEAMLKKLQKKKI  436 (758)
T ss_pred             ceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHHHHHHHHHcCC
Confidence            458999999999999999999999999999999999999999999999999999999854 4555544433

>KOG0347|consensus

Probab=99.67  E-value=1.1e-16  Score=121.50  Aligned_cols=68  Identities=25%  Similarity=0.368  Sum_probs=62.5

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      --||+|||+++||+|+|+|.+||||-.|.+..-|+||+||++|+++.|.++.++.+.+...+.++.+.
T Consensus       514 ~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~kt  581 (731)
T KOG0347|consen  514 SGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKT  581 (731)
T ss_pred             CeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHH
Confidence            45899999999999999999999999999999999999999999999999999999987766655543

>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=99.59  E-value=2.9e-16  Score=91.58  Aligned_cols=48  Identities=44%  Similarity=0.615  Sum_probs=45.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG   49 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~   49 (101)
                      +|+.+|||||+++++|+|+|++++||+++.|++...|.|++||+||.|
T Consensus        31 ~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen   31 SGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             TTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             ccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            466799999999999999999999999999999999999999999976

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

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.58  E-value=1.2e-15  Score=119.14  Aligned_cols=61  Identities=20%  Similarity=0.186  Sum_probs=55.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeC---CCC---------CccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWG---MPS---------SIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~---~p~---------~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|+.+||||||++++|+|+|+|++||++|   .|.         |.++|.||+||+||. ++|.|+.++++.+.
T Consensus       444 ~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        444 SKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             cCceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            57899999999999999999999999999   564         788999999999999 79999999987764

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

Probab=99.56  E-value=7.5e-15  Score=110.41  Aligned_cols=63  Identities=27%  Similarity=0.350  Sum_probs=58.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      +|+++|||||+++++|+|+|++++||.|+.-.|.-.++||.||+||. ++|.++++++.++.+.
T Consensus       423 ~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtrde  485 (542)
T COG1111         423 KGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTRDE  485 (542)
T ss_pred             cCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCchHH
Confidence            68999999999999999999999999999989999999999999998 7899999998885443

>KOG0327|consensus

Probab=99.56  E-value=3.2e-15  Score=109.09  Aligned_cols=71  Identities=30%  Similarity=0.440  Sum_probs=66.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|..+|||+|+.+++|+|+.+++.||||++|...++|+||+||+||.|.+|.++.+++..+...++.+-+.
T Consensus       311 ~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~  381 (397)
T KOG0327|consen  311 SGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKF  381 (397)
T ss_pred             cCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHh
Confidence            57899999999999999999999999999999999999999999999999999999999888877766644

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.53  E-value=9e-15  Score=113.71  Aligned_cols=58  Identities=29%  Similarity=0.481  Sum_probs=54.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-CccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+.+|||||+++++|+|+|++++||+++.|. +.++|.||+||+||.|..|.|++++.
T Consensus       506 ~g~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       506 EGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             cCCCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            58899999999999999999999999999885 68889999999999999999999983

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=9.4e-15  Score=113.66  Aligned_cols=59  Identities=25%  Similarity=0.175  Sum_probs=55.0

Q ss_pred             ceeEEEEccccccccCCC---Ccc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           4 EINVITATISFGMGIDRQ---NVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~---~v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      ..+|+||||+++||+|++   +|+     +||++++|.+...|.||+||+||.|..|.++.+++..|
T Consensus       521 ~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD  587 (656)
T PRK12898        521 RGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLED  587 (656)
T ss_pred             CCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhH
Confidence            457999999999999999   676     99999999999999999999999999999999999765

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.51  E-value=2.1e-14  Score=112.58  Aligned_cols=58  Identities=31%  Similarity=0.496  Sum_probs=54.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-CccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+++|||||+++++|+|+|++++||+++.|. +.++|.||.||+||.|..|.|++++.
T Consensus       529 ~g~~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        529 AGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             cCCCCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEEC
Confidence            58899999999999999999999999999986 67889999999999999999999995

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.51  E-value=6e-15  Score=117.39  Aligned_cols=64  Identities=27%  Similarity=0.352  Sum_probs=56.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCC------------------ccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSS------------------IPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~------------------~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|+.+||||||++++|+|+|+|++||++|+|..                  .++|.||+||+||. .+|.|+.++++.++
T Consensus       260 ~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~  338 (819)
T TIGR01970       260 QGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQH  338 (819)
T ss_pred             cCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHH
Confidence            578999999999999999999999999998752                  34588999999999 79999999998766


Q ss_pred             HHH
Q psy7959          64 KSL   66 (101)
Q Consensus        64 ~~~   66 (101)
                      ..+
T Consensus       339 ~~l  341 (819)
T TIGR01970       339 QRL  341 (819)
T ss_pred             Hhh
Confidence            543

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.

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.50  E-value=2e-14  Score=115.16  Aligned_cols=48  Identities=38%  Similarity=0.613  Sum_probs=46.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG   49 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~   49 (101)
                      +|+++|||||+++++|+|+|++++||+++.|.+..+|+||+||+||.+
T Consensus       338 ~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~  385 (876)
T PRK13767        338 RGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRL  385 (876)
T ss_pred             cCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCC
Confidence            588999999999999999999999999999999999999999999874

>KOG0346|consensus

Probab=99.49  E-value=3.3e-14  Score=105.85  Aligned_cols=51  Identities=22%  Similarity=0.400  Sum_probs=47.9

Q ss_pred             cccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959          14 FGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus        14 ~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      ++||+|+.+|..|+|||+|.++.+|+||+||++|.++.|.++.|+.+.+..
T Consensus       363 VsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~  413 (569)
T KOG0346|consen  363 VSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEF  413 (569)
T ss_pred             hhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHh
Confidence            348999999999999999999999999999999999999999999988765

>KOG0353|consensus

Probab=99.48  E-value=5.4e-14  Score=103.94  Aligned_cols=88  Identities=41%  Similarity=0.781  Sum_probs=74.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceee-----------------------------------------
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQ-----------------------------------------   40 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~q-----------------------------------------   40 (101)
                      .|++.|+|||-++++|+|-|+|++|||..+|++.++|+|                                         
T Consensus       365 a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfs  444 (695)
T KOG0353|consen  365 AGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFS  444 (695)
T ss_pred             ccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeec
Confidence            589999999999999999999999999999999999999                                         


Q ss_pred             --ecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHHHHHHHHHHHHHHHHHhc
Q psy7959          41 --ESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQ   97 (101)
Q Consensus        41 --r~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~m~~~~e~   97 (101)
                        .+||+||.+....||++|...|...+..+.......        ..++-+|++||..
T Consensus       445 ekesgragrd~~~a~cilyy~~~difk~ssmv~~e~~g--------~q~ly~mv~y~~d  495 (695)
T KOG0353|consen  445 EKESGRAGRDDMKADCILYYGFADIFKISSMVQMENTG--------IQKLYEMVRYAAD  495 (695)
T ss_pred             chhccccccCCCcccEEEEechHHHHhHHHHHHHHhhh--------HHHHHHHHHHHhh
Confidence              899999999999999999988887777666544322        2345567777654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.48  E-value=2.3e-14  Score=115.18  Aligned_cols=60  Identities=25%  Similarity=0.421  Sum_probs=55.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-CccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+++|||||+++++|+|+|++++||+++.|. +.++|+||+||+||.|+.|.|++++.+.
T Consensus       710 ~Gk~~ILVaT~iie~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       710 KGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             cCCCCEEEECChhhcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            68999999999999999999999999999864 6789999999999999999999998653

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.

>KOG4284|consensus

Probab=99.47  E-value=3.6e-14  Score=109.73  Aligned_cols=60  Identities=27%  Similarity=0.443  Sum_probs=56.8

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .++|||+||.-+||+|-++|++|||.|.|.+-..|.||+|||||+|..|.+|+|+.....
T Consensus       322 ~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  322 RVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             eEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            479999999999999999999999999999999999999999999999999999987643

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.47  E-value=3e-14  Score=113.43  Aligned_cols=63  Identities=27%  Similarity=0.334  Sum_probs=55.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC------------------CccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS------------------SIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~------------------~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|+.+||||||++++|+|+++|++||++++|.                  |.++|.||+||+||. .+|.|+.++++.++
T Consensus       263 ~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~  341 (812)
T PRK11664        263 AGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQA  341 (812)
T ss_pred             CCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHH
Confidence            57899999999999999999999999988764                  335799999999999 69999999997766


Q ss_pred             HH
Q psy7959          64 KS   65 (101)
Q Consensus        64 ~~   65 (101)
                      ..
T Consensus       342 ~~  343 (812)
T PRK11664        342 ER  343 (812)
T ss_pred             hh
Confidence            53

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.47  E-value=3.1e-14  Score=112.68  Aligned_cols=58  Identities=28%  Similarity=0.217  Sum_probs=54.9

Q ss_pred             eeEEEEccccccccCC---CCcc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDR---QNVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~---~~v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -+|+||||+++||+|+   ++|.     +||++++|.+...|.||+||+||.|..|.++.+++..|
T Consensus       477 g~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD  542 (790)
T PRK09200        477 GAVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLED  542 (790)
T ss_pred             CeEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchH
Confidence            3799999999999999   6998     99999999999999999999999999999999998765

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.45  E-value=4.3e-14  Score=115.95  Aligned_cols=64  Identities=23%  Similarity=0.278  Sum_probs=56.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC---------------C---CCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM---------------P---SSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~---------------p---~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|..+||||||++++|+|+|+|++||++|+               |   .|.++|.||+||+||. .+|.|+.++++.++
T Consensus       335 ~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~  413 (1294)
T PRK11131        335 HSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDF  413 (1294)
T ss_pred             cCCeeEEEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHH
Confidence            367899999999999999999999999873               3   4568899999999999 79999999998776


Q ss_pred             HHH
Q psy7959          64 KSL   66 (101)
Q Consensus        64 ~~~   66 (101)
                      ..+
T Consensus       414 ~~~  416 (1294)
T PRK11131        414 LSR  416 (1294)
T ss_pred             Hhh
Confidence            644

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.44  E-value=1.2e-13  Score=114.65  Aligned_cols=58  Identities=31%  Similarity=0.408  Sum_probs=50.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCC-CcceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG-LQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~-~~~~~i~~~~   59 (101)
                      +|++++||||+++++|||+++|++||+++.|.+.++|+||+||+||.. ..+.++++..
T Consensus       325 ~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~  383 (1490)
T PRK09751        325 SGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPR  383 (1490)
T ss_pred             hCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeC
Confidence            689999999999999999999999999999999999999999999973 3355554433

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.44  E-value=8.2e-14  Score=112.17  Aligned_cols=57  Identities=19%  Similarity=0.132  Sum_probs=51.6

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeC
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      |..+|||||+++++|+|++.+++|||||+|+++..|.||+||+||.|+.+.+.+++.
T Consensus       545 ~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~  601 (956)
T PRK04914        545 DGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVP  601 (956)
T ss_pred             CCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEc
Confidence            568999999999999999999999999999999999999999999998876544443

>KOG0334|consensus

Probab=99.43  E-value=9.5e-14  Score=110.75  Aligned_cols=71  Identities=24%  Similarity=0.422  Sum_probs=64.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|.+++||||+.+++|+|+.++.+|||||+|.-..+|+||+||+||.|+.|.|++|..+.+......+.+.
T Consensus       661 ~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~a  731 (997)
T KOG0334|consen  661 NGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKA  731 (997)
T ss_pred             ccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999776665555544

>PRK13766 Hef nuclease; Provisional

Probab=99.41  E-value=4.6e-13  Score=105.82  Aligned_cols=63  Identities=24%  Similarity=0.321  Sum_probs=56.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      +|+.+|||||+++++|+|+|++++||+||.|++..+|+||+||+||.+. +.++.++..+..+.
T Consensus       421 ~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t~ee  483 (773)
T PRK13766        421 AGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGTRDE  483 (773)
T ss_pred             cCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCChHH
Confidence            4789999999999999999999999999999999999999999999864 77777777665544

>PRK02362 ski2-like helicase; Provisional

Probab=99.40  E-value=1.9e-13  Score=107.79  Aligned_cols=73  Identities=26%  Similarity=0.404  Sum_probs=60.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC-----CCCCccceeeecceeccCCCc--ceEEEeeCccc-H-HHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG-----MPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHS-K-KSLEY   68 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~-----~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~-~-~~~~~   68 (101)
                      +|.++|||||+++++|+|+|.+++||+    ||     .|.+..+|.||+|||||.|.+  |.+++++...+ . +.++.
T Consensus       327 ~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~~~  406 (737)
T PRK02362        327 DRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYDELDELFER  406 (737)
T ss_pred             cCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCchhHHHHHHH
Confidence            689999999999999999999999997    66     588999999999999999865  88999987653 2 23445


Q ss_pred             HHHccc
Q psy7959          69 VIKTDT   74 (101)
Q Consensus        69 ~~~~~~   74 (101)
                      ++....
T Consensus       407 ~l~~~~  412 (737)
T PRK02362        407 YIWADP  412 (737)
T ss_pred             HHhCCC
Confidence            554333

>KOG0329|consensus

Probab=99.40  E-value=4.3e-14  Score=99.81  Aligned_cols=56  Identities=30%  Similarity=0.529  Sum_probs=53.5

Q ss_pred             EEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           8 ITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         8 lv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|||+.++||+|+..++.|+|||+|.+..+|+||+|||||.|..|.+|+|++..+.
T Consensus       302 ~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~d  357 (387)
T KOG0329|consen  302 LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  357 (387)
T ss_pred             hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhh
Confidence            89999999999999999999999999999999999999999999999999987643

>KOG0948|consensus

Probab=99.40  E-value=2.8e-13  Score=105.96  Aligned_cols=98  Identities=24%  Similarity=0.367  Sum_probs=85.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC----CCCCccceeeecceeccCCCc--ceEEEeeCcc-cHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG----MPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEH-SKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~----~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~-~~~~~~~~~   70 (101)
                      .|.+++|+||.++++|+++|.-++|+.    ||    ...+.-+|+|++|||||+|.+  |.+|.+++.. +....+.++
T Consensus       470 EGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrGivIlmiDekm~~~~ak~m~  549 (1041)
T KOG0948|consen  470 EGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRGIVILMIDEKMEPQVAKDML  549 (1041)
T ss_pred             ccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCCCceEEEEecCcCCHHHHHHHh
Confidence            478999999999999999998777765    33    256788999999999999964  9999999977 888999999


Q ss_pred             HcccchhHHHHHHHHHHHHHHHHHHhcCC
Q psy7959          71 KTDTSTKREQLELKFKNYLSMLEYCEQVP   99 (101)
Q Consensus        71 ~~~~~~~~~~~~~~~~~l~~m~~~~e~~~   99 (101)
                      +++.+.+...+...+.++.++++-.+-.|
T Consensus       550 kG~aD~LnSaFhLtYnMiLNLlRvEei~p  578 (1041)
T KOG0948|consen  550 KGSADPLNSAFHLTYNMILNLLRVEEISP  578 (1041)
T ss_pred             cCCCcchhhhhhhHHHHHHHHHHHccCCH
Confidence            99999999999999999999998766554

>KOG0339|consensus

Probab=99.39  E-value=1.7e-13  Score=103.72  Aligned_cols=72  Identities=19%  Similarity=0.268  Sum_probs=66.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTD   73 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~   73 (101)
                      ++...|||+||++++|+|+++++.|||||+..++..|.||+||+||.|..|.+++++++.|.+....+.++-
T Consensus       516 kk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnL  587 (731)
T KOG0339|consen  516 KKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNL  587 (731)
T ss_pred             hcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHHHH
Confidence            356889999999999999999999999999999999999999999999999999999999988777777653

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.39  E-value=4.4e-13  Score=104.79  Aligned_cols=61  Identities=23%  Similarity=0.326  Sum_probs=55.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeC-----CCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWG-----MPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~-----~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|+++|||||+.+++|+|+|++++|+++|     .|.+..+|+||+||+||. ..|.++++++..+.
T Consensus       490 ~G~i~VLV~t~~L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~  555 (655)
T TIGR00631       490 LGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITD  555 (655)
T ss_pred             cCCceEEEEcChhcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCH
Confidence            58899999999999999999999999988     799999999999999998 68999999887653

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

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.38  E-value=1.1e-13  Score=113.33  Aligned_cols=59  Identities=22%  Similarity=0.291  Sum_probs=51.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-CCCccceeeecceeccCCCcceEEEeeCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-p~~~~~~~qr~GR~gR~~~~~~~i~~~~~   60 (101)
                      +|+++|||||+++++|+|+|++++||..+. ..+.++|+||+||+||.|+.|.|++++..
T Consensus       859 ~Gk~~VLVaTdIierGIDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~  918 (1147)
T PRK10689        859 HQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  918 (1147)
T ss_pred             hcCCCEEEECchhhcccccccCCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCC
Confidence            589999999999999999999999994432 23456799999999999999999999864

>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=99.38  E-value=5.5e-13  Score=83.26  Aligned_cols=55  Identities=40%  Similarity=0.596  Sum_probs=50.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEE
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI   56 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~   56 (101)
                      +|..++|++|+++++|+|+|.+++||.++.|++...|.|++||++|.|+.+.+++
T Consensus        76 ~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~  130 (131)
T cd00079          76 EGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAIL  130 (131)
T ss_pred             cCCCcEEEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEe
Confidence            4568899999999999999999999999999999999999999999998777654

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.37  E-value=3.2e-13  Score=78.07  Aligned_cols=48  Identities=40%  Similarity=0.611  Sum_probs=45.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG   49 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~   49 (101)
                      +|..+||++|++++.|+|+++++.||.++.|++...|.|++||++|.|
T Consensus        35 ~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~g   82 (82)
T smart00490       35 NGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG   82 (82)
T ss_pred             cCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccCC
Confidence            366799999999999999999999999999999999999999999975

>KOG0354|consensus

Probab=99.37  E-value=8.9e-13  Score=103.21  Aligned_cols=56  Identities=32%  Similarity=0.463  Sum_probs=52.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+++|||||+++++|+|++.|++||-||...++-.++||.|| ||. ++|.++.+++
T Consensus       472 ~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa-~ns~~vll~t  527 (746)
T KOG0354|consen  472 DGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRA-RNSKCVLLTT  527 (746)
T ss_pred             CCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-ccc-cCCeEEEEEc
Confidence            5999999999999999999999999999999999999999999 998 5677777777

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.34  E-value=1.7e-12  Score=101.57  Aligned_cols=59  Identities=24%  Similarity=0.313  Sum_probs=53.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-----CCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-----PSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-----p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      .|++.|||||+.+++|+|+|++++||++|.     |.+..+|+||+||+||. ..|.++.+++..
T Consensus       494 ~g~i~vlV~t~~L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~  557 (652)
T PRK05298        494 LGEFDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKI  557 (652)
T ss_pred             cCCceEEEEeCHHhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCC
Confidence            578999999999999999999999999884     78999999999999996 689999999843

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.33  E-value=4.2e-13  Score=110.31  Aligned_cols=62  Identities=23%  Similarity=0.258  Sum_probs=54.7

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCC------------------CCccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMP------------------SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p------------------~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      ..+|||||++++.|+|+|+|++||++|++                  .|.++|.||+||+||.+ +|.|+.+++..++..
T Consensus       330 ~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~  408 (1283)
T TIGR01967       330 GRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNS  408 (1283)
T ss_pred             CceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHh
Confidence            46999999999999999999999999853                  35679999999999997 999999999877654


Q ss_pred             H
Q psy7959          66 L   66 (101)
Q Consensus        66 ~   66 (101)
                      .
T Consensus       409 ~  409 (1283)
T TIGR01967       409 R  409 (1283)
T ss_pred             h
Confidence            3

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.32  E-value=8.9e-13  Score=95.75  Aligned_cols=57  Identities=25%  Similarity=0.214  Sum_probs=46.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcc----eEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQS----YCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~----~~i~~~~~~   61 (101)
                      +|..+|||||+++++|+|++ +++||++..|  +.+|+||+||+||.|+..    ..+++....
T Consensus       276 ~~~~~ilvaT~~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       276 KNEKFVIVATQVIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             CCCCeEEEECcchhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence            46789999999999999995 8899998766  679999999999998642    455554433

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.32  E-value=1.2e-12  Score=103.21  Aligned_cols=58  Identities=26%  Similarity=0.244  Sum_probs=53.4

Q ss_pred             eeEEEEccccccccCCC---------CccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           5 INVITATISFGMGIDRQ---------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~---------~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      -+|+||||+++||+|++         ++.+|++++.|..... .||+||+||.|.+|.++.+++..|.
T Consensus       473 g~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       473 GAVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             CeEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            47999999999999999         9999999999988777 9999999999999999999987653

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.30  E-value=2.2e-12  Score=101.63  Aligned_cols=72  Identities=29%  Similarity=0.358  Sum_probs=56.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE-------eCCCC-CccceeeecceeccCC--CcceEEEeeCccc-HHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH-------WGMPS-SIPAYYQESGRAGRDG--LQSYCRIYHSEHS-KKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~-------~~~p~-~~~~~~qr~GR~gR~~--~~~~~i~~~~~~~-~~~~~~~~   70 (101)
                      +|.++|||||+++++|+|+|.+++||.       ++.|. +..+|.||+|||||.|  ..|.+++++...+ .+.+..++
T Consensus       319 ~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~~~~~~~~~~  398 (720)
T PRK00254        319 EGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMERYI  398 (720)
T ss_pred             CCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcchHHHHHHHH
Confidence            689999999999999999999999994       45543 5678999999999976  4589999987654 33455554


Q ss_pred             Hcc
Q psy7959          71 KTD   73 (101)
Q Consensus        71 ~~~   73 (101)
                      .+.
T Consensus       399 ~~~  401 (720)
T PRK00254        399 FGK  401 (720)
T ss_pred             hCC
Confidence            443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.29  E-value=1.8e-12  Score=101.92  Aligned_cols=61  Identities=26%  Similarity=0.192  Sum_probs=56.3

Q ss_pred             CceeEEEEccccccccCCCC-------ccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           3 GEINVITATISFGMGIDRQN-------VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~-------v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +...|+|||++++||+|++.       ..+||+++.|.+...|.|+.||+||.|.+|.+..+++..|.
T Consensus       452 ~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       452 RKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             CCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHH
Confidence            56899999999999999998       45999999999999999999999999999999999987653

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.

>KOG0337|consensus

Probab=99.27  E-value=4.1e-12  Score=94.41  Aligned_cols=63  Identities=14%  Similarity=0.226  Sum_probs=58.7

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      ++..+||.||+++||+|+|-.+.|||||+|.+..-|+||+||+.|+|+.|.++.++.+.+...
T Consensus       310 ~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~y  372 (529)
T KOG0337|consen  310 RKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPY  372 (529)
T ss_pred             CccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccchh
Confidence            567899999999999999999999999999999999999999999999999999998876543

>KOG0349|consensus

Probab=99.25  E-value=4.4e-12  Score=95.05  Aligned_cols=63  Identities=17%  Similarity=0.297  Sum_probs=58.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      ++++++|||||+++||+|+-.+.++||..+|.+..+|+||+||.||+.+-|.+|.++.....+
T Consensus       556 k~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~ek  618 (725)
T KOG0349|consen  556 KFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPEK  618 (725)
T ss_pred             hcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchhhhcceeEEEeeccchh
Confidence            467999999999999999999999999999999999999999999999999999998866444

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.23  E-value=1e-11  Score=97.57  Aligned_cols=77  Identities=22%  Similarity=0.238  Sum_probs=60.9

Q ss_pred             CCceeEEEEccccccccCCCCccEE--EEeCCCCCc----------cceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFV--VHWGMPSSI----------PAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~v--i~~~~p~~~----------~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|+.+|||+|+++++|+|+|+|++|  +++|.+.+.          ..|+|++||+||.+..|.++......+...++.+
T Consensus       478 ~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~~~~~~  557 (679)
T PRK05580        478 RGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQAL  557 (679)
T ss_pred             cCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCHHHHHH
Confidence            4789999999999999999999988  456655544          4589999999999999999988776666666666


Q ss_pred             HHcccchhH
Q psy7959          70 IKTDTSTKR   78 (101)
Q Consensus        70 ~~~~~~~~~   78 (101)
                      ...+.....
T Consensus       558 ~~~d~~~f~  566 (679)
T PRK05580        558 LAQDYDAFA  566 (679)
T ss_pred             HhCCHHHHH
Confidence            655554443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.23  E-value=4.8e-12  Score=100.24  Aligned_cols=58  Identities=31%  Similarity=0.245  Sum_probs=54.3

Q ss_pred             eeEEEEccccccccCC---CCcc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDR---QNVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~---~~v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -.|+|||++++||+|+   ++|.     +||++++|.+...|.|+.||+||.|.+|.+..+++..|
T Consensus       489 g~VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD  554 (796)
T PRK12906        489 GAVTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLED  554 (796)
T ss_pred             ceEEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccc
Confidence            4599999999999999   4899     99999999999999999999999999999999998764

>PRK01172 ski2-like helicase; Provisional

Probab=99.23  E-value=7.3e-12  Score=98.00  Aligned_cols=71  Identities=25%  Similarity=0.256  Sum_probs=54.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC---------CCCccceeeecceeccCCC--cceEEEeeCcc-cHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM---------PSSIPAYYQESGRAGRDGL--QSYCRIYHSEH-SKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~---------p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~-~~~~~~~~   69 (101)
                      +|.++|||||+++++|+|+|+..+|| .|.         |.+..+|.||+|||||.|.  .|.+++++... +.+.++.+
T Consensus       309 ~g~i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~~~~~~~~  387 (674)
T PRK01172        309 NRYIKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKKY  387 (674)
T ss_pred             cCCCeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcccHHHHHHH
Confidence            58899999999999999999875555 332         5678889999999999985  46677776654 35666666


Q ss_pred             HHcc
Q psy7959          70 IKTD   73 (101)
Q Consensus        70 ~~~~   73 (101)
                      +...
T Consensus       388 l~~~  391 (674)
T PRK01172        388 LSGE  391 (674)
T ss_pred             HcCC
Confidence            6443

>TIGR00595 priA primosomal protein N'

Probab=99.23  E-value=1.9e-11  Score=93.31  Aligned_cols=76  Identities=18%  Similarity=0.194  Sum_probs=57.8

Q ss_pred             CCceeEEEEccccccccCCCCccEE--EEeCCCCC----------ccceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFV--VHWGMPSS----------IPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~v--i~~~~p~~----------~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|+.+|||+|+++++|+|+|+|++|  +++|...+          ...|+|++||+||.+..|.+++.....+...+..+
T Consensus       310 ~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~~~~~~~  389 (505)
T TIGR00595       310 NGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAA  389 (505)
T ss_pred             cCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCCHHHHHH
Confidence            5789999999999999999999988  46665433          35679999999999989999877665555555555


Q ss_pred             HHcccchh
Q psy7959          70 IKTDTSTK   77 (101)
Q Consensus        70 ~~~~~~~~   77 (101)
                      ...++...
T Consensus       390 ~~~d~~~f  397 (505)
T TIGR00595       390 LTGDYEAF  397 (505)
T ss_pred             HhCCHHHH
Confidence            55444333

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).

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

Probab=99.21  E-value=1.3e-11  Score=97.99  Aligned_cols=59  Identities=34%  Similarity=0.564  Sum_probs=53.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccC-CCcceEEEeeCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD-GLQSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~-~~~~~~i~~~~~   60 (101)
                      +|+++++|||+.++.|||+.+|+.||+++.|.+.+.++||+||+|+. +..+.++.+..+
T Consensus       302 ~G~lravV~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         302 EGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             cCCceEEEEccchhhccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            68999999999999999999999999999999999999999999977 445777766655

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.19  E-value=2.5e-11  Score=92.39  Aligned_cols=58  Identities=22%  Similarity=0.148  Sum_probs=49.3

Q ss_pred             CCceeEEEEc-cccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITAT-ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T-~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+.+||||| +++++|+|+|+++.||+++.+.+...|+||+||++|.+.....+.+++
T Consensus       392 ~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K~~~~i~D  450 (501)
T PHA02558        392 GGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWD  450 (501)
T ss_pred             CCCCeEEEEEcceeccccccccccEEEEecCCcchhhhhhhhhccccCCCCCceEEEEE
Confidence            3667899998 899999999999999999999999999999999999976544444443

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.11  E-value=2.4e-11  Score=97.65  Aligned_cols=61  Identities=31%  Similarity=0.267  Sum_probs=54.2

Q ss_pred             CceeEEEEccccccccCCC---Ccc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           3 GEINVITATISFGMGIDRQ---NVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~---~v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +...|+|||++++||+|++   +|.     +||++..|.+...|.|+.||+||.|.+|.++.|++..|.
T Consensus       645 ~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        645 QKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             CCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHH
Confidence            4578999999999999999   564     458899999999999999999999999999999997653

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.11  E-value=6.1e-11  Score=93.56  Aligned_cols=62  Identities=18%  Similarity=0.077  Sum_probs=53.9

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCC-CCccceeeecceeccCCCcceE-------EEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMP-SSIPAYYQESGRAGRDGLQSYC-------RIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p-~~~~~~~qr~GR~gR~~~~~~~-------i~~~~~~~~~   64 (101)
                      |++++||+|+++.+|+|+|++++||+++.| .+..+|+||+||++|.+..+.+       +.+++.+..+
T Consensus       541 ~~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E  610 (732)
T TIGR00603       541 PKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQE  610 (732)
T ss_pred             CCccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchH
Confidence            478999999999999999999999999988 4999999999999999765443       7788876544

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).

>KOG0947|consensus

Probab=99.11  E-value=2.2e-10  Score=91.78  Aligned_cols=92  Identities=28%  Similarity=0.411  Sum_probs=75.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC---------CCCccceeeecceeccCCCc--ceEEEeeCcc--cHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM---------PSSIPAYYQESGRAGRDGLQ--SYCRIYHSEH--SKKSLEY   68 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~---------p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~--~~~~~~~   68 (101)
                      +|-+|||+||.++++|+++|.-.+|+. .+         -..+.+|.|++|||||+|-+  |.+|++....  +...++.
T Consensus       654 rGlVKVLFATETFAMGVNMPARtvVF~-Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~~vp~~a~l~~  732 (1248)
T KOG0947|consen  654 RGLVKVLFATETFAMGVNMPARTVVFS-SLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKDSVPSAATLKR  732 (1248)
T ss_pred             cCceEEEeehhhhhhhcCCCceeEEee-ehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecCCCCCHHHHhh
Confidence            588999999999999999998666654 22         35789999999999999964  7888877754  6778899


Q ss_pred             HHHcccchhHHHHHHHHHHHHHHHHH
Q psy7959          69 VIKTDTSTKREQLELKFKNYLSMLEY   94 (101)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~l~~m~~~   94 (101)
                      ++.+....+..++...+.++.++++-
T Consensus       733 li~G~~~~L~SQFRlTY~MILnLLRv  758 (1248)
T KOG0947|consen  733 LIMGGPTRLESQFRLTYGMILNLLRV  758 (1248)
T ss_pred             HhcCCCchhhhhhhhHHHHHHHHHHH
Confidence            99999999998888888877776653

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

Probab=99.10  E-value=4.2e-11  Score=95.48  Aligned_cols=52  Identities=17%  Similarity=0.085  Sum_probs=43.9

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc-ceEEEeeC
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ-SYCRIYHS   59 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~-~~~i~~~~   59 (101)
                      .+|||||+++++|+|++. ++||++..|  .++|+||+||+||.|+. +..++++.
T Consensus       337 ~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~  389 (844)
T TIGR02621       337 TVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVH  389 (844)
T ss_pred             ceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEe
Confidence            689999999999999986 889987766  58999999999999985 44466553

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.

>KOG0953|consensus

Probab=99.07  E-value=1.5e-10  Score=88.57  Aligned_cols=77  Identities=23%  Similarity=0.359  Sum_probs=63.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC---------CCCccceeeecceeccCCCc--ceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM---------PSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~---------p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~~~~~~~~   70 (101)
                      +++++||||||+++||+++ +++.||.+++         |.+.++..|-+|||||.|..  ..-++-+...|+..++.++
T Consensus       407 ~~e~dvlVAsDAIGMGLNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~~eDL~~L~~~l  485 (700)
T KOG0953|consen  407 SNECDVLVASDAIGMGLNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLHSEDLKLLKRIL  485 (700)
T ss_pred             CCccceEEeeccccccccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEeeHhhHHHHHHHH
Confidence            4689999999999999998 7999998885         56788899999999999753  3345555678889999999


Q ss_pred             HcccchhHH
Q psy7959          71 KTDTSTKRE   79 (101)
Q Consensus        71 ~~~~~~~~~   79 (101)
                      +...++...
T Consensus       486 ~~p~epi~~  494 (700)
T KOG0953|consen  486 KRPVEPIKN  494 (700)
T ss_pred             hCCchHHHh
Confidence            988877744

>KOG4150|consensus

Probab=99.06  E-value=1e-10  Score=90.17  Aligned_cols=62  Identities=32%  Similarity=0.445  Sum_probs=57.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|++.-++||++++.|+|+.+++.|++.++|.+.+++.|..|||||+++++.++.+......
T Consensus       581 ~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PV  642 (1034)
T KOG4150|consen  581 GGKLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPV  642 (1034)
T ss_pred             CCeeeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccch
Confidence            47889999999999999999999999999999999999999999999999998888776543

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.02  E-value=1.1e-10  Score=85.65  Aligned_cols=40  Identities=20%  Similarity=0.551  Sum_probs=35.8

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceec
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG   46 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~g   46 (101)
                      +.+||||||++++|+|++.+ +|| ++ |.+..+|+||+||+|
T Consensus       318 ~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       318 QFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             cCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            57899999999999999986 666 55 999999999999987

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.

>PRK14701 reverse gyrase; Provisional

Probab=98.95  E-value=3.2e-10  Score=95.55  Aligned_cols=71  Identities=18%  Similarity=0.292  Sum_probs=57.5

Q ss_pred             CCceeEEEEc----cccccccCCCC-ccEEEEeCCCC---Cccceeeec-------------ceeccCCCcceEEEeeCc
Q psy7959           2 RGEINVITAT----ISFGMGIDRQN-VRFVVHWGMPS---SIPAYYQES-------------GRAGRDGLQSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T----~~~~~G~d~~~-v~~vi~~~~p~---~~~~~~qr~-------------GR~gR~~~~~~~i~~~~~   60 (101)
                      +|+++|||||    ++++||||+|+ |++|||+|+|+   +...|.|..             ||+||.|..+.++..+..
T Consensus       376 ~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~~  455 (1638)
T PRK14701        376 EGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFP  455 (1638)
T ss_pred             cCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHHhHH
Confidence            6899999999    58999999999 99999999999   888888877             999999887666644444


Q ss_pred             ccHHHHHHHHHc
Q psy7959          61 HSKKSLEYVIKT   72 (101)
Q Consensus        61 ~~~~~~~~~~~~   72 (101)
                      .+...++.+++.
T Consensus       456 ~~~~~~~~~l~~  467 (1638)
T PRK14701        456 EDVEFLRSILKD  467 (1638)
T ss_pred             HHHHHHHHHhcc
Confidence            555555555544

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

Probab=98.82  E-value=5.9e-09  Score=82.43  Aligned_cols=78  Identities=23%  Similarity=0.271  Sum_probs=65.8

Q ss_pred             CCceeEEEEccccccccCCCCccEE--EEeCCCCC----------ccceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFV--VHWGMPSS----------IPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~v--i~~~~p~~----------~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|+.+|||.|+++++|.|+|+++.|  ++.|.-..          ...+.|-+|||||.+.+|.+++.....+...++.+
T Consensus       532 ~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~  611 (730)
T COG1198         532 NGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQAL  611 (730)
T ss_pred             CCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHHHHH
Confidence            5899999999999999999999977  45553322          33357999999999999999999999999999999


Q ss_pred             HHcccchhHH
Q psy7959          70 IKTDTSTKRE   79 (101)
Q Consensus        70 ~~~~~~~~~~   79 (101)
                      +.+++....+
T Consensus       612 ~~~dy~~F~~  621 (730)
T COG1198         612 KRGDYEAFYE  621 (730)
T ss_pred             HhcCHHHHHH
Confidence            9998877764

>KOG0922|consensus

Probab=98.77  E-value=3.6e-09  Score=82.09  Aligned_cols=72  Identities=25%  Similarity=0.293  Sum_probs=60.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|..||+++|++++-.+.++++.+||+-++                  |.|.++..||+|||||. .+|.|+.+|+..++
T Consensus       314 ~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt-~pGkcyRLYte~~~  392 (674)
T KOG0922|consen  314 PGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRT-GPGKCYRLYTESAY  392 (674)
T ss_pred             CCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCC-CCceEEEeeeHHHH
Confidence            378899999999999999999999998774                  66888899999999998 59999999998877


Q ss_pred             HHHHHHHHcccchh
Q psy7959          64 KSLEYVIKTDTSTK   77 (101)
Q Consensus        64 ~~~~~~~~~~~~~~   77 (101)
                      +   .+..+..++.
T Consensus       393 ~---~~~~~~~PEI  403 (674)
T KOG0922|consen  393 D---KMPLQTVPEI  403 (674)
T ss_pred             h---hcccCCCCce
Confidence            4   4444444444

>KOG0924|consensus

Probab=98.77  E-value=7e-09  Score=81.33  Aligned_cols=74  Identities=26%  Similarity=0.357  Sum_probs=60.2

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      |..+|+|||++++-.+.++++.+||..+.                  |.|.++..||+|||||.| +|.|+.+|+...+.
T Consensus       622 ~vRK~IvATNIAETSLTi~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~ay~  700 (1042)
T KOG0924|consen  622 GVRKCIVATNIAETSLTIPGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTEDAYK  700 (1042)
T ss_pred             CceeEEEeccchhhceeecceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCC-CcceeeehhhhHHH
Confidence            66899999999999999999999999774                  778888999999999984 99999999865433


Q ss_pred             HHHHHHHcccchhHH
Q psy7959          65 SLEYVIKTDTSTKRE   79 (101)
Q Consensus        65 ~~~~~~~~~~~~~~~   79 (101)
                        ..++....++..+
T Consensus       701 --~eml~stvPEIqR  713 (1042)
T KOG0924|consen  701 --NEMLPSTVPEIQR  713 (1042)
T ss_pred             --hhcccCCCchhhh
Confidence              2455555555543

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

Probab=98.76  E-value=8.6e-09  Score=80.39  Aligned_cols=61  Identities=31%  Similarity=0.467  Sum_probs=55.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-CCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +|+++|||||.+.+.|+|+|+.++.|-.+. -...+++.|--||.||.+..+.|+.++.+..
T Consensus       531 ~~e~~ILVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         531 EGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             cCCCcEEEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence            589999999999999999999998877764 3688999999999999999999999999765

>KOG0923|consensus

Probab=98.75  E-value=5.9e-09  Score=81.37  Aligned_cols=62  Identities=26%  Similarity=0.384  Sum_probs=54.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|..+|++||++++-.+.+++|.+||+-+.                  |.|-++..||+|||||.| +|.|+.+|+.+.+
T Consensus       530 ~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt~~aY  608 (902)
T KOG0923|consen  530 PGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYTAWAY  608 (902)
T ss_pred             CCceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeechhhh
Confidence            366899999999999999999999998664                  667888899999999985 9999999996654


Q ss_pred             H
Q psy7959          64 K   64 (101)
Q Consensus        64 ~   64 (101)
                      .
T Consensus       609 ~  609 (902)
T KOG0923|consen  609 E  609 (902)
T ss_pred             h
Confidence            4

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

Probab=98.75  E-value=5.6e-09  Score=83.64  Aligned_cols=61  Identities=30%  Similarity=0.372  Sum_probs=53.5

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      |+.||++||++++-+|.+++|++||+-+.                  |.|.++..||.|||||- ..|.|+-+|+..++.
T Consensus       312 ~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~-~pGicyRLyse~~~~  390 (845)
T COG1643         312 GKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRT-GPGICYRLYSEEDFL  390 (845)
T ss_pred             CcceEEEEccccccceeeCCeEEEecCCcccccccccccCceeeeEEEechhhhhhhccccccC-CCceEEEecCHHHHH
Confidence            34569999999999999999999998774                  56788899999999998 599999999976655

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

Probab=98.71  E-value=1.5e-08  Score=82.26  Aligned_cols=94  Identities=26%  Similarity=0.327  Sum_probs=76.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC----CCCCccceeeecceeccCCCc--ceEEEeeCcc--cHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG----MPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEH--SKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~----~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~--~~~~~~~~   69 (101)
                      .|.++|++||.+++.|+++|.-+.|+-    ||    .+.++.+|.|..|||||.|.+  |.+|++..+.  +......+
T Consensus       468 ~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~~~~~~~e~~~l  547 (1041)
T COG4581         468 EGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPPFESEPSEAAGL  547 (1041)
T ss_pred             ccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCCCCCChHHHHHh
Confidence            588999999999999999998666642    33    367899999999999999975  8888885543  46788899


Q ss_pred             HHcccchhHHHHHHHHHHHHHHHHHH
Q psy7959          70 IKTDTSTKREQLELKFKNYLSMLEYC   95 (101)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~l~~m~~~~   95 (101)
                      ...+...+...+...+.++.++++..
T Consensus       548 ~~~~~~~L~s~f~~sy~milnll~v~  573 (1041)
T COG4581         548 ASGKLDPLRSQFRLSYNMILNLLRVE  573 (1041)
T ss_pred             hcCCCccchhheecchhHHHhhhhhc
Confidence            99999999988888888877776653

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

Probab=98.67  E-value=5.8e-09  Score=83.90  Aligned_cols=62  Identities=31%  Similarity=0.510  Sum_probs=55.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-CccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|++.++++|++++.|+|+.+++.||..+.|. +..+++||+||+||.++.+..+.....+..
T Consensus       362 ~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~~~~  424 (851)
T COG1205         362 EGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRSDPL  424 (851)
T ss_pred             cCCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCCCcc
Confidence            58899999999999999999999999999999 899999999999999977777777764443

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

Probab=98.67  E-value=1.9e-08  Score=82.09  Aligned_cols=60  Identities=27%  Similarity=0.391  Sum_probs=53.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-CCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+.+|||||.+.+-|+|+|+++.+|--+. -...++++|--||.||..+.+.|+.++.+.
T Consensus       853 ~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         853 NGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             cCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            689999999999999999999997765442 478999999999999999999999998854

>PRK09401 reverse gyrase; Reviewed

Probab=98.59  E-value=1.9e-08  Score=83.20  Aligned_cols=45  Identities=24%  Similarity=0.302  Sum_probs=41.8

Q ss_pred             CCceeEEEE----ccccccccCCCC-ccEEEEeCCCC------Cccceeeecceec
Q psy7959           2 RGEINVITA----TISFGMGIDRQN-VRFVVHWGMPS------SIPAYYQESGRAG   46 (101)
Q Consensus         2 ~g~~~vlv~----T~~~~~G~d~~~-v~~vi~~~~p~------~~~~~~qr~GR~g   46 (101)
                      +|+++||||    ||+++||+|+|+ |++|||||+|.      ....|.||.||+-
T Consensus       374 ~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~  429 (1176)
T PRK09401        374 EGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLL  429 (1176)
T ss_pred             CCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHH
Confidence            689999999    699999999999 89999999998      6788999999985

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.55  E-value=1.1e-07  Score=75.98  Aligned_cols=60  Identities=23%  Similarity=0.448  Sum_probs=49.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC-----CCCCccceeeecceeccCCC--cceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG-----MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~-----~p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~   61 (101)
                      .|+++|||||++++.|++.|.-+.||-    |+     .+.+..+|.|+.|||||.|=  .|.++++.+..
T Consensus       338 ~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~~~~~  408 (766)
T COG1204         338 KGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSH  408 (766)
T ss_pred             cCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEEecCc
Confidence            589999999999999999998777663    66     56788899999999999984  36677776433

>KOG0926|consensus

Probab=98.54  E-value=6.2e-08  Score=77.17  Aligned_cols=60  Identities=28%  Similarity=0.336  Sum_probs=50.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      .|..-|+|||++++-.+.+|+|++||+.+.                  ..|.++.-||+|||||.| .|+|+.+|+..-
T Consensus       628 ~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSSAV  705 (1172)
T KOG0926|consen  628 KGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSSAV  705 (1172)
T ss_pred             CCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhhHH
Confidence            466779999999999999999999999774                  245666689999999985 899999998653

>KOG0949|consensus

Probab=98.53  E-value=1.2e-07  Score=76.67  Aligned_cols=79  Identities=19%  Similarity=0.289  Sum_probs=57.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeC-CCCCccceeeecceeccCCCc--ceEEEeeCcccHHHHHHHHHcccchhH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWG-MPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSKKSLEYVIKTDTSTKR   78 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~-~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~   78 (101)
                      +|.+.||+||.+++.|+++|.-++|.--| +-.++..|.|++|||||+|=+  |.++.+-  -.....+.++......+.
T Consensus       986 ~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~Fmg--iP~~kv~rLlts~L~diq 1063 (1330)
T KOG0949|consen  986 QGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFMG--IPRQKVQRLLTSLLPDIQ 1063 (1330)
T ss_pred             cCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEEe--CcHHHHHHHHHHhhhccc
Confidence            57899999999999999999766665555 567899999999999999854  5555443  234445555555555554


Q ss_pred             HHHH
Q psy7959          79 EQLE   82 (101)
Q Consensus        79 ~~~~   82 (101)
                      ...+
T Consensus      1064 G~~p 1067 (1330)
T KOG0949|consen 1064 GAYP 1067 (1330)
T ss_pred             CCCc
Confidence            4333

>KOG0950|consensus

Probab=98.51  E-value=1.1e-07  Score=76.36  Aligned_cols=78  Identities=22%  Similarity=0.307  Sum_probs=66.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC----CCCccceeeecceeccCCCc--ceEEEeeCcccHHHHHHHHHcccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM----PSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSKKSLEYVIKTDTS   75 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~----p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~~~~~~~~~~~~~   75 (101)
                      .|-+.|++||+.++-|++.|..+++|-+-.    ..+..+|.|++|||||.|.+  |.+|+.+...+......++.....
T Consensus       546 ~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~~~~lv~~~~~  625 (1008)
T KOG0950|consen  546 EGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRVRELVNSPLK  625 (1008)
T ss_pred             hcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhHHHHHHhcccc
Confidence            578999999999999999999999887553    46788999999999999864  889999999998877788887776


Q ss_pred             hhHH
Q psy7959          76 TKRE   79 (101)
Q Consensus        76 ~~~~   79 (101)
                      ....
T Consensus       626 ~~~S  629 (1008)
T KOG0950|consen  626 PLNS  629 (1008)
T ss_pred             cccc
Confidence            6654

>PRK09694 helicase Cas3; Provisional

Probab=98.44  E-value=7.1e-08  Score=77.86  Aligned_cols=43  Identities=19%  Similarity=0.273  Sum_probs=38.8

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCC
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL   50 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~   50 (101)
                      .+|||||+++++|+|+ +++++|....|  ..+++||+||+||.+.
T Consensus       622 ~~ILVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        622 GRILVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             CeEEEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            4799999999999999 58999998777  5799999999999975

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

Probab=98.39  E-value=3.8e-07  Score=67.03  Aligned_cols=58  Identities=24%  Similarity=0.253  Sum_probs=45.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE-eCC-CCCccceeeecceeccCCC-c-ceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH-WGM-PSSIPAYYQESGRAGRDGL-Q-SYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~-~~~-p~~~~~~~qr~GR~gR~~~-~-~~~i~~~~   59 (101)
                      +|++++|++|.+++||+.+|+|++.+. ..- -.+.+.++|.+||+||.-. + |..+.|..
T Consensus       353 ~G~~~lLiTTTILERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH~  414 (441)
T COG4098         353 DGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFHY  414 (441)
T ss_pred             cCceEEEEEeehhhcccccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEec
Confidence            689999999999999999999996554 332 3678889999999999854 3 55555543

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

Probab=98.39  E-value=2.2e-07  Score=70.06  Aligned_cols=47  Identities=21%  Similarity=0.297  Sum_probs=44.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD   48 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~   48 (101)
                      +|++++||++.++.+|+|+|+++.+|......|...|+||+||.-|.
T Consensus       330 ~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         330 TGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             cCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            35689999999999999999999999999999999999999999993

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.35  E-value=4.6e-07  Score=74.23  Aligned_cols=59  Identities=19%  Similarity=0.185  Sum_probs=50.9

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcc--eEEEeeCcccH
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQS--YCRIYHSEHSK   63 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~--~~i~~~~~~~~   63 (101)
                      .-+|++|.+++.|||+...++||+||.|+++....|+.||+-|.|+..  .++.++..+..
T Consensus       541 ~VfLLSTrAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTI  601 (1033)
T PLN03142        541 FVFLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTI  601 (1033)
T ss_pred             eEEEEeccccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcH
Confidence            457899999999999999999999999999999999999999999763  35556666543

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

Probab=98.30  E-value=4.5e-07  Score=74.92  Aligned_cols=45  Identities=27%  Similarity=0.189  Sum_probs=42.7

Q ss_pred             eEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCC
Q psy7959           6 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL   50 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~   50 (101)
                      +|+|+++++..|+|+|.|..||.+..+.|...|+|++||+.|...
T Consensus       758 ~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~~~  802 (1123)
T PRK11448        758 NIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRLCP  802 (1123)
T ss_pred             eEEEEecccccCCCcccccEEEEecCCCCHHHHHHHHhhhccCCc
Confidence            699999999999999999999999999999999999999999743

>KOG0920|consensus

Probab=98.23  E-value=4.6e-07  Score=73.18  Aligned_cols=62  Identities=26%  Similarity=0.284  Sum_probs=52.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|..||+++|++++-.|-+++|-+||+.+.                  +.+.++..||.|||||. .+|.|+.+++...+
T Consensus       468 ~g~RKIIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~  546 (924)
T KOG0920|consen  468 KGTRKIILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRY  546 (924)
T ss_pred             CCcchhhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhh
Confidence            467899999999999999999999998764                  23556668999999998 79999999987655


Q ss_pred             H
Q psy7959          64 K   64 (101)
Q Consensus        64 ~   64 (101)
                      +
T Consensus       547 ~  547 (924)
T KOG0920|consen  547 E  547 (924)
T ss_pred             h
Confidence            4

>KOG0925|consensus

Probab=98.14  E-value=1.6e-06  Score=66.24  Aligned_cols=60  Identities=25%  Similarity=0.315  Sum_probs=52.4

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      ..||+|+|++++-.+.+++|.+||+-++                  |.|.++..||.||+||. .+|.|+.+|++..+.
T Consensus       313 ~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~~~  390 (699)
T KOG0925|consen  313 GRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAFE  390 (699)
T ss_pred             cceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHhhh
Confidence            3689999999999999999999998764                  78888999999999997 689999999865443

>TIGR01054 rgy reverse gyrase

Probab=98.13  E-value=1.9e-06  Score=71.62  Aligned_cols=32  Identities=34%  Similarity=0.619  Sum_probs=29.9

Q ss_pred             CCceeEEEE----ccccccccCCCC-ccEEEEeCCCC
Q psy7959           2 RGEINVITA----TISFGMGIDRQN-VRFVVHWGMPS   33 (101)
Q Consensus         2 ~g~~~vlv~----T~~~~~G~d~~~-v~~vi~~~~p~   33 (101)
                      +|+++||||    ||+++||+|+|+ |++|||||+|.
T Consensus       373 ~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~  409 (1171)
T TIGR01054       373 EGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPK  409 (1171)
T ss_pred             cCCCCEEEEeccccCcccccCCCCccccEEEEECCCC
Confidence            689999999    599999999999 89999999995

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.

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

Probab=98.06  E-value=6.5e-06  Score=63.47  Aligned_cols=58  Identities=24%  Similarity=0.345  Sum_probs=50.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeC-----CCCCccceeeecceeccCCCcceEEEeeCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWG-----MPSSIPAYYQESGRAGRDGLQSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~-----~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~   60 (101)
                      .|.++|||+-+.+-+|+|+|.|.+|-..|     +..|..+++|-+|||+|+ -+|.+|.+.+.
T Consensus       494 ~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN-~~GkvIlYAD~  556 (663)
T COG0556         494 LGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADK  556 (663)
T ss_pred             cCCccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhc-cCCeEEEEchh
Confidence            48899999999999999999999997766     467899999999999997 47888877653

>KOG0952|consensus

Probab=98.00  E-value=1.8e-05  Score=64.68  Aligned_cols=85  Identities=21%  Similarity=0.244  Sum_probs=65.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCC-----------CCccceeeecceeccCC--CcceEEEeeCcccHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMP-----------SSIPAYYQESGRAGRDG--LQSYCRIYHSEHSKKSLEY   68 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p-----------~~~~~~~qr~GR~gR~~--~~~~~i~~~~~~~~~~~~~   68 (101)
                      .|-++||+||..++-|+++|+ -.||..+-+           .+....+|..|||||.+  ..|.++++.+.+-.+.+-.
T Consensus       420 ~G~i~vL~cTaTLAwGVNLPA-~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~s  498 (1230)
T KOG0952|consen  420 EGHIKVLCCTATLAWGVNLPA-YAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYES  498 (1230)
T ss_pred             cCCceEEEecceeeeccCCcc-eEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHH
Confidence            578999999999999999997 455554432           13455689999999985  5688888888888889999


Q ss_pred             HHHcccchhHHHHHHHHHH
Q psy7959          69 VIKTDTSTKREQLELKFKN   87 (101)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~   87 (101)
                      ++.+..+...+-.....+.
T Consensus       499 Ll~~~~piES~~~~~L~dn  517 (1230)
T KOG0952|consen  499 LLTGQNPIESQLLPCLIDN  517 (1230)
T ss_pred             HHcCCChhHHHHHHHHHHh
Confidence            9999887766544444443

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=97.98  E-value=6.6e-06  Score=66.21  Aligned_cols=60  Identities=28%  Similarity=0.167  Sum_probs=49.6

Q ss_pred             CceeEEEEccccccccCCCCc--------------------------------------cEEEEeCCCCCccceeeecce
Q psy7959           3 GEINVITATISFGMGIDRQNV--------------------------------------RFVVHWGMPSSIPAYYQESGR   44 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v--------------------------------------~~vi~~~~p~~~~~~~qr~GR   44 (101)
                      +...|+||||+++||+|++==                                      -+||-...|.|.--=.|-.||
T Consensus       477 ~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGR  556 (830)
T PRK12904        477 RPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGR  556 (830)
T ss_pred             CCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcc
Confidence            568999999999999998621                                      167777777777767899999


Q ss_pred             eccCCCcceEEEeeCccc
Q psy7959          45 AGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus        45 ~gR~~~~~~~i~~~~~~~   62 (101)
                      +||-|.+|.+-.+++-.|
T Consensus       557 agRQGdpGss~f~lSleD  574 (830)
T PRK12904        557 SGRQGDPGSSRFYLSLED  574 (830)
T ss_pred             cccCCCCCceeEEEEcCc
Confidence            999999999999888654

>KOG0951|consensus

Probab=97.97  E-value=9.3e-06  Score=67.47  Aligned_cols=85  Identities=15%  Similarity=0.187  Sum_probs=68.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC------CCCCccceeeecceeccCCCc--ceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG------MPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~------~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~~~~~~~   69 (101)
                      +|.++|||+|-.++.|++.|.-+++|-    ||      .+.++.+.+|+.|||||.+-+  |..+......++..+..+
T Consensus       631 ~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls~  710 (1674)
T KOG0951|consen  631 DGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLSL  710 (1674)
T ss_pred             cCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHHh
Confidence            588999999999999999999877774    33      256788899999999998754  777888778888888888


Q ss_pred             HHcccchhHHHHHHHHH
Q psy7959          70 IKTDTSTKREQLELKFK   86 (101)
Q Consensus        70 ~~~~~~~~~~~~~~~~~   86 (101)
                      +.++.+...+-.++...
T Consensus       711 mn~qLpiesq~~~rl~d  727 (1674)
T KOG0951|consen  711 MNQQLPIESQFVSRLAD  727 (1674)
T ss_pred             hhhcCCChHHHHHHhhh
Confidence            88888777664444433

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=97.86  E-value=6.5e-06  Score=65.63  Aligned_cols=56  Identities=23%  Similarity=0.345  Sum_probs=43.8

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCC--CcceEEEeeCcc
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG--LQSYCRIYHSEH   61 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~--~~~~~i~~~~~~   61 (101)
                      +...|+|||++++.|+|++ .+++|.-  +..+.+.+||+||.+|.|  ..|..+.+....
T Consensus       493 ~~~~IvVaTQVIEagvDid-fd~mITe--~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         493 NEGFIVVATQVIEAGVDID-FDVLITE--LAPIDSLIQRAGRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             cCCeEEEEeeEEEEEeccc-cCeeeec--CCCHHHHHHHHHHHhhcccccCCceeEeeccc
Confidence            4678999999999999984 6666653  455788999999999999  456666665543

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

Probab=97.85  E-value=1.9e-06  Score=67.06  Aligned_cols=59  Identities=22%  Similarity=0.271  Sum_probs=47.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEe----C-CCCCccceeeecceeccCC--CcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHW----G-MPSSIPAYYQESGRAGRDG--LQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~----~-~p~~~~~~~qr~GR~gR~~--~~~~~i~~~~~~   61 (101)
                      ++++.++|+|-+++-|+|+|.-. ||.-    + -+.++..|.|+.|||||.+  ..|.+++++.++
T Consensus       488 ~q~l~~VVTTAAL~AGVDFPASQ-VIFEsLaMG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         488 AQELAAVVTTAALAAGVDFPASQ-VIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             cCCcceEeehhhhhcCCCCchHH-HHHHHHHcccccCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            46789999999999999999744 4432    2 2678999999999999997  358888888764

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.58  E-value=5.1e-05  Score=61.43  Aligned_cols=58  Identities=26%  Similarity=0.229  Sum_probs=47.6

Q ss_pred             eeEEEEccccccccCCCCcc--------EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDRQNVR--------FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~--------~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -.|.|||++++||.|+.=-.        +||....|.|.--=-|-.||+||-|.+|.+-.|++-.|
T Consensus       475 GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD  540 (925)
T PRK12903        475 GAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDD  540 (925)
T ss_pred             CeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecch
Confidence            46899999999999985221        88988888776666799999999999999888887554

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.48  E-value=5.9e-05  Score=60.14  Aligned_cols=58  Identities=29%  Similarity=0.238  Sum_probs=48.2

Q ss_pred             eeEEEEccccccccCCC----------Ccc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDRQ----------NVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~----------~v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -.|.|||++++||.|+.          .|.     +||-...+.|.--=.|-.||+||-|.+|.+-.|++-.|
T Consensus       476 gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleD  548 (764)
T PRK12326        476 GAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLED  548 (764)
T ss_pred             CcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            35889999999999975          222     78888888888777899999999999999988888554

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=97.47  E-value=0.00012  Score=59.48  Aligned_cols=56  Identities=32%  Similarity=0.241  Sum_probs=45.0

Q ss_pred             EEEEccccccccCCCC--------------------------------c-----cEEEEeCCCCCccceeeecceeccCC
Q psy7959           7 VITATISFGMGIDRQN--------------------------------V-----RFVVHWGMPSSIPAYYQESGRAGRDG   49 (101)
Q Consensus         7 vlv~T~~~~~G~d~~~--------------------------------v-----~~vi~~~~p~~~~~~~qr~GR~gR~~   49 (101)
                      |+|||++++||+|+.=                                |     -+||-...+.|.--=.|-.||+||-|
T Consensus       500 VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQG  579 (908)
T PRK13107        500 VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQG  579 (908)
T ss_pred             EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCC
Confidence            9999999999999751                                1     16676666666555578999999999


Q ss_pred             CcceEEEeeCccc
Q psy7959          50 LQSYCRIYHSEHS   62 (101)
Q Consensus        50 ~~~~~i~~~~~~~   62 (101)
                      .+|.+-.|++-.|
T Consensus       580 DPGss~f~lSlED  592 (908)
T PRK13107        580 DAGSSRFYLSMED  592 (908)
T ss_pred             CCCceeEEEEeCc
Confidence            9999999988655

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=97.38  E-value=0.00016  Score=58.85  Aligned_cols=57  Identities=32%  Similarity=0.221  Sum_probs=44.0

Q ss_pred             eEEEEccccccccCCCC---------------------------------c-----cEEEEeCCCCCccceeeecceecc
Q psy7959           6 NVITATISFGMGIDRQN---------------------------------V-----RFVVHWGMPSSIPAYYQESGRAGR   47 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~---------------------------------v-----~~vi~~~~p~~~~~~~qr~GR~gR   47 (101)
                      .|+|||++++||+|+-=                                 |     -+||-...+.|.--=.|-.||+||
T Consensus       494 ~VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGR  573 (896)
T PRK13104        494 AVTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGR  573 (896)
T ss_pred             cEEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhcccccc
Confidence            59999999999999751                                 1     155655556555555688999999


Q ss_pred             CCCcceEEEeeCccc
Q psy7959          48 DGLQSYCRIYHSEHS   62 (101)
Q Consensus        48 ~~~~~~~i~~~~~~~   62 (101)
                      -|.+|.+-.|++-.|
T Consensus       574 QGDPGss~f~lSleD  588 (896)
T PRK13104        574 QGDPGSSRFYLSLED  588 (896)
T ss_pred             CCCCCceEEEEEcCc
Confidence            999999999888554

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.26  E-value=0.00025  Score=58.41  Aligned_cols=57  Identities=30%  Similarity=0.254  Sum_probs=48.4

Q ss_pred             eEEEEccccccccCCC---Cc-----cEEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           6 NVITATISFGMGIDRQ---NV-----RFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~---~v-----~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      .|.|||++++||.|+.   .|     -+||-...+.|.---.|-.||+||-|.+|.+-.|++-.|
T Consensus       678 aVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLED  742 (1112)
T PRK12901        678 TVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLED  742 (1112)
T ss_pred             cEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEccc
Confidence            5889999999999985   12     388888888888888899999999999999988888554

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.23  E-value=0.00026  Score=57.88  Aligned_cols=58  Identities=24%  Similarity=0.141  Sum_probs=49.0

Q ss_pred             eeEEEEccccccccCCCC---cc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDRQN---VR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~---v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -.|.|||++++||.|+.=   |.     +||-...|.|.---.|-.||+||-|.+|.+..|++-.|
T Consensus       617 g~VTIATNmAGRGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlED  682 (970)
T PRK12899        617 GAVTVATNMAGRGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFED  682 (970)
T ss_pred             CcEEEeeccccCCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcch
Confidence            468999999999998742   22     78888889888888999999999999999998888654

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.13  E-value=0.00028  Score=57.47  Aligned_cols=58  Identities=31%  Similarity=0.225  Sum_probs=46.3

Q ss_pred             eeEEEEccccccccCCC--------------------------------Ccc-----EEEEeCCCCCccceeeecceecc
Q psy7959           5 INVITATISFGMGIDRQ--------------------------------NVR-----FVVHWGMPSSIPAYYQESGRAGR   47 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~--------------------------------~v~-----~vi~~~~p~~~~~~~qr~GR~gR   47 (101)
                      -.|.|||++++||.|+.                                .|.     +||-...+.|.--=.|-.||+||
T Consensus       498 GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGR  577 (913)
T PRK13103        498 GALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGR  577 (913)
T ss_pred             CcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhcccccc
Confidence            35889999999999983                                122     67777777766666788999999


Q ss_pred             CCCcceEEEeeCccc
Q psy7959          48 DGLQSYCRIYHSEHS   62 (101)
Q Consensus        48 ~~~~~~~i~~~~~~~   62 (101)
                      -|.+|.+-.|++-.|
T Consensus       578 QGDPGsS~f~lSlED  592 (913)
T PRK13103        578 QGDPGSSRFYLSLED  592 (913)
T ss_pred             CCCCCceEEEEEcCc
Confidence            999999999888654

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.42  E-value=0.0045  Score=44.53  Aligned_cols=51  Identities=25%  Similarity=0.266  Sum_probs=42.5

Q ss_pred             CCCceeEEEEccccccccCCC--------CccEEEEeCCCCCccceeeecceeccCCCc
Q psy7959           1 MRGEINVITATISFGMGIDRQ--------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQ   51 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~--------~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~   51 (101)
                      |+|+.+|+|-|++++.|+-+-        .-++-|...+||+....+|..||+-|.++.
T Consensus        58 ~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~  116 (278)
T PF13871_consen   58 MDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQV  116 (278)
T ss_pred             hCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccc
Confidence            689999999999999997543        123446788999999999999999999874

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

Probab=96.27  E-value=0.0092  Score=48.61  Aligned_cols=74  Identities=19%  Similarity=0.109  Sum_probs=50.1

Q ss_pred             CCceeEEEEccccccccCCCCcc--EEEEeCCCCC-c-----------------------------cceeeecceeccCC
Q psy7959           2 RGEINVITATISFGMGIDRQNVR--FVVHWGMPSS-I-----------------------------PAYYQESGRAGRDG   49 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~--~vi~~~~p~~-~-----------------------------~~~~qr~GR~gR~~   49 (101)
                      +|+..||+||+.+.+|+|+++..  .||-..+|.. +                             ..+.|-+||.=|..
T Consensus       723 ~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~  802 (850)
T TIGR01407       723 NGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRE  802 (850)
T ss_pred             hCCCeEEEEcceeecccccCCCceEEEEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccC
Confidence            35678999999999999999765  6677777642 1                             22368999999998


Q ss_pred             CcceEEEeeCcc-cHHHHHHHHHcccc
Q psy7959          50 LQSYCRIYHSEH-SKKSLEYVIKTDTS   75 (101)
Q Consensus        50 ~~~~~i~~~~~~-~~~~~~~~~~~~~~   75 (101)
                      ++..++++++.- ....+...+-...+
T Consensus       803 ~D~G~v~ilD~R~~~~~Yg~~~~~sLp  829 (850)
T TIGR01407       803 NDRGSIVILDRRLVGKRYGKRFEKSLP  829 (850)
T ss_pred             CceEEEEEEccccccchHHHHHHHhCC
Confidence            776666666644 33344344444333

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.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.16  E-value=0.01  Score=47.31  Aligned_cols=71  Identities=8%  Similarity=0.037  Sum_probs=49.1

Q ss_pred             CCceeEEEEcc----ccccccCCCCccEEEEeCC------CC------CccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           2 RGEINVITATI----SFGMGIDRQNVRFVVHWGM------PS------SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         2 ~g~~~vlv~T~----~~~~G~d~~~v~~vi~~~~------p~------~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      .++.+|||+|.    +++     ++++.|+..|.      |.      ....+.|-+||+||....|.+++.. ..+...
T Consensus       469 ~~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfRA~Er~~qll~qvagragr~~~~G~V~iq~-~p~~~~  542 (665)
T PRK14873        469 DAGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVA-ESSLPT  542 (665)
T ss_pred             ccCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcChHHHHHHHHHHHHHhhcCCCCCCEEEEEe-CCCCHH
Confidence            35789999999    555     35676655442      21      2344579999999998889988885 444466


Q ss_pred             HHHHHHcccchhH
Q psy7959          66 LEYVIKTDTSTKR   78 (101)
Q Consensus        66 ~~~~~~~~~~~~~   78 (101)
                      ++.+...++....
T Consensus       543 ~~~l~~~d~~~F~  555 (665)
T PRK14873        543 VQALIRWDPVGHA  555 (665)
T ss_pred             HHHHHhCCHHHHH
Confidence            7777777765554

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=96.06  E-value=0.0074  Score=39.10  Aligned_cols=28  Identities=32%  Similarity=0.507  Sum_probs=24.1

Q ss_pred             eEEEEccccccccCCCC--ccEEEEeCCCC
Q psy7959           6 NVITATISFGMGIDRQN--VRFVVHWGMPS   33 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~--v~~vi~~~~p~   33 (101)
                      -||++|..+++|+|+++  ++.||-.++|.
T Consensus        50 ~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492       50 AILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             EEEEEccceecceecCCCCeeEEEEEecCC
Confidence            58999988999999996  67899888874

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

Probab=95.89  E-value=0.014  Score=46.43  Aligned_cols=56  Identities=14%  Similarity=0.073  Sum_probs=42.6

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccC-C--C-cceEEEeeC
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD-G--L-QSYCRIYHS   59 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~-~--~-~~~~i~~~~   59 (101)
                      +.++|||++|++..|.|.|.+..++..- |..-..++|.+||+-|. .  + .|..+-++.
T Consensus       590 ~~~~ilIVvdmllTGFDaP~l~tLyldK-plk~h~LlQai~R~nR~~~~~K~~g~IvDy~g  649 (667)
T TIGR00348       590 ENPKLLIVVDMLLTGFDAPILNTLYLDK-PLKYHGLLQAIARTNRIDGKDKTFGLIVDYRG  649 (667)
T ss_pred             CCceEEEEEcccccccCCCccceEEEec-cccccHHHHHHHHhccccCCCCCCEEEEECcC
Confidence            4689999999999999999998887666 54445689999999993 3  2 245555543

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

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=95.73  E-value=0.011  Score=38.22  Aligned_cols=54  Identities=26%  Similarity=0.215  Sum_probs=38.8

Q ss_pred             eEEEEccc--cccccCCCC--ccEEEEeCCCCC-c------------------------------cceeeecceeccCCC
Q psy7959           6 NVITATIS--FGMGIDRQN--VRFVVHWGMPSS-I------------------------------PAYYQESGRAGRDGL   50 (101)
Q Consensus         6 ~vlv~T~~--~~~G~d~~~--v~~vi~~~~p~~-~------------------------------~~~~qr~GR~gR~~~   50 (101)
                      -||+++.-  +++|+|+++  ++.||-.++|.. +                              ....|-+||.=|..+
T Consensus        49 ~iL~~v~~G~~~EGiD~~g~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~Qa~GR~iR~~~  128 (142)
T smart00491       49 ALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRHKN  128 (142)
T ss_pred             EEEEEEeCCeeecceecCCCccEEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHhCccccCcc
Confidence            48888887  899999997  679999888732 1                              112478888888876


Q ss_pred             cceEEEeeC
Q psy7959          51 QSYCRIYHS   59 (101)
Q Consensus        51 ~~~~i~~~~   59 (101)
                      +-.+++++.
T Consensus       129 D~g~i~l~D  137 (142)
T smart00491      129 DYGVVVLLD  137 (142)
T ss_pred             ceEEEEEEe
Confidence            655555554

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

Probab=95.72  E-value=0.011  Score=39.06  Aligned_cols=58  Identities=29%  Similarity=0.287  Sum_probs=37.2

Q ss_pred             CceeEEEEcc--ccccccCCCC--ccEEEEeCCCCC-cc-----------------------------ceeeecceeccC
Q psy7959           3 GEINVITATI--SFGMGIDRQN--VRFVVHWGMPSS-IP-----------------------------AYYQESGRAGRD   48 (101)
Q Consensus         3 g~~~vlv~T~--~~~~G~d~~~--v~~vi~~~~p~~-~~-----------------------------~~~qr~GR~gR~   48 (101)
                      +.--||+|+.  .+.+|+|+++  ++.||-.++|.. +.                             ...|-+||+=|.
T Consensus        58 ~~~~il~~v~~g~~~EGiD~~~~~~r~vii~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~  137 (167)
T PF13307_consen   58 GEGAILLAVAGGSFSEGIDFPGDLLRAVIIVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRS  137 (167)
T ss_dssp             SSSEEEEEETTSCCGSSS--ECESEEEEEEES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--S
T ss_pred             ccCeEEEEEecccEEEeecCCCchhheeeecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceec
Confidence            4456899998  8999999996  889999998842 11                             114789999998


Q ss_pred             CCcceEEEeeCc
Q psy7959          49 GLQSYCRIYHSE   60 (101)
Q Consensus        49 ~~~~~~i~~~~~   60 (101)
                      .++-.++++++.
T Consensus       138 ~~D~g~i~llD~  149 (167)
T PF13307_consen  138 EDDYGVIILLDS  149 (167)
T ss_dssp             TT-EEEEEEESG
T ss_pred             cCCcEEEEEEcC
Confidence            877666777664

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=95.62  E-value=0.0047  Score=51.33  Aligned_cols=45  Identities=27%  Similarity=0.380  Sum_probs=36.3

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCC
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL   50 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~   50 (101)
                      +...|+|+|++++.|+|+ +.+++|-  -|.+..+.+|+.||..|.+.
T Consensus       837 ~~~~i~v~Tqv~E~g~D~-dfd~~~~--~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       837 NHLFIVLATPVEEVGRDH-DYDWAIA--DPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CCCeEEEEeeeEEEEecc-cCCeeee--ccCcHHHHHHHhhccccccc
Confidence            467899999999999997 3444443  36788899999999999875

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.

>KOG0390|consensus

Probab=95.58  E-value=0.01  Score=47.90  Aligned_cols=55  Identities=16%  Similarity=0.134  Sum_probs=47.3

Q ss_pred             EEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc--ceEEEeeCcc
Q psy7959           7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEH   61 (101)
Q Consensus         7 vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~   61 (101)
                      +|.+|-+.+.||++=+.+.||.+|..|+|+.=.|-.+|+-|.|+.  -.++.++..+
T Consensus       651 fLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatG  707 (776)
T KOG0390|consen  651 FLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATG  707 (776)
T ss_pred             EEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEEeecCC
Confidence            456777999999999999999999999999999999999999986  4555666655

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=95.24  E-value=0.015  Score=47.46  Aligned_cols=24  Identities=38%  Similarity=0.479  Sum_probs=20.6

Q ss_pred             eeecceeccCCCcceEEEeeCccc
Q psy7959          39 YQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus        39 ~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -|-.||+||-|.+|.+-.|++-.|
T Consensus       609 nQLrGRaGRQGDPG~s~f~lSLED  632 (870)
T CHL00122        609 NQLRGRAGRQGDPGSSRFFLSLED  632 (870)
T ss_pred             HHHhccccCCCCCCcceEEEEecc
Confidence            488899999999999988888554

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

Probab=95.10  E-value=0.041  Score=45.42  Aligned_cols=73  Identities=18%  Similarity=0.107  Sum_probs=50.1

Q ss_pred             CceeEEEEccccccccCCCC--ccEEEEeCCCCC-c-----------------------------cceeeecceeccCCC
Q psy7959           3 GEINVITATISFGMGIDRQN--VRFVVHWGMPSS-I-----------------------------PAYYQESGRAGRDGL   50 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~--v~~vi~~~~p~~-~-----------------------------~~~~qr~GR~gR~~~   50 (101)
                      ++-.||++|..+.+|+|+|+  ++.||-..+|.. +                             ..+.|-+||.=|..+
T Consensus       803 ~~~~iLlG~~sFwEGVD~pg~~l~~viI~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~  882 (928)
T PRK08074        803 FDKAILLGTSSFWEGIDIPGDELSCLVIVRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTET  882 (928)
T ss_pred             cCCeEEEecCcccCccccCCCceEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCC
Confidence            34569999999999999996  578888887742 1                             123688899999887


Q ss_pred             cceEEEeeCcc-cHHHHHHHHHcccc
Q psy7959          51 QSYCRIYHSEH-SKKSLEYVIKTDTS   75 (101)
Q Consensus        51 ~~~~i~~~~~~-~~~~~~~~~~~~~~   75 (101)
                      +-.++++++.- ....+...+-+..+
T Consensus       883 D~G~v~ilD~R~~~k~Yg~~~l~sLP  908 (928)
T PRK08074        883 DRGTVFVLDRRLTTTSYGKYFLESLP  908 (928)
T ss_pred             ceEEEEEecCccccchHHHHHHHhCC
Confidence            75566666644 33445444444444

>KOG0387|consensus

Probab=95.02  E-value=0.023  Score=46.09  Aligned_cols=57  Identities=16%  Similarity=0.076  Sum_probs=48.8

Q ss_pred             EEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcce--EEEeeCcccH
Q psy7959           7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY--CRIYHSEHSK   63 (101)
Q Consensus         7 vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~--~i~~~~~~~~   63 (101)
                      +|++|-+.+.|+++-..+-||-||.-|+|+.=.|-.-||.|.|+.-.  ++.+++.+..
T Consensus       602 FLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTI  660 (923)
T KOG0387|consen  602 FLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTI  660 (923)
T ss_pred             EEEEecccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcH
Confidence            68899999999999999999999999999999999999999998633  4556666543

>COG4889 Predicted helicase [General function prediction only]

Probab=94.80  E-value=0.013  Score=48.47  Aligned_cols=56  Identities=20%  Similarity=0.265  Sum_probs=44.9

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCC---cceEEEeeC
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL---QSYCRIYHS   59 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~---~~~~i~~~~   59 (101)
                      +++||-----+++|+|+|.++.||.|+.-.+.-+.+|-+||.=|...   -|..|+.+.
T Consensus       528 eckIlSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIa  586 (1518)
T COG4889         528 ECKILSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIA  586 (1518)
T ss_pred             hheeeccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEec
Confidence            56777666678999999999999999977888899999999988742   266555443

>KOG0385|consensus

Probab=94.72  E-value=0.034  Score=45.15  Aligned_cols=60  Identities=18%  Similarity=0.148  Sum_probs=48.3

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc--ceEEEeeCcccHH
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSKK   64 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~~   64 (101)
                      .=+|++|=+.+.||++-..+.||.||.-|+|..=.|-.-||-|-|+.  =.++.+++.+..+
T Consensus       541 FiFlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVE  602 (971)
T KOG0385|consen  541 FIFLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVE  602 (971)
T ss_pred             EEEEEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHH
Confidence            44789999999999999999999999999998888877777777764  4466677766443

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

Probab=94.47  E-value=0.044  Score=43.21  Aligned_cols=67  Identities=21%  Similarity=0.226  Sum_probs=47.2

Q ss_pred             eEEEEccccccccCCCC--ccEEEEeCCCCC------------------------------ccceeeecceeccCCCcce
Q psy7959           6 NVITATISFGMGIDRQN--VRFVVHWGMPSS------------------------------IPAYYQESGRAGRDGLQSY   53 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~--v~~vi~~~~p~~------------------------------~~~~~qr~GR~gR~~~~~~   53 (101)
                      -++|+|..+++|+|+++  .+.||-.++|..                              ...+.|-+||.=|..++..
T Consensus       530 ~~lv~~gsf~EGVD~~g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G  609 (654)
T COG1199         530 LILVGGGSFWEGVDFPGDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRG  609 (654)
T ss_pred             eEEEeeccccCcccCCCCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCce
Confidence            68999999999999996  578888888743                              1223699999999877766


Q ss_pred             EEEeeCcc-cHHHHHHHHHc
Q psy7959          54 CRIYHSEH-SKKSLEYVIKT   72 (101)
Q Consensus        54 ~i~~~~~~-~~~~~~~~~~~   72 (101)
                      ++++++.- ....++..+..
T Consensus       610 ~ivllD~R~~~~~y~~~l~~  629 (654)
T COG1199         610 VIVLLDKRYATKRYGKLLLD  629 (654)
T ss_pred             EEEEecccchhhhHHHHHHH
Confidence            66666543 33334444444

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=94.46  E-value=0.051  Score=43.57  Aligned_cols=59  Identities=22%  Similarity=0.179  Sum_probs=43.6

Q ss_pred             CceeEEEEccccccccCCCC--ccEEEEeCCCCC-cc-----------------------------ceeeecceeccCCC
Q psy7959           3 GEINVITATISFGMGIDRQN--VRFVVHWGMPSS-IP-----------------------------AYYQESGRAGRDGL   50 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~--v~~vi~~~~p~~-~~-----------------------------~~~qr~GR~gR~~~   50 (101)
                      |+-.||++|..+.+|+|+|+  ++.||-..+|.. +.                             .+.|-+||.=|..+
T Consensus       584 ~~~~VL~g~~sf~EGVD~pGd~l~~vII~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~  663 (697)
T PRK11747        584 GEGSVLFGLQSFAEGLDLPGDYLTQVIITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQ  663 (697)
T ss_pred             CCCeEEEEeccccccccCCCCceEEEEEEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCC
Confidence            45569999999999999986  789998887742 11                             12588899988876


Q ss_pred             cceEEEeeCcc
Q psy7959          51 QSYCRIYHSEH   61 (101)
Q Consensus        51 ~~~~i~~~~~~   61 (101)
                      +-.++++++.-
T Consensus       664 D~G~i~ilD~R  674 (697)
T PRK11747        664 DRGRVTILDRR  674 (697)
T ss_pred             ceEEEEEEccc
Confidence            65566666543

>KOG1015|consensus

Probab=94.30  E-value=0.065  Score=44.78  Aligned_cols=57  Identities=16%  Similarity=0.067  Sum_probs=48.8

Q ss_pred             eEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc--ceEEEeeCccc
Q psy7959           6 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHS   62 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~   62 (101)
                      -.||+|-+.+.|+++-..+.||.||..|+++-=.|-+=|+-|+|+.  -.++.|+..+.
T Consensus      1220 l~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYRfiAqGT 1278 (1567)
T KOG1015|consen 1220 LFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYRFIAQGT 1278 (1567)
T ss_pred             EEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehhhhhccc
Confidence            3689999999999999999999999999999999999999999974  55555666553

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

Probab=93.87  E-value=0.13  Score=42.12  Aligned_cols=73  Identities=23%  Similarity=0.159  Sum_probs=47.5

Q ss_pred             CceeEEEEccccccccCCC--CccEEEEeCCCCC------------------------------ccceeeecceeccCCC
Q psy7959           3 GEINVITATISFGMGIDRQ--NVRFVVHWGMPSS------------------------------IPAYYQESGRAGRDGL   50 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~--~v~~vi~~~~p~~------------------------------~~~~~qr~GR~gR~~~   50 (101)
                      ++-.||++|..+.+|+|+|  +...||-..+|..                              ...+.|-+||.=|..+
T Consensus       693 ~~~~vLlG~~sFwEGVD~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~  772 (820)
T PRK07246        693 GEQQILLGLGSFWEGVDFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRRED  772 (820)
T ss_pred             CCCeEEEecchhhCCCCCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCC
Confidence            4456999999999999997  3556666776632                              1123688999999877


Q ss_pred             cceEEEeeCcc-cHHHHHHHHHcccc
Q psy7959          51 QSYCRIYHSEH-SKKSLEYVIKTDTS   75 (101)
Q Consensus        51 ~~~~i~~~~~~-~~~~~~~~~~~~~~   75 (101)
                      +..+++++++- ....+...+-+..+
T Consensus       773 D~Gvv~ilD~R~~~k~Yg~~~l~sLP  798 (820)
T PRK07246        773 QKSAVLILDRRILTKSYGKQILASLA  798 (820)
T ss_pred             CcEEEEEECCcccccHHHHHHHHhCC
Confidence            65566666644 33344333333333

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

Probab=93.83  E-value=0.016  Score=47.04  Aligned_cols=44  Identities=20%  Similarity=0.117  Sum_probs=39.9

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccC
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD   48 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~   48 (101)
                      -+|.++.+++.-|+|+|.|..++.+-.-.|-..|.|++||+=|.
T Consensus       482 P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         482 PRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             CceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            46889999999999999999999988889999999999999775

>KOG0384|consensus

Probab=93.72  E-value=0.11  Score=43.99  Aligned_cols=61  Identities=16%  Similarity=0.153  Sum_probs=51.6

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcce--EEEeeCcccH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY--CRIYHSEHSK   63 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~--~i~~~~~~~~   63 (101)
                      ..+-+|+||=+.+.||++-..+.||.||.-|+|.+=+|--.||-|-|+...  ++.+++.+..
T Consensus       751 ddFvFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~Tv  813 (1373)
T KOG0384|consen  751 DDFVFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTV  813 (1373)
T ss_pred             CceEEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCch
Confidence            356789999999999999999999999999999999998888888887643  6677776644

>KOG1513|consensus

Probab=93.23  E-value=0.052  Score=44.55  Aligned_cols=50  Identities=30%  Similarity=0.289  Sum_probs=42.3

Q ss_pred             CCCceeEEEEccccccccCCCCccEE--------EEeCCCCCccceeeecceeccCCC
Q psy7959           1 MRGEINVITATISFGMGIDRQNVRFV--------VHWGMPSSIPAYYQESGRAGRDGL   50 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~~v~~v--------i~~~~p~~~~~~~qr~GR~gR~~~   50 (101)
                      |+|+.-|-|-+.+++-||-++.=+.|        |...+||+....+|..||+-|.++
T Consensus       854 M~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQ  911 (1300)
T KOG1513|consen  854 MDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQ  911 (1300)
T ss_pred             ccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccc
Confidence            78998999999999999877654444        456789999999999999999875

>KOG0388|consensus

Probab=92.80  E-value=0.2  Score=40.94  Aligned_cols=57  Identities=19%  Similarity=0.125  Sum_probs=44.7

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcc--eEEEeeCcc
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQS--YCRIYHSEH   61 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~--~~i~~~~~~   61 (101)
                      +=+|++|-+.+.||++-..+.||.||.-|++..=.|---||-|.|+.-  .++.++..+
T Consensus      1096 FvFLLSTRAGGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rg 1154 (1185)
T KOG0388|consen 1096 FVFLLSTRAGGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRG 1154 (1185)
T ss_pred             EEEEEecccCcccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccc
Confidence            457899999999999999999999999999888778777887777643  344444333

>KOG0701|consensus

Probab=92.19  E-value=0.013  Score=50.60  Aligned_cols=45  Identities=31%  Similarity=0.504  Sum_probs=42.0

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccC
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRD   48 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~   48 (101)
                      ++++|++|.+++.|+|++.++.|+.++.|....+|+|+.||+-+.
T Consensus       354 ~ln~L~~~~~~~e~~d~~~~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  354 ELNLLIATSVLEEGVDVPKCNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhHHHHHHHHHhhcchhhhhhheeccCcchHHHHHHhhcccccc
Confidence            578999999999999999999999999999999999999998554

>KOG0921|consensus

Probab=91.62  E-value=0.14  Score=42.53  Aligned_cols=63  Identities=24%  Similarity=0.241  Sum_probs=48.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .|..+++++|.+++-.+.+.++.+||..+.                  ..+..+..||.||+||. +.|.|..++...-+
T Consensus       698 ~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs~arF  776 (1282)
T KOG0921|consen  698 EGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCSRARF  776 (1282)
T ss_pred             ccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccHHHHH
Confidence            367899999999999998888888876552                  23556678999999997 67888777765544


Q ss_pred             HH
Q psy7959          64 KS   65 (101)
Q Consensus        64 ~~   65 (101)
                      +.
T Consensus       777 ~~  778 (1282)
T KOG0921|consen  777 EA  778 (1282)
T ss_pred             HH
Confidence            43

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

Probab=91.24  E-value=0.14  Score=41.02  Aligned_cols=58  Identities=14%  Similarity=0.048  Sum_probs=47.2

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc--ceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~   62 (101)
                      .-++++|.+.+.|++.-..+.||.+|..+++....|...|+-|.|+.  =.++.+...+.
T Consensus       764 ~v~lls~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~t  823 (866)
T COG0553         764 KVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGT  823 (866)
T ss_pred             ceEEEEecccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCCc
Confidence            44667778999999999999999999999999999999999888765  33555555554

>KOG0389|consensus

Probab=91.23  E-value=1.1  Score=36.84  Aligned_cols=71  Identities=15%  Similarity=0.078  Sum_probs=52.6

Q ss_pred             eEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCC--cceEEEeeCcccHH-HHHHHHHcccch
Q psy7959           6 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSKK-SLEYVIKTDTST   76 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~~~~-~~~~~~~~~~~~   76 (101)
                      =+|++|-+.+-||++-..+.||.+|+-.+|-.=.|---|+-|.|+  .=.++.+++.+..+ .+..+.+.+...
T Consensus       831 VFLLSTKAGG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIEE~I~~lA~~KL~L  904 (941)
T KOG0389|consen  831 VFLLSTKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIEEGILRLAKTKLAL  904 (941)
T ss_pred             EEEEeeccCcceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecCcHHHHHHHHHHHhhhh
Confidence            468999999999999999999999998887777776666666665  35577777777544 444555544433

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

Probab=90.98  E-value=0.46  Score=37.99  Aligned_cols=59  Identities=19%  Similarity=0.013  Sum_probs=42.6

Q ss_pred             CceeEEEEccccccccCC----------CCccEEEEeCCCCCc-------------------------cceeeecceecc
Q psy7959           3 GEINVITATISFGMGIDR----------QNVRFVVHWGMPSSI-------------------------PAYYQESGRAGR   47 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~----------~~v~~vi~~~~p~~~-------------------------~~~~qr~GR~gR   47 (101)
                      |.-.||++|+.+-+|+|+          ..++.||..-+|..+                         -.+.|-+||.=|
T Consensus       521 ~~~~vL~gt~sfweGvDv~~~~~~p~~G~~Ls~ViI~kLPF~~~dp~a~~~~~~~~g~~~f~~~p~a~i~lkQg~GRLIR  600 (636)
T TIGR03117       521 GIQPVLIAAGGAWTGIDLTHKPVSPDKDNLLTDLIITCAPFGLNRSLSMLKRIRKTSVRPWEIINESLMMLRQGLGRLVR  600 (636)
T ss_pred             CCCcEEEeCCccccccccCCccCCCCCCCcccEEEEEeCCCCcCChHHHHHHHHhcCCChHhhhHHHHHHHHHhcCceee
Confidence            557899999999999999          248889887777432                         123588888888


Q ss_pred             CCCc--ceEEEeeCcc
Q psy7959          48 DGLQ--SYCRIYHSEH   61 (101)
Q Consensus        48 ~~~~--~~~i~~~~~~   61 (101)
                      ...+  -..|.++++-
T Consensus       601 ~~~D~~~G~i~ilD~R  616 (636)
T TIGR03117       601 HPDMPQNRRIHMLDGR  616 (636)
T ss_pred             cCCCcCceEEEEEeCC
Confidence            8766  5555555533

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.

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=90.94  E-value=0.53  Score=38.67  Aligned_cols=58  Identities=19%  Similarity=0.136  Sum_probs=39.0

Q ss_pred             EEccccccccCCCC----------------------c----------cEEEEeCCCCCccceee--ecceeccCCCcceE
Q psy7959           9 TATISFGMGIDRQN----------------------V----------RFVVHWGMPSSIPAYYQ--ESGRAGRDGLQSYC   54 (101)
Q Consensus         9 v~T~~~~~G~d~~~----------------------v----------~~vi~~~~p~~~~~~~q--r~GR~gR~~~~~~~   54 (101)
                      |+|+..+.|+|++.                      +          ++||.|+.-.+.-.-+|  |+||.||.   +.+
T Consensus       431 ~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~---~rV  507 (814)
T TIGR00596       431 FEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRP---LRV  507 (814)
T ss_pred             ccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCC---cEE
Confidence            67888888999886                      5          79999995444444455  66666664   567


Q ss_pred             EEeeCcccHHHHHHH
Q psy7959          55 RIYHSEHSKKSLEYV   69 (101)
Q Consensus        55 i~~~~~~~~~~~~~~   69 (101)
                      +.++..+..+...++
T Consensus       508 yfL~y~~S~EEq~yl  522 (814)
T TIGR00596       508 YFLYYGGSIEEQRYL  522 (814)
T ss_pred             EEEEECCcHHHHHHH
Confidence            777776655544333

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

>KOG1000|consensus

Probab=90.84  E-value=0.29  Score=38.40  Aligned_cols=45  Identities=22%  Similarity=0.197  Sum_probs=38.4

Q ss_pred             EEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcce
Q psy7959           9 TATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY   53 (101)
Q Consensus         9 v~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~   53 (101)
                      ++-.+++.|+++...+.|+...+++++.-++|-=-|+-|.|+.+.
T Consensus       549 lsItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkss  593 (689)
T KOG1000|consen  549 LSITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSS  593 (689)
T ss_pred             EEEeecccceeeeccceEEEEEecCCCceEEechhhhhhccccce
Confidence            445678899999999999999999999999998888888887533

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

Probab=90.01  E-value=0.31  Score=40.90  Aligned_cols=32  Identities=28%  Similarity=0.698  Sum_probs=27.5

Q ss_pred             CCceeEEEEcc----ccccccCCCC-ccEEEEeCCCC
Q psy7959           2 RGEINVITATI----SFGMGIDRQN-VRFVVHWGMPS   33 (101)
Q Consensus         2 ~g~~~vlv~T~----~~~~G~d~~~-v~~vi~~~~p~   33 (101)
                      .|++++||+..    ++-||+|+|+ ++++|.++.|+
T Consensus       381 ~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         381 EGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             cCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            58999998764    6779999996 88999999984

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=89.61  E-value=0.59  Score=37.52  Aligned_cols=55  Identities=24%  Similarity=0.140  Sum_probs=41.9

Q ss_pred             eeEEEEc--cccccccCCCC--ccEEEEeCCCC-Ccc------------------------------ceeeecceeccCC
Q psy7959           5 INVITAT--ISFGMGIDRQN--VRFVVHWGMPS-SIP------------------------------AYYQESGRAGRDG   49 (101)
Q Consensus         5 ~~vlv~T--~~~~~G~d~~~--v~~vi~~~~p~-~~~------------------------------~~~qr~GR~gR~~   49 (101)
                      --||+|+  ..+++|+|+++  .+.||-.++|. ++.                              ...|-+||+=|..
T Consensus       583 gavL~av~gGk~sEGIDf~~~~~r~ViivGlPf~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~~  662 (705)
T TIGR00604       583 GAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQDFYEFDAMRAVNQAIGRVIRHK  662 (705)
T ss_pred             ceEEEEecCCcccCccccCCCCCcEEEEEccCCCCCCCHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHHHHhCccccCc
Confidence            3489998  78999999997  78999999885 211                              1248889999987


Q ss_pred             CcceEEEeeC
Q psy7959          50 LQSYCRIYHS   59 (101)
Q Consensus        50 ~~~~~i~~~~   59 (101)
                      ++-.++++++
T Consensus       663 ~D~G~iillD  672 (705)
T TIGR00604       663 DDYGSIVLLD  672 (705)
T ss_pred             CceEEEEEEe
Confidence            7766677765

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).

>KOG0391|consensus

Probab=88.48  E-value=0.99  Score=38.99  Aligned_cols=56  Identities=20%  Similarity=0.132  Sum_probs=41.8

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCcc------ceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIP------AYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~------~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      +.++++|-..+.|+++-..+.||+||.-|++.      +..||+|++    ++=+.+.+++....+
T Consensus      1329 fcfILSTrSggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqt----RDVHIYRLISe~TIE 1390 (1958)
T KOG0391|consen 1329 FCFILSTRSGGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT----RDVHIYRLISERTIE 1390 (1958)
T ss_pred             EEEEEeccCCccccccccCceEEEecCCCCchhhhHHHHHHHhhcCc----cceEEEEeeccchHH
Confidence            45688999999999999999999999877643      455666665    456677777765433

>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=88.34  E-value=1.3  Score=31.22  Aligned_cols=67  Identities=15%  Similarity=0.194  Sum_probs=52.4

Q ss_pred             ceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceec-cCCCcceEEEeeCcccHHHHHHHH
Q psy7959           4 EINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAG-RDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         4 ~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~g-R~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      ...|+|+=+.++||+-++++.......-+.+...+.|+.=+-| |.|=...|=+++++.-.+.+..+.
T Consensus       135 ~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~  202 (239)
T PF10593_consen  135 LNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYEDLCRIYMPEELYDWFRHIA  202 (239)
T ss_pred             ceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCcccccceEEecCHHHHHHHHHHH
Confidence            4789999999999999999988888888888889999988888 555466777777655555554444

This domain is found associated with a helicase domain of superfamily type II [].

>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=87.94  E-value=0.81  Score=35.12  Aligned_cols=73  Identities=16%  Similarity=0.213  Sum_probs=52.7

Q ss_pred             CCceeEEEEcccc--ccccCCCCccEEEEeCCCCCccceeeecceeccCC------CcceEEEeeCcccHHHHHHHHHcc
Q psy7959           2 RGEINVITATISF--GMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG------LQSYCRIYHSEHSKKSLEYVIKTD   73 (101)
Q Consensus         2 ~g~~~vlv~T~~~--~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~------~~~~~i~~~~~~~~~~~~~~~~~~   73 (101)
                      +|+.+||+-|.=+  =+-..+.+++.||.|++|..+.=|-..+...+...      ....+.++++..|.-.+..++..+
T Consensus       348 ~G~~~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIVGt~  427 (442)
T PF06862_consen  348 HGRKPILLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIVGTE  427 (442)
T ss_pred             cCCceEEEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHhCHH
Confidence            6889999999622  13456788999999999988777655444443332      257899999988888777776654


Q ss_pred             c
Q psy7959          74 T   74 (101)
Q Consensus        74 ~   74 (101)
                      .
T Consensus       428 r  428 (442)
T PF06862_consen  428 R  428 (442)
T ss_pred             H
Confidence            4

; GO: 0005634 nucleus

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

Probab=86.01  E-value=0.25  Score=40.51  Aligned_cols=55  Identities=31%  Similarity=0.235  Sum_probs=34.9

Q ss_pred             eEEEEccccccccCCCCcc-----------EEEEeCCCCCccce-eeecceeccCCCcceEEEeeCcc
Q psy7959           6 NVITATISFGMGIDRQNVR-----------FVVHWGMPSSIPAY-YQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~-----------~vi~~~~p~~~~~~-~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      -|-|||++++||.|+.=-.           +||-...-. .... -|--||+||-|..|.+..+++-.
T Consensus       479 aVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhE-SRRIDnQLRGRsGRQGDpG~S~F~lSle  545 (822)
T COG0653         479 AVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHE-SRRIDNQLRGRAGRQGDPGSSRFYLSLE  545 (822)
T ss_pred             ccccccccccCCcccccCCCHHHHHHhCCcEEEecccch-hhHHHHHhhcccccCCCcchhhhhhhhH
Confidence            3569999999999975211           222221111 1112 27889999999888887777644

>KOG0386|consensus

Probab=84.45  E-value=0.83  Score=38.40  Aligned_cols=51  Identities=22%  Similarity=0.208  Sum_probs=45.2

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEE
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR   55 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i   55 (101)
                      ..+|.+|-+.+.|++....+.||.||.-+++-...|+.-||-|.|+.-.+-
T Consensus       780 f~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evR  830 (1157)
T KOG0386|consen  780 FIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVR  830 (1157)
T ss_pred             eeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhhee
Confidence            567899999999999999999999999999999999999999988754433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	101
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		7e-15
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		1e-14
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		5e-14
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-04
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		9e-04

>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase Length = 591

Iteration: 1
 Score = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 31/56 (55%), Positives = 43/56 (76%)
Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH 58
            EI V+ AT++FGMGID+ +VRFV+H  M  S+  YYQESGRAGRD +++ C +Y+
Sbjct: 316 NEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYY 371

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 29/57 (50%), Positives = 46/57 (80%)
Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH 58
           R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL +   +++
Sbjct: 284 RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 28/57 (49%), Positives = 45/57 (78%)
Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYH 58
           R ++ ++ AT++FG GI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL +   +++
Sbjct: 284 RDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAXLFY 340

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           G + V+ AT     G+D +N++ V+++ MPS I  Y    GR GR G
Sbjct: 349 GSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVG 395

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           RGE   + AT     GID +N+  V+++ +P    +Y   +GR GR G
Sbjct: 83  RGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAG 130

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	101
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	1e-33
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	1e-31
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	3e-05
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	4e-04

>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 =  120 bits (304), Expect = 1e-33
 Identities = 35/98 (35%), Positives = 58/98 (59%), Gaps = 8/98 (8%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
              EI V+ AT++FGMGID+ +VRFV+H  M  S+  YYQESGRAGRD +++ C +Y+  
Sbjct: 314 SANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGF 373

Query: 61  HSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCEQV 98
                +  ++  + +  +++L         M+ YC+ +
Sbjct: 374 GDIFRISSMVVME-NVGQQKLY-------EMVSYCQNI 403

>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 =  114 bits (288), Expect = 1e-31
 Identities = 32/96 (33%), Positives = 58/96 (60%), Gaps = 2/96 (2%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
            R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL +   +++  
Sbjct: 283 QRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342

Query: 61  HSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 96
                L   +  +   + +  +++     +M  + E
Sbjct: 343 ADMAWLRRCL--EEKPQGQLQDIERHKLNAMGAFAE 376

>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 = 40.2 bits (93), Expect = 3e-05
 Identities = 18/46 (39%), Positives = 21/46 (45%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 47
           RGE NV+ AT     G+D   V  VV +    S     Q  GR GR
Sbjct: 417 RGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 15/47 (31%), Positives = 24/47 (51%)

Query: 3   GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
           G+ +V+ AT     G+D   ++ V+++ MP  I  Y    GR G  G
Sbjct: 103 GKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSG 149

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	101
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.84
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.82
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.82
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.81
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.81
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.8
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.79
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.79
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.78
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.78
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.63
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.76
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.76
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.74
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.74
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.73
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.73
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.72
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.71
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.71
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.71
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.7
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.7
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.69
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.69
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.69
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.67
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.66
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.66
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.62
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.61
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.6
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.6
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.59
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.59
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.59
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.58
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.57
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.56
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.55
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.54
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.54
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.54
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.52
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.52
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.51
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.51
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.5
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.5
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.49
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.48
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.48
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.46
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.45
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.45
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.44
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.42
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.41
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.38
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.37
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.36
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.36
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.33
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.27
3h1t_A	590	Type I site-specific restriction-modification syst	99.24
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.23
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.13
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.96
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.82
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.81
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.14
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	96.55
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	87.27
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	82.69

>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=99.84  E-value=4.1e-21  Score=144.68  Aligned_cols=95  Identities=34%  Similarity=0.654  Sum_probs=83.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQL   81 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (101)
                      +|+.+|||||+++++|+|+|+|++||++|+|.+.++|+||+||+||.|..+.+++++.+.|....+.++.....+.  ..
T Consensus       284 ~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~~~~~~~--~~  361 (523)
T 1oyw_A          284 RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQ--LQ  361 (523)
T ss_dssp             TTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHHTSCCSH--HH
T ss_pred             cCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHhccCcHH--HH
Confidence            5789999999999999999999999999999999999999999999999999999999999998888888744433  23


Q ss_pred             HHHHHHHHHHHHHHhcC
Q psy7959          82 ELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        82 ~~~~~~l~~m~~~~e~~   98 (101)
                      ......+++|..||++.
T Consensus       362 ~~~~~~l~~m~~~~~~~  378 (523)
T 1oyw_A          362 DIERHKLNAMGAFAEAQ  378 (523)
T ss_dssp             HHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            45567788999998763

>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=99.82  E-value=8e-21  Score=128.67  Aligned_cols=69  Identities=30%  Similarity=0.509  Sum_probs=62.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++++.+...+..+.
T Consensus        79 ~g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~  147 (212)
T 3eaq_A           79 QGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALE  147 (212)
T ss_dssp             SSSCCEEEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHH
T ss_pred             CCCCeEEEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHH
Confidence            578999999999999999999999999999999999999999999999999999999998876655544

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.82  E-value=1.1e-20  Score=122.99  Aligned_cols=70  Identities=27%  Similarity=0.468  Sum_probs=64.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus        83 ~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~  152 (163)
T 2hjv_A           83 RGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEE  152 (163)
T ss_dssp             TTSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             cCCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999888776665544

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.81  E-value=2.3e-20  Score=121.59  Aligned_cols=70  Identities=23%  Similarity=0.409  Sum_probs=59.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus        78 ~g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~  147 (165)
T 1fuk_A           78 SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  147 (165)
T ss_dssp             TTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHH
T ss_pred             cCCCEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999888776665543

>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=99.81  E-value=1.5e-20  Score=143.69  Aligned_cols=89  Identities=38%  Similarity=0.738  Sum_probs=78.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQL   81 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (101)
                      +|+++|||||+++++|+|+|+|++||++++|.+.++|+||+||+||.|..|.|++++.+.|...+..++.....      
T Consensus       315 ~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~~~~~~~------  388 (591)
T 2v1x_A          315 ANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENV------  388 (591)
T ss_dssp             TTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHTTTSTT------
T ss_pred             cCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHHHhhhhh------
Confidence            57899999999999999999999999999999999999999999999999999999999998888888765322      


Q ss_pred             HHHHHHHHHHHHHHhcC
Q psy7959          82 ELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        82 ~~~~~~l~~m~~~~e~~   98 (101)
                        ....+.+|..||++.
T Consensus       389 --~~~~l~~~~~~~~~~  403 (591)
T 2v1x_A          389 --GQQKLYEMVSYCQNI  403 (591)
T ss_dssp             --HHHHHHHHHHHHTCS
T ss_pred             --hHHHHHHHHHHHhcc
Confidence              235567888888743

>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=99.80  E-value=2.5e-20  Score=122.40  Aligned_cols=70  Identities=26%  Similarity=0.360  Sum_probs=60.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCC------CCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMP------SSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p------~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|      .+..+|+||+||+||.|+.|.+++++.+.+...+..+.+
T Consensus        82 ~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~  157 (175)
T 2rb4_A           82 DGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQD  157 (175)
T ss_dssp             TTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHH
T ss_pred             cCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHH
Confidence            5789999999999999999999999999999      899999999999999999999999999888776655544

>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=99.79  E-value=3e-20  Score=123.64  Aligned_cols=69  Identities=26%  Similarity=0.471  Sum_probs=56.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+++|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++++.+...++.+.
T Consensus        94 ~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~  162 (185)
T 2jgn_A           94 SGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLL  162 (185)
T ss_dssp             HTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHH
T ss_pred             cCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHH
Confidence            478899999999999999999999999999999999999999999999999999999988765444443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.79  E-value=7.5e-20  Score=130.16  Aligned_cols=69  Identities=32%  Similarity=0.516  Sum_probs=58.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|.+..+|+||+||+||.|+.|.++.++++.+...+..+.
T Consensus        76 ~g~~~vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie  144 (300)
T 3i32_A           76 QGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALE  144 (300)
T ss_dssp             HTSCCEEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHH
T ss_pred             cCCceEEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHH
Confidence            478999999999999999999999999999999999999999999999999999999988866554443

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.78  E-value=5.6e-20  Score=120.90  Aligned_cols=61  Identities=26%  Similarity=0.455  Sum_probs=58.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++.+.+
T Consensus        79 ~g~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~  139 (172)
T 1t5i_A           79 DFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  139 (172)
T ss_dssp             TTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             CCCCcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChh
Confidence            5789999999999999999999999999999999999999999999999999999998653

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.78  E-value=8.3e-20  Score=122.18  Aligned_cols=64  Identities=23%  Similarity=0.443  Sum_probs=56.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcc-cHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH-SKKS   65 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~-~~~~   65 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++++. +...
T Consensus       102 ~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~  166 (191)
T 2p6n_A          102 EGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESV  166 (191)
T ss_dssp             HTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHH
T ss_pred             cCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHH
Confidence            478899999999999999999999999999999999999999999999999999999876 4443

>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=99.63  E-value=2.6e-20  Score=121.97  Aligned_cols=70  Identities=30%  Similarity=0.390  Sum_probs=63.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|+++.+|+||+||+||.|+.|.+++++.+.+...++.+.+
T Consensus        78 ~g~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~  147 (170)
T 2yjt_D           78 EGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGR  147 (170)
Confidence            4788999999999999999999999999999999999999999999999999999998887665544443

>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=99.76  E-value=2e-19  Score=132.31  Aligned_cols=60  Identities=30%  Similarity=0.556  Sum_probs=57.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+.+|||||+++++|+|+|++++||+||+|.+..+|+||+||+||.|+.|.+++|+++.
T Consensus       348 ~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~  407 (434)
T 2db3_A          348 NGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPE  407 (434)
T ss_dssp             TSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTT
T ss_pred             cCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEecc
Confidence            578999999999999999999999999999999999999999999999999999999854

>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=99.76  E-value=4.9e-19  Score=132.93  Aligned_cols=71  Identities=21%  Similarity=0.338  Sum_probs=66.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|+.+|||||+++++|+|+|+|++||++|+|.++.+|+||+||+||.|+.|.+++++.+.+...++.+.+.
T Consensus       390 ~g~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~  460 (563)
T 3i5x_A          390 KDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA  460 (563)
T ss_dssp             HCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHH
T ss_pred             cCCCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999998888777643

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.74  E-value=1.3e-18  Score=131.75  Aligned_cols=71  Identities=21%  Similarity=0.338  Sum_probs=66.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|+.+|||||+++++|+|+|+|++||++|+|.++.+|+||+||+||.|+.|.+++++.+.+...++.+.+.
T Consensus       339 ~g~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~  409 (579)
T 3sqw_A          339 KDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDA  409 (579)
T ss_dssp             HCSSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHH
T ss_pred             cCCCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999998887777653

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.74  E-value=4.7e-19  Score=127.81  Aligned_cols=69  Identities=26%  Similarity=0.471  Sum_probs=61.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+.+|||||+++++|+|+|++++||++|.|.+..+|+||+||+||.|+.|.+++++++.+...+..+.
T Consensus       324 ~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~  392 (417)
T 2i4i_A          324 SGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLL  392 (417)
T ss_dssp             HTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHH
T ss_pred             cCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHH
Confidence            478899999999999999999999999999999999999999999999999999999988876555444

>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=99.73  E-value=2.3e-18  Score=123.78  Aligned_cols=70  Identities=21%  Similarity=0.356  Sum_probs=65.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|.|.+..+|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus       306 ~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~  375 (400)
T 1s2m_A          306 QGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQ  375 (400)
T ss_dssp             TTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             cCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999998877666554

>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=99.73  E-value=1.4e-18  Score=125.46  Aligned_cols=69  Identities=20%  Similarity=0.404  Sum_probs=63.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+.+|||||+++++|+|+|++++||++|.|.+..+|+||+||+||.|+.|.+++++.+.+...++.+.
T Consensus       324 ~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~  392 (410)
T 2j0s_A          324 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIE  392 (410)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHH
T ss_pred             CCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHH
Confidence            478899999999999999999999999999999999999999999999999999999998877665543

>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=99.72  E-value=1.4e-18  Score=125.09  Aligned_cols=70  Identities=27%  Similarity=0.436  Sum_probs=53.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||++|.|.+..+|+||+||+||.|+.|.+++++++.+...++.+.+
T Consensus       328 ~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~  397 (414)
T 3eiq_A          328 SGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIET  397 (414)
T ss_dssp             CC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHH
T ss_pred             cCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999988776665544

>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=99.71  E-value=1.5e-18  Score=124.63  Aligned_cols=61  Identities=25%  Similarity=0.409  Sum_probs=56.7

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC------CccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS------SIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~------~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|.      +..+|+||+||+||.|+.|.+++++.+.+
T Consensus       314 ~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          314 EGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             TTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             CCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            57899999999999999999999999999994      56899999999999999999999998664

>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=99.71  E-value=5e-18  Score=120.01  Aligned_cols=71  Identities=24%  Similarity=0.453  Sum_probs=65.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      +|+.+|||||+++++|+|+|++++||+++.|.+..+|+||+||+||.|+.|.++.++++.+...+..+.+.
T Consensus       286 ~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~  356 (367)
T 1hv8_A          286 QKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERA  356 (367)
T ss_dssp             TTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHH
T ss_pred             cCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHH
Confidence            47889999999999999999999999999999999999999999999999999999999988877666543

>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=99.71  E-value=8.4e-18  Score=119.85  Aligned_cols=64  Identities=25%  Similarity=0.443  Sum_probs=59.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC------CccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS------SIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~------~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|.      +..+|+||+||+||.|+.|.+++++.+.+...
T Consensus       291 ~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~  360 (395)
T 3pey_A          291 EGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFN  360 (395)
T ss_dssp             TTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHH
T ss_pred             CCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHH
Confidence            57899999999999999999999999999998      99999999999999999999999998765443

>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=99.70  E-value=4.6e-18  Score=119.18  Aligned_cols=67  Identities=22%  Similarity=0.314  Sum_probs=61.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|+.+|||||+++++|+|+|++++||+++.|.+..+|+||+||+||.|+.|.+++++. .+....+.+
T Consensus       264 ~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i  330 (337)
T 2z0m_A          264 EGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEV  330 (337)
T ss_dssp             TTSCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHH
T ss_pred             cCCCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999998 665555444

>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=99.70  E-value=9.3e-19  Score=129.38  Aligned_cols=61  Identities=25%  Similarity=0.409  Sum_probs=0.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC------CccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS------SIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~------~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|.      +..+|+||+||+||.|+.|.+++++.+.+
T Consensus       381 ~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~  447 (479)
T 3fmp_B          381 EGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  447 (479)
T ss_dssp             -------------------------------------------------------------------
T ss_pred             cCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcc
Confidence            57899999999999999999999999999994      66899999999999999999999998765

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.69  E-value=5.3e-17  Score=120.25  Aligned_cols=61  Identities=26%  Similarity=0.376  Sum_probs=56.3

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      |+++|||||+++++|+|+|++++||+||+|+++.+|+||+|| ||. +.|.++.++++.+.+.
T Consensus       451 g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~  511 (555)
T 3tbk_A          451 GDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIE  511 (555)
T ss_dssp             -CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHH
T ss_pred             CCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHH
Confidence            789999999999999999999999999999999999999999 998 8899999998876543

>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=99.69  E-value=1.2e-17  Score=119.40  Aligned_cols=62  Identities=26%  Similarity=0.450  Sum_probs=58.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|+.+|||||+++++|+|+|++++||+++.|.+..+|+||+||+||.|+.|.+++++.+.+.
T Consensus       298 ~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  359 (391)
T 1xti_A          298 DFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  359 (391)
T ss_dssp             TTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHH
T ss_pred             cCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccch
Confidence            57889999999999999999999999999999999999999999999999999999987643

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.69  E-value=2e-17  Score=120.03  Aligned_cols=70  Identities=26%  Similarity=0.519  Sum_probs=59.4

Q ss_pred             CCceeEEEE----ccccccccCCCC-ccEEEEeCCC--CCccceeeecceeccCC----CcceEEEeeCccc-HHHHHHH
Q psy7959           2 RGEINVITA----TISFGMGIDRQN-VRFVVHWGMP--SSIPAYYQESGRAGRDG----LQSYCRIYHSEHS-KKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~----T~~~~~G~d~~~-v~~vi~~~~p--~~~~~~~qr~GR~gR~~----~~~~~i~~~~~~~-~~~~~~~   69 (101)
                      +|+++||||    |+++++|+|+|+ |++||++|+|  .+..+|+||+||+||.|    ..|.+++++.+.. +..+...
T Consensus       295 ~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~~~~~~~~~l~~~  374 (414)
T 3oiy_A          295 VGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTR  374 (414)
T ss_dssp             TTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEECCCHHHHHHHHHH
T ss_pred             CCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEEccHHHHHHHHHH
Confidence            588999999    999999999999 9999999999  99999999999999997    4799999994332 2344444


Q ss_pred             HH
Q psy7959          70 IK   71 (101)
Q Consensus        70 ~~   71 (101)
                      ++
T Consensus       375 ~~  376 (414)
T 3oiy_A          375 LL  376 (414)
T ss_dssp             HH
T ss_pred             hc
Confidence            44

>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=99.67  E-value=4.8e-18  Score=121.41  Aligned_cols=70  Identities=23%  Similarity=0.409  Sum_probs=0.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.+|||||+++++|+|+|++++||+++.|.+..+|+||+||+||.|+.|.+++++++.+...+..+.+
T Consensus       307 ~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~  376 (394)
T 1fuu_A          307 SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  376 (394)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             CCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHH
Confidence            4788999999999999999999999999999999999999999999999999999999888766555443

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.66  E-value=1.1e-16  Score=122.50  Aligned_cols=60  Identities=27%  Similarity=0.376  Sum_probs=41.8

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      |+.+|||||+++++|+|+|++++||+||+|.++.+|+||+|| ||. +.|.++.+++..+..
T Consensus       460 g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~  519 (696)
T 2ykg_A          460 GDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVI  519 (696)
T ss_dssp             -CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHH
T ss_pred             CCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHH
Confidence            889999999999999999999999999999999999999999 998 788999999877663

>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=99.66  E-value=4e-17  Score=121.25  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=36.6

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      |+++|||||+++++|+|+|++++||+||+|+++.+|+||+|| ||. +.|.++.++...+.+
T Consensus       452 g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~  511 (556)
T 4a2p_A          452 KDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  511 (556)
T ss_dssp             --CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHH
T ss_pred             CceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchH
Confidence            889999999999999999999999999999999999999999 998 789999999887654

>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=99.61  E-value=1.3e-16  Score=118.00  Aligned_cols=56  Identities=25%  Similarity=0.216  Sum_probs=51.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE-------------------eCCCCCccceeeecceeccC-CCcceEEEee
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH-------------------WGMPSSIPAYYQESGRAGRD-GLQSYCRIYH   58 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~-------------------~~~p~~~~~~~qr~GR~gR~-~~~~~~i~~~   58 (101)
                      +|+++|||||+++++|+|+| +++||+                   ++.|.+.++|+||+||+||. +..|.|++++
T Consensus       221 ~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~  296 (440)
T 1yks_A          221 QKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  296 (440)
T ss_dssp             -CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             CCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEe
Confidence            58899999999999999999 999986                   88899999999999999998 6789999997

>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=99.60  E-value=2.2e-16  Score=116.93  Aligned_cols=58  Identities=17%  Similarity=0.228  Sum_probs=53.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeC--------------------CCCCccceeeecceeccCCC-cceEEEeeCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWG--------------------MPSSIPAYYQESGRAGRDGL-QSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~--------------------~p~~~~~~~qr~GR~gR~~~-~~~~i~~~~~   60 (101)
                      +|+.+|||||+++++|+|+|+ ++||++|                    .|.+..+|+||+||+||.|. .|.++.++..
T Consensus       232 ~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          232 LTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             SSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             cCCceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence            588999999999999999999 9999999                    99999999999999999998 7888888753

>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=99.60  E-value=2.2e-16  Score=120.99  Aligned_cols=48  Identities=31%  Similarity=0.477  Sum_probs=42.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG   49 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~   49 (101)
                      +|+++|||||+++++|+|+|++++||+||+|+++.+|+||+||+||.|
T Consensus       462 ~g~~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g  509 (699)
T 4gl2_A          462 TGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE  509 (699)
T ss_dssp             C---CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS
T ss_pred             cCCCcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC
Confidence            588999999999999999999999999999999999999999976654

>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=99.59  E-value=1.4e-16  Score=118.29  Aligned_cols=59  Identities=20%  Similarity=0.186  Sum_probs=52.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE--------------------eCCCCCccceeeecceeccCCC-cceEEEeeCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH--------------------WGMPSSIPAYYQESGRAGRDGL-QSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~--------------------~~~p~~~~~~~qr~GR~gR~~~-~~~~i~~~~~   60 (101)
                      +|+.+|||||+++++|+|+|+ ++||+                    ++.|.+.++|+||+||+||.|. .|.+++++.+
T Consensus       234 ~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~  312 (459)
T 2z83_A          234 NGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGA  312 (459)
T ss_dssp             SCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             CCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEcc
Confidence            588999999999999999999 99999                    6799999999999999999997 8999999987


Q ss_pred             c
Q psy7959          61 H   61 (101)
Q Consensus        61 ~   61 (101)
                      .
T Consensus       313 ~  313 (459)
T 2z83_A          313 T  313 (459)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.59  E-value=1.9e-16  Score=126.93  Aligned_cols=74  Identities=28%  Similarity=0.406  Sum_probs=66.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eCC----CCCccceeeecceeccCCC--cceEEEeeCcc-cHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WGM----PSSIPAYYQESGRAGRDGL--QSYCRIYHSEH-SKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~~----p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~-~~~~~~~~~   70 (101)
                      +|.++|||||+++++|+|+|++++||+    ||.    |.++.+|+||+||+||.|.  .|.+++++++. +...+..++
T Consensus       430 ~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~G~vi~l~~~~~e~~~~~~l~  509 (1010)
T 2xgj_A          430 EGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMV  509 (1010)
T ss_dssp             TTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSSEEEEEEECSCCCHHHHHHHH
T ss_pred             cCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCceEEEEEECCCCCHHHHHHHH
Confidence            588999999999999999999999999    998    8999999999999999996  49999999876 667777777


Q ss_pred             Hcccc
Q psy7959          71 KTDTS   75 (101)
Q Consensus        71 ~~~~~   75 (101)
                      .+..+
T Consensus       510 ~~~~~  514 (1010)
T 2xgj_A          510 KGQAD  514 (1010)
T ss_dssp             SCCCC
T ss_pred             hCCCc
Confidence            76655

>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=99.59  E-value=7.1e-16  Score=120.59  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=42.2

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      |+++|||||+++++|+|+|++++||+||+|+++.+|+||+|| ||. +.|.++.+++..+.+
T Consensus       693 g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~e  752 (797)
T 4a2q_A          693 KDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (797)
T ss_dssp             -CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHHH
T ss_pred             CCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHH
Confidence            889999999999999999999999999999999999999999 998 889999999877654

>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=99.58  E-value=4.2e-16  Score=112.61  Aligned_cols=63  Identities=30%  Similarity=0.346  Sum_probs=58.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKS   65 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~   65 (101)
                      +|+.+|||||+++++|+|+|++++||++|.|+++..|+||+||+||.|+ |.++.++.+++.+.
T Consensus       417 ~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~ee  479 (494)
T 1wp9_A          417 RGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDE  479 (494)
T ss_dssp             HTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHHH
T ss_pred             cCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHHH
Confidence            3678999999999999999999999999999999999999999999998 99999999886654

>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=99.57  E-value=4.4e-16  Score=119.59  Aligned_cols=62  Identities=16%  Similarity=0.214  Sum_probs=54.6

Q ss_pred             CCceeEEEEccccccccCCCCccEE--------------------EEeCCCCCccceeeecceeccCCC-cceEEEeeC-
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFV--------------------VHWGMPSSIPAYYQESGRAGRDGL-QSYCRIYHS-   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~v--------------------i~~~~p~~~~~~~qr~GR~gR~~~-~~~~i~~~~-   59 (101)
                      +|+.+||||||++++|+|+| +++|                    |+++.|.+.++|+||+||+||.|. .|.+++++. 
T Consensus       399 ~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~  477 (618)
T 2whx_A          399 LTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  477 (618)
T ss_dssp             HSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             CCCcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccC
Confidence            47899999999999999997 8888                    777889999999999999999975 899999997 


Q ss_pred             --cccHH
Q psy7959          60 --EHSKK   64 (101)
Q Consensus        60 --~~~~~   64 (101)
                        +.+..
T Consensus       478 ~~~~d~~  484 (618)
T 2whx_A          478 PLKNDED  484 (618)
T ss_dssp             CCCCCTT
T ss_pred             CchhhHH
Confidence              55543

>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=99.56  E-value=3.1e-16  Score=126.72  Aligned_cols=80  Identities=24%  Similarity=0.279  Sum_probs=63.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCC--------CCccceeeecceeccCC--CcceEEEeeCcc-cHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMP--------SSIPAYYQESGRAGRDG--LQSYCRIYHSEH-SKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p--------~~~~~~~qr~GR~gR~~--~~~~~i~~~~~~-~~~~~~~~~   70 (101)
                      +|.++|||||+++++|+|+|++++||+++.|        .++.+|+||+||+||.|  ..|.+++++.+. +...+..++
T Consensus       528 ~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~G~~ill~~~~~~~~~~~~l~  607 (1108)
T 3l9o_A          528 EGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDRGIVIMMIDEKMEPQVAKGMV  607 (1108)
T ss_dssp             HTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSSEEEEEEECCCCCHHHHHHHH
T ss_pred             CCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCceEEEEEecCCcCHHHHHHHh
Confidence            4889999999999999999999999987764        35666999999999999  579999999876 566777788


Q ss_pred             HcccchhHHHH
Q psy7959          71 KTDTSTKREQL   81 (101)
Q Consensus        71 ~~~~~~~~~~~   81 (101)
                      ......+...+
T Consensus       608 ~~~~~~L~S~f  618 (1108)
T 3l9o_A          608 KGQADRLDSAF  618 (1108)
T ss_dssp             HCCCCCCCCCC
T ss_pred             cCCCccccccc
Confidence            77665554433

>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=99.55  E-value=2.7e-15  Score=119.42  Aligned_cols=60  Identities=25%  Similarity=0.325  Sum_probs=42.6

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      |+++|||||+++++|+|+|++++||+||+|+++.+|+||+|| ||. ..|.++.++...+.+
T Consensus       693 g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          693 KDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             -CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             CCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence            889999999999999999999999999999999999999999 998 788899998876543

>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=99.54  E-value=8.8e-16  Score=120.39  Aligned_cols=61  Identities=26%  Similarity=0.308  Sum_probs=57.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC------------------CCCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM------------------PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|..+|||||+++++|+|+|+|++||++|+                  |.+.++|+||+||+||. ..|.|+.++++.++
T Consensus       367 ~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          367 RPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             SCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             CCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            588999999999999999999999999888                  88999999999999999 78999999987665

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.54  E-value=1.4e-15  Score=117.80  Aligned_cols=56  Identities=20%  Similarity=0.178  Sum_probs=52.3

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE--------------------eCCCCCccceeeecceeccC-CCcceEEEee
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH--------------------WGMPSSIPAYYQESGRAGRD-GLQSYCRIYH   58 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~--------------------~~~p~~~~~~~qr~GR~gR~-~~~~~~i~~~   58 (101)
                      +|+++|||||+++++|+|+| +++||+                    +++|.+.++|+||+||+||. ++.|.+++++
T Consensus       454 ~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~  530 (673)
T 2wv9_A          454 NGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYG  530 (673)
T ss_dssp             TCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEEC
T ss_pred             CCCceEEEECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEE
Confidence            58899999999999999999 999998                    56899999999999999999 6789999996

>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=99.54  E-value=1.5e-15  Score=119.68  Aligned_cols=58  Identities=29%  Similarity=0.180  Sum_probs=55.0

Q ss_pred             eeEEEEccccccccCCC--------CccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDRQ--------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~--------~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      .+|+||||+++||+|++        ++.+||++++|.+...|+||+||+||.|.+|.++.|++..|
T Consensus       481 g~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD  546 (844)
T 1tf5_A          481 GAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  546 (844)
T ss_dssp             TCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             CeEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHH
Confidence            57999999999999999        78899999999999999999999999999999999998665

>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=99.52  E-value=5.2e-15  Score=114.29  Aligned_cols=62  Identities=23%  Similarity=0.291  Sum_probs=57.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-----CCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-----PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-----p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      +|+++|||||+++++|+|+|++++||++|.     |.+..+|+||+||+||. ..|.+++++++.+..
T Consensus       493 ~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~  559 (661)
T 2d7d_A          493 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKS  559 (661)
T ss_dssp             HTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHH
T ss_pred             cCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHH
Confidence            378999999999999999999999999997     99999999999999998 789999999887654

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.52  E-value=8.1e-15  Score=113.69  Aligned_cols=74  Identities=22%  Similarity=0.372  Sum_probs=61.1

Q ss_pred             CceeEEEEccccccccCCCCccEEEEeCC--------------CCCccceeeecceeccCCCc---ceEEEeeCcccHHH
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVVHWGM--------------PSSIPAYYQESGRAGRDGLQ---SYCRIYHSEHSKKS   65 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi~~~~--------------p~~~~~~~qr~GR~gR~~~~---~~~i~~~~~~~~~~   65 (101)
                      |+++|||||+++++|+|+ ++++||++|+              |.+.++|+||+||+||.|..   |.++.+ .+.+...
T Consensus       371 g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l-~~~d~~~  448 (677)
T 3rc3_A          371 DPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTM-NHEDLSL  448 (677)
T ss_dssp             SSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEES-STTHHHH
T ss_pred             CCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEE-ecchHHH
Confidence            789999999999999999 9999999998              78999999999999999964   555554 4556666


Q ss_pred             HHHHHHcccchhH
Q psy7959          66 LEYVIKTDTSTKR   78 (101)
Q Consensus        66 ~~~~~~~~~~~~~   78 (101)
                      +..++.....+..
T Consensus       449 ~~~~~~~~~~~i~  461 (677)
T 3rc3_A          449 LKEILKRPVDPIR  461 (677)
T ss_dssp             HHHHHHSCCCCCC
T ss_pred             HHHHHhcCcchhh
Confidence            7777776655543

>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=99.51  E-value=7e-15  Score=113.65  Aligned_cols=64  Identities=20%  Similarity=0.241  Sum_probs=57.9

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-----CCCccceeeecceeccCCCcceEEEeeCcccHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-----PSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSL   66 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-----p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~   66 (101)
                      +|+++|||||+++++|+|+|++++||++|.     |.+..+|+||+||+||.+ .|.+++++++.+....
T Consensus       487 ~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~  555 (664)
T 1c4o_A          487 LGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQ  555 (664)
T ss_dssp             TTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHH
T ss_pred             cCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHH
Confidence            478999999999999999999999999997     899999999999999994 8999999988765443

>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=99.51  E-value=1.5e-15  Score=117.61  Aligned_cols=58  Identities=21%  Similarity=0.271  Sum_probs=52.1

Q ss_pred             CceeEEEEccccccccCCCCccEEE----------EeC-----------CCCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           3 GEINVITATISFGMGIDRQNVRFVV----------HWG-----------MPSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         3 g~~~vlv~T~~~~~G~d~~~v~~vi----------~~~-----------~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +..+||||||++++|+|++ +++||          |||           +|.+.++|+||+||+|| ++.|. +.|+++.
T Consensus       438 ~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~  514 (666)
T 3o8b_A          438 IGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPG  514 (666)
T ss_dssp             SSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCC
T ss_pred             CCCcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecc
Confidence            5569999999999999996 99998          677           89999999999999999 88899 9998876


Q ss_pred             cH
Q psy7959          62 SK   63 (101)
Q Consensus        62 ~~   63 (101)
                      +.
T Consensus       515 e~  516 (666)
T 3o8b_A          515 ER  516 (666)
T ss_dssp             CB
T ss_pred             hh
Confidence            54

>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=99.50  E-value=4.2e-15  Score=116.73  Aligned_cols=60  Identities=23%  Similarity=0.427  Sum_probs=55.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-CccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+++|||||+++++|+|+|++++||++|.|. +.++|.||+||+||.|..|.|++++.+.
T Consensus       637 ~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~  697 (780)
T 1gm5_A          637 EGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDV  697 (780)
T ss_dssp             TTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSC
T ss_pred             CCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCC
Confidence            58899999999999999999999999999985 7889999999999999999999999743

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.50  E-value=5.6e-15  Score=114.06  Aligned_cols=61  Identities=26%  Similarity=0.386  Sum_probs=52.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC-------CCCCccceeeecceeccCCC--cceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG-------MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~-------~p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~~   62 (101)
                      +|.++|||||+++++|+|+|++++||+    ||       .|.+..+|.||+|||||.|.  .|.|+.++++.+
T Consensus       336 ~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  409 (715)
T 2va8_A          336 QRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKE  409 (715)
T ss_dssp             TTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSCGG
T ss_pred             cCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCCch
Confidence            588999999999999999999999999    99       89999999999999999884  699999998765

>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=99.49  E-value=6.6e-15  Score=118.45  Aligned_cols=66  Identities=27%  Similarity=0.350  Sum_probs=50.0

Q ss_pred             CCceeEEEE----ccccccccCCCCc-cEEEEeCCC--------------------------------------------
Q psy7959           2 RGEINVITA----TISFGMGIDRQNV-RFVVHWGMP--------------------------------------------   32 (101)
Q Consensus         2 ~g~~~vlv~----T~~~~~G~d~~~v-~~vi~~~~p--------------------------------------------   32 (101)
                      +|+.+||||    |+++++|+|+|+| ++||++|+|                                            
T Consensus       317 ~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  396 (1054)
T 1gku_B          317 EGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEV  396 (1054)
T ss_dssp             HTSCSEEEEECC------CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHH
T ss_pred             cCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence            478999999    9999999999995 999999999                                            


Q ss_pred             ---------------------------CCccceeeecceeccCCCcc--eEEEeeCcccHHHHH
Q psy7959          33 ---------------------------SSIPAYYQESGRAGRDGLQS--YCRIYHSEHSKKSLE   67 (101)
Q Consensus        33 ---------------------------~~~~~~~qr~GR~gR~~~~~--~~i~~~~~~~~~~~~   67 (101)
                                                 .+..+|+||+||+||.|..|  .++.++...+...+.
T Consensus       397 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~  460 (1054)
T 1gku_B          397 REILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLS  460 (1054)
T ss_dssp             HHHHHHHHTTSCCSCSSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHH
T ss_pred             HHHHHHHhccccccccceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHH
Confidence                                       78999999999999987664  356666555554443

>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=99.48  E-value=1.1e-14  Score=112.77  Aligned_cols=71  Identities=23%  Similarity=0.286  Sum_probs=60.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC----CCCCccceeeecceeccCC--CcceEEEeeCcccHHH-HHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG----MPSSIPAYYQESGRAGRDG--LQSYCRIYHSEHSKKS-LEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~----~p~~~~~~~qr~GR~gR~~--~~~~~i~~~~~~~~~~-~~~~~   70 (101)
                      +|.++|||||+++++|+|+|++++||+    ||    .|.+..+|+||+|||||.|  ..|.|+.++++.+... +..++
T Consensus       318 ~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~~~~~~~~  397 (720)
T 2zj8_A          318 KGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYI  397 (720)
T ss_dssp             TTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSCHHHHHHHHT
T ss_pred             CCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCccHHHHHHHHh
Confidence            588999999999999999999999999    66    5899999999999999998  4689999999877443 33444


Q ss_pred             Hc
Q psy7959          71 KT   72 (101)
Q Consensus        71 ~~   72 (101)
                      ..
T Consensus       398 ~~  399 (720)
T 2zj8_A          398 FG  399 (720)
T ss_dssp             TS
T ss_pred             cC
Confidence            33

>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=99.48  E-value=1.2e-14  Score=113.57  Aligned_cols=58  Identities=26%  Similarity=0.131  Sum_probs=54.5

Q ss_pred             eeEEEEccccccccCCC--------CccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           5 INVITATISFGMGIDRQ--------NVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~--------~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      -.|+||||+++||+|++        +..+||++++|.+...|.||+||+||.|.+|.++.|++..|
T Consensus       523 g~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD  588 (822)
T 3jux_A          523 GMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLED  588 (822)
T ss_dssp             TCEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTS
T ss_pred             CeEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhH
Confidence            47999999999999997        56699999999999999999999999999999999999776

>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=99.46  E-value=2.2e-14  Score=110.74  Aligned_cols=63  Identities=29%  Similarity=0.489  Sum_probs=57.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC---CCCCccceeeecceeccCC--CcceEEEeeCcccHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG---MPSSIPAYYQESGRAGRDG--LQSYCRIYHSEHSKK   64 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~---~p~~~~~~~qr~GR~gR~~--~~~~~i~~~~~~~~~   64 (101)
                      +|+++|||||+++++|+|+|++++||+    ||   .|.+..+|.||+||+||.|  ..|.|+.+++..+.+
T Consensus       320 ~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~~~  391 (702)
T 2p6r_A          320 RGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDRE  391 (702)
T ss_dssp             TTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHH
T ss_pred             CCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCccHH
Confidence            588999999999999999999999999    76   6899999999999999998  468999999988754

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.45  E-value=1.4e-14  Score=116.14  Aligned_cols=74  Identities=26%  Similarity=0.320  Sum_probs=57.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCC---------CCccceeeecceeccCC--CcceEEEeeC--cccHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMP---------SSIPAYYQESGRAGRDG--LQSYCRIYHS--EHSKKSLEY   68 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p---------~~~~~~~qr~GR~gR~~--~~~~~i~~~~--~~~~~~~~~   68 (101)
                      +|.++|||||+++++|+|+|+ ..||..++|         .++.+|+||+|||||.|  ..|.+++++.  ..+...++.
T Consensus       423 ~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~~~~G~vi~l~~~~~~~~~~~~~  501 (997)
T 4a4z_A          423 KGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKE  501 (997)
T ss_dssp             TTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTTCSSEEEEEECCSSCCCHHHHHH
T ss_pred             CCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCCCcceEEEEecCCCcchHHHHHH
Confidence            588999999999999999999 555554444         49999999999999998  4588888883  335666666


Q ss_pred             HHHcccch
Q psy7959          69 VIKTDTST   76 (101)
Q Consensus        69 ~~~~~~~~   76 (101)
                      ++......
T Consensus       502 ~i~~~~~~  509 (997)
T 4a4z_A          502 VTMGVPTR  509 (997)
T ss_dssp             HHHSCCCC
T ss_pred             HhcCCCcc
Confidence            66655444

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.45  E-value=2e-14  Score=116.13  Aligned_cols=32  Identities=31%  Similarity=0.755  Sum_probs=30.8

Q ss_pred             CCceeEEEE----ccccccccCCCC-ccEEEEeCCCC
Q psy7959           2 RGEINVITA----TISFGMGIDRQN-VRFVVHWGMPS   33 (101)
Q Consensus         2 ~g~~~vlv~----T~~~~~G~d~~~-v~~vi~~~~p~   33 (101)
                      +|+++||||    |+++++|+|+|+ |++|||||+|.
T Consensus       352 ~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          352 VGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             HTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            488999999    999999999999 99999999998

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.44  E-value=2e-14  Score=105.91  Aligned_cols=56  Identities=16%  Similarity=0.138  Sum_probs=47.8

Q ss_pred             CCceeEEEEccccccccCCCCccE-----------------EEEeCCCCCccceeeecceeccCCCc-ceEEEee
Q psy7959           2 RGEINVITATISFGMGIDRQNVRF-----------------VVHWGMPSSIPAYYQESGRAGRDGLQ-SYCRIYH   58 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~-----------------vi~~~~p~~~~~~~qr~GR~gR~~~~-~~~i~~~   58 (101)
                      +|+.+|||||+++++|+|+| +..                 ||+++.|.+.++|+||+||+||.|.. +.++++.
T Consensus       215 ~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          215 SEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             HSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             CCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence            47899999999999999999 544                 67889999999999999999999854 4555554

>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=99.42  E-value=2.8e-14  Score=105.10  Aligned_cols=60  Identities=22%  Similarity=0.176  Sum_probs=52.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc---ceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ---SYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~---~~~i~~~~~~   61 (101)
                      +|+++|||||+++++|+|+|++++||++|.|+++..|+||+||+||.|+.   ...+.++..+
T Consensus       392 ~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          392 TGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             HSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             CCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            37899999999999999999999999999999999999999999999854   3344455544

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.41  E-value=2e-14  Score=106.81  Aligned_cols=58  Identities=24%  Similarity=0.129  Sum_probs=52.3

Q ss_pred             CCceeEEEEc-cccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITAT-ISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T-~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+.+||||| +++++|+|+|++++||+++.|+++.+|+|++||+||.|..+.++.+++
T Consensus       395 ~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          395 NGKGIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             HCCSCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             CCCCCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            4788999999 999999999999999999999999999999999999998764555554

>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=99.38  E-value=9.7e-14  Score=109.42  Aligned_cols=57  Identities=30%  Similarity=0.235  Sum_probs=53.5

Q ss_pred             eEEEEccccccccCCCC--------------------------------c-----cEEEEeCCCCCccceeeecceeccC
Q psy7959           6 NVITATISFGMGIDRQN--------------------------------V-----RFVVHWGMPSSIPAYYQESGRAGRD   48 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~--------------------------------v-----~~vi~~~~p~~~~~~~qr~GR~gR~   48 (101)
                      .|+||||+++||+|++.                                |     .+||++++|.+...|.||+||+||.
T Consensus       491 ~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRq  570 (853)
T 2fsf_A          491 AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQ  570 (853)
T ss_dssp             CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccC
Confidence            79999999999999987                                4     6999999999999999999999999


Q ss_pred             CCcceEEEeeCccc
Q psy7959          49 GLQSYCRIYHSEHS   62 (101)
Q Consensus        49 ~~~~~~i~~~~~~~   62 (101)
                      |.+|.++.|++..|
T Consensus       571 Gd~G~s~~fls~eD  584 (853)
T 2fsf_A          571 GDAGSSRFYLSMED  584 (853)
T ss_dssp             GCCEEEEEEEETTS
T ss_pred             CCCeeEEEEecccH
Confidence            99999999998665

>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=99.37  E-value=1.3e-13  Score=110.25  Aligned_cols=53  Identities=21%  Similarity=0.148  Sum_probs=49.4

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEe
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIY   57 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~   57 (101)
                      ++|||||+++++|+|+|++++||++|+|+++..|+||+||+||.|+.+.++++
T Consensus       557 ~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~  609 (968)
T 3dmq_A          557 AQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIH  609 (968)
T ss_dssp             CEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEE
T ss_pred             ccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEE
Confidence            99999999999999999999999999999999999999999999988754444

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.36  E-value=3.2e-13  Score=94.59  Aligned_cols=60  Identities=17%  Similarity=0.137  Sum_probs=39.0

Q ss_pred             cee-EEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcce--EEEeeCcccH
Q psy7959           4 EIN-VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY--CRIYHSEHSK   63 (101)
Q Consensus         4 ~~~-vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~--~i~~~~~~~~   63 (101)
                      ..+ +|++|+++++|+|++.+++||+||+|+++..|.|++||++|.|+.+.  ++.++..+..
T Consensus       164 ~~~v~L~st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~Ti  226 (271)
T 1z5z_A          164 SVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTL  226 (271)
T ss_dssp             TCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSH
T ss_pred             CCCEEEEehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCCH
Confidence            455 78999999999999999999999999999999999999999998644  4556666543

>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=99.36  E-value=2.4e-13  Score=110.22  Aligned_cols=60  Identities=22%  Similarity=0.280  Sum_probs=55.6

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-CCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-PSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+++|||||+++++|+|+|++++||.++. +.++.+|+||+||+||.|+.|.|++++.+.
T Consensus       862 ~g~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          862 HQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             TTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             cCCCcEEEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            588999999999999999999999999887 578999999999999999999999998764

>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=99.33  E-value=3.4e-13  Score=106.82  Aligned_cols=59  Identities=29%  Similarity=0.183  Sum_probs=54.5

Q ss_pred             eeEEEEccccccccCCCCc----------------------------------------------------cEEEEeCCC
Q psy7959           5 INVITATISFGMGIDRQNV----------------------------------------------------RFVVHWGMP   32 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v----------------------------------------------------~~vi~~~~p   32 (101)
                      -.|+||||+++||+|++.+                                                    .+||++++|
T Consensus       509 G~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~p  588 (922)
T 1nkt_A          509 GGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERH  588 (922)
T ss_dssp             TCEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCC
T ss_pred             CeEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCC
Confidence            3799999999999999975                                                    599999999


Q ss_pred             CCccceeeecceeccCCCcceEEEeeCcccH
Q psy7959          33 SSIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus        33 ~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      .+...|.||.||+||.|.+|.++.|++..|.
T Consensus       589 es~riy~qr~GRTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          589 ESRRIDNQLRGRSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             SSHHHHHHHHHTSSGGGCCEEEEEEEETTSH
T ss_pred             CCHHHHHHHhcccccCCCCeeEEEEechhHH
Confidence            9999999999999999999999999987654

>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=99.27  E-value=9.3e-13  Score=110.10  Aligned_cols=73  Identities=19%  Similarity=0.245  Sum_probs=63.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC------CCCCccceeeecceeccCCC--cceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG------MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~------~p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|.++|||||+++++|+|+|.+++||.    ||      .|.++.+|.||+|||||.|.  .|.+++++.+.+...++++
T Consensus      1237 ~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~l 1316 (1724)
T 4f92_B         1237 SGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKF 1316 (1724)
T ss_dssp             HTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHH
T ss_pred             CCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHHHHHHH
Confidence            588999999999999999999999984    22      46789999999999999986  5999999999888888888


Q ss_pred             HHccc
Q psy7959          70 IKTDT   74 (101)
Q Consensus        70 ~~~~~   74 (101)
                      +....
T Consensus      1317 l~~~~ 1321 (1724)
T 4f92_B         1317 LYEPL 1321 (1724)
T ss_dssp             TTSCB
T ss_pred             hCCCC
Confidence            76644

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.24  E-value=2.2e-12  Score=97.65  Aligned_cols=44  Identities=23%  Similarity=0.276  Sum_probs=42.4

Q ss_pred             EEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCC
Q psy7959           7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGL   50 (101)
Q Consensus         7 vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~   50 (101)
                      |||||+++++|+|+|++++||+++.|.+...|+||+||+||.+.
T Consensus       502 ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          502 ILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             EEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             EEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            88999999999999999999999999999999999999999874

>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=99.23  E-value=1.1e-12  Score=109.73  Aligned_cols=73  Identities=15%  Similarity=0.207  Sum_probs=62.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----eC------CCCCccceeeecceeccCCC--cceEEEeeCcccHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----WG------MPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSKKSLEYV   69 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----~~------~p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~~~~~~~~~   69 (101)
                      +|.++|||||++++.|+|+|.+++||.    |+      .|.++.+|.||+|||||.|.  .|.++++....+...+..+
T Consensus       402 ~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~l  481 (1724)
T 4f92_B          402 DKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL  481 (1724)
T ss_dssp             TTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHH
T ss_pred             CCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchhHHHHHHH
Confidence            689999999999999999999999986    43      36789999999999999874  5999999988887777676


Q ss_pred             HHccc
Q psy7959          70 IKTDT   74 (101)
Q Consensus        70 ~~~~~   74 (101)
                      +.+..
T Consensus       482 l~~~~  486 (1724)
T 4f92_B          482 LNQQL  486 (1724)
T ss_dssp             TTTCS
T ss_pred             HcCCC
Confidence            66543

>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=99.13  E-value=2.1e-11  Score=90.27  Aligned_cols=61  Identities=16%  Similarity=0.141  Sum_probs=47.6

Q ss_pred             cee-EEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcce--EEEeeCcccHH
Q psy7959           4 EIN-VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSY--CRIYHSEHSKK   64 (101)
Q Consensus         4 ~~~-vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~--~i~~~~~~~~~   64 (101)
                      ..+ +|++|+++++|+|+++++.||++|.|+++..|.|++||++|.|+...  ++.++..+..+
T Consensus       393 ~~~vil~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~tie  456 (500)
T 1z63_A          393 SVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLE  456 (500)
T ss_dssp             TCCCCEEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTSHH
T ss_pred             CCCEEEEecccccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCCHH
Confidence            344 79999999999999999999999999999999999999999997644  45566655443

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.96  E-value=2.6e-10  Score=87.67  Aligned_cols=58  Identities=17%  Similarity=0.111  Sum_probs=50.8

Q ss_pred             eEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcc--eEEEeeCcccH
Q psy7959           6 NVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQS--YCRIYHSEHSK   63 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~--~~i~~~~~~~~   63 (101)
                      .+|++|+++++|+|++++++||++|.|+++..|.|++||++|.|+..  .++.++..+..
T Consensus       471 v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~ti  530 (644)
T 1z3i_X          471 IFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTI  530 (644)
T ss_dssp             EEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSH
T ss_pred             EEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCCH
Confidence            58999999999999999999999999999999999999999999754  45556666543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.82  E-value=1.2e-09  Score=85.81  Aligned_cols=59  Identities=22%  Similarity=0.151  Sum_probs=51.6

Q ss_pred             eeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc--ceEEEeeCcccH
Q psy7959           5 INVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSK   63 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~   63 (101)
                      ..+|++|.+++.|+|++.++.||++|.|+++..+.|+.||+.|.|+.  -.++.++..+..
T Consensus       626 ~v~LlSt~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~Ti  686 (800)
T 3mwy_W          626 FVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTV  686 (800)
T ss_dssp             CCEEEEHHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTSH
T ss_pred             eEEEEecccccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCCH
Confidence            45999999999999999999999999999999999999999999975  445566666643

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=98.81  E-value=1.4e-09  Score=87.76  Aligned_cols=57  Identities=12%  Similarity=0.075  Sum_probs=51.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc----ceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ----SYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~----~~~i~~~~   59 (101)
                      +|+++|||+|+++.+|+|+|.+ .++.+|.|.+...|+|++||++|.+..    |.++.|..
T Consensus       647 ~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~  707 (1038)
T 2w00_A          647 NQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRD  707 (1038)
T ss_dssp             TTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSC
T ss_pred             cCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEccc
Confidence            4789999999999999999999 788999999999999999999998753    77777765

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.14  E-value=0.00017  Score=54.40  Aligned_cols=54  Identities=19%  Similarity=0.115  Sum_probs=30.1

Q ss_pred             eEEE--EccccccccCCCC----ccEEEEeCCCCCcc------------------------------ceeeecceeccCC
Q psy7959           6 NVIT--ATISFGMGIDRQN----VRFVVHWGMPSSIP------------------------------AYYQESGRAGRDG   49 (101)
Q Consensus         6 ~vlv--~T~~~~~G~d~~~----v~~vi~~~~p~~~~------------------------------~~~qr~GR~gR~~   49 (101)
                      .||+  +|+.+++|+|+|+    ++.||.+++|....                              .+.|-+||.-|..
T Consensus       430 ~il~~V~~~~~~EGiD~~~~~~~~~~Vii~~lPf~~~~d~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~Q~~GR~iR~~  509 (540)
T 2vl7_A          430 YLVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDP  509 (540)
T ss_dssp             CEEEEEC---------------CEEEEEEESCCCCCTTSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCCST
T ss_pred             eEEEEEecCceecceecCCCcccccEEEEECCCCCCCCCHHHHHHHHHHHHhhCCChhHHHHHHHHHHHHHHhCCcccCC
Confidence            4666  8999999999997    89999999985322                              2358899999987


Q ss_pred             CcceEEEeeC
Q psy7959          50 LQSYCRIYHS   59 (101)
Q Consensus        50 ~~~~~i~~~~   59 (101)
                      ++-.+++++.
T Consensus       510 ~D~g~v~llD  519 (540)
T 2vl7_A          510 NDYVKIYLCD  519 (540)
T ss_dssp             TCCCEEEEES
T ss_pred             CccEEEEEEc
Confidence            7655566655

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=96.55  E-value=0.0011  Score=53.34  Aligned_cols=38  Identities=32%  Similarity=0.300  Sum_probs=30.0

Q ss_pred             EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959          25 FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus        25 ~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +||-...+.|.--=.|-.||+||-|.+|.+..|++-.|
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeD  699 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDD  699 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSS
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECCh
Confidence            66666666666666789999999999999988887554

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=87.27  E-value=0.36  Score=37.02  Aligned_cols=57  Identities=21%  Similarity=0.274  Sum_probs=35.0

Q ss_pred             ceeEEEEcc--ccccccCCCC--ccEEEEeCCCCCcc-----------------------------ceeeecceeccCCC
Q psy7959           4 EINVITATI--SFGMGIDRQN--VRFVVHWGMPSSIP-----------------------------AYYQESGRAGRDGL   50 (101)
Q Consensus         4 ~~~vlv~T~--~~~~G~d~~~--v~~vi~~~~p~~~~-----------------------------~~~qr~GR~gR~~~   50 (101)
                      +--||++|.  .+.+|+|+++  .+.||-.++|....                             .+.|-+||.=|..+
T Consensus       494 ~~~vL~~v~~gsf~EGiD~~g~~l~~viI~~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~  573 (620)
T 4a15_A          494 DHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAE  573 (620)
T ss_dssp             SCCEEEEETTSCC--------CCCCEEEESSCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTT
T ss_pred             CCcEEEEEecCceeccccCCCCceEEEEEEcCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCC
Confidence            346889975  8999999996  77999999885321                             12588999989877


Q ss_pred             cceEEEeeCc
Q psy7959          51 QSYCRIYHSE   60 (101)
Q Consensus        51 ~~~~i~~~~~   60 (101)
                      +-.++++++.
T Consensus       574 D~G~v~llD~  583 (620)
T 4a15_A          574 DTGACVILDK  583 (620)
T ss_dssp             CCEEEEEECG
T ss_pred             ceEEEEEEcc
Confidence            7666777654

>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=82.69  E-value=7.9  Score=27.60  Aligned_cols=68  Identities=6%  Similarity=-0.164  Sum_probs=43.1

Q ss_pred             eeEEEEccccccccC-----CCCccEEEEeCCCCCccc-eeeecceeccC----CCcceEEEeeCcccHHHHHHHHHc
Q psy7959           5 INVITATISFGMGID-----RQNVRFVVHWGMPSSIPA-YYQESGRAGRD----GLQSYCRIYHSEHSKKSLEYVIKT   72 (101)
Q Consensus         5 ~~vlv~T~~~~~G~d-----~~~v~~vi~~~~p~~~~~-~~qr~GR~gR~----~~~~~~i~~~~~~~~~~~~~~~~~   72 (101)
                      ..|-+.|...+-|++     ....+.||-||.-+++.. .+|..-|+-|.    ++.-.++.++..+..++....+..
T Consensus       171 ~~i~Lltsag~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh~~l~~~~  248 (328)
T 3hgt_A          171 CTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGK  248 (328)
T ss_dssp             EEEEEEESSCCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHHHHHHccC
Confidence            444455666666675     567889999998888876 36644444333    345678899988877766555543

---

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	101
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	1e-10
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	1e-09
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	3e-07
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	2e-06
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-06
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	1e-05
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	1e-05
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	2e-05
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	2e-05
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	6e-05
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	1e-04
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	2e-04
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	7e-04
d2eyqa5	211	c.37.1.19 (A:779-989) Transcription-repair couplin	8e-04
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	0.001

>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 = 53.7 bits (128), Expect = 1e-10
 Identities = 18/56 (32%), Positives = 22/56 (39%)

Query: 2   RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIY 57
           RGE NV+ AT     G+D   V  VV +    S     Q  GR GR        + 
Sbjct: 217 RGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIILM 272

>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 = 51.1 bits (122), Expect = 1e-09
 Identities = 7/42 (16%), Positives = 11/42 (26%), Gaps = 1/42 (2%)

Query: 7   VITATISFGM-GIDRQNVRFVVHWGMPSSIPAYYQESGRAGR 47
           +   T               +    +P    +  Q  GR GR
Sbjct: 101 IDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR 142

>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 = 44.4 bits (104), Expect = 3e-07
 Identities = 14/84 (16%), Positives = 28/84 (33%), Gaps = 9/84 (10%)

Query: 1   MRGEINVITATISFGMGIDR-----QNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR 55
           + GEI+ +  T  +   + R     + +RF V  G PS    +            Q    
Sbjct: 66  VEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKL 121

Query: 56  IYHSEHSKKSLEYVIKTDTSTKRE 79
           + +   +   +E ++        E
Sbjct: 122 LAYLYRNVDEIERLLPAVERHIDE 145

>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 = 40.8 bits (95), Expect = 2e-06
 Identities = 13/63 (20%), Positives = 18/63 (28%), Gaps = 3/63 (4%)

Query: 1   MRGEINVITATISFGMGIDRQN---VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIY 57
                 V+ AT +   G        +      G P    +  Q  GR GR     Y  + 
Sbjct: 75  PTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGRGKPGIYRFVA 134

Query: 58  HSE 60
             E
Sbjct: 135 PGE 137

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 41.8 bits (97), Expect = 3e-06
 Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 2/56 (3%)

Query: 7   VITATISFGMGIDRQN-VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCR-IYHSE 60
           VI         I      R ++   MP +  +  Q  GR GR+      + IY  E
Sbjct: 245 VIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE 300

>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 = 39.6 bits (91), Expect = 1e-05
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
            + +I ++ AT     GID  ++  V+++ +P +  +Y    GR GR G +       + 
Sbjct: 75  KQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINR 134

Query: 61  HSKKSLEYVIKTDTSTKREQLE 82
              K L Y I+     K ++L+
Sbjct: 135 REYKKLRY-IERAMKLKIKKLK 155

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

 Score = 39.3 bits (91), Expect = 1e-05
 Identities = 13/90 (14%), Positives = 30/90 (33%), Gaps = 9/90 (10%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSI-----PAYYQESGRAGRDGLQSYCR 55
             G  + +        G+D   V  V               +  Q  GRA R+       
Sbjct: 78  RLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA--RGEV 135

Query: 56  IYHSEHSKKSLEYVIKTDTSTKREQLELKF 85
             +++   ++++  I  + + +R  L+  +
Sbjct: 136 WLYADRVSEAMQRAI--EETNRRRALQEAY 163

>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 = 39.1 bits (90), Expect = 2e-05
 Identities = 12/49 (24%), Positives = 15/49 (30%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDG 49
             G    I ++     GID  +    V      S   Y Q  GR  R  
Sbjct: 135 RTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS 183

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 39.0 bits (90), Expect = 2e-05
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYY-QESGRAGRDGLQSYCRIYHS 59
             G  +++ +T    +GID      +V         A   Q  GR GR G ++YC +   
Sbjct: 87  AEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVG 146

Query: 60  EH 61
           + 
Sbjct: 147 DV 148

>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 = 37.6 bits (86), Expect = 6e-05
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 9/75 (12%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVH-------WGMPSSIPAYYQESGRAGRDGL--Q 51
            RG I V+ AT +   G++    R +V        +     +  Y Q +GRAGR G+  +
Sbjct: 117 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDER 176

Query: 52  SYCRIYHSEHSKKSL 66
               I   +  ++  
Sbjct: 177 GEAIIIVGKRDREIA 191

>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 = 36.8 bits (84), Expect = 1e-04
 Identities = 14/71 (19%), Positives = 31/71 (43%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             G   V+ +T  +  G+D   V  ++++ +P++   Y    GR+GR G +     +   
Sbjct: 81  RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKN 140

Query: 61  HSKKSLEYVIK 71
              + L  + +
Sbjct: 141 DDIRILRDIEQ 151

>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 = 36.6 bits (83), Expect = 2e-04
 Identities = 34/96 (35%), Positives = 58/96 (60%), Gaps = 2/96 (2%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
            R ++ ++ AT++FGMGI++ NVRFVVH+ +P +I +YYQE+GRAGRDGL +   +++  
Sbjct: 77  QRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 136

Query: 61  HSKKSLEYVIKTDTSTKREQLELKFKNYLSMLEYCE 96
                L   ++     + + +E    N  +M  + E
Sbjct: 137 ADMAWLRRCLEEKPQGQLQDIERHKLN--AMGAFAE 170

>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 = 34.8 bits (79), Expect = 7e-04
 Identities = 14/90 (15%), Positives = 26/90 (28%), Gaps = 3/90 (3%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQES--GRAGRDGLQSYCRIYH 58
             G+ +V+        G+D   V  V             + S     GR    +   +  
Sbjct: 78  RLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 137

Query: 59  SEHSKKSLEYVIKTDTSTKRE-QLELKFKN 87
              +      +   +T  +R  Q E   K+
Sbjct: 138 YADTITKSMEIAIQETKRRRAIQEEYNRKH 167

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 211

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

 Score = 34.6 bits (79), Expect = 8e-04
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 7/80 (8%)

Query: 1   MRGEINVITATISFGMGIDRQNVR-FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRI--- 56
                NV+  T     GID       ++       +   +Q  GR GR   Q+Y  +   
Sbjct: 80  HHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTP 139

Query: 57  ---YHSEHSKKSLEYVIKTD 73
                +  ++K LE +   +
Sbjct: 140 HPKAMTTDAQKRLEAIASLE 159

>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 = 33.7 bits (76), Expect = 0.001
 Identities = 16/71 (22%), Positives = 31/71 (43%)

Query: 1   MRGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSE 60
             G   ++ +T     GID Q V  V+++ +P++   Y    GR GR G +     + + 
Sbjct: 74  RSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN 133

Query: 61  HSKKSLEYVIK 71
               ++  + K
Sbjct: 134 EDVGAMRELEK 144

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	101
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.92
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.88
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.87
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.86
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.85
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.84
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.78
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.76
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.75
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.71
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.7
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.65
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.6
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.59
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.45
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.35
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.33
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.2
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.07
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.39
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.35
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.23
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	97.06
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	87.16

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.92  E-value=1.2e-25  Score=150.62  Aligned_cols=95  Identities=34%  Similarity=0.652  Sum_probs=83.2

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccchhHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTSTKREQL   81 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (101)
                      +|+++|||||+++++|+|+|+|++|||||+|.++.+|+||+||+||.|+.|.+++++.+.|...+++++.+......  .
T Consensus        78 ~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i~~~~~~~~--~  155 (200)
T d1oywa3          78 RDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQL--Q  155 (200)
T ss_dssp             TTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHHTSCCSHH--H
T ss_pred             cccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhhhccccccc--h
Confidence            68999999999999999999999999999999999999999999999999999999999999999888887766553  3


Q ss_pred             HHHHHHHHHHHHHHhcC
Q psy7959          82 ELKFKNYLSMLEYCEQV   98 (101)
Q Consensus        82 ~~~~~~l~~m~~~~e~~   98 (101)
                      ......+++|..|+++.
T Consensus       156 ~~~~~~~~~m~~~~~~~  172 (200)
T d1oywa3         156 DIERHKLNAMGAFAEAQ  172 (200)
T ss_dssp             HHHHHHHHHHHHHHTCS
T ss_pred             hhhHHHHHHHHHHHhch
Confidence            44445567777787653

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=1.1e-23  Score=136.77  Aligned_cols=70  Identities=23%  Similarity=0.409  Sum_probs=60.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      .|+.+||||||+++||+|+|+|++|||||+|++++.|+||+||+||.|+.|.+++++++.|...+..+.+
T Consensus        75 ~~~~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~  144 (162)
T d1fuka_          75 SGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEK  144 (162)
T ss_dssp             TTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHH
T ss_pred             hcccceeeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999988876665544

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.2e-23  Score=137.22  Aligned_cols=70  Identities=20%  Similarity=0.405  Sum_probs=64.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.++|||||++++|+|+|++++|||||+|++..+|+||+||+||.|+.|.+++++.+.+...++.+.+
T Consensus        82 ~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~  151 (168)
T d2j0sa2          82 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQ  151 (168)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHH
T ss_pred             cCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999999999999999998877665533

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.86  E-value=8e-23  Score=131.39  Aligned_cols=69  Identities=25%  Similarity=0.450  Sum_probs=64.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVI   70 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~   70 (101)
                      +|+.+|||||+++++|+|+|++++||+||+|+++.+|+||+||+||.|+.|.+++++++.|...++.+.
T Consensus        76 ~~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~  144 (155)
T d1hv8a2          76 QKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIE  144 (155)
T ss_dssp             TTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHH
T ss_pred             cccceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHH
Confidence            578999999999999999999999999999999999999999999999999999999998877665443

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=2e-22  Score=131.43  Aligned_cols=70  Identities=21%  Similarity=0.356  Sum_probs=64.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~   71 (101)
                      +|+.++||||+++++|+|+|++++|||||+|+++.+|+||+||+||.|+.|.+++|+++.+...+..+.+
T Consensus        80 ~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~  149 (171)
T d1s2ma2          80 QGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQ  149 (171)
T ss_dssp             TTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             cCccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999999999998876665543

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.7e-20  Score=122.06  Aligned_cols=61  Identities=26%  Similarity=0.455  Sum_probs=58.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +|+.+|||||+++++|+|+|++++||++|+|.++.+|+||+||+||.|+.|.+++++++.+
T Consensus        75 ~g~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~  135 (168)
T d1t5ia_          75 DFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  135 (168)
T ss_dssp             TTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             cccceeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchH
Confidence            5889999999999999999999999999999999999999999999999999999998754

>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=99.76  E-value=1.9e-19  Score=118.62  Aligned_cols=59  Identities=22%  Similarity=0.255  Sum_probs=49.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-----CccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-----SIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-----~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+++|||||+++++|+|+|+|++|||||+|.     +..+|+||+||+||.|.. .++.++...
T Consensus        79 ~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~-~~~~~~~~~  142 (181)
T d1t5la2          79 LGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANG-HVIMYADTI  142 (181)
T ss_dssp             HTSCSEEEESCCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTC-EEEEECSSC
T ss_pred             CCCCCEEEehhHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCc-eeEeecchh
Confidence            58999999999999999999999999999996     577899999999998754 444444433

>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=99.75  E-value=1.8e-19  Score=114.21  Aligned_cols=58  Identities=21%  Similarity=0.244  Sum_probs=51.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeC----CCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWG----MPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~----~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +|+.+||||||++++|+| +++++|||+|    +|.+.++|+||+||+|| |+.|. +.|+.++|
T Consensus        76 ~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_          76 TNGDVVVVATDALMTGFT-GDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             TSSCEEEEESSSSCSSSC-CCBSEEEECSEETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             hhhcceeehhHHHHhccc-cccceEEEEEecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            578999999999999999 9999999966    59999999999999999 88885 66776654

>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=99.71  E-value=8.1e-19  Score=121.33  Aligned_cols=62  Identities=31%  Similarity=0.395  Sum_probs=56.4

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      +|+++|||||+++++|+|+|++++||+||+|+++.+|+||+||+||. ++|.++.++.++..+
T Consensus       217 ~g~~~vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~-~~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         217 RGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGTRD  278 (286)
T ss_dssp             HTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSC-CCSEEEEEEETTSHH
T ss_pred             cCCCcEEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCC-CCCEEEEEEeCCCHH
Confidence            47889999999999999999999999999999999999999999997 478888888877554

>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=99.70  E-value=4.4e-18  Score=111.44  Aligned_cols=61  Identities=21%  Similarity=0.261  Sum_probs=51.8

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCC-----CccceeeecceeccCCCcceEEEeeCcccH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPS-----SIPAYYQESGRAGRDGLQSYCRIYHSEHSK   63 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-----~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~   63 (101)
                      +|+++|||||+++++|+|+|+|++||++|.|.     +..+|+||+||+||.+. |.++++......
T Consensus        79 ~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~  144 (174)
T d1c4oa2          79 LGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSE  144 (174)
T ss_dssp             TTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCH
T ss_pred             CCCeEEEEeeeeeeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCCCH
Confidence            68999999999999999999999999999775     45779999999999865 666666654443

>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=99.65  E-value=1.5e-17  Score=111.44  Aligned_cols=64  Identities=22%  Similarity=0.411  Sum_probs=58.2

Q ss_pred             CCCceeEEEEccccccccCCCCccEEEEeCCCC-CccceeeecceeccCCCcceEEEeeCcccHH
Q psy7959           1 MRGEINVITATISFGMGIDRQNVRFVVHWGMPS-SIPAYYQESGRAGRDGLQSYCRIYHSEHSKK   64 (101)
Q Consensus         1 ~~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~-~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~   64 (101)
                      .+|+++|||||+++++|+|+|+++++|+++.|. ..++|.|..||+||.+..|.|++++++.+..
T Consensus        87 ~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~  151 (206)
T d1gm5a4          87 AEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEE  151 (206)
T ss_dssp             TTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHH
T ss_pred             HCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeecccccc
Confidence            368999999999999999999999999999885 7999999999999999999999999865543

>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=99.60  E-value=1.1e-16  Score=108.75  Aligned_cols=71  Identities=20%  Similarity=0.212  Sum_probs=57.2

Q ss_pred             CCceeEEEEc----cccccccCCCC-ccEEEEeCCCCCccceeeecceeccCCCcceEEEeeCcccHHHHHHHHHcccch
Q psy7959           2 RGEINVITAT----ISFGMGIDRQN-VRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHSKKSLEYVIKTDTST   76 (101)
Q Consensus         2 ~g~~~vlv~T----~~~~~G~d~~~-v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~~~~~~~~~~~~~~~   76 (101)
                      +|+++|||||    +++++|+|+|+ |++|||||+|+    |.||+||+||.|..+.++.++...+......+.......
T Consensus        67 ~g~~~vLVaT~a~~~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~~~~~~~  142 (248)
T d1gkub2          67 EGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERH  142 (248)
T ss_dssp             HTSCSEEEEECC------CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSC
T ss_pred             hCCCeEEEEeccccchhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHHHHHHHh
Confidence            5899999999    78999999996 99999999994    999999999999999999998888877666555444433

>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=99.59  E-value=8.9e-17  Score=106.91  Aligned_cols=70  Identities=27%  Similarity=0.466  Sum_probs=59.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE-------eCCCCCccceeeecceeccCCC--cceEEEeeCcccHHH-HHHHHH
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH-------WGMPSSIPAYYQESGRAGRDGL--QSYCRIYHSEHSKKS-LEYVIK   71 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~-------~~~p~~~~~~~qr~GR~gR~~~--~~~~i~~~~~~~~~~-~~~~~~   71 (101)
                      +|.++|||||+++++|+|+|..++||+       ++.|.+..+|+||+|||||.|.  .|.+++++.+.+.+. ++.++.
T Consensus       118 ~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~~~~~k~~~~  197 (201)
T d2p6ra4         118 RGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIF  197 (201)
T ss_dssp             TTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHHHHHHTTTS
T ss_pred             CCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCChHHHHHHHhc
Confidence            588999999999999999999999996       5678999999999999999985  588998888776653 444443

>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=99.45  E-value=3.7e-15  Score=98.14  Aligned_cols=50  Identities=24%  Similarity=0.258  Sum_probs=47.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ   51 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~   51 (101)
                      +|+++|||+|+++++|+|+|.+++||+++.|+++.+|+||+||++|.|+.
T Consensus       136 ~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         136 TGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             HSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTT
T ss_pred             cCCeeeeeecchhhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCC
Confidence            47889999999999999999999999999999999999999999999864

>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=99.35  E-value=8.1e-14  Score=97.16  Aligned_cols=57  Identities=16%  Similarity=0.218  Sum_probs=49.3

Q ss_pred             CCceeEEEEcccccc---ccCCCCccEEEEeCCCCCccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITATISFGM---GIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~---G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+++++|+|+++++   |+|++.+.+||++++|.++++|+||+||+|| |++|....++.
T Consensus        94 ~G~~dvVVaT~~~a~g~~giDid~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~  153 (299)
T d1a1va2          94 TGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAP  153 (299)
T ss_dssp             CCCBSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCS
T ss_pred             cCCCcEEEEEeehhccCCCCCCCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEec
Confidence            578999999999998   5677778899999999999999999999999 78886654443

>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=99.33  E-value=2.8e-13  Score=90.54  Aligned_cols=59  Identities=22%  Similarity=0.293  Sum_probs=55.0

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCCC-CCccceeeecceeccCCCcceEEEeeCc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGMP-SSIPAYYQESGRAGRDGLQSYCRIYHSE   60 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~p-~~~~~~~qr~GR~gR~~~~~~~i~~~~~   60 (101)
                      +|+++|||||.+++.|+|+|+++++|..+.. ...+++.|..||.||.+..+.|+.++..
T Consensus        81 ~g~~~ILv~TtvIEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~  140 (211)
T d2eyqa5          81 HQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPH  140 (211)
T ss_dssp             TTSCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECC
T ss_pred             cCCcceEEEehhhhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecC
Confidence            6899999999999999999999999988876 6899999999999999999999999864

>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=99.20  E-value=2.5e-12  Score=87.70  Aligned_cols=59  Identities=19%  Similarity=0.199  Sum_probs=47.1

Q ss_pred             CCceeEEEEccccccccCCCCccEEEE----------eC----------CCCCccceeeecceeccCCCcceEEEeeCcc
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVH----------WG----------MPSSIPAYYQESGRAGRDGLQSYCRIYHSEH   61 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~----------~~----------~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~   61 (101)
                      +|+.+++|||+++++|+|+ +++.||.          +|          .|.|.++|+||+||+||.|+.+....++...
T Consensus       222 ~~~~~~lvaT~~~~~G~~~-~~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         222 TNDWDFVVTTDISEMGANF-KAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             TSCCSEEEECGGGGTTCCC-CCSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             ccchhhhhhhHHHHhcCCC-CccEEEEcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence            5788999999999999998 4566553          33          3567889999999999999888777666543

>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=99.07  E-value=1.9e-11  Score=85.32  Aligned_cols=57  Identities=26%  Similarity=0.188  Sum_probs=45.5

Q ss_pred             CCceeEEEEccccccccCCCCccEEEEeCC-------------------CCCccceeeecceeccCCCcceEEEeeC
Q psy7959           2 RGEINVITATISFGMGIDRQNVRFVVHWGM-------------------PSSIPAYYQESGRAGRDGLQSYCRIYHS   59 (101)
Q Consensus         2 ~g~~~vlv~T~~~~~G~d~~~v~~vi~~~~-------------------p~~~~~~~qr~GR~gR~~~~~~~i~~~~   59 (101)
                      +|+.+|||||+++++|+|+ +|.+||++++                   |.+.++..||.||+||.+....++.++.
T Consensus        80 ~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2          80 QKKPDFILATDIAEMGANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             -CCCSEEEESSSTTCCTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             cCCcCEEEEechhhhceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence            5788999999999999999 6999998775                   2455666899999999976655555554

>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=98.39  E-value=7e-08  Score=67.95  Aligned_cols=57  Identities=18%  Similarity=0.129  Sum_probs=48.6

Q ss_pred             EEEEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCcc--eEEEeeCcccH
Q psy7959           7 VITATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQS--YCRIYHSEHSK   63 (101)
Q Consensus         7 vlv~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~~--~~i~~~~~~~~   63 (101)
                      +|++|.+++.|+|+...+.||.+|.++++..+.|+.||+-|.|+..  .++.++..+..
T Consensus       174 lLls~~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~Ti  232 (346)
T d1z3ix1         174 FMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTI  232 (346)
T ss_dssp             EEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTSH
T ss_pred             eeecchhhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCCCH
Confidence            6788999999999999999999999999999999999999999763  34555555543

>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=98.35  E-value=1.9e-07  Score=62.19  Aligned_cols=60  Identities=18%  Similarity=0.124  Sum_probs=36.2

Q ss_pred             ceeEE-EEccccccccCCCCccEEEEeCCCCCccceeeecceeccCCCc--ceEEEeeCcccH
Q psy7959           4 EINVI-TATISFGMGIDRQNVRFVVHWGMPSSIPAYYQESGRAGRDGLQ--SYCRIYHSEHSK   63 (101)
Q Consensus         4 ~~~vl-v~T~~~~~G~d~~~v~~vi~~~~p~~~~~~~qr~GR~gR~~~~--~~~i~~~~~~~~   63 (101)
                      ..++| ++|.+.+.|+|+..++.||+++.|+++..+.|+.||+-|.|+.  -.++.++..+..
T Consensus       137 ~~~vll~~~~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~Ti  199 (244)
T d1z5za1         137 SVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTL  199 (244)
T ss_dssp             TCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTSH
T ss_pred             cchhccccccccccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCCCH
Confidence            35566 4557899999999999999999999999999999999999864  334445555543

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.23  E-value=2.5e-07  Score=59.57  Aligned_cols=57  Identities=32%  Similarity=0.277  Sum_probs=49.3

Q ss_pred             eEEEEccccccccCCC---Ccc-----EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959           6 NVITATISFGMGIDRQ---NVR-----FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus         6 ~vlv~T~~~~~G~d~~---~v~-----~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      .|.|||++++||.|+.   .|.     +||..-.|.+..--.|-.||+||-|.+|.+..+++-.|
T Consensus        84 ~VtIATNmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          84 AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             ceeehhhHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            5899999999999874   233     88888899999999999999999999999988887544

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.06  E-value=6.3e-05  Score=49.46  Aligned_cols=38  Identities=29%  Similarity=0.269  Sum_probs=26.5

Q ss_pred             EEEEeCCCCCccceeeecceeccCCCcceEEEeeCccc
Q psy7959          25 FVVHWGMPSSIPAYYQESGRAGRDGLQSYCRIYHSEHS   62 (101)
Q Consensus        25 ~vi~~~~p~~~~~~~qr~GR~gR~~~~~~~i~~~~~~~   62 (101)
                      +||-...-.|.--=.|-.||+||-|.+|.+..|++-.|
T Consensus       155 ~VIGTErHeSrRIDnQLRGRsGRQGDPGsSrFflSLeD  192 (219)
T d1nkta4         155 YVLGTERHESRRIDNQLRGRSGRQGDPGESRFYLSLGD  192 (219)
T ss_dssp             EEEECSCCSSHHHHHHHHHTSSGGGCCEEEEEEEETTS
T ss_pred             EEEeccccccccccccccccccccCCCccceeEEeccH
Confidence            45544443333333577899999999999999987554

>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=87.16  E-value=0.062  Score=33.55  Aligned_cols=14  Identities=14%  Similarity=-0.009  Sum_probs=11.4

Q ss_pred             ceeeecceeccCCC
Q psy7959          37 AYYQESGRAGRDGL   50 (101)
Q Consensus        37 ~~~qr~GR~gR~~~   50 (101)
                      ++.|++||+||.|+
T Consensus       116 s~~~yi~R~GRagR  129 (181)
T d1t5la2         116 SERSLIQTIGRAAR  129 (181)
T ss_dssp             SHHHHHHHHGGGTT
T ss_pred             cHHHHHHHHHhhcc
Confidence            35688999999975