Psyllid ID: psy4494

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230----
Protein Sequence
MFALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHcccccHHHHHHccccHHHHHHHHHHHcccccccEEEEEcccccHHHHHHHHHHHHHcccccccEEEEccccHHHHHHHHHHHccccccccccccccccEEccccccccccccEEEEcccccccHHHHHHccccccccccccEEEccccccHHHHHHHHHccHHHHHHHHHHHHHHHcccccHHHHHHHHccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHcccccEEEEEccccHHHHHHHHHHHccccccEEEEEEcccccccHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHHHcccccEEEcccccccEEEEEccccccccEEEEEEccccccHHHHHHcccccccccccccEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccccHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
MFALLYTIAYLNLWRTSFYQVSIAfglgidkpnvRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRnqsgiiyttSIKECEDLREELRNRGLRVSAYHAKLESNVSIAfglgidkpnvRFVIHHCLSKSMENFYQesgragrdgqIAHCILYYrlpdvfklssmVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFdeawsdtecrgmcdhcrggrrdakrvdv
Flexible Loop (DISEMBL)
MFALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRrfrnqsgiiyttsikecEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYfdeawsdtecrgmcdhcrggrrdakrvdv
Low Complexity Region (SEG)
MFALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV
Disordered region (IsUnstruct)
*FALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTT******************VSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCR***********
Disordered Region (DISOPRED)
*FALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF******ANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRR*****DV
Disordered Region (DISEMBL)
MFALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRG**********
Disordered Region (DISPRO)
*FALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGG*********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFALLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV
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	234	2.2.26 [Sep-21-2011]
Q9TXJ8	631	Putative ATP-dependent DN	yes	N/A	0.820	0.304	0.433	4e-51
A8WK63	618	Putative ATP-dependent DN	N/A	N/A	0.803	0.304	0.427	7e-49
Q5RF63	649	ATP-dependent DNA helicas	yes	N/A	0.743	0.268	0.468	2e-48
P46063	649	ATP-dependent DNA helicas	yes	N/A	0.743	0.268	0.463	4e-48
Q6AYJ1	621	ATP-dependent DNA helicas	yes	N/A	0.743	0.280	0.463	1e-47
Q9Z129	648	ATP-dependent DNA helicas	yes	N/A	0.743	0.268	0.458	3e-47
Q9FT73	705	Mediator of RNA polymeras	yes	N/A	0.833	0.276	0.428	1e-45
P35187	1447	ATP-dependent helicase SG	yes	N/A	0.743	0.120	0.339	2e-32
Q9VGI8	1487	Bloom syndrome protein ho	yes	N/A	0.769	0.121	0.370	5e-31
O88700	1416	Bloom syndrome protein ho	no	N/A	0.619	0.102	0.412	1e-30

>sp|Q9TXJ8|RECQ1_CAEEL Putative ATP-dependent DNA helicase Q1 OS=Caenorhabditis elegans GN=K02F3.12 PE=3 SV=3

 Score =  201 bits (510), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 97/224 (43%), Positives = 135/224 (60%), Gaps = 32/224 (14%)

Query: 20  QVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSG 79
           Q ++ F  G ++ N++              Y+V  KP ++ +C +E+A  + R F  Q+G
Sbjct: 290 QAALTFRAGFNRSNLK--------------YKVVQKPGSEDECTEEIAKTIKRDFAGQTG 335

Query: 80  IIYTTSIKECEDLREELRNRGLRVSAYHAKLESN------------------VSIAFGLG 121
           IIY  S  +CE + + L++ G++   YHA +E                     ++AFG+G
Sbjct: 336 IIYCLSRNDCEKVAKALKSHGIKAKHYHAYMEPVDRSGAHQGWISGKIQVIVATVAFGMG 395

Query: 122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGL 181
           IDKPNVRFVIHH L KS+EN+YQESGRAGRDGQ A CILYYRL D+FK SSMV  ++TG+
Sbjct: 396 IDKPNVRFVIHHSLPKSIENYYQESGRAGRDGQPATCILYYRLADIFKQSSMVQQERTGI 455

Query: 182 ANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGG 225
            NLYN+V Y  D + CRR  +A +F+EAW  + C+  CD C  G
Sbjct: 456 QNLYNMVRYAADSSTCRRVKLAEHFEEAWEPSWCQKQCDTCENG 499

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 elegans (taxid: 6239)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

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

 Score =  193 bits (491), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 94/220 (42%), Positives = 132/220 (60%), Gaps = 32/220 (14%)

Query: 21  VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGI 80
           V+I F  G ++ N+               Y+V  KP ++ +C++++   + R+F  ++GI
Sbjct: 268 VAIVFRAGFNRANLN--------------YKVLTKPGSEDECVEKIVRTIKRKFSGKTGI 313

Query: 81  IYTTSIKECEDLREELRNRGLRVSAYHAKLESN------------------VSIAFGLGI 122
           IY  S  +CE L + L+  G+R   YHA +E                     ++AFG+GI
Sbjct: 314 IYCLSRNDCEKLAKSLKANGIRAKHYHAYMEPVDRSAAHQKWVSGEIQVIVATVAFGMGI 373

Query: 123 DKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLA 182
           DKP+VRFVIHH L KS+EN+YQESGRAGRDG  A CILYYR+ D+FK SSM+  +QTG+A
Sbjct: 374 DKPDVRFVIHHSLPKSIENYYQESGRAGRDGLPATCILYYRMSDIFKQSSMIQQEQTGIA 433

Query: 183 NLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
           NLYN+V Y  D   CRR  +A +F+EAW  + C+  CD C
Sbjct: 434 NLYNMVRYASDTVTCRRVKLAEHFEEAWEPSWCQKQCDVC 473

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|Q5RF63|RECQ1_PONAB ATP-dependent DNA helicase Q1 OS=Pongo abelii GN=RECQL PE=2 SV=1

 Score =  192 bits (488), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 90/192 (46%), Positives = 124/192 (64%), Gaps = 18/192 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KP+  +D ++++  L++ R++ QSGIIY  S K+ E +   LRN G+   AYHA
Sbjct: 287 YYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLRNLGIHAGAYHA 346

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE                     ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 347 NLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 406

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RD   A CILYY   D+F++SSMV  +  G   LY +VSYC + ++CRR ++A +FDE W
Sbjct: 407 RDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRLLMAQHFDEVW 466

Query: 211 SDTECRGMCDHC 222
           +   C  MCD+C
Sbjct: 467 NSEACNKMCDNC 478

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.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P46063|RECQ1_HUMAN ATP-dependent DNA helicase Q1 OS=Homo sapiens GN=RECQL PE=1 SV=3

 Score =  191 bits (485), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 89/192 (46%), Positives = 124/192 (64%), Gaps = 18/192 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KP+  +D ++++  L++ R++ QSGIIY  S K+ E +   L+N G+   AYHA
Sbjct: 287 YYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHA 346

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE                     ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 347 NLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 406

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RD   A CILYY   D+F++SSMV  +  G   LY +VSYC + ++CRR ++A +FDE W
Sbjct: 407 RDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVW 466

Query: 211 SDTECRGMCDHC 222
           +   C  MCD+C
Sbjct: 467 NSEACNKMCDNC 478

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.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q6AYJ1|RECQ1_RAT ATP-dependent DNA helicase Q1 OS=Rattus norvegicus GN=Recql PE=2 SV=1

 Score =  189 bits (481), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 89/192 (46%), Positives = 126/192 (65%), Gaps = 18/192 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KP++ +D ++ +A+L++ R++ +SGIIY  S K+ E +   L+  G+R   YHA
Sbjct: 287 YYEVRQKPSSAEDFIENIANLINGRYKGKSGIIYCFSQKDSEQVTISLQKLGVRAGTYHA 346

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            +E                     ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 347 NMEPEDRTKVHTQWSANELQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 406

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RD   A CILYY   D+F++SSMV  +  G   LY +VSYC + ++CRRA+IA +FDE W
Sbjct: 407 RDDWRADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRALIAQHFDEVW 466

Query: 211 SDTECRGMCDHC 222
           +   C  MCD+C
Sbjct: 467 NADACNKMCDNC 478

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.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9Z129|RECQ1_MOUSE ATP-dependent DNA helicase Q1 OS=Mus musculus GN=Recql PE=1 SV=2

 Score =  188 bits (478), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 88/192 (45%), Positives = 122/192 (63%), Gaps = 18/192 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY+VR KP++ +D  +++  L++ R++ QSGIIY  S K+ E +   L+  G+    YHA
Sbjct: 287 FYEVRQKPSSAEDFTEDIVKLINGRYKGQSGIIYCFSQKDSEQITISLQKLGIHAGTYHA 346

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            +E                     ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 347 NMEPEDKTKVHTQWSANELQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 406

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RD   A CILYY   D+F++SSMV  +  G   LY +VSYC + ++CRR +IA +FDE W
Sbjct: 407 RDDSRADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNVSKCRRVLIAQHFDEVW 466

Query: 211 SDTECRGMCDHC 222
           +   C  MCD+C
Sbjct: 467 NADACNKMCDNC 478

Isoform alpha is a DNA helicase that may play a role in the repair of DNA that is damaged by ultraviolet light or other mutagens. Isoform beta may have important roles in the meiotic process. Both isoforms exhibit 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|Q9FT73|MED34_ARATH Mediator of RNA polymerase II transcription subunit 34 OS=Arabidopsis thaliana GN=MED34 PE=1 SV=1

 Score =  182 bits (463), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 99/231 (42%), Positives = 137/231 (59%), Gaps = 36/231 (15%)

Query: 23  IAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF-RNQSGII 81
           + F   +++PN+              FY VR K A  K  +DE+A+ +   +  N+SGI+
Sbjct: 273 VKFVSSVNRPNL--------------FYSVREKSAVGKLVVDEIAEFIRESYSNNESGIV 318

Query: 82  YTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGID 123
           Y  S KECE +  +LR RG+    YHA +++N+                  ++AFG+GI+
Sbjct: 319 YCFSRKECEQIAGDLRERGISADYYHADMDANMREKVHMRWSKNKLQVIVGTVAFGMGIN 378

Query: 124 KPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLAN 183
           KP+VRFVIHH LSKSME +YQESGRAGRDG  + CIL++R  DV + SSMVF + +GL N
Sbjct: 379 KPDVRFVIHHSLSKSMETYYQESGRAGRDGLPSECILFFRSADVPRQSSMVFYEYSGLQN 438

Query: 184 LYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV 234
           LY+IV YC  +T+CRR+    +F E   D  C GMCD+C     + K VDV
Sbjct: 439 LYDIVRYCQSKTKCRRSAFFRHFGEPSQD--CNGMCDNC-ALSSEVKEVDV 486

3'-5' DNA helicase that may play a role in the repair of DNA. Exhibits a magnesium-dependent ATP or dATP-dependent DNA-helicase activity. Can use GTP/dGTP, CTP/dCTP or UTP/dUTP as nucleotide cofactors. Catalyzes Holliday junction branch migration and replication fork regression. Disrupts D-loop structures.

Arabidopsis thaliana (taxid: 3702)

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 =  139 bits (350), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 69/203 (33%), Positives = 114/203 (56%), Gaps = 29/203 (14%)

Query: 49   FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
            +Y+V  K    K+ + E+ D +  RF+NQ+GIIY  S K CE    +++  G++ + YHA
Sbjct: 876  YYEVNKK---TKNTIFEICDAVKSRFKNQTGIIYCHSKKSCEQTSAQMQRNGIKCAYYHA 932

Query: 109  KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
             +E +                   ++AFG+GIDKP+VRFV H  + +++E +YQE+GRAG
Sbjct: 933  GMEPDERLSVQKAWQADEIQVICATVAFGMGIDKPDVRFVYHFTVPRTLEGYYQETGRAG 992

Query: 151  RDGQIAHCILYYRLPDVFKLSSMV--------FDQQTGLANLYNIVSYCLDQTRCRRAII 202
            RDG  ++CI Y+   D+  + +M+         +++  L  L  +++YC + T CRR ++
Sbjct: 993  RDGNYSYCITYFSFRDIRTMQTMIQKDKNLDRENKEKHLNKLQQVMAYCDNVTDCRRKLV 1052

Query: 203  ASYFDEAWSDTECRGMCDHCRGG 225
             SYF+E +    C   CD+CR  
Sbjct: 1053 LSYFNEDFDSKLCHKNCDNCRNS 1075

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

 Score =  134 bits (337), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 79/213 (37%), Positives = 114/213 (53%), Gaps = 33/213 (15%)

Query: 53   RIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES 112
            R+ P      LD+++  +  + ++ SGIIY  S KEC++  +++   G+R  +YHA L  
Sbjct: 935  RVLPKKGVSTLDDISRYIRSKPQHFSGIIYCLSRKECDETSKKMCKDGVRAVSYHAGLTD 994

Query: 113  N------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQ 154
                                ++AFG+GIDKP+VRFV+H+ L KS+E +YQE+GRAGRDG 
Sbjct: 995  TDRESRQKDWLTGKMRVICATVAFGMGIDKPDVRFVLHYSLPKSIEGYYQEAGRAGRDGD 1054

Query: 155  IAHCILYYRLPDVFKLSSMVFDQQTGLA---------NLYNIVSYCLDQTRCRRAIIASY 205
            +A CILYY   D+ ++  M+ D    L          NLY IV YC + T CRRA    Y
Sbjct: 1055 VADCILYYNYSDMLRIKKML-DSDKALQYNVKKIHVDNLYRIVGYCENLTDCRRAQQLDY 1113

Query: 206  FDEAWSDTEC----RGMCDHCRGGRRDAKRVDV 234
            F E ++  +C       CD+C   +R  K VD 
Sbjct: 1114 FGEHFTSEQCLENRETACDNCI-NKRAYKAVDA 1145

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

 Score =  133 bits (334), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 73/177 (41%), Positives = 102/177 (57%), Gaps = 32/177 (18%)

Query: 78   SGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-------------------SIAF 118
            SGIIY  S +EC+ + + L+  GL   AYHA L  +                    +IAF
Sbjct: 898  SGIIYCLSRRECDTMADTLQREGLAALAYHAGLSDSARDEVQHKWINQDNCQVICATIAF 957

Query: 119  GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF--- 175
            G+GIDKP+VRFVIH  L KSME +YQESGRAGRDG+I+HC+L+Y   DV +L  ++    
Sbjct: 958  GMGIDKPDVRFVIHASLPKSMEGYYQESGRAGRDGEISHCVLFYTYHDVTRLKRLIMMEK 1017

Query: 176  -----DQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTE-CRG----MCDHC 222
                  ++T + NLY++V YC + T CRR  + +YF E   + + C+      CD+C
Sbjct: 1018 DGNYHTKETHVNNLYSMVHYCENITECRRIQLLAYFGEKGFNPDFCKKYPDVSCDNC 1074

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

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	234
321475158	624	RecQ1-like protein [Daphnia pulex]	0.799	0.299	0.529	2e-62
193606281	599	PREDICTED: ATP-dependent DNA helicase Q1	0.739	0.288	0.578	7e-62
322779042	596	hypothetical protein SINV_80478 [Solenop	0.794	0.312	0.548	3e-61
238859683	598	RecQ protein 1 [Nasonia vitripennis]	0.743	0.290	0.572	6e-61
383853399	597	PREDICTED: ATP-dependent DNA helicase Q1	0.790	0.309	0.534	3e-60
332027185	599	ATP-dependent DNA helicase Q1 [Acromyrme	0.794	0.310	0.529	4e-60
242022338	652	ATP-dependent DNA helicase Q1, putative	0.747	0.268	0.544	6e-60
340717015	596	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.790	0.310	0.539	6e-59
350408702	602	PREDICTED: ATP-dependent DNA helicase Q1	0.790	0.307	0.539	1e-58
380018171	596	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.747	0.293	0.538	3e-58

>gi|321475158|gb|EFX86121.1| RecQ1-like protein [Daphnia pulex]

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 116/219 (52%), Positives = 147/219 (67%), Gaps = 32/219 (14%)

Query: 22  SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGII 81
           S+ F    ++PN+              +Y+VRIKP+ QK+C+DEL  L++ RF  QSGII
Sbjct: 264 SLVFKASFNRPNL--------------YYEVRIKPSTQKECIDELVQLLTNRFHGQSGII 309

Query: 82  YTTSIKECEDLREELRNRGLRVSAYHAKLESN------------------VSIAFGLGID 123
           YTTS+K+C+ L  ELR +  RV++YHA LE                     +IAFG+GID
Sbjct: 310 YTTSVKDCDQLASELRQQKCRVASYHASLEPADRTEVHTGWRENRYQAVVATIAFGMGID 369

Query: 124 KPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLAN 183
           KP+VRFVIHH +SKSMENFYQESGRAGRD   A CI+Y+RL D+F+LS+MVF +QTGL N
Sbjct: 370 KPDVRFVIHHSISKSMENFYQESGRAGRDDLQACCIVYWRLSDLFRLSTMVFTEQTGLRN 429

Query: 184 LYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
           LY + +YCLD  RCRR IIAS+FDE W  + C  MCDHC
Sbjct: 430 LYAMAAYCLDPERCRREIIASHFDERWESSSCNKMCDHC 468

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193606281|ref|XP_001943152.1| PREDICTED: ATP-dependent DNA helicase Q1-like [Acyrthosiphon pisum]

 Score =  242 bits (618), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 111/192 (57%), Positives = 143/192 (74%), Gaps = 19/192 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+V+ KP  +K C+DELA L+  +F+NQSGIIYTTSIK+CE LR++L+  G RV +YHA
Sbjct: 282 YYEVKWKPEGKK-CVDELASLLKNKFKNQSGIIYTTSIKDCESLRKDLKEHGCRVGSYHA 340

Query: 109 KLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
           +LE  +                  +IAFGLGIDKPNVRFVIHH LSKS+ENFYQESGRAG
Sbjct: 341 QLEGPLRSKVHRKWLNDEYQAVVATIAFGLGIDKPNVRFVIHHTLSKSIENFYQESGRAG 400

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ + C+LYY+L DVFKLS+MVF  QTGL NLY+I+ YCL+   CRR +I+++FDE+W
Sbjct: 401 RDGKPSTCLLYYKLSDVFKLSTMVFTTQTGLPNLYSIIKYCLNVKECRRKLISTHFDESW 460

Query: 211 SDTECRGMCDHC 222
              +C  MCD+C
Sbjct: 461 ESIDCDAMCDNC 472

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322779042|gb|EFZ09441.1| hypothetical protein SINV_80478 [Solenopsis invicta]

 Score =  240 bits (613), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 113/206 (54%), Positives = 149/206 (72%), Gaps = 20/206 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KPA ++ CL  + +L+  RF  +SGIIYTT+IK+ E L  +LR RG++V  YHA
Sbjct: 287 YYEVRRKPAEKETCLAMMENLLKTRFNGKSGIIYTTTIKDAEQLTSDLRGRGIKVGCYHA 346

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE++                   +IAFGLGIDKP+VRFVIHHCLSKSMENFYQESGRAG
Sbjct: 347 MLEADYRSEVYSKWMSGKYQAVIATIAFGLGIDKPDVRFVIHHCLSKSMENFYQESGRAG 406

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ + C++ YRL D FKLS+MVF  + GL NLY +++YCLD+T CRR++IA++F+E W
Sbjct: 407 RDGKKSVCLVLYRLADTFKLSTMVFQDKVGLQNLYKMLAYCLDRTSCRRSLIATHFEENW 466

Query: 211 SDTECRGMCDHCRGGR--RDAKRVDV 234
             T+C  MCDHCR  +  R+AKR+DV
Sbjct: 467 KVTDCAEMCDHCRKPKDDRNAKRIDV 492

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|238859683|ref|NP_001154966.1| RecQ protein 1 [Nasonia vitripennis]

 Score =  239 bits (610), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 110/192 (57%), Positives = 140/192 (72%), Gaps = 18/192 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY+VR KP+ ++ CL+ +  L+  RF  +SGIIYTT+IKE E L  +LR RGLR+  YHA
Sbjct: 292 FYEVRRKPSDKEACLEMIVSLLKNRFEGKSGIIYTTTIKESEQLTTDLRARGLRIGCYHA 351

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE                     +IAFGLGIDKP+VRFVIHHCLSKSMEN YQESGRAG
Sbjct: 352 MLEPEYRTKVYSKWFSGEYQAVVATIAFGLGIDKPDVRFVIHHCLSKSMENLYQESGRAG 411

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ ++CIL YRL DVFKLS+MVF  + GL NLY I++YCLDQ+ CRR++IA++F+E W
Sbjct: 412 RDGEKSYCILLYRLMDVFKLSTMVFQDKVGLQNLYKILNYCLDQSSCRRSLIATHFEETW 471

Query: 211 SDTECRGMCDHC 222
           + ++C+ MCDHC
Sbjct: 472 AKSDCKEMCDHC 483

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383853399|ref|XP_003702210.1| PREDICTED: ATP-dependent DNA helicase Q1-like [Megachile rotundata]

 Score =  237 bits (605), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 109/204 (53%), Positives = 147/204 (72%), Gaps = 19/204 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY+VR KP+ +  CL  + +L+  RF+++SGIIYTT+IK+ E L  ELR+ G++V  YHA
Sbjct: 291 FYEVRRKPSDKSTCLAMIENLLKNRFKDKSGIIYTTTIKDAEQLTTELRSLGIKVGCYHA 350

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE                     +IAFGLGIDKP+VRFVIHHC+SKSMENFYQESGRAG
Sbjct: 351 MLEPEYRSEVYSKWISGKYQAVVATIAFGLGIDKPDVRFVIHHCISKSMENFYQESGRAG 410

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ + CI+ YRLPDVFKLS+MVF  + GL NLY +++YCLD + CRR++IA++F+E W
Sbjct: 411 RDGKKSACIVLYRLPDVFKLSTMVFQDKVGLQNLYKMLAYCLDLSSCRRSLIATHFEETW 470

Query: 211 SDTECRGMCDHCRGGRRDAKRVDV 234
           + ++C  MCDHCR   ++ K V++
Sbjct: 471 TKSDCAEMCDHCRKP-KEKKEVNI 493

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027185|gb|EGI67277.1| ATP-dependent DNA helicase Q1 [Acromyrmex echinatior]

 Score =  236 bits (603), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 108/204 (52%), Positives = 145/204 (71%), Gaps = 18/204 (8%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KPA ++ CL  + +L+  RF  +SGIIYTT+IK+ E L  +LR RG++   YHA
Sbjct: 291 YYEVRRKPADKETCLAMIENLLKNRFNGKSGIIYTTTIKDAEQLTTDLRGRGIKAGCYHA 350

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE+N                   +IAFGLGIDKP+VRFVIHHC+SKSMENFYQESGRAG
Sbjct: 351 MLEANYRSEVYSKWMSGKYQVVVATIAFGLGIDKPDVRFVIHHCVSKSMENFYQESGRAG 410

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ + C++ YRL D+FKLS+MVF  + GL NLY +++YCLD+T CRR++IA++F+E W
Sbjct: 411 RDGKKSVCLVLYRLADIFKLSTMVFQDKVGLQNLYKVLAYCLDETSCRRSLIATHFEENW 470

Query: 211 SDTECRGMCDHCRGGRRDAKRVDV 234
            + +C  MCDHCR      K++DV
Sbjct: 471 KENDCAEMCDHCRKSVSVRKQIDV 494

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022338|ref|XP_002431597.1| ATP-dependent DNA helicase Q1, putative [Pediculus humanus corporis] gi|212516905|gb|EEB18859.1| ATP-dependent DNA helicase Q1, putative [Pediculus humanus corporis]

 Score =  236 bits (602), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 105/193 (54%), Positives = 142/193 (73%), Gaps = 18/193 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+V +KP++Q + LD L + +  +F N+SGIIYTT+IKECE+L +ELR RG++   YHA
Sbjct: 278 YYEVVLKPSSQSENLDLLENWLKNKFSNKSGIIYTTAIKECEELTKELRKRGIKAGVYHA 337

Query: 109 KLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            L++ V                  ++AFG+GIDKP+VRFVIHH LSKSMENFYQESGRAG
Sbjct: 338 MLDAEVRSKMHTKWMSNEYQVIVATVAFGMGIDKPDVRFVIHHSLSKSMENFYQESGRAG 397

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ +HCI+ +RL DVFKLS+MVF QQ GL NLY+++++CL+   CRR++IA +FDE W
Sbjct: 398 RDGKNSHCIVMFRLADVFKLSTMVFTQQKGLENLYSMLNFCLNNDTCRRSLIAEHFDEVW 457

Query: 211 SDTECRGMCDHCR 223
           +   C  MCDHC+
Sbjct: 458 NSNFCNKMCDHCK 470

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340717015|ref|XP_003396985.1| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent DNA helicase Q1-like [Bombus terrestris]

 Score =  233 bits (593), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 110/204 (53%), Positives = 148/204 (72%), Gaps = 19/204 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY+VR KP  ++ CL  + +L+  RF+++SGIIYTT+IK+ E L  +LR  GL+V  YHA
Sbjct: 290 FYEVRRKPTDKETCLAMIENLLKNRFKDKSGIIYTTTIKDAEQLTTDLRALGLKVGCYHA 349

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE++                   +IAFGLGIDKP+VRFVIHHC+SKSMENFYQESGRAG
Sbjct: 350 MLEADYRSEVYSKWISGKYQAVVATIAFGLGIDKPDVRFVIHHCISKSMENFYQESGRAG 409

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ A  I+ YRL DVFKLS+MVF  + GL NLY ++ YCLDQT CRR++IA +F+E+W
Sbjct: 410 RDGKKAVSIVLYRLLDVFKLSTMVFQDKVGLQNLYKMLEYCLDQTSCRRSLIAVHFEESW 469

Query: 211 SDTECRGMCDHCRGGRRDAKRVDV 234
           + ++C  MCDHCR   +++K+V++
Sbjct: 470 TRSDCAEMCDHCRKP-KESKQVNI 492

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408702|ref|XP_003488482.1| PREDICTED: ATP-dependent DNA helicase Q1-like [Bombus impatiens]

 Score =  231 bits (590), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 110/204 (53%), Positives = 146/204 (71%), Gaps = 19/204 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY+VR KP  +  CL  + +L+  RF+++SGIIYTT+IK+ E L  +LR  GL+V  YHA
Sbjct: 296 FYEVRRKPTDKDTCLAMIENLLKNRFKDKSGIIYTTTIKDAEQLTTDLRALGLKVGCYHA 355

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE++                   +IAFGLGIDKP+VRFVIHHC+SKSMENFYQESGRAG
Sbjct: 356 MLEADYRSEVYSKWISGKYQAVVATIAFGLGIDKPDVRFVIHHCISKSMENFYQESGRAG 415

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ A  I+ YRL DVFKLS+MVF  + GL NLY ++ YCLDQT CRR++IA +F+E+W
Sbjct: 416 RDGKKAVSIVLYRLLDVFKLSTMVFQDKVGLQNLYKMLEYCLDQTSCRRSLIAVHFEESW 475

Query: 211 SDTECRGMCDHCRGGRRDAKRVDV 234
           +  +C  MCDHCR   +++K+V++
Sbjct: 476 TRNDCAEMCDHCRKP-KESKQVNI 498

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380018171|ref|XP_003693009.1| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent DNA helicase Q1-like [Apis florea]

 Score =  230 bits (587), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 104/193 (53%), Positives = 142/193 (73%), Gaps = 18/193 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY+VR KP  +  CL  + +L+  RF+++SGIIYTT+IK+ E L  +LR  GL+V  YHA
Sbjct: 290 FYEVRRKPTDKDTCLAMIENLLKNRFKDKSGIIYTTTIKDAEQLTTDLRAVGLKVGCYHA 349

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE++                   +IAFGLGIDKP+VR+VIHHC+SKSME+FYQESGRAG
Sbjct: 350 MLEADYRSEVYSKWISGKYQAVVATIAFGLGIDKPDVRYVIHHCISKSMESFYQESGRAG 409

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RDG+ + CI+ Y+L D+FKLS+MVF  + GL NLY +++YCLDQT CRR++IA++F+E+W
Sbjct: 410 RDGKKSMCIVLYKLQDIFKLSTMVFQDKVGLQNLYKMLAYCLDQTSCRRSLIATHFEESW 469

Query: 211 SDTECRGMCDHCR 223
           + ++C  MCDHCR
Sbjct: 470 TRSDCAEMCDHCR 482

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	234
WB|WBGene00019334	631	K02F3.12 [Caenorhabditis elega	0.474	0.175	0.630	1.1e-47
UNIPROTKB|F1SR01	649	RECQL "Uncharacterized protein	0.461	0.166	0.611	1.2e-45
UNIPROTKB|P46063	649	RECQL "ATP-dependent DNA helic	0.461	0.166	0.583	2.2e-45
RGD|1311071	621	Recql "RecQ protein-like (DNA	0.461	0.173	0.601	2.9e-45
UNIPROTKB|Q6AYJ1	621	Recql "ATP-dependent DNA helic	0.461	0.173	0.601	2.9e-45
ZFIN|ZDB-GENE-050809-134	640	recql "RecQ protein-like (DNA	0.508	0.185	0.541	1.1e-44
UNIPROTKB|A0JN36	649	RECQL "Uncharacterized protein	0.461	0.166	0.601	1.1e-44
MGI|MGI:103021	648	Recql "RecQ protein-like" [Mus	0.461	0.166	0.592	1.2e-44
UNIPROTKB|F1PNP1	646	RECQL "Uncharacterized protein	0.461	0.167	0.574	3.3e-44
UNIPROTKB|F1NPI7	661	RECQL "Uncharacterized protein	0.743	0.263	0.442	5.9e-43

WB|WBGene00019334 K02F3.12 [Caenorhabditis elegans (taxid:6239)]

 Score = 394 (143.8 bits), Expect = 1.1e-47, Sum P(2) = 1.1e-47
 Identities = 70/111 (63%), Positives = 86/111 (77%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKPNVRFVIHH L KS+EN+YQESGRAGRDGQ A CILYYRL D+FK SSMV
Sbjct:   389 TVAFGMGIDKPNVRFVIHHSLPKSIENYYQESGRAGRDGQPATCILYYRLADIFKQSSMV 448

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGG 225
               ++TG+ NLYN+V Y  D + CRR  +A +F+EAW  + C+  CD C  G
Sbjct:   449 QQERTGIQNLYNMVRYAADSSTCRRVKLAEHFEEAWEPSWCQKQCDTCENG 499

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:0003677 "DNA binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|F1SR01 RECQL "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 376 (137.4 bits), Expect = 1.2e-45, Sum P(2) = 1.2e-45
 Identities = 66/108 (61%), Positives = 83/108 (76%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDTKADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC + ++CRR +IA +FDE WS  EC  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNISKCRRVLIAQHFDEVWSPEECNKMCDNC 478

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000733 "DNA strand renaturation" evidence=IEA

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:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|P46063 RECQL "ATP-dependent DNA helicase Q1" [Homo sapiens (taxid:9606)]

 Score = 366 (133.9 bits), Expect = 2.2e-45, Sum P(2) = 2.2e-45
 Identities = 63/108 (58%), Positives = 82/108 (75%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC + ++CRR ++A +FDE W+   C  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNC 478

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0000733 "DNA strand renaturation" evidence=IDA

GO:0003678 "DNA helicase activity" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0015630 "microtubule cytoskeleton" evidence=IDA

GO:0032508 "DNA duplex unwinding" evidence=IDA;TAS

RGD|1311071 Recql "RecQ protein-like (DNA helicase Q1-like)" [Rattus norvegicus (taxid:10116)]

 Score = 369 (135.0 bits), Expect = 2.9e-45, Sum P(2) = 2.9e-45
 Identities = 65/108 (60%), Positives = 83/108 (76%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDWRADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC + ++CRRA+IA +FDE W+   C  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNISKCRRALIAQHFDEVWNADACNKMCDNC 478

GO:0000733 "DNA strand renaturation" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0015630 "microtubule cytoskeleton" evidence=IEA;ISO

GO:0032508 "DNA duplex unwinding" evidence=ISO

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

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q6AYJ1 Recql "ATP-dependent DNA helicase Q1" [Rattus norvegicus (taxid:10116)]

 Score = 369 (135.0 bits), Expect = 2.9e-45, Sum P(2) = 2.9e-45
 Identities = 65/108 (60%), Positives = 83/108 (76%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDWRADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC + ++CRRA+IA +FDE W+   C  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNISKCRRALIAQHFDEVWNADACNKMCDNC 478

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

ZFIN|ZDB-GENE-050809-134 recql "RecQ protein-like (DNA helicase Q1-like)" [Danio rerio (taxid:7955)]

 Score = 364 (133.2 bits), Expect = 1.1e-44, Sum P(2) = 1.1e-44
 Identities = 65/120 (54%), Positives = 90/120 (75%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDK +VRFVIHH +SKS+EN+YQESGRAGRD   A CI+++   D+F++S+MV
Sbjct:   375 TVAFGMGIDKADVRFVIHHTISKSIENYYQESGRAGRDDSPADCIVFFGFMDIFRISTMV 434

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV 234
               + TG   L+N+V+YC +  RCRRA++A +FDE W+D EC  MCD CR G  D   +D+
Sbjct:   435 VMENTGQQKLHNMVAYCQNVDRCRRAMMAIHFDEVWNDEECNEMCDVCRHGN-DYITMDI 493

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

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

GO:0006281 "DNA repair" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|A0JN36 RECQL "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 370 (135.3 bits), Expect = 1.1e-44, Sum P(2) = 1.1e-44
 Identities = 65/108 (60%), Positives = 81/108 (75%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC +  +CRR +IA +FDE WS   C  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNINKCRRVLIAQHFDEVWSPEACNKMCDNC 478

GO:0015630 "microtubule cytoskeleton" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=IEA

GO:0000733 "DNA strand renaturation" 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

MGI|MGI:103021 Recql "RecQ protein-like" [Mus musculus (taxid:10090)]

 Score = 368 (134.6 bits), Expect = 1.2e-44, Sum P(2) = 1.2e-44
 Identities = 64/108 (59%), Positives = 82/108 (75%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDSRADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC + ++CRR +IA +FDE W+   C  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNVSKCRRVLIAQHFDEVWNADACNKMCDNC 478

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000733 "DNA strand renaturation" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=ISO

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0032508 "DNA duplex unwinding" evidence=ISO

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

UNIPROTKB|F1PNP1 RECQL "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 362 (132.5 bits), Expect = 3.3e-44, Sum P(2) = 3.3e-44
 Identities = 62/108 (57%), Positives = 82/108 (75%)

Query:   115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV 174
             ++AFG+GIDKP+VRF+IHH +SKS+EN+YQESGRAGRD   A CILYY   D+F++SSMV
Sbjct:   371 TVAFGMGIDKPDVRFIIHHSMSKSIENYYQESGRAGRDDMKADCILYYGFGDIFRISSMV 430

Query:   175 FDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
               +  G   LY +VSYC + ++CRR +IA +FDE W+   C  MCD+C
Sbjct:   431 VMENVGQQKLYEMVSYCQNISKCRRVLIAQHFDEVWNAEACNRMCDNC 478

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:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NPI7 RECQL "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 455 (165.2 bits), Expect = 5.9e-43, P = 5.9e-43
 Identities = 85/192 (44%), Positives = 123/192 (64%)

Query:    49 FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
             +Y+VR KP+  +D ++++  L++ R++  SGI+Y  S K+ E +   L+  G++   YHA
Sbjct:   287 YYEVRHKPSNNEDFIEDIVKLINGRYKGLSGIVYCFSQKDSEQVTVSLQKLGIKAGTYHA 346

Query:   109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
              +++                    ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct:   347 NMDAKYKTKVHKGWAANQIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 406

Query:   151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
             RD Q A CILYY   D+F++SSMV  +  G   LY++VSYC +  +CRR +IA +FDE W
Sbjct:   407 RDDQKADCILYYGFGDIFRISSMVVMENVGQEKLYDMVSYCQNMNKCRRVLIARHFDEVW 466

Query:   211 SDTECRGMCDHC 222
                 C  MCD+C
Sbjct:   467 ESANCNRMCDNC 478

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:0000733 "DNA strand renaturation" evidence=IEA

GO:0003678 "DNA helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0015630 "microtubule cytoskeleton" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

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

---

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	234
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	1e-55
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	2e-42
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-39
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	6e-36
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-32
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-20
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	3e-11
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	4e-11
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	5e-11
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	1e-10
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-08
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	1e-08
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	8e-08
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	1e-06
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	2e-05
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	8e-04
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	0.001

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

 Score =  183 bits (467), Expect = 1e-55
 Identities = 84/238 (35%), Positives = 122/238 (51%), Gaps = 46/238 (19%)

Query: 25  FGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTT 84
           F    D+PN+               Y+VR K       L++L   + + F+ +SGIIY  
Sbjct: 192 FCTSFDRPNLY--------------YEVRRKTP---KILEDLLRFIRKEFKGKSGIIYCP 234

Query: 85  SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPN 126
           S K+ E +   L+N G+   AYHA LE +                   ++AFG+GI+KP+
Sbjct: 235 SRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPD 294

Query: 127 VRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFD-----QQTGL 181
           VRFVIH+ L KSME++YQESGRAGRDG  + C L+Y   D+ +L  ++ +     Q+T  
Sbjct: 295 VRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLMEEPDGQQRTYK 354

Query: 182 ANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTE-----CRGMCDHCRGGRRDAKRVDV 234
             LY ++ YCL+ + CRR I+ S+F E   +           CD+C   R D K  DV
Sbjct: 355 LKLYEMMEYCLNSSTCRRLILLSHFGEKQLNKSFGIMGTEKCCDNCC-KRLDYKTKDV 411

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

 Score =  151 bits (383), Expect = 2e-42
 Identities = 73/236 (30%), Positives = 106/236 (44%), Gaps = 42/236 (17%)

Query: 26  GLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSR-RFRNQSGIIYTT 84
            LG+   N+ F              +V  K     +  D+LA L +     ++SGIIY  
Sbjct: 187 QLGLQDANI-FRGSFDRP---NLALKVVEKG----EPSDQLAFLATVLPQLSKSGIIYCL 238

Query: 85  SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPN 126
           + K+ E+L E LR  G+   AYHA L +                    + AFG+GIDKP+
Sbjct: 239 TRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPD 298

Query: 127 VRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYN 186
           VRFVIH+ L  S+E++YQE+GRAGRDG  A  IL Y   D+     ++ +Q         
Sbjct: 299 VRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLI-EQSKPDEEQKQ 357

Query: 187 I--------VSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKRVDV 234
           I        ++YC +   CRR ++  YF E     +    C +C       K+ D 
Sbjct: 358 IELAKLRQMIAYC-ETQTCRRLVLLKYFGE-----DEPEPCGNCDNCLDTPKQFDG 407

Length = 590

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

 Score =  143 bits (363), Expect = 1e-39
 Identities = 79/199 (39%), Positives = 105/199 (52%), Gaps = 33/199 (16%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
            + V  K   QK  LD L     ++ R QSGIIY +S K+ E+L E L ++G+   AYHA
Sbjct: 202 RFSVVKKNNKQKFLLDYL-----KKHRGQSGIIYASSRKKVEELAERLESQGISALAYHA 256

Query: 109 KLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            L + V                  + AFG+GIDKPNVRFVIH+ +  ++E++YQE+GRAG
Sbjct: 257 GLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAG 316

Query: 151 RDGQIAHCILYYRLPDV------FKLSSMVFD-QQTGLANLYNIVSYCLDQTRCRRAIIA 203
           RDG  A  IL Y   D+       + S    D +Q     L  +++YC  QT CRRA I 
Sbjct: 317 RDGLPAEAILLYSPADIALLKRRIEQSEADDDYKQIEREKLRAMIAYCETQT-CRRAYIL 375

Query: 204 SYFDEAWSDTECRGMCDHC 222
            YF E      C G CD+C
Sbjct: 376 RYFGEN-EVEPC-GNCDNC 392

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 =  134 bits (338), Expect = 6e-36
 Identities = 70/202 (34%), Positives = 106/202 (52%), Gaps = 39/202 (19%)

Query: 60  KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYH------------ 107
           K CL+++   +     ++ GIIY  S  +CE + E L+  G + + YH            
Sbjct: 664 KKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQ 723

Query: 108 ---AKLESNV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY 161
              +K E N+   ++AFG+GI+KP+VRFVIHH L KS+E ++QE GRAGRDGQ + C+LY
Sbjct: 724 KQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLY 783

Query: 162 YRLPDVFKLSSMV----FDQ-----------------QTGLANLYNIVSYCLDQTRCRRA 200
           Y   D  ++  M+     +Q                 +T   NL  +VSYC ++  CRR 
Sbjct: 784 YSYSDYIRVKHMISQGGVEQSPMAMGYNRMASSGRILETNTENLLRMVSYCENEVDCRRF 843

Query: 201 IIASYFDEAWSDTECRGMCDHC 222
           +   +F E +  T C+  CD+C
Sbjct: 844 LQLVHFGEKFDSTNCKKTCDNC 865

Length = 1195

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

 Score =  123 bits (311), Expect = 1e-32
 Identities = 74/219 (33%), Positives = 115/219 (52%), Gaps = 50/219 (22%)

Query: 30  DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC 89
           D+PN+R+ +       +E F     KP      LD+L   +  + R +SGIIY  S  + 
Sbjct: 209 DRPNIRYTL-------VEKF-----KP------LDQLMRYVQEQ-RGKSGIIYCNSRAKV 249

Query: 90  EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVI 131
           ED    L++RG+  +AYHA L+++V                  ++AFG+GI+KPNVRFV+
Sbjct: 250 EDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV 309

Query: 132 HHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYC 191
           H  + +++E++YQE+GRAGRDG  A  +L+Y   D+  L   + ++  G     +I  + 
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAG--QQQDIERHK 367

Query: 192 LD--------QTRCRRAIIASYFDEAWSDTECRGMCDHC 222
           L+        QT CRR ++ +YF E      C G CD C
Sbjct: 368 LNAMGAFAEAQT-CRRLVLLNYFGE-GRQEPC-GNCDIC 403

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 = 83.4 bits (207), Expect = 1e-20
 Identities = 39/131 (29%), Positives = 54/131 (41%), Gaps = 20/131 (15%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
              V      + + L EL  L     +    +I+  S K  ++L E LR  G++V+A H 
Sbjct: 3   KQYVLPVEDEKLEALLEL--LKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60

Query: 109 KL---------------ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
                            E  V +A      GID PNV  VI++ L  S  ++ Q  GRAG
Sbjct: 61  DGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAG 120

Query: 151 RDGQIAHCILY 161
           R GQ    IL 
Sbjct: 121 RAGQKGTAILL 131

Length = 131

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

 Score = 62.1 bits (151), Expect = 3e-11
 Identities = 20/30 (66%), Positives = 28/30 (93%)

Query: 22  SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
           ++AFG+GI+KP+VRFVIH+ L KSME++YQ
Sbjct: 283 TVAFGMGINKPDVRFVIHYSLPKSMESYYQ 312

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|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score = 56.8 bits (138), Expect = 4e-11
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 18/78 (23%)

Query: 94  EELRNRGLRVSAYHAKLESN-----------------VSI-AFGLGIDKPNVRFVIHHCL 135
           + LR  G++V+  H  L                    V+    G GID P+V  VI++ L
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 136 SKSMENFYQESGRAGRDG 153
             +  ++ Q  GRAGR G
Sbjct: 61  PWNPASYIQRIGRAGRAG 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 = 56.8 bits (138), Expect = 5e-11
 Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 18/82 (21%)

Query: 90  EDLREELRNRGLRVSAYHAKLESN-----------------VSI-AFGLGIDKPNVRFVI 131
           E+L E L+  G++V+  H  L                    V+      G+D P V  VI
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 132 HHCLSKSMENFYQESGRAGRDG 153
            + L  S  ++ Q  GRAGR G
Sbjct: 61  IYDLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 60.4 bits (147), Expect = 1e-10
 Identities = 19/29 (65%), Positives = 25/29 (86%)

Query: 23  IAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
            AFG+GIDKP+VRFVIH+ L  S+E++YQ
Sbjct: 288 NAFGMGIDKPDVRFVIHYDLPGSIESYYQ 316

Length = 590

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

 Score = 54.7 bits (132), Expect = 1e-08
 Identities = 18/30 (60%), Positives = 26/30 (86%)

Query: 22  SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
           + AFG+GIDKPNVRFVIH+ +  ++E++YQ
Sbjct: 281 TNAFGMGIDKPNVRFVIHYDMPGNLESYYQ 310

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 = 54.5 bits (131), Expect = 1e-08
 Identities = 19/30 (63%), Positives = 27/30 (90%)

Query: 22  SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
           ++AFG+GI+KP+VRFVIHH L KS+E ++Q
Sbjct: 737 TVAFGMGINKPDVRFVIHHSLPKSIEGYHQ 766

Length = 1195

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

 Score = 52.1 bits (125), Expect = 8e-08
 Identities = 42/208 (20%), Positives = 78/208 (37%), Gaps = 25/208 (12%)

Query: 44  KSMENFYQVRIKPAAQK-DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR 102
           K ++ FY + ++   +K + L +L             I++  + +  E+L E LR RG +
Sbjct: 245 KKIKQFY-LEVESEEEKLELLLKLLKDE----DEGRVIVFVRTKRLVEELAESLRKRGFK 299

Query: 103 VSAYHAKL---------------ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ 144
           V+A H  L               E  V +A      G+D P+V  VI++ L    E++  
Sbjct: 300 VAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVH 359

Query: 145 ESGRAGRDGQIAHCI-LYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIA 203
             GR GR G+    I       +V KL  +    +  L +   +     +  +  +    
Sbjct: 360 RIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRP 419

Query: 204 SYFDEAWSDTECRGMCDHCRGGRRDAKR 231
              +E+    E + +    +   R    
Sbjct: 420 GLEEESDISDEIKKLKSSKKALLRGLGV 447

Length = 513

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

 Score = 48.6 bits (116), Expect = 1e-06
 Identities = 16/30 (53%), Positives = 27/30 (90%)

Query: 22  SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
           ++AFG+GI+KPNVRFV+H  + +++E++YQ
Sbjct: 293 TVAFGMGINKPNVRFVVHFDIPRNIESYYQ 322

Length = 607

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

 Score = 44.4 bits (105), Expect = 2e-05
 Identities = 30/106 (28%), Positives = 46/106 (43%), Gaps = 25/106 (23%)

Query: 71  SRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN----------------- 113
           S+ +R Q+ I++T S + C +L + L  +GL+ + YHA L                    
Sbjct: 436 SKGYRGQT-IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAV 494

Query: 114 -VSIAFGLGIDKPNVRFVIHHCLSK-----SMENFYQESGRAGRDG 153
             + A   G+D P  + VI   L+      S+  F Q  GRAGR  
Sbjct: 495 VTTAALAAGVDFPASQ-VIFESLAMGIEWLSVREFQQMLGRAGRPD 539

Length = 830

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

 Score = 36.7 bits (86), Expect = 8e-04
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 24 AFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
            G GID P+V  VI++ L  +  ++ Q
Sbjct: 42 VAGRGIDLPDVNLVINYDLPWNPASYIQ 69

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|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 34/129 (26%), Positives = 54/129 (41%), Gaps = 19/129 (14%)

Query: 63  LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE----------- 111
            D L DL       Q+ IIY  + ++ + L +++  R   VS  H  ++           
Sbjct: 255 FDTLCDLYETLTITQA-IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREF 313

Query: 112 ----SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRL 164
               + V I   L   GID   V  VI++ L  S EN+    GR+GR G+    I +   
Sbjct: 314 RSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTP 373

Query: 165 PDVFKLSSM 173
            D+ +L  +
Sbjct: 374 DDIEQLKEI 382

Length = 401

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	234
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG0353|consensus	695		100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
KOG0351|consensus	941		100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
KOG0352|consensus	641		99.97
KOG0333|consensus	673		99.94
KOG0330|consensus	476		99.94
KOG0331|consensus	519		99.94
KOG0328|consensus	400		99.94
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.94
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.91
PTZ00110	545	helicase; Provisional	99.91
KOG0345|consensus	567		99.91
KOG0326|consensus	459		99.9
KOG0332|consensus	477		99.9
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.9
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.89
KOG0341|consensus	610		99.89
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.89
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.89
KOG0342|consensus	543		99.89
KOG0340|consensus	442		99.89
KOG0335|consensus	482		99.88
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.88
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.88
KOG0336|consensus	629		99.88
KOG0338|consensus	691		99.88
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.87
KOG0343|consensus	758		99.85
KOG0344|consensus	593		99.85
PTZ00424	401	helicase 45; Provisional	99.85
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.84
KOG0327|consensus	397		99.84
KOG0346|consensus	569		99.82
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.8
KOG0334|consensus	997		99.8
KOG0339|consensus	731		99.8
KOG4284|consensus	980		99.8
KOG0347|consensus	731		99.79
KOG0350|consensus	620		99.78
KOG0348|consensus	708		99.76
KOG0337|consensus	529		99.75
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.75
PHA02653	675	RNA helicase NPH-II; Provisional	99.71
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.69
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.67
PRK04914	956	ATP-dependent helicase HepA; Validated	99.67
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.66
PRK10689	1147	transcription-repair coupling factor; Provisional	99.65
PRK13767	876	ATP-dependent helicase; Provisional	99.64
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.64
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.64
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.64
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.63
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.63
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.62
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.62
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.61
PRK05298	652	excinuclease ABC subunit B; Provisional	99.6
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.58
KOG0329|consensus	387		99.58
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.56
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.55
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.53
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.51
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.51
PRK13766	773	Hef nuclease; Provisional	99.51
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.49
PRK02362	737	ski2-like helicase; Provisional	99.48
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.48
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.47
PRK14701	1638	reverse gyrase; Provisional	99.45
KOG0349|consensus	725		99.43
PHA02558	501	uvsW UvsW helicase; Provisional	99.42
PRK09401	1176	reverse gyrase; Reviewed	99.38
PRK00254	720	ski2-like helicase; Provisional	99.35
COG1202	830	Superfamily II helicase, archaea-specific [General	99.33
PRK01172	674	ski2-like helicase; Provisional	99.27
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.25
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.23
KOG0354|consensus	746		99.15
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.15
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.13
KOG4150|consensus	1034		99.09
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.06
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.02
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.01
PRK09694	878	helicase Cas3; Provisional	99.01
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.98
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.84
KOG0948|consensus	1041		98.77
COG1205	851	Distinct helicase family with a unique C-terminal	98.77
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.76
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.73
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.72
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.67
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.67
COG1204	766	Superfamily II helicase [General function predicti	98.61
PRK05580	679	primosome assembly protein PriA; Validated	98.61
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.51
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.47
KOG0950|consensus	1008		98.46
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.41
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.41
KOG0952|consensus	1230		98.37
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.35
KOG0922|consensus	674		98.35
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.34
KOG0947|consensus	1248		98.32
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.2
KOG0923|consensus	902		98.16
KOG0951|consensus	1674		98.15
KOG0953|consensus	700		98.04
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.04
KOG0390|consensus	776		97.73
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.68
KOG0920|consensus	924		97.63
COG4096	875	HsdR Type I site-specific restriction-modification	97.63
KOG0924|consensus	1042		97.61
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	97.41
KOG0384|consensus	1373		97.37
KOG0387|consensus	923		97.26
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.18
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.11
KOG0385|consensus	971		97.08
KOG0926|consensus	1172		96.97
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	96.89
KOG0925|consensus	699		96.38
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	96.32
KOG1000|consensus	689		96.28
COG4889	1518	Predicted helicase [General function prediction on	96.27
KOG0949|consensus	1330		96.16
KOG0391|consensus	1958		96.05
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	96.04
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	95.99
KOG0388|consensus	1185		95.87
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	95.61
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	95.57
KOG0389|consensus	941		95.57
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.98
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	94.56
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	94.52
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	94.38
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	93.75
KOG0351|consensus	941		93.71
KOG0353|consensus	695		93.2
KOG0392|consensus	1549		92.98
KOG0386|consensus	1157		92.79
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	92.46
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	92.24
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	92.04
KOG1002|consensus	791		91.61
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	90.07
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	88.89
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	86.98
KOG1015|consensus	1567		86.64
KOG0352|consensus	641		86.25
PRK14701	1638	reverse gyrase; Provisional	84.96
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	84.73
KOG2340|consensus	698		84.28
KOG0701|consensus	1606		83.44
KOG1123|consensus	776		82.88
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	82.13
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	81.9
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	81.13
cd01522	117	RHOD_1 Member of the Rhodanese Homology Domain sup	80.21

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

Probab=100.00  E-value=1.3e-38  Score=289.56  Aligned_cols=212  Identities=37%  Similarity=0.552  Sum_probs=166.7

Q ss_pred             HHHhhhccCchhHHHHhhCCCCCcEEE-----------EEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCc
Q psy4494          10 YLNLWRTSFYQVSIAFGLGIDKPNVRF-----------VIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQS   78 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~~~~~i~~-----------~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~   78 (234)
                      +++-+...+|+.++++.+.+..+.++.           .+.....++.|++|.++.+. +...++..+.+.  .....++
T Consensus       156 ~lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfdRpNi~~~v~~~~-~~~~q~~fi~~~--~~~~~~~  232 (590)
T COG0514         156 RLGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKG-EPSDQLAFLATV--LPQLSKS  232 (590)
T ss_pred             HHHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCCCchhhhhhhhcc-cHHHHHHHHHhh--ccccCCC
Confidence            344455555554444444443333221           12234567889999998776 333333333331  1335677


Q ss_pred             EEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHh
Q psy4494          79 GIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSME  140 (234)
Q Consensus        79 ~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~  140 (234)
                      +||||.|++.+|.++++|...|+.+..|||+|+.++                  |.|||||||.|||++|||||+|.+++
T Consensus       233 GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~E  312 (590)
T COG0514         233 GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIE  312 (590)
T ss_pred             eEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHH
Confidence            999999999999999999999999999999999877                  99999999999999999999999999


Q ss_pred             HhhhhhcccccCCCceEEEEEeecccHHHhhhhHHhh-------hhhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCC
Q psy4494         141 NFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQ-------QTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDT  213 (234)
Q Consensus       141 ~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~  213 (234)
                      +|+|++|||||||.++.|+++|++.|......++...       +....+++.|..|++ +..|||..++.||||. .+.
T Consensus       313 sYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~~~~~~~~~~~~~~kl~~~~~~~e-~~~crr~~ll~yfge~-~~~  390 (590)
T COG0514         313 SYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQSKPDEEQKQIELAKLRQMIAYCE-TQTCRRLVLLKYFGED-EPE  390 (590)
T ss_pred             HHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHhhcchHHHHHHHHHHHHHHHHhcc-cccchHHHHHHhcCcc-ccc
Confidence            9999999999999999999999999988877776653       233478999999996 5669999999999998 667


Q ss_pred             ccCCCCCCCCCCCC
Q psy4494         214 ECRGMCDHCRGGRR  227 (234)
Q Consensus       214 ~c~~~Cd~C~~~~~  227 (234)
                      +| +.||+|...+.
T Consensus       391 ~c-~~c~~c~~~~~  403 (590)
T COG0514         391 PC-GNCDNCLDTPK  403 (590)
T ss_pred             cc-cCCCcccCcch
Confidence            79 67999998873

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

Probab=100.00  E-value=4.4e-38  Score=300.95  Aligned_cols=181  Identities=38%  Similarity=0.780  Sum_probs=154.2

Q ss_pred             CCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------
Q psy4494          43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------  114 (234)
Q Consensus        43 ~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------  114 (234)
                      ..+.|++|.|.++.   ...+..|.+++.......++||||+|++.|+.++..|+..|+.+..|||+|++++        
T Consensus       650 f~RpNL~y~Vv~k~---kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F  726 (1195)
T PLN03137        650 FNRPNLWYSVVPKT---KKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQW  726 (1195)
T ss_pred             cCccceEEEEeccc---hhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHH
Confidence            34567889887653   2234566677765445678999999999999999999999999999999999877        


Q ss_pred             ----------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHHhh-------
Q psy4494         115 ----------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQ-------  177 (234)
Q Consensus       115 ----------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~-------  177 (234)
                                |+++|||||+|+|++||||++|.++++|+||+|||||+|.+|.|++||...|+.....++...       
T Consensus       727 ~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI~~~~~~~s~~  806 (1195)
T PLN03137        727 SKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPM  806 (1195)
T ss_pred             hcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHHhccccccchh
Confidence                      999999999999999999999999999999999999999999999999999988877776421       


Q ss_pred             --------------hhhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCCCC
Q psy4494         178 --------------QTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGR  226 (234)
Q Consensus       178 --------------~~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~~~  226 (234)
                                    ....++|.+|..||++...|||+.|+.||||.+.+..|...||||....
T Consensus       807 ~~~~~r~~~s~~~~e~~~~~L~~m~~yce~~~~CRR~~lL~yFGE~~~~~~C~~~CDnC~~~~  869 (1195)
T PLN03137        807 AMGYNRMASSGRILETNTENLLRMVSYCENEVDCRRFLQLVHFGEKFDSTNCKKTCDNCSSSK  869 (1195)
T ss_pred             hhhhcccchhHHHHHHHHHHHHHHHHHHhChHhhHHHHHHHHcccccCccCCCCCCCCCCCCC
Confidence                          1133678999999976568999999999999976667966799999877

>KOG0353|consensus

Probab=100.00  E-value=4e-37  Score=262.64  Aligned_cols=218  Identities=44%  Similarity=0.783  Sum_probs=194.1

Q ss_pred             HHHHhhhccCchhHHHHhhCCCCCcEEEEE-----------eeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCC
Q psy4494           9 AYLNLWRTSFYQVSIAFGLGIDKPNVRFVI-----------HHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQ   77 (234)
Q Consensus         9 a~l~l~~at~p~~~i~~~~~~~~~~i~~~~-----------~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~   77 (234)
                      .-|+++...||.+++.-.+.....+|--.+           ....-.+.|++|+|+.+|++.++..+.+.++++..+.++
T Consensus       239 ~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gq  318 (695)
T KOG0353|consen  239 KALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQ  318 (695)
T ss_pred             HHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeecccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCC
Confidence            347778888888776555444333321110           112234678999999999999999999999999888899


Q ss_pred             cEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCH
Q psy4494          78 SGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSM  139 (234)
Q Consensus        78 ~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~  139 (234)
                      .+||||-|++.||.++..|+.+|+.+.+||+.|.++.                  |.++|||||.|+|++|||..+|.++
T Consensus       319 sgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksi  398 (695)
T KOG0353|consen  319 SGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSI  398 (695)
T ss_pred             cceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhH
Confidence            9999999999999999999999999999999999877                  9999999999999999999999999


Q ss_pred             hHhhh-------------------------------------------hhcccccCCCceEEEEEeecccHHHhhhhHHh
Q psy4494         140 ENFYQ-------------------------------------------ESGRAGRDGQIAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       140 ~~y~q-------------------------------------------r~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      +.|+|                                           +.||+||++.++.||+||...|+.+.+.+++.
T Consensus       399 enyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cilyy~~~difk~ssmv~~  478 (695)
T KOG0353|consen  399 ENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFADIFKISSMVQM  478 (695)
T ss_pred             HHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEEechHHHHhHHHHHHH
Confidence            99999                                           89999999999999999999999999999999


Q ss_pred             hhhhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCCCC
Q psy4494         177 QQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGR  226 (234)
Q Consensus       177 ~~~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~~~  226 (234)
                      +..+.++|.+|++|+.+.+.|||..+.++|+|..++..|+.+||+|....
T Consensus       479 e~~g~q~ly~mv~y~~d~s~crrv~laehfde~w~~~~c~k~cd~c~~~n  528 (695)
T KOG0353|consen  479 ENTGIQKLYEMVRYAADISKCRRVKLAEHFDEAWEPEACNKMCDNCCKDN  528 (695)
T ss_pred             HhhhHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCHHHHHHHhhhhccCc
Confidence            99999999999999999999999999999999999999999999998766

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=6.5e-34  Score=259.02  Aligned_cols=205  Identities=35%  Similarity=0.595  Sum_probs=157.4

Q ss_pred             hhccCchh---HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHH
Q psy4494          14 WRTSFYQV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECE   90 (234)
Q Consensus        14 ~~at~p~~---~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~   90 (234)
                      ++||.+..   .+...+++..+.+.    .....+.|.+|.+..+..   ..+..+.+++.....++++||||+|++.++
T Consensus       168 lTAT~~~~~~~di~~~l~l~~~~~~----~~s~~r~nl~~~v~~~~~---~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e  240 (470)
T TIGR00614       168 LTATASPSVREDILRQLNLKNPQIF----CTSFDRPNLYYEVRRKTP---KILEDLLRFIRKEFKGKSGIIYCPSRKKSE  240 (470)
T ss_pred             EecCCCHHHHHHHHHHcCCCCCcEE----eCCCCCCCcEEEEEeCCc---cHHHHHHHHHHHhcCCCceEEEECcHHHHH
Confidence            45555543   33444455544332    123345677888876643   245556666654445677899999999999


Q ss_pred             HHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccC
Q psy4494          91 DLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRD  152 (234)
Q Consensus        91 ~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~  152 (234)
                      .++..|+..|+.+..|||+|++++                  |++++||||+|+|++||||++|.++++|+||+||+||+
T Consensus       241 ~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~  320 (470)
T TIGR00614       241 QVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRD  320 (470)
T ss_pred             HHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCC
Confidence            999999999999999999999876                  99999999999999999999999999999999999999


Q ss_pred             CCceEEEEEeecccHHHhhhhHHhhhh------hhHhHHHHHHHhhcCcccHHHHHHhHcCCCCC-----CCccCCCCCC
Q psy4494         153 GQIAHCILYYRLPDVFKLSSMVFDQQT------GLANLYNIVSYCLDQTRCRRAIIASYFDEAWS-----DTECRGMCDH  221 (234)
Q Consensus       153 g~~~~~i~~~~~~d~~~~~~~~~~~~~------~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~-----~~~c~~~Cd~  221 (234)
                      |.+|.+++|+++.|...+..++.....      ..+.+++|..|+ ++..|||+.|++||||...     ...|..+|||
T Consensus       321 G~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~crr~~l~~~f~~~~~~~~~~~~~~~~~C~~  399 (470)
T TIGR00614       321 GLPSECHLFYAPADINRLRRLLMEEPDGQQRTYKLKLYEMMEYCL-NSSTCRRLILLSHFGEKQLNKSFGIMGTEKCCDN  399 (470)
T ss_pred             CCCceEEEEechhHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHh-ccccCHHHHHHHHcCCcccccccccccCCCCCCC
Confidence            999999999999999888877654322      124456666665 6889999999999999632     2235567888


Q ss_pred             CCCCC
Q psy4494         222 CRGGR  226 (234)
Q Consensus       222 C~~~~  226 (234)
                      |....
T Consensus       400 C~~~~  404 (470)
T TIGR00614       400 CCKRL  404 (470)
T ss_pred             CCCcc
Confidence            87665

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

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=2.3e-33  Score=262.16  Aligned_cols=201  Identities=34%  Similarity=0.598  Sum_probs=157.2

Q ss_pred             hhccCchh---HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHH
Q psy4494          14 WRTSFYQV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECE   90 (234)
Q Consensus        14 ~~at~p~~---~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~   90 (234)
                      ++||.+..   .+...+++..|.+..    ....+.|..|.+..+..    .+..+..++.. ..+.++||||+|++.|+
T Consensus       180 lTAT~~~~~~~di~~~l~l~~~~~~~----~~~~r~nl~~~v~~~~~----~~~~l~~~l~~-~~~~~~IIFc~tr~~~e  250 (607)
T PRK11057        180 LTATADDTTRQDIVRLLGLNDPLIQI----SSFDRPNIRYTLVEKFK----PLDQLMRYVQE-QRGKSGIIYCNSRAKVE  250 (607)
T ss_pred             EecCCChhHHHHHHHHhCCCCeEEEE----CCCCCCcceeeeeeccc----hHHHHHHHHHh-cCCCCEEEEECcHHHHH
Confidence            45555543   233444444443322    12234566777755432    34445555543 35678999999999999


Q ss_pred             HHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccC
Q psy4494          91 DLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRD  152 (234)
Q Consensus        91 ~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~  152 (234)
                      .++..|+..|+.+..|||+|++++                  |++++||||+|+|++|||||+|.++++|+||+|||||+
T Consensus       251 ~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~  330 (607)
T PRK11057        251 DTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRD  330 (607)
T ss_pred             HHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCC
Confidence            999999999999999999999876                  99999999999999999999999999999999999999


Q ss_pred             CCceEEEEEeecccHHHhhhhHHhhh------hhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCCCC
Q psy4494         153 GQIAHCILYYRLPDVFKLSSMVFDQQ------TGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGR  226 (234)
Q Consensus       153 g~~~~~i~~~~~~d~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~~~  226 (234)
                      |.+|.+++|+++.|...+..++....      ....++..|..|++ +..|||+.|++||||... ..| ++||+|....
T Consensus       331 G~~~~~ill~~~~d~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~Crr~~~l~yf~e~~~-~~c-~~cd~c~~~~  407 (607)
T PRK11057        331 GLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERHKLNAMGAFAE-AQTCRRLVLLNYFGEGRQ-EPC-GNCDICLDPP  407 (607)
T ss_pred             CCCceEEEEeCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHh-cccCHHHHHHHHhCCCCC-CCC-CCCCCCCCcc
Confidence            99999999999999887776664321      23457899999996 678999999999999864 347 6899998865

>KOG0351|consensus

Probab=100.00  E-value=9e-34  Score=270.43  Aligned_cols=199  Identities=40%  Similarity=0.716  Sum_probs=171.3

Q ss_pred             HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCC
Q psy4494          22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGL  101 (234)
Q Consensus        22 ~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~  101 (234)
                      +++..+++..+.    +......+.|++|+|.++...  +....+...++...+.+++||||.++++|+.++..|++.|+
T Consensus       437 DIi~~L~l~~~~----~~~~sfnR~NL~yeV~~k~~~--~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~  510 (941)
T KOG0351|consen  437 DVIRSLGLRNPE----LFKSSFNRPNLKYEVSPKTDK--DALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGK  510 (941)
T ss_pred             HHHHHhCCCCcc----eecccCCCCCceEEEEeccCc--cchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhch
Confidence            455555555544    335567788999999887642  23445555666666789999999999999999999999999


Q ss_pred             ceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEee
Q psy4494         102 RVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       102 ~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                      ++.+||+||++++                  |.|||||||.|||+.||||++|++++.|+|++|||||+|.++.|++||+
T Consensus       511 ~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~  590 (941)
T KOG0351|consen  511 SAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYG  590 (941)
T ss_pred             hhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecc
Confidence            9999999999987                  9999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHhhhhHHhhh--------hhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccC--CCCCCCCCCC
Q psy4494         164 LPDVFKLSSMVFDQQ--------TGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECR--GMCDHCRGGR  226 (234)
Q Consensus       164 ~~d~~~~~~~~~~~~--------~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~--~~Cd~C~~~~  226 (234)
                      ..|...+..++..+.        .....+.+|..||++.+.|||+.++.||||.+....|.  ..||+|....
T Consensus       591 ~~D~~~l~~ll~s~~~~~~~~~~~~~~~l~~~~~yCen~t~crr~~~l~~fge~f~~~~c~~~k~cd~C~~~~  663 (941)
T KOG0351|consen  591 YADISELRRLLTSGNRLSGVKKFTRLLELVQVVTYCENETDCRRKQILEYFGEEFDSKHCKKHKTCDNCRESL  663 (941)
T ss_pred             hhHHHHHHHHHHccccccchhhccchhhHHHHHHhhcCccchhHHHHHHhcccccchhhccCCchHHHhhccc
Confidence            999999888876651        23467899999999999999999999999998888897  5899999887

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=1.5e-32  Score=256.50  Aligned_cols=176  Identities=41%  Similarity=0.667  Sum_probs=148.7

Q ss_pred             CCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------
Q psy4494          43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------  114 (234)
Q Consensus        43 ~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------  114 (234)
                      ..+.|.+|.+..+..    +...+.+++... .+.++||||+|++.++.+++.|...|+.+..|||+|++++        
T Consensus       196 ~~r~nl~~~v~~~~~----~~~~l~~~l~~~-~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F  270 (591)
T TIGR01389       196 FDRPNLRFSVVKKNN----KQKFLLDYLKKH-RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDF  270 (591)
T ss_pred             CCCCCcEEEEEeCCC----HHHHHHHHHHhc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHH
Confidence            445678888866532    344556666533 4678999999999999999999999999999999999866        


Q ss_pred             ----------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHHhh-------
Q psy4494         115 ----------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQ-------  177 (234)
Q Consensus       115 ----------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~-------  177 (234)
                                |++++||||+|+|++||||++|.++++|+||+|||||+|.++.++++|++.|......++...       
T Consensus       271 ~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~~i~~~~~~~~~~  350 (591)
T TIGR01389       271 LYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQSEADDDYK  350 (591)
T ss_pred             HcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHHHHhccCCcHHHH
Confidence                      999999999999999999999999999999999999999999999999999988877766541       


Q ss_pred             hhhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCCCC
Q psy4494         178 QTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGR  226 (234)
Q Consensus       178 ~~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~~~  226 (234)
                      .....++++|..|++ +..|||..++.||||.. ...| +.||||....
T Consensus       351 ~~~~~~l~~~~~~~~-~~~c~r~~~~~~f~~~~-~~~c-~~cd~c~~~~  396 (591)
T TIGR01389       351 QIEREKLRAMIAYCE-TQTCRRAYILRYFGENE-VEPC-GNCDNCLDPP  396 (591)
T ss_pred             HHHHHHHHHHHHHHc-ccccHhHHHHHhcCCCC-CCCC-CCCCCCCCCC
Confidence            223467899999996 68999999999999974 3458 6899998765

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.

>KOG0352|consensus

Probab=99.97  E-value=8.9e-31  Score=226.24  Aligned_cols=198  Identities=37%  Similarity=0.674  Sum_probs=155.3

Q ss_pred             HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhc------------CCCcEEEEecchHHH
Q psy4494          22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF------------RNQSGIIYTTSIKEC   89 (234)
Q Consensus        22 ~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~------------~~~~~iIf~~t~~~~   89 (234)
                      ++.+.+.+..|...   ..++.-+-|++|.+..+..- ++.+..|.++-...+            ..+.+||||.|++.|
T Consensus       193 Di~~qL~L~~PVAi---FkTP~FR~NLFYD~~~K~~I-~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~c  268 (641)
T KOG0352|consen  193 DIAFQLKLRNPVAI---FKTPTFRDNLFYDNHMKSFI-TDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNEC  268 (641)
T ss_pred             HHHHHHhhcCcHHh---ccCcchhhhhhHHHHHHHHh-hhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHH
Confidence            45555555544222   23445556788877554322 334555555543221            135689999999999


Q ss_pred             HHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccccc
Q psy4494          90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR  151 (234)
Q Consensus        90 ~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR  151 (234)
                      |.++-.|..+|+.+.+||+++...+                  |..||||+|.|+|++||||++|+++..|+|+.|||||
T Consensus       269 Eq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGR  348 (641)
T KOG0352|consen  269 EQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGR  348 (641)
T ss_pred             HHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhcccccc
Confidence            9999999999999999999998766                  9999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEeecccHHHhhhhHHhhhh--------------hhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCC
Q psy4494         152 DGQIAHCILYYRLPDVFKLSSMVFDQQT--------------GLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRG  217 (234)
Q Consensus       152 ~g~~~~~i~~~~~~d~~~~~~~~~~~~~--------------~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~  217 (234)
                      +|.++.|-+||+.+|...+.-++..+..              .....+.|+.||+ ...||+..+.+|||+...  +|.+
T Consensus       349 DGk~SyCRLYYsR~D~~~i~FLi~~e~aklrek~~ke~~~k~~I~~F~k~~eFCE-~~~CRH~~ia~fFgD~~p--~ckg  425 (641)
T KOG0352|consen  349 DGKRSYCRLYYSRQDKNALNFLVSGELAKLREKAKKEMQIKSIITGFAKMLEFCE-SARCRHVSIASFFDDTEC--PCKT  425 (641)
T ss_pred             CCCccceeeeecccchHHHHHHHhhHHHHHHHhcchhhhHHHHHHHHHHHHHHHH-HcccchHHHHHhcCCCCC--CCCC
Confidence            9999999999999998887766654321              1123588999996 589999999999999753  5779


Q ss_pred             CCCCCCCCC
Q psy4494         218 MCDHCRGGR  226 (234)
Q Consensus       218 ~Cd~C~~~~  226 (234)
                      +||+|.+..
T Consensus       426 ~cd~c~~p~  434 (641)
T KOG0352|consen  426 NCDYCRDPT  434 (641)
T ss_pred             CccccCCHH
Confidence            999999865

>KOG0333|consensus

Probab=99.94  E-value=5e-27  Score=207.17  Aligned_cols=158  Identities=20%  Similarity=0.276  Sum_probs=129.9

Q ss_pred             HHhhhccCchh--HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          11 LNLWRTSFYQV--SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        11 l~l~~at~p~~--~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      .-+|.+|.|.+  -++...-.++..+.......+..++++....+.    .+++...|..++.+. ...++|||+|+++.
T Consensus       455 T~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~----ed~k~kkL~eil~~~-~~ppiIIFvN~kk~  529 (673)
T KOG0333|consen  455 TVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVS----EDEKRKKLIEILESN-FDPPIIIFVNTKKG  529 (673)
T ss_pred             EEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEec----chHHHHHHHHHHHhC-CCCCEEEEEechhh
Confidence            34688888875  344444455555666655666667776666533    345677888888754 56789999999999


Q ss_pred             HHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccc
Q psy4494          89 CEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG  150 (234)
Q Consensus        89 ~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~g  150 (234)
                      |+.||+.|.+.|+.+..|||+.++++                  |+++|||||+|+|.+|||||+++++++|+||+||+|
T Consensus       530 ~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieDYtHRIGRTg  609 (673)
T KOG0333|consen  530 ADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIEDYTHRIGRTG  609 (673)
T ss_pred             HHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHHHHHHhcccc
Confidence            99999999999999999999999987                  999999999999999999999999999999999999


Q ss_pred             cCCCceEEEEEeecccHHHhhhh
Q psy4494         151 RDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       151 R~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      |+|+.|+++.|+++.|-..+..+
T Consensus       610 RAGk~GtaiSflt~~dt~v~ydL  632 (673)
T KOG0333|consen  610 RAGKSGTAISFLTPADTAVFYDL  632 (673)
T ss_pred             ccccCceeEEEeccchhHHHHHH
Confidence            99999999999999886554443

>KOG0330|consensus

Probab=99.94  E-value=3.6e-27  Score=201.76  Aligned_cols=164  Identities=16%  Similarity=0.213  Sum_probs=133.9

Q ss_pred             HHHHHhhhccCchhH-HHHhhCCCCC-cEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecc
Q psy4494           8 IAYLNLWRTSFYQVS-IAFGLGIDKP-NVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTS   85 (234)
Q Consensus         8 ~a~l~l~~at~p~~~-i~~~~~~~~~-~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t   85 (234)
                      ..++-||+||+|+.. -......+.| .|.+.-.++.-..+.++|..++...+...    |+.++.. ..+.+.||||+|
T Consensus       235 erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~y----LV~ll~e-~~g~s~iVF~~t  309 (476)
T KOG0330|consen  235 ERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTY----LVYLLNE-LAGNSVIVFCNT  309 (476)
T ss_pred             cceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchh----HHHHHHh-hcCCcEEEEEec
Confidence            345668999999862 2234444443 45554456666777888888776655443    4444442 356889999999


Q ss_pred             hHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhc
Q psy4494          86 IKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESG  147 (234)
Q Consensus        86 ~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~G  147 (234)
                      ...++.++-.|+..|+.+..+||+|+++.                  |++.+||+|+|+|++|||||+|.+..+|+||+|
T Consensus       310 ~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvG  389 (476)
T KOG0330|consen  310 CNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVG  389 (476)
T ss_pred             cchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcc
Confidence            99999999999999999999999999977                  999999999999999999999999999999999


Q ss_pred             ccccCCCceEEEEEeecccHHHhhhhHHh
Q psy4494         148 RAGRDGQIAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       148 R~gR~g~~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      |+||+|++|.+|.+++.+|+..+.+|...
T Consensus       390 RtaRaGrsG~~ItlVtqyDve~~qrIE~~  418 (476)
T KOG0330|consen  390 RTARAGRSGKAITLVTQYDVELVQRIEHA  418 (476)
T ss_pred             cccccCCCcceEEEEehhhhHHHHHHHHH
Confidence            99999999999999999999988777543

>KOG0331|consensus

Probab=99.94  E-value=2.9e-27  Score=212.12  Aligned_cols=163  Identities=17%  Similarity=0.269  Sum_probs=127.0

Q ss_pred             HHHhhhccCchhHH--HHhhCCCCCcEEEEEee--ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhc--CCCcEEEEe
Q psy4494          10 YLNLWRTSFYQVSI--AFGLGIDKPNVRFVIHH--CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF--RNQSGIIYT   83 (234)
Q Consensus        10 ~l~l~~at~p~~~i--~~~~~~~~~~i~~~~~~--~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~--~~~~~iIf~   83 (234)
                      |+-+|++|+|....  +...-.++..+.+.-..  ...+++.+...+..    ..++...|.++|.+..  +..++||||
T Consensus       273 Qtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~----~~~K~~~l~~lL~~~~~~~~~KvIIFc  348 (519)
T KOG0331|consen  273 QTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCD----ETAKLRKLGKLLEDISSDSEGKVIIFC  348 (519)
T ss_pred             cEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcC----HHHHHHHHHHHHHHHhccCCCcEEEEe
Confidence            67899999999743  22222244444433222  22334444544432    3455566666665443  567899999


Q ss_pred             cchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhh
Q psy4494          84 TSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQE  145 (234)
Q Consensus        84 ~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr  145 (234)
                      +|++.|++|+..|+..++.+..+||+.++++                  |++++||+|+|+|++|||||+|.++++|+||
T Consensus       349 ~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHR  428 (519)
T KOG0331|consen  349 ETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHR  428 (519)
T ss_pred             cchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcccccccCCCccccEEEeCCCCCCHHHHHhh
Confidence            9999999999999999999999999999988                  9999999999999999999999999999999


Q ss_pred             hcccccCCCceEEEEEeecccHHHhhhhHHh
Q psy4494         146 SGRAGRDGQIAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       146 ~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      +||+||+|+.|.+++|++..+......++..
T Consensus       429 iGRTGRa~~~G~A~tfft~~~~~~a~~l~~~  459 (519)
T KOG0331|consen  429 IGRTGRAGKKGTAITFFTSDNAKLARELIKV  459 (519)
T ss_pred             cCccccCCCCceEEEEEeHHHHHHHHHHHHH
Confidence            9999999999999999999888776665543

>KOG0328|consensus

Probab=99.94  E-value=2.9e-27  Score=195.27  Aligned_cols=170  Identities=20%  Similarity=0.248  Sum_probs=133.9

Q ss_pred             chHHHHHHHhhhccCchhHH--HHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEE
Q psy4494           4 LLYTIAYLNLWRTSFYQVSI--AFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGII   81 (234)
Q Consensus         4 ~~~~~a~l~l~~at~p~~~i--~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iI   81 (234)
                      ++.+-+|.-++|||+|....  ......||..+-+.-..-+...+.+||..+.++   +.|...|.++.. .+.-.+++|
T Consensus       196 ~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~E---ewKfdtLcdLYd-~LtItQavI  271 (400)
T KOG0328|consen  196 YLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKE---EWKFDTLCDLYD-TLTITQAVI  271 (400)
T ss_pred             hCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechh---hhhHhHHHHHhh-hhehheEEE
Confidence            34445667789999999733  333334443333222233344577877765443   346666666653 345667999


Q ss_pred             EecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhh
Q psy4494          82 YTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFY  143 (234)
Q Consensus        82 f~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~  143 (234)
                      ||||++.++.|.+.|++..+.+..+||+|.+++                  |++.+||+|+|.|.+|||||+|.+.+.|+
T Consensus       272 FcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YI  351 (400)
T KOG0328|consen  272 FCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYI  351 (400)
T ss_pred             EecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHh
Confidence            999999999999999999999999999999988                  99999999999999999999999999999


Q ss_pred             hhhcccccCCCceEEEEEeecccHHHhhhhHHhh
Q psy4494         144 QESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQ  177 (234)
Q Consensus       144 qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~  177 (234)
                      ||+||.||.|++|.+|.|+...|+..+..+.+.-
T Consensus       352 HRIGRSGRFGRkGvainFVk~~d~~~lrdieq~y  385 (400)
T KOG0328|consen  352 HRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYY  385 (400)
T ss_pred             hhhccccccCCcceEEEEecHHHHHHHHHHHHHH
Confidence            9999999999999999999999998887766443

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

Probab=99.94  E-value=1.3e-26  Score=212.69  Aligned_cols=162  Identities=23%  Similarity=0.337  Sum_probs=130.6

Q ss_pred             HHHHhhhccCchh--HHHHhhCCCCCcEEEEEeec--cCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEec
Q psy4494           9 AYLNLWRTSFYQV--SIAFGLGIDKPNVRFVIHHC--LSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTT   84 (234)
Q Consensus         9 a~l~l~~at~p~~--~i~~~~~~~~~~i~~~~~~~--~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~   84 (234)
                      -|..+||||+|..  .++.....++..+.+.....  ....+.++|..+...   .+++..|..++... ...++||||+
T Consensus       206 ~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~---~~k~~~L~~ll~~~-~~~~~IVF~~  281 (513)
T COG0513         206 RQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESE---EEKLELLLKLLKDE-DEGRVIVFVR  281 (513)
T ss_pred             cEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCH---HHHHHHHHHHHhcC-CCCeEEEEeC
Confidence            5667899999995  22333333555555543333  556677777664432   24788888888743 4557999999


Q ss_pred             chHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhh
Q psy4494          85 SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQES  146 (234)
Q Consensus        85 t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~  146 (234)
                      |++.++.++..|...|+.+..+||++++++                  |++++||||+|+|++|||||+|.+.++|+||+
T Consensus       282 tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRi  361 (513)
T COG0513         282 TKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRI  361 (513)
T ss_pred             cHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeEEccCCCCHHHheecc
Confidence            999999999999999999999999999987                  99999999999999999999999999999999


Q ss_pred             cccccCCCceEEEEEeecc-cHHHhhhhH
Q psy4494         147 GRAGRDGQIAHCILYYRLP-DVFKLSSMV  174 (234)
Q Consensus       147 GR~gR~g~~~~~i~~~~~~-d~~~~~~~~  174 (234)
                      ||+||+|+.|.+++|+.+. |...+..+.
T Consensus       362 GRTgRaG~~G~ai~fv~~~~e~~~l~~ie  390 (513)
T COG0513         362 GRTGRAGRKGVAISFVTEEEEVKKLKRIE  390 (513)
T ss_pred             CccccCCCCCeEEEEeCcHHHHHHHHHHH
Confidence            9999999999999999985 666555543

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.91  E-value=5.1e-24  Score=191.80  Aligned_cols=157  Identities=17%  Similarity=0.234  Sum_probs=119.3

Q ss_pred             HhhhccCchhHH-HHhhCC-CCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHH
Q psy4494          12 NLWRTSFYQVSI-AFGLGI-DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC   89 (234)
Q Consensus        12 ~l~~at~p~~~i-~~~~~~-~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~   89 (234)
                      -+||||++.... .....+ ++..+.+.........+...+..    ....++...|..++... ...++||||+|++.|
T Consensus       194 ~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~----~~~~~k~~~l~~ll~~~-~~~~~lVF~~t~~~~  268 (423)
T PRK04837        194 MLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFY----PSNEEKMRLLQTLIEEE-WPDRAIIFANTKHRC  268 (423)
T ss_pred             EEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEe----CCHHHHHHHHHHHHHhc-CCCeEEEEECCHHHH
Confidence            367888886522 222222 33233322222222333333332    23355777777777643 567899999999999


Q ss_pred             HHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccccc
Q psy4494          90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR  151 (234)
Q Consensus        90 ~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR  151 (234)
                      +.++..|...|+.+..+||++++++                  |++++||||+|+|++|||||+|.+..+|+||+||+||
T Consensus       269 ~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR  348 (423)
T PRK04837        269 EEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGR  348 (423)
T ss_pred             HHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccC
Confidence            9999999999999999999999876                  9999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEeecccHHHhhhh
Q psy4494         152 DGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       152 ~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      +|+.|.+++|+.+.|...+..+
T Consensus       349 ~G~~G~ai~~~~~~~~~~~~~i  370 (423)
T PRK04837        349 AGASGHSISLACEEYALNLPAI  370 (423)
T ss_pred             CCCCeeEEEEeCHHHHHHHHHH
Confidence            9999999999998877665544

>PTZ00110 helicase; Provisional

Probab=99.91  E-value=1.5e-23  Score=193.97  Aligned_cols=185  Identities=16%  Similarity=0.224  Sum_probs=130.7

Q ss_pred             HHhhhccCchhHHHHhhC-CCCCcEEEEEee---ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhc-CCCcEEEEecc
Q psy4494          11 LNLWRTSFYQVSIAFGLG-IDKPNVRFVIHH---CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF-RNQSGIIYTTS   85 (234)
Q Consensus        11 l~l~~at~p~~~i~~~~~-~~~~~i~~~~~~---~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~-~~~~~iIf~~t   85 (234)
                      +-+|+||+|......... .....+.+.+..   .....+.+.+.+..    ..++...|.+++.... ...++||||+|
T Consensus       311 ~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~----~~~k~~~L~~ll~~~~~~~~k~LIF~~t  386 (545)
T PTZ00110        311 TLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVE----EHEKRGKLKMLLQRIMRDGDKILIFVET  386 (545)
T ss_pred             EEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEe----chhHHHHHHHHHHHhcccCCeEEEEecC
Confidence            356899998753222111 111123333221   12233444444432    2345555666655433 46789999999


Q ss_pred             hHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhc
Q psy4494          86 IKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESG  147 (234)
Q Consensus        86 ~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~G  147 (234)
                      ++.|+.++..|+..++.+..+||++++++                  |++++||||+|+|++|||||+|.++++|+||+|
T Consensus       387 ~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiG  466 (545)
T PTZ00110        387 KKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIG  466 (545)
T ss_pred             hHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhc
Confidence            99999999999999999999999999876                  999999999999999999999999999999999


Q ss_pred             ccccCCCceEEEEEeecccHHHhhhhHHhhhhh----hHhHHHHHHHhhcCcccHH
Q psy4494         148 RAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTG----LANLYNIVSYCLDQTRCRR  199 (234)
Q Consensus       148 R~gR~g~~~~~i~~~~~~d~~~~~~~~~~~~~~----~~~l~~~~~~~~~~~~Crr  199 (234)
                      |+||+|+.|.+++|+++.|......++..-...    ...|..|.....+...|++
T Consensus       467 RtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~~~~~~~~~~~~~  522 (545)
T PTZ00110        467 RTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERSNGTERRR  522 (545)
T ss_pred             ccccCCCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHHHHHHhcCCccccc
Confidence            999999999999999998877666554432221    2455566555444446663

>KOG0345|consensus

Probab=99.91  E-value=3.7e-24  Score=187.03  Aligned_cols=157  Identities=17%  Similarity=0.241  Sum_probs=130.9

Q ss_pred             HHHHHhhhccCchh-HHHHhhCCCCC-cEEEEEeec--cCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEe
Q psy4494           8 IAYLNLWRTSFYQV-SIAFGLGIDKP-NVRFVIHHC--LSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYT   83 (234)
Q Consensus         8 ~a~l~l~~at~p~~-~i~~~~~~~~~-~i~~~~~~~--~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~   83 (234)
                      =-..||||||-.+. .-.+..|+..| .|.+.....  .|.++..+|.++    ...+++..+.+++.. ...+++|||.
T Consensus       188 QRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~----~a~eK~~~lv~~L~~-~~~kK~iVFF  262 (567)
T KOG0345|consen  188 QRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVC----EADEKLSQLVHLLNN-NKDKKCIVFF  262 (567)
T ss_pred             ccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEe----cHHHHHHHHHHHHhc-cccccEEEEe
Confidence            33579999998885 55777787443 344444333  677788888884    346788899999875 3678999999


Q ss_pred             cchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhh
Q psy4494          84 TSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFY  143 (234)
Q Consensus        84 ~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~  143 (234)
                      +|...++.....|...  ...+..+||.|++..                  |++++||||+|+|++||+||+|.+++.|+
T Consensus       263 ~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~Fv  342 (567)
T KOG0345|consen  263 PTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFV  342 (567)
T ss_pred             cCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHH
Confidence            9999999999998765  678999999999985                  99999999999999999999999999999


Q ss_pred             hhhcccccCCCceEEEEEeecccHHH
Q psy4494         144 QESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       144 qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                      ||+||+||.|+.|.||+|+.+.+...
T Consensus       343 HR~GRTaR~gr~G~Aivfl~p~E~aY  368 (567)
T KOG0345|consen  343 HRCGRTARAGREGNAIVFLNPREEAY  368 (567)
T ss_pred             hhcchhhhccCccceEEEecccHHHH
Confidence            99999999999999999999966544

>KOG0326|consensus

Probab=99.90  E-value=1.2e-24  Score=182.44  Aligned_cols=171  Identities=22%  Similarity=0.311  Sum_probs=138.6

Q ss_pred             cchHHHHHHHhhhccCchhHHHHh-hCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEE
Q psy4494           3 ALLYTIAYLNLWRTSFYQVSIAFG-LGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGII   81 (234)
Q Consensus         3 ~~~~~~a~l~l~~at~p~~~i~~~-~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iI   81 (234)
                      +++...-|..|||||||-....|. --+.+|...--...-....+.+||..+..    .+|+.-|..++. .+.-...||
T Consensus       253 ~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~eLtl~GvtQyYafV~e----~qKvhCLntLfs-kLqINQsII  327 (459)
T KOG0326|consen  253 SFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEELTLKGVTQYYAFVEE----RQKVHCLNTLFS-KLQINQSII  327 (459)
T ss_pred             HhCCccceeeEEecccchhHHHHHHHhccCcceeehhhhhhhcchhhheeeech----hhhhhhHHHHHH-HhcccceEE
Confidence            455566677889999998654444 33455644333344556778888887543    456666666654 345667899


Q ss_pred             EecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhh
Q psy4494          82 YTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFY  143 (234)
Q Consensus        82 f~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~  143 (234)
                      ||||.+.+|-+|+.+.+.|+.+.++|+.|.++.                  |+.+-||||++.|+.|||||+|++.++|+
T Consensus       328 FCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYL  407 (459)
T KOG0326|consen  328 FCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYL  407 (459)
T ss_pred             EeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHH
Confidence            999999999999999999999999999999877                  99999999999999999999999999999


Q ss_pred             hhhcccccCCCceEEEEEeecccHHHhhhhHHhhh
Q psy4494         144 QESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQ  178 (234)
Q Consensus       144 qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~~  178 (234)
                      ||+||+||.|..|.||.+++.+|...+..+.++-.
T Consensus       408 HRIGRsGRFGhlGlAInLityedrf~L~~IE~eLG  442 (459)
T KOG0326|consen  408 HRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELG  442 (459)
T ss_pred             HHccCCccCCCcceEEEEEehhhhhhHHHHHHHhc
Confidence            99999999999999999999999888777665443

>KOG0332|consensus

Probab=99.90  E-value=6.1e-24  Score=181.21  Aligned_cols=157  Identities=24%  Similarity=0.291  Sum_probs=126.6

Q ss_pred             HHHHHhhhccCchhHHHHhhCCCCC-c-EEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecc
Q psy4494           8 IAYLNLWRTSFYQVSIAFGLGIDKP-N-VRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTS   85 (234)
Q Consensus         8 ~a~l~l~~at~p~~~i~~~~~~~~~-~-i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t   85 (234)
                      -.|+-|||+||......|...+-+. + +.+.-.......+.++|.+...   .++|...|.+++- -..-+++||||.|
T Consensus       264 ~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~---~~~K~~~l~~lyg-~~tigqsiIFc~t  339 (477)
T KOG0332|consen  264 NQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCAC---RDDKYQALVNLYG-LLTIGQSIIFCHT  339 (477)
T ss_pred             cceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccc---hhhHHHHHHHHHh-hhhhhheEEEEee
Confidence            4577899999999888777776443 2 3333233344566777776444   4567777777543 2346789999999


Q ss_pred             hHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCC------CHhH
Q psy4494          86 IKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSK------SMEN  141 (234)
Q Consensus        86 ~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~------~~~~  141 (234)
                      ++.+..++..|.+.|.++..+||+|..++                  |++++||||++.|..|||||+|.      +.+.
T Consensus       340 k~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~et  419 (477)
T KOG0332|consen  340 KATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYET  419 (477)
T ss_pred             hhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHH
Confidence            99999999999999999999999999877                  99999999999999999999995      6789


Q ss_pred             hhhhhcccccCCCceEEEEEeecccHH
Q psy4494         142 FYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       142 y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      |+||+||+||.|+.|.++.++...+..
T Consensus       420 YlHRiGRtGRFGkkG~a~n~v~~~~s~  446 (477)
T KOG0332|consen  420 YLHRIGRTGRFGKKGLAINLVDDKDSM  446 (477)
T ss_pred             HHHHhcccccccccceEEEeecccCcH
Confidence            999999999999999999999876543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.90  E-value=7.5e-23  Score=186.05  Aligned_cols=158  Identities=18%  Similarity=0.272  Sum_probs=120.7

Q ss_pred             HHHhhhccCchhHH--HHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchH
Q psy4494          10 YLNLWRTSFYQVSI--AFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIK   87 (234)
Q Consensus        10 ~l~l~~at~p~~~i--~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~   87 (234)
                      +.-+||||+|....  ......++..+.+.... ....+.++|....    ..++...+..++.. ..+.++||||+|++
T Consensus       180 q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~----~~~k~~~l~~ll~~-~~~~~~lVF~~t~~  253 (460)
T PRK11776        180 QTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVS----PDERLPALQRLLLH-HQPESCVVFCNTKK  253 (460)
T ss_pred             EEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeC----cHHHHHHHHHHHHh-cCCCceEEEECCHH
Confidence            34568999987532  22222233333332222 2233444443322    23467777777753 35678999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccc
Q psy4494          88 ECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus        88 ~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      .++.++..|...++.+..+||++++.+                  |+++++|+|+|+|++|||||+|.+..+|+||+||+
T Consensus       254 ~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRt  333 (460)
T PRK11776        254 ECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRT  333 (460)
T ss_pred             HHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccc
Confidence            999999999999999999999999876                  99999999999999999999999999999999999


Q ss_pred             ccCCCceEEEEEeecccHHHhhhh
Q psy4494         150 GRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      ||+|+.|.+++|+.+.|...+..+
T Consensus       334 GR~g~~G~ai~l~~~~e~~~~~~i  357 (460)
T PRK11776        334 GRAGSKGLALSLVAPEEMQRANAI  357 (460)
T ss_pred             cCCCCcceEEEEEchhHHHHHHHH
Confidence            999999999999999887665544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.89  E-value=1.1e-22  Score=184.71  Aligned_cols=159  Identities=16%  Similarity=0.222  Sum_probs=119.6

Q ss_pred             HHhhhccCchhH--HHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          11 LNLWRTSFYQVS--IAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        11 l~l~~at~p~~~--i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      .-+|+||++...  +...+..++..+.+.........+..++...    +...+...+..++.. ....++||||+|++.
T Consensus       183 ~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~----~~~~k~~~l~~l~~~-~~~~~~lVF~~t~~~  257 (456)
T PRK10590        183 NLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFV----DKKRKRELLSQMIGK-GNWQQVLVFTRTKHG  257 (456)
T ss_pred             EEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEc----CHHHHHHHHHHHHHc-CCCCcEEEEcCcHHH
Confidence            346889988742  2222333333343332233334444444432    223445555555543 345789999999999


Q ss_pred             HHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccc
Q psy4494          89 CEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG  150 (234)
Q Consensus        89 ~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~g  150 (234)
                      ++.+++.|...++.+..+||++++++                  |+++++|||+|+|++||||++|.++.+|+||+||+|
T Consensus       258 ~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaG  337 (456)
T PRK10590        258 ANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTG  337 (456)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccc
Confidence            99999999999999999999999866                  999999999999999999999999999999999999


Q ss_pred             cCCCceEEEEEeecccHHHhhhhH
Q psy4494         151 RDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       151 R~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      |+|..|.+++|+...|...+..+.
T Consensus       338 R~g~~G~ai~l~~~~d~~~~~~ie  361 (456)
T PRK10590        338 RAAATGEALSLVCVDEHKLLRDIE  361 (456)
T ss_pred             cCCCCeeEEEEecHHHHHHHHHHH
Confidence            999999999999988876655443

>KOG0341|consensus

Probab=99.89  E-value=1e-23  Score=180.83  Aligned_cols=153  Identities=18%  Similarity=0.280  Sum_probs=121.4

Q ss_pred             HHHHhhhccCchh-HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchH
Q psy4494           9 AYLNLWRTSFYQV-SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIK   87 (234)
Q Consensus         9 a~l~l~~at~p~~-~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~   87 (234)
                      -|.-|||+|.|.. .+.+...+-+| |.+.+...-..++|..-+|..  .+.+.++-.|++.+++  ...+++|||..+.
T Consensus       358 RQTLLFSATMP~KIQ~FAkSALVKP-vtvNVGRAGAAsldViQevEy--VkqEaKiVylLeCLQK--T~PpVLIFaEkK~  432 (610)
T KOG0341|consen  358 RQTLLFSATMPKKIQNFAKSALVKP-VTVNVGRAGAASLDVIQEVEY--VKQEAKIVYLLECLQK--TSPPVLIFAEKKA  432 (610)
T ss_pred             hheeeeeccccHHHHHHHHhhcccc-eEEecccccccchhHHHHHHH--HHhhhhhhhHHHHhcc--CCCceEEEecccc
Confidence            3566899999986 55555566555 445555545555553322210  1234456666666664  3567999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccc
Q psy4494          88 ECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus        88 ~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      .++.++++|--.|..+..+||+.++++                  |++++-|+|+|+|.+|||||+|.++++|+||+||+
T Consensus       433 DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRT  512 (610)
T KOG0341|consen  433 DVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRT  512 (610)
T ss_pred             ChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhccc
Confidence            999999999999999999999999987                  99999999999999999999999999999999999


Q ss_pred             ccCCCceEEEEEeeccc
Q psy4494         150 GRDGQIAHCILYYRLPD  166 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d  166 (234)
                      ||.|+.|.+.+|++...
T Consensus       513 GRsg~~GiATTfINK~~  529 (610)
T KOG0341|consen  513 GRSGKTGIATTFINKNQ  529 (610)
T ss_pred             CCCCCcceeeeeecccc
Confidence            99999999999998753

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.89  E-value=1.9e-22  Score=182.18  Aligned_cols=159  Identities=18%  Similarity=0.220  Sum_probs=121.0

Q ss_pred             HHHhhhccCchh---HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecch
Q psy4494          10 YLNLWRTSFYQV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSI   86 (234)
Q Consensus        10 ~l~l~~at~p~~---~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~   86 (234)
                      ++-+||||++..   .+...+..++..+...........+.++|...   .....+...|..++.. ....++||||+|+
T Consensus       180 q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~---~~~~~k~~~l~~l~~~-~~~~~~lVF~~s~  255 (434)
T PRK11192        180 QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRA---DDLEHKTALLCHLLKQ-PEVTRSIVFVRTR  255 (434)
T ss_pred             EEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEe---CCHHHHHHHHHHHHhc-CCCCeEEEEeCCh
Confidence            345688888753   22333333443343332223333444444432   2234567777777753 2567899999999


Q ss_pred             HHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcc
Q psy4494          87 KECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGR  148 (234)
Q Consensus        87 ~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR  148 (234)
                      +.++.++..|+..++.+..+||+|++.+                  |+++++|+|+|+|++|||||+|.+...|+||+||
T Consensus       256 ~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR  335 (434)
T PRK11192        256 ERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGR  335 (434)
T ss_pred             HHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccc
Confidence            9999999999999999999999999876                  9999999999999999999999999999999999


Q ss_pred             cccCCCceEEEEEeecccHHHhhh
Q psy4494         149 AGRDGQIAHCILYYRLPDVFKLSS  172 (234)
Q Consensus       149 ~gR~g~~~~~i~~~~~~d~~~~~~  172 (234)
                      +||+|..|.+++++...|...+.+
T Consensus       336 ~gR~g~~g~ai~l~~~~d~~~~~~  359 (434)
T PRK11192        336 TGRAGRKGTAISLVEAHDHLLLGK  359 (434)
T ss_pred             cccCCCCceEEEEecHHHHHHHHH
Confidence            999999999999998877765544

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.89  E-value=1.8e-22  Score=189.02  Aligned_cols=159  Identities=14%  Similarity=0.230  Sum_probs=122.1

Q ss_pred             HHHhhhccCchhH--HHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchH
Q psy4494          10 YLNLWRTSFYQVS--IAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIK   87 (234)
Q Consensus        10 ~l~l~~at~p~~~--i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~   87 (234)
                      ++.+||||+|...  +......++..+.+.........+.+.|..+.    ..++...|..++.. ....++||||+|+.
T Consensus       182 q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~----~~~k~~~L~~~L~~-~~~~~~IVF~~tk~  256 (629)
T PRK11634        182 QTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVW----GMRKNEALVRFLEA-EDFDAAIIFVRTKN  256 (629)
T ss_pred             eEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEec----hhhHHHHHHHHHHh-cCCCCEEEEeccHH
Confidence            4567899998852  33333334444443322223333444444322    23466667777653 24578999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccc
Q psy4494          88 ECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus        88 ~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      .++.++..|...|+.+..+||+|++.+                  |+++++|||+|+|++|||||+|.++++|+||+||+
T Consensus       257 ~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRt  336 (629)
T PRK11634        257 ATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRT  336 (629)
T ss_pred             HHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccc
Confidence            999999999999999999999999876                  99999999999999999999999999999999999


Q ss_pred             ccCCCceEEEEEeecccHHHhhhh
Q psy4494         150 GRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      ||.|+.|.+++|+.+.|...+..+
T Consensus       337 GRaGr~G~ai~~v~~~e~~~l~~i  360 (629)
T PRK11634        337 GRAGRAGRALLFVENRERRLLRNI  360 (629)
T ss_pred             cCCCCcceEEEEechHHHHHHHHH
Confidence            999999999999998776555444

>KOG0342|consensus

Probab=99.89  E-value=1.1e-22  Score=178.66  Aligned_cols=161  Identities=16%  Similarity=0.154  Sum_probs=131.3

Q ss_pred             HHHHHhhhccCchh-HHHHhhCCCCCcEEEEEee----ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEE
Q psy4494           8 IAYLNLWRTSFYQV-SIAFGLGIDKPNVRFVIHH----CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIY   82 (234)
Q Consensus         8 ~a~l~l~~at~p~~-~i~~~~~~~~~~i~~~~~~----~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf   82 (234)
                      --|..|||||.|.. .-.+...+.+..+.+.+..    ...+++++-|.+.+..    ..+..+..++++....+++|||
T Consensus       261 ~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~----~~f~ll~~~LKk~~~~~KiiVF  336 (543)
T KOG0342|consen  261 QRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSD----SRFSLLYTFLKKNIKRYKIIVF  336 (543)
T ss_pred             cceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEecccc----chHHHHHHHHHHhcCCceEEEE
Confidence            34567899999985 3444444544444444432    3445677878885543    3366777788766555899999


Q ss_pred             ecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhh
Q psy4494          83 TTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ  144 (234)
Q Consensus        83 ~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~q  144 (234)
                      |+|...+..+++.|+...+++..+||++++..                  |++.+||+|+|+|++||+||+|.+.++|+|
T Consensus       337 ~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIH  416 (543)
T KOG0342|consen  337 FSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIH  416 (543)
T ss_pred             echhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHH
Confidence            99999999999999999999999999999977                  999999999999999999999999999999


Q ss_pred             hhcccccCCCceEEEEEeecccHHHhhh
Q psy4494         145 ESGRAGRDGQIAHCILYYRLPDVFKLSS  172 (234)
Q Consensus       145 r~GR~gR~g~~~~~i~~~~~~d~~~~~~  172 (234)
                      |+||+||.|..|.++++..|+++.-+..
T Consensus       417 RvGRTaR~gk~G~alL~l~p~El~Flr~  444 (543)
T KOG0342|consen  417 RVGRTAREGKEGKALLLLAPWELGFLRY  444 (543)
T ss_pred             HhccccccCCCceEEEEeChhHHHHHHH
Confidence            9999999999999999999998765543

>KOG0340|consensus

Probab=99.89  E-value=8.9e-23  Score=173.17  Aligned_cols=163  Identities=21%  Similarity=0.326  Sum_probs=119.7

Q ss_pred             HHhhhccCchh-HHHHhhCCCCCcEEEEEee----ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecc
Q psy4494          11 LNLWRTSFYQV-SIAFGLGIDKPNVRFVIHH----CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTS   85 (234)
Q Consensus        11 l~l~~at~p~~-~i~~~~~~~~~~i~~~~~~----~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t   85 (234)
                      .-||++|.-+. .-.+...+.++ +-+.+..    ..+..+.+.|...+...... .+..++.-..+. ..+.++||+||
T Consensus       187 tLlfSATitd~i~ql~~~~i~k~-~a~~~e~~~~vstvetL~q~yI~~~~~vkda-YLv~~Lr~~~~~-~~~simIFvnt  263 (442)
T KOG0340|consen  187 TLLFSATITDTIKQLFGCPITKS-IAFELEVIDGVSTVETLYQGYILVSIDVKDA-YLVHLLRDFENK-ENGSIMIFVNT  263 (442)
T ss_pred             eEEEEeehhhHHHHhhcCCcccc-cceEEeccCCCCchhhhhhheeecchhhhHH-HHHHHHhhhhhc-cCceEEEEeeh
Confidence            33556655543 22333444443 2222221    22333445555544333222 222333333322 46789999999


Q ss_pred             hHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhc
Q psy4494          86 IKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESG  147 (234)
Q Consensus        86 ~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~G  147 (234)
                      ...|+.++..|+..++++..+||.|++++                  |++++||+|||.|++|||||+|.++.+|+||+|
T Consensus       264 tr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvG  343 (442)
T KOG0340|consen  264 TRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVG  343 (442)
T ss_pred             hHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhc
Confidence            99999999999999999999999999988                  999999999999999999999999999999999


Q ss_pred             ccccCCCceEEEEEeecccHHHhhhhHHh
Q psy4494         148 RAGRDGQIAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       148 R~gR~g~~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      |+.|+|+.|.+|.++++.|...+.++.+.
T Consensus       344 RtARAGR~G~aiSivt~rDv~l~~aiE~~  372 (442)
T KOG0340|consen  344 RTARAGRKGMAISIVTQRDVELLQAIEEE  372 (442)
T ss_pred             chhcccCCcceEEEechhhHHHHHHHHHH
Confidence            99999999999999999999888776543

>KOG0335|consensus

Probab=99.88  E-value=1.4e-22  Score=179.68  Aligned_cols=157  Identities=15%  Similarity=0.187  Sum_probs=118.0

Q ss_pred             HHHhhhccCchhH-H-HHhhCCC-CCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhc---C-----CCc
Q psy4494          10 YLNLWRTSFYQVS-I-AFGLGID-KPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF---R-----NQS   78 (234)
Q Consensus        10 ~l~l~~at~p~~~-i-~~~~~~~-~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~---~-----~~~   78 (234)
                      +.-|||||||... - ++..-.+ .-.+++......++.+.+....+.+    .++...|.+++....   .     ...
T Consensus       264 qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~----~~kr~~Lldll~~~~~~~~~~~~~~e~  339 (482)
T KOG0335|consen  264 QTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNE----MEKRSKLLDLLNKDDGPPSDGEPKWEK  339 (482)
T ss_pred             eEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecc----hhhHHHHHHHhhcccCCcccCCcccce
Confidence            4568999999862 2 2222222 2233444344455555444444333    345555666654322   1     237


Q ss_pred             EEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHh
Q psy4494          79 GIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSME  140 (234)
Q Consensus        79 ~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~  140 (234)
                      ++|||.|++.+..|+..|...++++..+||..++.+                  |++++||+|+|+|++|||||+|.+..
T Consensus       340 tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d  419 (482)
T KOG0335|consen  340 TLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADID  419 (482)
T ss_pred             EEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcchh
Confidence            999999999999999999999999999999999877                  99999999999999999999999999


Q ss_pred             HhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         141 NFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       141 ~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                      +|+||+||+||+|+.|.++.|++..+-...
T Consensus       420 ~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~  449 (482)
T KOG0335|consen  420 DYVHRIGRTGRVGNGGRATSFFNEKNQNIA  449 (482)
T ss_pred             hHHHhccccccCCCCceeEEEeccccchhH
Confidence            999999999999999999999996544433

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.88  E-value=3.6e-22  Score=185.56  Aligned_cols=158  Identities=15%  Similarity=0.205  Sum_probs=119.3

Q ss_pred             HHhhhccCchhHHH-HhhCCCCC-cEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          11 LNLWRTSFYQVSIA-FGLGIDKP-NVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        11 l~l~~at~p~~~i~-~~~~~~~~-~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      ..+||+|++..... ....+..| .+.+.........+.+++..    ....+++..|..++.. ....++||||+|++.
T Consensus       195 ~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~----~~~~~k~~~L~~ll~~-~~~~k~LVF~nt~~~  269 (572)
T PRK04537        195 TLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYF----PADEEKQTLLLGLLSR-SEGARTMVFVNTKAF  269 (572)
T ss_pred             EEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEe----cCHHHHHHHHHHHHhc-ccCCcEEEEeCCHHH
Confidence            45688998875322 22222333 22222222222333343333    2234567777777753 356789999999999


Q ss_pred             HHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccc
Q psy4494          89 CEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG  150 (234)
Q Consensus        89 ~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~g  150 (234)
                      ++.+++.|...++.+..+||+|++.+                  |+++++|||+|+|++|||||+|.++++|+||+||+|
T Consensus       270 ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaG  349 (572)
T PRK04537        270 VERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTA  349 (572)
T ss_pred             HHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccc
Confidence            99999999999999999999999876                  999999999999999999999999999999999999


Q ss_pred             cCCCceEEEEEeecccHHHhhhh
Q psy4494         151 RDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       151 R~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      |.|+.|.+++|+.+.+...+..+
T Consensus       350 R~G~~G~ai~~~~~~~~~~l~~i  372 (572)
T PRK04537        350 RLGEEGDAISFACERYAMSLPDI  372 (572)
T ss_pred             cCCCCceEEEEecHHHHHHHHHH
Confidence            99999999999988776655544

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

Probab=99.88  E-value=2.1e-22  Score=185.44  Aligned_cols=161  Identities=17%  Similarity=0.247  Sum_probs=116.2

Q ss_pred             HHHhhhccCchhHHHHhhCCCCCcEEEEEee--ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhc-CCCcEEEEecch
Q psy4494          10 YLNLWRTSFYQVSIAFGLGIDKPNVRFVIHH--CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF-RNQSGIIYTTSI   86 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~~~~~i~~~~~~--~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~-~~~~~iIf~~t~   86 (234)
                      +..+||||+|.........+....+.+.+..  .....+.+.+....    ..++...+.+++.... ...++||||+|+
T Consensus       302 q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~----~~~k~~~l~~~l~~~~~~~~~~iVFv~s~  377 (518)
T PLN00206        302 QVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVE----TKQKKQKLFDILKSKQHFKPPAVVFVSSR  377 (518)
T ss_pred             cEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEecc----chhHHHHHHHHHHhhcccCCCEEEEcCCc
Confidence            4457899998763222222222223333222  12222333333321    2234455666665321 235799999999


Q ss_pred             HHHHHHHHHHHH-cCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhc
Q psy4494          87 KECEDLREELRN-RGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESG  147 (234)
Q Consensus        87 ~~~~~l~~~L~~-~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~G  147 (234)
                      ..++.++..|.. .++.+..+||++++++                  |++++||||+|+|++|||||+|.++.+|+||+|
T Consensus       378 ~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiG  457 (518)
T PLN00206        378 LGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIG  457 (518)
T ss_pred             hhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhcc
Confidence            999999999975 5899999999999876                  999999999999999999999999999999999


Q ss_pred             ccccCCCceEEEEEeecccHHHhhhhH
Q psy4494         148 RAGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       148 R~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      |+||.|..|.+++|+++.|...+..++
T Consensus       458 RaGR~g~~G~ai~f~~~~~~~~~~~l~  484 (518)
T PLN00206        458 RASRMGEKGTAIVFVNEEDRNLFPELV  484 (518)
T ss_pred             ccccCCCCeEEEEEEchhHHHHHHHHH
Confidence            999999999999999988766555444

>KOG0336|consensus

Probab=99.88  E-value=1.8e-22  Score=174.18  Aligned_cols=164  Identities=15%  Similarity=0.223  Sum_probs=127.9

Q ss_pred             HHHhhhccCchhHHHHhhCC-CCCcEEEEEe--eccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecch
Q psy4494          10 YLNLWRTSFYQVSIAFGLGI-DKPNVRFVIH--HCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSI   86 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~-~~~~i~~~~~--~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~   86 (234)
                      +..++|||+|.-........ ..|.+-++-.  -...+++.+...|    ....+++..+..++.....+.++||||..+
T Consensus       400 qtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v----~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K  475 (629)
T KOG0336|consen  400 QTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIV----TTDSEKLEIVQFFVANMSSNDKVIIFVSRK  475 (629)
T ss_pred             eeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEe----cccHHHHHHHHHHHHhcCCCceEEEEEech
Confidence            34568999998643333333 2333322211  1223445555544    234567777777776666788999999999


Q ss_pred             HHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcc
Q psy4494          87 KECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGR  148 (234)
Q Consensus        87 ~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR  148 (234)
                      ..++.|..-|.-.|+.+..+||+-++..                  |+.++||+|+++|.||+|||+|.+++.|+||+||
T Consensus       476 ~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGr  555 (629)
T KOG0336|consen  476 VMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGR  555 (629)
T ss_pred             hhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcc
Confidence            9999999999999999999999988765                  9999999999999999999999999999999999


Q ss_pred             cccCCCceEEEEEeecccHHHhhhhHHhh
Q psy4494         149 AGRDGQIAHCILYYRLPDVFKLSSMVFDQ  177 (234)
Q Consensus       149 ~gR~g~~~~~i~~~~~~d~~~~~~~~~~~  177 (234)
                      +||+|+.|+++.|++.+|......+++--
T Consensus       556 tGRaGr~G~sis~lt~~D~~~a~eLI~IL  584 (629)
T KOG0336|consen  556 TGRAGRTGTSISFLTRNDWSMAEELIQIL  584 (629)
T ss_pred             cccCCCCcceEEEEehhhHHHHHHHHHHH
Confidence            99999999999999999998887776543

>KOG0338|consensus

Probab=99.88  E-value=1.1e-22  Score=179.34  Aligned_cols=163  Identities=22%  Similarity=0.335  Sum_probs=129.1

Q ss_pred             HHHhhhccCchh-HHHHhhCCCCCcEEEEEee--ccCCCc-ceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecc
Q psy4494          10 YLNLWRTSFYQV-SIAFGLGIDKPNVRFVIHH--CLSKSM-ENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTS   85 (234)
Q Consensus        10 ~l~l~~at~p~~-~i~~~~~~~~~~i~~~~~~--~~~~~~-~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t   85 (234)
                      |.-|||||+... .-...+++++| |++.+..  .....+ +.|..+++..  ..+.-..+..++.. ....++|||+.|
T Consensus       360 QTmLFSATMteeVkdL~slSL~kP-vrifvd~~~~~a~~LtQEFiRIR~~r--e~dRea~l~~l~~r-tf~~~~ivFv~t  435 (691)
T KOG0338|consen  360 QTMLFSATMTEEVKDLASLSLNKP-VRIFVDPNKDTAPKLTQEFIRIRPKR--EGDREAMLASLITR-TFQDRTIVFVRT  435 (691)
T ss_pred             cceeehhhhHHHHHHHHHhhcCCC-eEEEeCCccccchhhhHHHheecccc--ccccHHHHHHHHHH-hcccceEEEEeh
Confidence            567899999885 56778888887 4544432  222222 3455554322  12222233444443 346789999999


Q ss_pred             hHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhc
Q psy4494          86 IKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESG  147 (234)
Q Consensus        86 ~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~G  147 (234)
                      ++.|+++.=.|--.|+++.-+||++++++                  |++++||+||++|..||||++|.+.+.|+||+|
T Consensus       436 Kk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVG  515 (691)
T KOG0338|consen  436 KKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVG  515 (691)
T ss_pred             HHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhh
Confidence            99999999999999999999999999988                  999999999999999999999999999999999


Q ss_pred             ccccCCCceEEEEEeecccHHHhhhhHHh
Q psy4494         148 RAGRDGQIAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       148 R~gR~g~~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      |+.|+|+.|.+|+|++..|...++.+++.
T Consensus       516 RTARAGRaGrsVtlvgE~dRkllK~iik~  544 (691)
T KOG0338|consen  516 RTARAGRAGRSVTLVGESDRKLLKEIIKS  544 (691)
T ss_pred             hhhhcccCcceEEEeccccHHHHHHHHhh
Confidence            99999999999999999998888877765

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.87  E-value=1.8e-21  Score=177.78  Aligned_cols=110  Identities=20%  Similarity=0.359  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCC
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGI  122 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gi  122 (234)
                      ++...+.+++... ...++||||++++.++.++..|...++.+..+||++++++                  |+++++||
T Consensus       321 ~k~~~l~~ll~~~-~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GI  399 (475)
T PRK01297        321 DKYKLLYNLVTQN-PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGI  399 (475)
T ss_pred             hHHHHHHHHHHhc-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCC
Confidence            3555566666532 4568999999999999999999999999999999999876                  99999999


Q ss_pred             CCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhh
Q psy4494         123 DKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLS  171 (234)
Q Consensus       123 d~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~  171 (234)
                      |+++|++|||||+|.+..+|+||+||+||.|+.|.+++|+...|...+.
T Consensus       400 Di~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~  448 (475)
T PRK01297        400 HIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLP  448 (475)
T ss_pred             cccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHH
Confidence            9999999999999999999999999999999999999999877655433

>KOG0343|consensus

Probab=99.85  E-value=4e-21  Score=170.96  Aligned_cols=163  Identities=17%  Similarity=0.224  Sum_probs=133.3

Q ss_pred             hHHHHHHHhhhccCchh-HHHHhhCCCCC-cEEEE--EeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEE
Q psy4494           5 LYTIAYLNLWRTSFYQV-SIAFGLGIDKP-NVRFV--IHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGI   80 (234)
Q Consensus         5 ~~~~a~l~l~~at~p~~-~i~~~~~~~~~-~i~~~--~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~i   80 (234)
                      +...-|.-|||||--.. .-.+.+.+..| .|.+.  .....|..++++|.+++.    .+++..|+.++..+ ...+.|
T Consensus       243 lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l----~~Ki~~L~sFI~sh-lk~K~i  317 (758)
T KOG0343|consen  243 LPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL----EDKIDMLWSFIKSH-LKKKSI  317 (758)
T ss_pred             CChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEeh----hhHHHHHHHHHHhc-cccceE
Confidence            33445666888886553 44566666444 34332  125678888999988664    57899999999865 567899


Q ss_pred             EEecchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHh
Q psy4494          81 IYTTSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSME  140 (234)
Q Consensus        81 If~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~  140 (234)
                      ||+.|.+++..++..++..  |++...+||.|++..                  |++.+||+|+|.|++||++|+|.+++
T Consensus       318 VF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~  397 (758)
T KOG0343|consen  318 VFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVD  397 (758)
T ss_pred             EEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHH
Confidence            9999999999999999876  899999999999976                  99999999999999999999999999


Q ss_pred             HhhhhhcccccCCCceEEEEEeecccHHHhhh
Q psy4494         141 NFYQESGRAGRDGQIAHCILYYRLPDVFKLSS  172 (234)
Q Consensus       141 ~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~  172 (234)
                      +|+||+||+.|.+..|.+++++.|.+...+..
T Consensus       398 tYIHRvGRtAR~~~~G~sll~L~psEeE~~l~  429 (758)
T KOG0343|consen  398 TYIHRVGRTARYKERGESLLMLTPSEEEAMLK  429 (758)
T ss_pred             HHHHHhhhhhcccCCCceEEEEcchhHHHHHH
Confidence            99999999999999999999999988544433

>KOG0344|consensus

Probab=99.85  E-value=7.7e-21  Score=170.21  Aligned_cols=161  Identities=20%  Similarity=0.259  Sum_probs=131.2

Q ss_pred             HHHhhhccCchh--HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchH
Q psy4494          10 YLNLWRTSFYQV--SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIK   87 (234)
Q Consensus        10 ~l~l~~at~p~~--~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~   87 (234)
                      ..++||+|++..  .++-..-.+...|-+..+......+++-....   ++...++..+.+++... -..+++||+.+.+
T Consensus       323 ~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~sa~~~V~QelvF~---gse~~K~lA~rq~v~~g-~~PP~lIfVQs~e  398 (593)
T KOG0344|consen  323 RVALFSATISVYVEEWAELIKSDLKRVIVGLRNSANETVDQELVFC---GSEKGKLLALRQLVASG-FKPPVLIFVQSKE  398 (593)
T ss_pred             hhhhhhccccHHHHHHHHHhhccceeEEEecchhHhhhhhhhheee---ecchhHHHHHHHHHhcc-CCCCeEEEEecHH
Confidence            578999999985  45555555555555555555555555433332   33456777888888765 4567999999999


Q ss_pred             HHHHHHHHH-HHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcc
Q psy4494          88 ECEDLREEL-RNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGR  148 (234)
Q Consensus        88 ~~~~l~~~L-~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR  148 (234)
                      .|.+|...| .-.++.+..+||..++.+                  |+.++||+|+.+|+.|||||+|.+..+|+||+||
T Consensus       399 Rak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGR  478 (593)
T KOG0344|consen  399 RAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGR  478 (593)
T ss_pred             HHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhc
Confidence            999999999 677999999999998876                  9999999999999999999999999999999999


Q ss_pred             cccCCCceEEEEEeecccHHHhhhhH
Q psy4494         149 AGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       149 ~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      +||+|+.|.|++||+.+|...++.+.
T Consensus       479 tgRag~~g~Aitfytd~d~~~ir~ia  504 (593)
T KOG0344|consen  479 TGRAGRSGKAITFYTDQDMPRIRSIA  504 (593)
T ss_pred             cCCCCCCcceEEEeccccchhhhhHH
Confidence            99999999999999999988776654

>PTZ00424 helicase 45; Provisional

Probab=99.85  E-value=1e-20  Score=168.88  Aligned_cols=160  Identities=21%  Similarity=0.314  Sum_probs=116.6

Q ss_pred             HHHhhhccCchhHHH--HhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchH
Q psy4494          10 YLNLWRTSFYQVSIA--FGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIK   87 (234)
Q Consensus        10 ~l~l~~at~p~~~i~--~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~   87 (234)
                      ++-+++||+|+....  .....++..+.+.........++.+|....   ....+...+..++.. ....++||||+|++
T Consensus       203 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~-~~~~~~ivF~~t~~  278 (401)
T PTZ00424        203 QVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVE---KEEWKFDTLCDLYET-LTITQAIIYCNTRR  278 (401)
T ss_pred             EEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecC---hHHHHHHHHHHHHHh-cCCCeEEEEecCcH
Confidence            345578888875322  122222222211111122333444444322   123345555555543 34568999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccc
Q psy4494          88 ECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus        88 ~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      .++.++..|...++.+..+||++++++                  |+++++|+|+|++++||+||+|.+..+|+||+||+
T Consensus       279 ~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRa  358 (401)
T PTZ00424        279 KVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRS  358 (401)
T ss_pred             HHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeeccccc
Confidence            999999999999999999999999876                  99999999999999999999999999999999999


Q ss_pred             ccCCCceEEEEEeecccHHHhhhh
Q psy4494         150 GRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      ||.|+.|.+++++++.|...+..+
T Consensus       359 gR~g~~G~~i~l~~~~~~~~~~~~  382 (401)
T PTZ00424        359 GRFGRKGVAINFVTPDDIEQLKEI  382 (401)
T ss_pred             ccCCCCceEEEEEcHHHHHHHHHH
Confidence            999999999999998887655543

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

Probab=99.84  E-value=2.2e-20  Score=177.95  Aligned_cols=101  Identities=29%  Similarity=0.374  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc--------CCceeeeccCCCchh------------------
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR--------GLRVSAYHAKLESNV------------------  114 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~--------~~~~~~~h~~~~~~~------------------  114 (234)
                      ++...+.+++.   .+.++||||+|++.++.++..|++.        +.++..|||++++++                  
T Consensus       259 ~~~~~l~~l~~---~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVa  335 (742)
T TIGR03817       259 EAADLLADLVA---EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVAT  335 (742)
T ss_pred             HHHHHHHHHHH---CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEE
Confidence            34555666655   3578999999999999999998764        567899999999977                  


Q ss_pred             hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       115 T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      |+++++|||+++|++|||||.|.+..+|+||+||+||.|+.|.++++.+.
T Consensus       336 Td~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~  385 (742)
T TIGR03817       336 TNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARD  385 (742)
T ss_pred             CchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCC
Confidence            99999999999999999999999999999999999999999999999863

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.

>KOG0327|consensus

Probab=99.84  E-value=5.6e-21  Score=163.73  Aligned_cols=164  Identities=24%  Similarity=0.325  Sum_probs=130.5

Q ss_pred             hHHHHHHHhhhccCchhHHHHh--hCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEE
Q psy4494           5 LYTIAYLNLWRTSFYQVSIAFG--LGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIY   82 (234)
Q Consensus         5 ~~~~a~l~l~~at~p~~~i~~~--~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf   82 (234)
                      +.+-.|..|+|||.|.......  .+.++..|.+.......+.+.++|.-+.++.    |+..|.++..   .-..++||
T Consensus       197 lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~----k~~~l~dl~~---~~~q~~if  269 (397)
T KOG0327|consen  197 LPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEE----KLDTLCDLYR---RVTQAVIF  269 (397)
T ss_pred             cCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccc----cccHHHHHHH---hhhcceEE
Confidence            3344578899999999744333  3334433333322333455667776655443    6666776665   45678999


Q ss_pred             ecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhh
Q psy4494          83 TTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ  144 (234)
Q Consensus        83 ~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~q  144 (234)
                      |||++.+..+...|..+++++.++||+|.+.+                  |+.++||+|+..+..||||++|...++|+|
T Consensus       270 ~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yih  349 (397)
T KOG0327|consen  270 CNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIH  349 (397)
T ss_pred             ecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhh
Confidence            99999999999999999999999999999977                  889999999999999999999999999999


Q ss_pred             hhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         145 ESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       145 r~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      |+||+||.|++|.++.+++..|...++++.+
T Consensus       350 R~gr~gr~grkg~~in~v~~~d~~~lk~ie~  380 (397)
T KOG0327|consen  350 RIGRAGRFGRKGVAINFVTEEDVRDLKDIEK  380 (397)
T ss_pred             hcccccccCCCceeeeeehHhhHHHHHhHHH
Confidence            9999999999999999999998887776653

>KOG0346|consensus

Probab=99.82  E-value=1.6e-19  Score=157.03  Aligned_cols=159  Identities=17%  Similarity=0.260  Sum_probs=120.3

Q ss_pred             hHHHHHHHhhhccCchh-HHHHhhCCCCCcEEEEEe-eccC--CCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEE
Q psy4494           5 LYTIAYLNLWRTSFYQV-SIAFGLGIDKPNVRFVIH-HCLS--KSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGI   80 (234)
Q Consensus         5 ~~~~a~l~l~~at~p~~-~i~~~~~~~~~~i~~~~~-~~~~--~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~i   80 (234)
                      +.+..|.-|.|||+.+. ..+..+-...|.+ .... ...+  +.+.+|+.. ..   ..+++..++.+++-.+-.++.|
T Consensus       198 LPr~~Q~~LmSATl~dDv~~LKkL~l~nPvi-Lkl~e~el~~~dqL~Qy~v~-cs---e~DKflllyallKL~LI~gKsl  272 (569)
T KOG0346|consen  198 LPRIYQCFLMSATLSDDVQALKKLFLHNPVI-LKLTEGELPNPDQLTQYQVK-CS---EEDKFLLLYALLKLRLIRGKSL  272 (569)
T ss_pred             CCchhhheeehhhhhhHHHHHHHHhccCCeE-EEeccccCCCcccceEEEEE-ec---cchhHHHHHHHHHHHHhcCceE
Confidence            45566777788888764 3333344455544 3222 2222  333444443 33   3456666777766555678899


Q ss_pred             EEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------------------------------------
Q psy4494          81 IYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------------------------------------  114 (234)
Q Consensus        81 If~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------------------------------------  114 (234)
                      ||+||++.|-++--.|+..|++...++|.++...                                              
T Consensus       273 iFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkk  352 (569)
T KOG0346|consen  273 IFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKK  352 (569)
T ss_pred             EEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccc
Confidence            9999999999999999999999999999988654                                              


Q ss_pred             -------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         115 -------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       115 -------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                             ....+||||+.+|..|+|||+|.+.++|+||+||++|++++|.++.|+.|.+..
T Consensus       353 skkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P~e~~  413 (569)
T KOG0346|consen  353 SKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSPKEEF  413 (569)
T ss_pred             cccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecchHHh
Confidence                   345689999999999999999999999999999999999999999999987655

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=4.6e-19  Score=164.58  Aligned_cols=110  Identities=24%  Similarity=0.220  Sum_probs=97.5

Q ss_pred             hHHHHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...|.+++.... .+.++||||+|++.++.++..|...|+++..+||.+++.+                |+.+|||
T Consensus       455 ~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~rE~~ii~~ag~~g~VlVATdmAgRG  534 (656)
T PRK12898        455 AAAKWAAVAARVRELHAQGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDAEEAAIVARAGQRGRITVATNMAGRG  534 (656)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHHHHHHHHHHcCCCCcEEEEccchhcc
Confidence            4567777887776422 3578999999999999999999999999999999987655                9999999


Q ss_pred             CCCC---Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         122 IDKP---NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       122 id~~---~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      +|++   +|.     +||||++|.+...|.||+||+||.|.+|.+++|++.+|..
T Consensus       535 tDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD~l  589 (656)
T PRK12898        535 TDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLEDDL  589 (656)
T ss_pred             cCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhHHH
Confidence            9999   776     9999999999999999999999999999999999987743

>KOG0334|consensus

Probab=99.80  E-value=4.6e-19  Score=167.48  Aligned_cols=164  Identities=15%  Similarity=0.293  Sum_probs=132.5

Q ss_pred             HHHHHHhhhccCchhHHHHh-hCCCCC-cEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEec
Q psy4494           7 TIAYLNLWRTSFYQVSIAFG-LGIDKP-NVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTT   84 (234)
Q Consensus         7 ~~a~l~l~~at~p~~~i~~~-~~~~~~-~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~   84 (234)
                      +--|+-+||+|||....... .-..+| .|.+..+....+.+++.+.|...   +.+++..|.++|.......++||||.
T Consensus       545 pdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~---e~eKf~kL~eLl~e~~e~~~tiiFv~  621 (997)
T KOG0334|consen  545 PDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAI---ENEKFLKLLELLGERYEDGKTIIFVD  621 (997)
T ss_pred             hhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecC---chHHHHHHHHHHHHHhhcCCEEEEEc
Confidence            34578899999999733222 222344 34444455666677777777542   34577777778776667889999999


Q ss_pred             chHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhh
Q psy4494          85 SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQES  146 (234)
Q Consensus        85 t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~  146 (234)
                      +...|..+...|.+.|+.+..+||+.++.+                  |+.+++|+|++++.+|||||+|....+|+||+
T Consensus       622 ~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~  701 (997)
T KOG0334|consen  622 KQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRV  701 (997)
T ss_pred             CchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHh
Confidence            999999999999999999999999999966                  99999999999999999999999999999999


Q ss_pred             cccccCCCceEEEEEeecccHHHhhhh
Q psy4494         147 GRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       147 GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      ||+||+|++|.|++|+.+.+......+
T Consensus       702 gRTgragrkg~AvtFi~p~q~~~a~dl  728 (997)
T KOG0334|consen  702 GRTGRAGRKGAAVTFITPDQLKYAGDL  728 (997)
T ss_pred             cccccCCccceeEEEeChHHhhhHHHH
Confidence            999999999999999999665544333

>KOG0339|consensus

Probab=99.80  E-value=5.8e-19  Score=155.96  Aligned_cols=163  Identities=17%  Similarity=0.194  Sum_probs=127.5

Q ss_pred             HHHhhhccCchh--HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchH
Q psy4494          10 YLNLWRTSFYQV--SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIK   87 (234)
Q Consensus        10 ~l~l~~at~p~~--~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~   87 (234)
                      |.-+|++||+..  ..+...-.++.++...-...-..-+.+...|.+   +...|+.+|..-|-.....+++|||+..+.
T Consensus       403 QtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~---s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~  479 (731)
T KOG0339|consen  403 QTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCP---SEEKKLNWLLRHLVEFSSEGKVLIFVTKKA  479 (731)
T ss_pred             eEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeecc---CcHHHHHHHHHHhhhhccCCcEEEEEeccC
Confidence            345699999885  233333345544332222222333334444433   345688888887766556789999999999


Q ss_pred             HHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccc
Q psy4494          88 ECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus        88 ~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      .+++++..|+..++.+..+||+|++.+                  |++..||+|+++++.|||||+-.+++.|.||+||+
T Consensus       480 ~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrt  559 (731)
T KOG0339|consen  480 DAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRT  559 (731)
T ss_pred             CHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhc
Confidence            999999999999999999999998876                  99999999999999999999999999999999999


Q ss_pred             ccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         150 GRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      ||+|..|++++++++.|....-.++.
T Consensus       560 gRag~kGvayTlvTeKDa~fAG~LVn  585 (731)
T KOG0339|consen  560 GRAGEKGVAYTLVTEKDAEFAGHLVN  585 (731)
T ss_pred             ccccccceeeEEechhhHHHhhHHHH
Confidence            99999999999999999876555554

>KOG4284|consensus

Probab=99.80  E-value=1.1e-19  Score=164.33  Aligned_cols=160  Identities=17%  Similarity=0.265  Sum_probs=127.8

Q ss_pred             HHHHHHHhhhccCchh--HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCCh----HHHHHHHHHHHHhhcCCCcE
Q psy4494           6 YTIAYLNLWRTSFYQV--SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQ----KDCLDELADLMSRRFRNQSG   79 (234)
Q Consensus         6 ~~~a~l~l~~at~p~~--~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~----~~~~~~l~~~l~~~~~~~~~   79 (234)
                      ...-|...||||.|+-  .......-++.-|++.....-.-.+.+||.+.+.+...    ..++..|-+++. ..+...+
T Consensus       197 P~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~-~ipy~QA  275 (980)
T KOG4284|consen  197 PQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFK-SIPYVQA  275 (980)
T ss_pred             chhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHh-hCchHHH
Confidence            3344566789999985  22333333555577665554455677888776665432    235566666665 3466789


Q ss_pred             EEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhH
Q psy4494          80 IIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMEN  141 (234)
Q Consensus        80 iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~  141 (234)
                      ||||+....|+-++.+|.+.|+++..+.|.|++.+                  |+..+||||-++|++|||.|+|.+-++
T Consensus       276 lVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eT  355 (980)
T KOG4284|consen  276 LVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEET  355 (980)
T ss_pred             HhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHH
Confidence            99999999999999999999999999999999988                  999999999999999999999999999


Q ss_pred             hhhhhcccccCCCceEEEEEeeccc
Q psy4494         142 FYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       142 y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      |+||+|||||.|..|.+|+|.....
T Consensus       356 Y~HRIGRAgRFG~~G~aVT~~~~~~  380 (980)
T KOG4284|consen  356 YFHRIGRAGRFGAHGAAVTLLEDER  380 (980)
T ss_pred             HHHHhhhcccccccceeEEEeccch
Confidence            9999999999999999999997653

>KOG0347|consensus

Probab=99.79  E-value=7.9e-20  Score=162.67  Aligned_cols=98  Identities=21%  Similarity=0.299  Sum_probs=93.0

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCC
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSK  137 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~  137 (234)
                      ++++|||||+++.+.+|+..|...+++...+|+.|.+++                  |++++||+|||+|+|||||..|.
T Consensus       463 PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPr  542 (731)
T KOG0347|consen  463 PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPR  542 (731)
T ss_pred             CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCC
Confidence            788999999999999999999999999999999999987                  99999999999999999999999


Q ss_pred             CHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         138 SMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       138 ~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      +.+-|+||.||+.|++..|.++++..|.+...+.++
T Consensus       543 tseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL  578 (731)
T KOG0347|consen  543 TSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKL  578 (731)
T ss_pred             ccceeEecccccccccCCCeEEEEeChHHhHHHHHH
Confidence            999999999999999999999999999887655544

>KOG0350|consensus

Probab=99.78  E-value=7.7e-19  Score=154.89  Aligned_cols=167  Identities=19%  Similarity=0.214  Sum_probs=127.3

Q ss_pred             hHHHHHHHhhhccCchhHH-HHhhCCCCCcEEEE-----EeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCc
Q psy4494           5 LYTIAYLNLWRTSFYQVSI-AFGLGIDKPNVRFV-----IHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQS   78 (234)
Q Consensus         5 ~~~~a~l~l~~at~p~~~i-~~~~~~~~~~i~~~-----~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~   78 (234)
                      +|..-..-+|++++.+.+. ...+.+.-|.+..+     ..+..|..+.+++.+....    .+...+..++... ...+
T Consensus       357 ~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~----~kpl~~~~lI~~~-k~~r  431 (620)
T KOG0350|consen  357 LYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPK----FKPLAVYALITSN-KLNR  431 (620)
T ss_pred             cCchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeecccc----cchHhHHHHHHHh-hcce
Confidence            3444455567888877642 33344444433322     3466777777777764322    2334455555532 5678


Q ss_pred             EEEEecchHHHHHHHHHHH----HcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecC
Q psy4494          79 GIIYTTSIKECEDLREELR----NRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLS  136 (234)
Q Consensus        79 ~iIf~~t~~~~~~l~~~L~----~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P  136 (234)
                      +|+|+++.+.+.+++..|.    +..+.+..|.|+++.+.                  +++++||||+.+|+.|||||+|
T Consensus       432 ~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~P  511 (620)
T KOG0350|consen  432 TLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDPP  511 (620)
T ss_pred             EEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCCC
Confidence            9999999999999999998    23667788888888765                  9999999999999999999999


Q ss_pred             CCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHHh
Q psy4494         137 KSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       137 ~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      .+..+|+||+||++|+|+.|.|+.+....+...+.+++..
T Consensus       512 ~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~  551 (620)
T KOG0350|consen  512 ASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKK  551 (620)
T ss_pred             chhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHH
Confidence            9999999999999999999999999999998888877654

>KOG0348|consensus

Probab=99.76  E-value=3.7e-18  Score=151.68  Aligned_cols=129  Identities=16%  Similarity=0.191  Sum_probs=102.4

Q ss_pred             ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc---------------------
Q psy4494          41 CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR---------------------   99 (234)
Q Consensus        41 ~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~---------------------   99 (234)
                      ..|..+.+.|.|++..-..-.+...|.+..+ ....+++|||+.+.+.++-=++.|...                     
T Consensus       391 ~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k-~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~  469 (708)
T KOG0348|consen  391 AIPEQLLQRYTVVPPKLRLVALAALLLNKVK-FEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLF  469 (708)
T ss_pred             cCcHHhhhceEecCCchhHHHHHHHHHHHhh-hhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhh
Confidence            3456667788887654332223333333333 234568999999999999888777531                     


Q ss_pred             -CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEE
Q psy4494         100 -GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCIL  160 (234)
Q Consensus       100 -~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~  160 (234)
                       +.+..-+||+|++++                  |++++||+|+|+|++||.||+|.+..+|+||+||+.|.|..|.+++
T Consensus       470 ~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alL  549 (708)
T KOG0348|consen  470 MDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALL  549 (708)
T ss_pred             hcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEE
Confidence             345788999999988                  9999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHh
Q psy4494         161 YYRLPDVFKL  170 (234)
Q Consensus       161 ~~~~~d~~~~  170 (234)
                      |..|.+...+
T Consensus       550 fL~P~Eaey~  559 (708)
T KOG0348|consen  550 FLLPSEAEYV  559 (708)
T ss_pred             EecccHHHHH
Confidence            9999887643

>KOG0337|consensus

Probab=99.75  E-value=9.3e-19  Score=151.66  Aligned_cols=162  Identities=17%  Similarity=0.176  Sum_probs=136.0

Q ss_pred             HHHHHHhhhccCchhHH-HHhhCCCC-CcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEec
Q psy4494           7 TIAYLNLWRTSFYQVSI-AFGLGIDK-PNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTT   84 (234)
Q Consensus         7 ~~a~l~l~~at~p~~~i-~~~~~~~~-~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~   84 (234)
                      .-+|.-+||+|.|+..+ ....|..+ ..||+.+.......++..+..+.+    +++...|..++.+...+++++||+.
T Consensus       194 ~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~----a~K~aaLl~il~~~~~~~~t~vf~~  269 (529)
T KOG0337|consen  194 ESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRK----AEKEAALLSILGGRIKDKQTIVFVA  269 (529)
T ss_pred             CcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeecc----HHHHHHHHHHHhccccccceeEEec
Confidence            33466789999999743 34466644 468988888787777776665433    4567777777776556778999999


Q ss_pred             chHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhh
Q psy4494          85 SIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQES  146 (234)
Q Consensus        85 t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~  146 (234)
                      |+..+|.+...|+..|+.+..++|++++..                  |++++||+|+|..+.|||||+|.+..-|+||+
T Consensus       270 tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRV  349 (529)
T KOG0337|consen  270 TKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRV  349 (529)
T ss_pred             ccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEe
Confidence            999999999999999999999999999876                  99999999999999999999999999999999


Q ss_pred             cccccCCCceEEEEEeecccHHHhhh
Q psy4494         147 GRAGRDGQIAHCILYYRLPDVFKLSS  172 (234)
Q Consensus       147 GR~gR~g~~~~~i~~~~~~d~~~~~~  172 (234)
                      ||+.|+|+.|.++.++.+.|...+.+
T Consensus       350 gr~aragrtg~aYs~V~~~~~~yl~D  375 (529)
T KOG0337|consen  350 GRVARAGRTGRAYSLVASTDDPYLLD  375 (529)
T ss_pred             cchhhccccceEEEEEecccchhhhh
Confidence            99999999999999999987665443

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=8.4e-18  Score=159.20  Aligned_cols=110  Identities=23%  Similarity=0.241  Sum_probs=98.3

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...|.+.+... ..+.++||||+|++.++.++..|...|+++..+||.+.+++                |+.+|||
T Consensus       410 ~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g~VlIATdmAgRG  489 (790)
T PRK09200        410 LDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKGAVTVATNMAGRG  489 (790)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCCeEEEEccchhcC
Confidence            356777777777542 35788999999999999999999999999999999987765                9999999


Q ss_pred             CCC---CCcc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         122 IDK---PNVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       122 id~---~~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      +|+   ++|.     +||||++|.+...|.||+||+||.|.+|.+++|++..|..
T Consensus       490 ~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~l  544 (790)
T PRK09200        490 TDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDDL  544 (790)
T ss_pred             cCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHHH
Confidence            999   6999     9999999999999999999999999999999999986643

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.71  E-value=6.2e-17  Score=152.00  Aligned_cols=153  Identities=16%  Similarity=0.196  Sum_probs=108.2

Q ss_pred             HHHhhhccCchh--HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcC-CC-----hHHHHHHHHHHHHhh--cCCCcE
Q psy4494          10 YLNLWRTSFYQV--SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKP-AA-----QKDCLDELADLMSRR--FRNQSG   79 (234)
Q Consensus        10 ~l~l~~at~p~~--~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~-~~-----~~~~~~~l~~~l~~~--~~~~~~   79 (234)
                      ++-++|||+|..  .+...++ +++.+.+  .......++++|...... ..     ..++. .+...+...  ..++++
T Consensus       323 q~ILmSATl~~dv~~l~~~~~-~p~~I~I--~grt~~pV~~~yi~~~~~~~~~~~y~~~~k~-~~l~~L~~~~~~~~g~i  398 (675)
T PHA02653        323 SLFLMTATLEDDRDRIKEFFP-NPAFVHI--PGGTLFPISEVYVKNKYNPKNKRAYIEEEKK-NIVTALKKYTPPKGSSG  398 (675)
T ss_pred             EEEEEccCCcHhHHHHHHHhc-CCcEEEe--CCCcCCCeEEEEeecCcccccchhhhHHHHH-HHHHHHHHhhcccCCcE
Confidence            577899999864  2222222 3443432  222234556666432210 00     11111 222222211  134689


Q ss_pred             EEEecchHHHHHHHHHHHHc--CCceeeeccCCCchh-----------------hhhcccCCCCCCccEEEEee---cCC
Q psy4494          80 IIYTTSIKECEDLREELRNR--GLRVSAYHAKLESNV-----------------SIAFGLGIDKPNVRFVIHHC---LSK  137 (234)
Q Consensus        80 iIf~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~-----------------T~~~~~Gid~~~v~~Vi~~~---~P~  137 (234)
                      |||++++++++.+++.|.+.  ++.+..+||++++.+                 |+.+++|+|+|+|++||++|   .|.
T Consensus       399 LVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~  478 (675)
T PHA02653        399 IVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNIDEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPE  478 (675)
T ss_pred             EEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHHHHHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCCC
Confidence            99999999999999999987  789999999999753                 99999999999999999999   665


Q ss_pred             ---------CHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         138 ---------SMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       138 ---------~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                               +..+|.||+|||||. ++|.|+.+++..+.
T Consensus       479 ~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        479 PFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             cccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence                     778999999999999 78999999998775

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.69  E-value=5.8e-16  Score=149.98  Aligned_cols=91  Identities=27%  Similarity=0.400  Sum_probs=84.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEee
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHC  134 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~  134 (234)
                      .+++++||||+++.++.+++.|+..  ++++..+||+|++++                  |+++++|+|+|++++||+++
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VIi~~  738 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIER  738 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEEEec
Confidence            4678999999999999999999985  788999999999876                  99999999999999999999


Q ss_pred             cCC-CHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         135 LSK-SMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       135 ~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      .|. +..+|+||+||+||.|+.|.|++++++.
T Consensus       739 a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       739 ADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             CCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            976 6789999999999999999999999764

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.67  E-value=3.1e-16  Score=147.58  Aligned_cols=109  Identities=19%  Similarity=0.204  Sum_probs=96.9

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+.+.+. ..+.++||||+|++.++.++..|...|+++..+||.+++++                |+.+|||
T Consensus       406 ~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g~VlIATdmAgRG  485 (762)
T TIGR03714       406 LPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKGAVTVATSMAGRG  485 (762)
T ss_pred             HHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCCeEEEEccccccc
Confidence            356777777776542 35789999999999999999999999999999999999766                9999999


Q ss_pred             CCCC---------CccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         122 IDKP---------NVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       122 id~~---------~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      +|++         ++.+|++|++|....+ .||+||+||.|.+|.+++|++..|..
T Consensus       486 tDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~l  540 (762)
T TIGR03714       486 TDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDDL  540 (762)
T ss_pred             cCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchhh
Confidence            9999         9999999999988777 99999999999999999999987643

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.67  E-value=2.9e-16  Score=151.88  Aligned_cols=104  Identities=17%  Similarity=0.189  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHH-HcCCceeeeccCCCchh--------------------hhhc
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELR-NRGLRVSAYHAKLESNV--------------------SIAF  118 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~-~~~~~~~~~h~~~~~~~--------------------T~~~  118 (234)
                      +.|+..|.++++. ..+.++||||++++.+..+++.|+ ..|+++..+||+|++.+                    |++.
T Consensus       478 d~Ki~~L~~~L~~-~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvg  556 (956)
T PRK04914        478 DPRVEWLIDFLKS-HRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIG  556 (956)
T ss_pred             CHHHHHHHHHHHh-cCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhh
Confidence            3466777777764 357899999999999999999995 56999999999999866                    8999


Q ss_pred             ccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         119 GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       119 ~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      |+|+|++.+++|||||+|+++..|.||+||+||.|+++.+.+++..
T Consensus       557 seGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~  602 (956)
T PRK04914        557 SEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPY  602 (956)
T ss_pred             ccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEcc
Confidence            9999999999999999999999999999999999999877666644

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.66  E-value=6.4e-16  Score=136.18  Aligned_cols=88  Identities=13%  Similarity=0.253  Sum_probs=74.2

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCC--ceeeeccCCCchh----------------------hhhcccCCCCCCccEE
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGL--RVSAYHAKLESNV----------------------SIAFGLGIDKPNVRFV  130 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~--~~~~~h~~~~~~~----------------------T~~~~~Gid~~~v~~V  130 (234)
                      .++++||||+|++.++.++..|++.+.  .+..+||++++.+                      |+++++|+|++ ++.|
T Consensus       221 ~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~v  299 (358)
T TIGR01587       221 KGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVM  299 (358)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEE
Confidence            568899999999999999999998766  4999999997643                      99999999996 8899


Q ss_pred             EEeecCCCHhHhhhhhcccccCCCc----eEEEEEeecc
Q psy4494         131 IHHCLSKSMENFYQESGRAGRDGQI----AHCILYYRLP  165 (234)
Q Consensus       131 i~~~~P~~~~~y~qr~GR~gR~g~~----~~~i~~~~~~  165 (234)
                      |++..|  +++|+||+||+||.|+.    |..++|....
T Consensus       300 i~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       300 ITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             EEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence            998776  78999999999998764    3555555443

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.65  E-value=3.1e-15  Score=147.79  Aligned_cols=91  Identities=20%  Similarity=0.255  Sum_probs=80.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEee
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHC  134 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~  134 (234)
                      .+++++||||+++.++.+++.|.+.  ++.+..+||+|++++                  |+++++|+|+|+|++||..+
T Consensus       808 r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi~~  887 (1147)
T PRK10689        808 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  887 (1147)
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEEec
Confidence            4678999999999999999999987  788999999999876                  99999999999999999544


Q ss_pred             cC-CCHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         135 LS-KSMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       135 ~P-~~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      .. -++.+|+||+||+||.|+.|.|+++++..
T Consensus       888 ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        888 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             CCCCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            32 25567999999999999999999998653

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.64  E-value=8.9e-16  Score=149.09  Aligned_cols=97  Identities=27%  Similarity=0.432  Sum_probs=80.4

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc------CCceeeeccCCCchh------------------hhhc
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR------GLRVSAYHAKLESNV------------------SIAF  118 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~------~~~~~~~h~~~~~~~------------------T~~~  118 (234)
                      ...+.+++.   ..+++||||||++.|+.++..|+..      +..+..+||++++++                  |+++
T Consensus       274 ~~~L~~~i~---~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~L  350 (876)
T PRK13767        274 YETLHELIK---EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSL  350 (876)
T ss_pred             HHHHHHHHh---cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChH
Confidence            334444443   3578999999999999999999873      467999999999876                  9999


Q ss_pred             ccCCCCCCccEEEEeecCCCHhHhhhhhcccccC-CCceEEEEEe
Q psy4494         119 GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRD-GQIAHCILYY  162 (234)
Q Consensus       119 ~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~-g~~~~~i~~~  162 (234)
                      ++|||+|+|++||+|+.|.++.+|+||+||+||. |..+.++++.
T Consensus       351 e~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~  395 (876)
T PRK13767        351 ELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIV  395 (876)
T ss_pred             HhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEE
Confidence            9999999999999999999999999999999985 4444444444

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.64  E-value=1.4e-15  Score=145.78  Aligned_cols=155  Identities=16%  Similarity=0.154  Sum_probs=108.9

Q ss_pred             HHHhhhccCchhHHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHH-HHHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          10 YLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKD-CLDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~-~~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      ++-++|||++...+...++ +.+.|...   .....++++|........... ....+..++..  ..+.+|||++++++
T Consensus       148 qlIlmSATl~~~~l~~~l~-~~~vI~~~---gr~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~~e  221 (819)
T TIGR01970       148 KILAMSATLDGERLSSLLP-DAPVVESE---GRSFPVEIRYLPLRGDQRLEDAVSRAVEHALAS--ETGSILVFLPGQAE  221 (819)
T ss_pred             eEEEEeCCCCHHHHHHHcC-CCcEEEec---CcceeeeeEEeecchhhhHHHHHHHHHHHHHHh--cCCcEEEEECCHHH
Confidence            3456788888664433332 23333321   112235566654322111111 12234444432  35789999999999


Q ss_pred             HHHHHHHHHH---cCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCC---------
Q psy4494          89 CEDLREELRN---RGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKS---------  138 (234)
Q Consensus        89 ~~~l~~~L~~---~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~---------  138 (234)
                      ++.+++.|++   .++.+..+||++++++                  |+++++|||+|+|++||++|+|..         
T Consensus       222 I~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~  301 (819)
T TIGR01970       222 IRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGI  301 (819)
T ss_pred             HHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCC
Confidence            9999999987   4788999999999866                  999999999999999999999863         


Q ss_pred             ---------HhHhhhhhcccccCCCceEEEEEeecccHHHhh
Q psy4494         139 ---------MENFYQESGRAGRDGQIAHCILYYRLPDVFKLS  171 (234)
Q Consensus       139 ---------~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~  171 (234)
                               -.+|.||+||+||. .+|.|+.+|+..++..+.
T Consensus       302 ~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~~l~  342 (819)
T TIGR01970       302 TRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQRLP  342 (819)
T ss_pred             ceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHHhhh
Confidence                     23589999999999 899999999987765443

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

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

Probab=99.64  E-value=3.1e-15  Score=112.38  Aligned_cols=101  Identities=34%  Similarity=0.491  Sum_probs=88.7

Q ss_pred             HHHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          61 DCLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        61 ~~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      .+...+.+++.+.. ..+++||||++.+.++.+++.|...+..+..+||++++.+                  |.++++|
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G   91 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARG   91 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcC
Confidence            46666777766432 4678999999999999999999988889999999998765                  8899999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEE
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY  161 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~  161 (234)
                      +|+|++++||.++.|++...|.|++||++|.|+.|.++++
T Consensus        92 ~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          92 IDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             cChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            9999999999999999999999999999999988876653

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.64  E-value=1.8e-15  Score=151.05  Aligned_cols=90  Identities=27%  Similarity=0.380  Sum_probs=77.4

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcC---------------------------------CceeeeccCCCchh-------
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRG---------------------------------LRVSAYHAKLESNV-------  114 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~---------------------------------~~~~~~h~~~~~~~-------  114 (234)
                      ...++||||||++.||.++..|++..                                 ..+..+||++++++       
T Consensus       243 ~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~  322 (1490)
T PRK09751        243 RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQA  322 (1490)
T ss_pred             cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHH
Confidence            46789999999999999999997531                                 12578999999987       


Q ss_pred             -----------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccC-CCceEEEEEeec
Q psy4494         115 -----------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRD-GQIAHCILYYRL  164 (234)
Q Consensus       115 -----------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~-g~~~~~i~~~~~  164 (234)
                                 |+++++|||+++|++||||+.|.++.+|+||+||+||. |..+.++++...
T Consensus       323 fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~~  384 (1490)
T PRK09751        323 LKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPRT  384 (1490)
T ss_pred             HHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeCc
Confidence                       99999999999999999999999999999999999995 555666755544

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.63  E-value=1.3e-15  Score=143.88  Aligned_cols=109  Identities=23%  Similarity=0.259  Sum_probs=97.7

Q ss_pred             hHHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+.+.. ...+.|+||||+|+..++.++..|.+.|++...+||.+.+.+                |+.+|||
T Consensus       422 ~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~VtIATnmAGRG  501 (796)
T PRK12906        422 LDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGAVTIATNMAGRG  501 (796)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCceEEEEeccccCC
Confidence            35677777777753 235789999999999999999999999999999999988766                9999999


Q ss_pred             CCCC---Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         122 IDKP---NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       122 id~~---~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      +||+   +|.     +||+++.|.+...|.|++||+||.|.+|.+.+|++.+|-
T Consensus       502 tDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~  555 (796)
T PRK12906        502 TDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  555 (796)
T ss_pred             CCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccch
Confidence            9994   899     999999999999999999999999999999999998763

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.63  E-value=5.7e-15  Score=138.91  Aligned_cols=98  Identities=24%  Similarity=0.321  Sum_probs=87.4

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEee--
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHC--  134 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~--  134 (234)
                      .+.++||||+|++.++.+++.|.+.|+++..+||++++.+                  |+.+++|+|+|++++||++|  
T Consensus       441 ~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lVvi~Dad  520 (655)
T TIGR00631       441 RNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDAD  520 (655)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEEEEeCcc
Confidence            4678999999999999999999999999999999988643                  88999999999999999998  


Q ss_pred             ---cCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         135 ---LSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       135 ---~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                         .|.+..+|+||+||+||. ..|.+++|++..+......+
T Consensus       521 ifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~ai  561 (655)
T TIGR00631       521 KEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQKAI  561 (655)
T ss_pred             cccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHHHH
Confidence               799999999999999998 57999999987765544433

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

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.62  E-value=2.2e-15  Score=144.66  Aligned_cols=153  Identities=17%  Similarity=0.209  Sum_probs=108.2

Q ss_pred             HHHhhhccCchhHHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHH-HHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          10 YLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDC-LDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~-~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      ++-++|||++...+...++ +.+.+...   .....++.+|..........+. ...+..++..  ..+.+|||++++++
T Consensus       151 qlilmSATl~~~~l~~~~~-~~~~I~~~---gr~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~--~~g~iLVFlpg~~e  224 (812)
T PRK11664        151 KLLIMSATLDNDRLQQLLP-DAPVIVSE---GRSFPVERRYQPLPAHQRFDEAVARATAELLRQ--ESGSLLLFLPGVGE  224 (812)
T ss_pred             eEEEEecCCCHHHHHHhcC-CCCEEEec---CccccceEEeccCchhhhHHHHHHHHHHHHHHh--CCCCEEEEcCCHHH
Confidence            4567899988754433322 33333221   1122356666532221111111 1234444432  35789999999999


Q ss_pred             HHHHHHHHHH---cCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCH--------
Q psy4494          89 CEDLREELRN---RGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSM--------  139 (234)
Q Consensus        89 ~~~l~~~L~~---~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~--------  139 (234)
                      ++.+++.|+.   .++.+..+||++++++                  |+.+++|||+++|++||++|.|...        
T Consensus       225 i~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~  304 (812)
T PRK11664        225 IQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGL  304 (812)
T ss_pred             HHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCc
Confidence            9999999987   5788999999999865                  9999999999999999998887643        


Q ss_pred             ----------hHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         140 ----------ENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       140 ----------~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                                .+|.||+||+||. .+|.|+.+|+..+...
T Consensus       305 ~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~~~  343 (812)
T PRK11664        305 TRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQAER  343 (812)
T ss_pred             ceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHHhh
Confidence                      4899999999999 6999999999877654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.62  E-value=3.5e-15  Score=139.94  Aligned_cols=110  Identities=25%  Similarity=0.294  Sum_probs=94.7

Q ss_pred             hHHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+.+.+ ...+.|+||||+|++.++.++..|.+.|++...+||.....+                |+.+|||
T Consensus       387 ~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~q~~rEa~ii~~ag~~g~VtIATnmAgRG  466 (745)
T TIGR00963       387 EEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAKNHEREAEIIAQAGRKGAVTIATNMAGRG  466 (745)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCChHHHHHHHHHhcCCCceEEEEeccccCC
Confidence            34566666665532 336889999999999999999999999999999999844433                9999999


Q ss_pred             CCCCC--c-----cEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         122 IDKPN--V-----RFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       122 id~~~--v-----~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      +|++.  |     -+||+++.|.+...|.|++||+||.|.+|.+.+|++..|..
T Consensus       467 tDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~l  520 (745)
T TIGR00963       467 TDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDNL  520 (745)
T ss_pred             cCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHHH
Confidence            99998  4     49999999999999999999999999999999999987643

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.61  E-value=4.4e-15  Score=146.18  Aligned_cols=156  Identities=19%  Similarity=0.271  Sum_probs=109.2

Q ss_pred             HHHhhhccCchhHHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCC--hHHHHHHHHHHHHh--hcCCCcEEEEecc
Q psy4494          10 YLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAA--QKDCLDELADLMSR--RFRNQSGIIYTTS   85 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~--~~~~~~~l~~~l~~--~~~~~~~iIf~~t   85 (234)
                      ++-++|||++...+....+ +.|.+.+  ... ...++.+|.......+  ..+.+..+...+..  ...++.+|||+++
T Consensus       220 KvILmSATid~e~fs~~F~-~apvI~V--~Gr-~~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg  295 (1294)
T PRK11131        220 KVIITSATIDPERFSRHFN-NAPIIEV--SGR-TYPVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSG  295 (1294)
T ss_pred             eEEEeeCCCCHHHHHHHcC-CCCEEEE--cCc-cccceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCC
Confidence            4567888887544333332 2333332  211 2235666654322111  23344444443321  1245789999999


Q ss_pred             hHHHHHHHHHHHHcCCc---eeeeccCCCchh----------------hhhcccCCCCCCccEEEEee------------
Q psy4494          86 IKECEDLREELRNRGLR---VSAYHAKLESNV----------------SIAFGLGIDKPNVRFVIHHC------------  134 (234)
Q Consensus        86 ~~~~~~l~~~L~~~~~~---~~~~h~~~~~~~----------------T~~~~~Gid~~~v~~Vi~~~------------  134 (234)
                      +++++.+++.|+..+++   +.++||++++++                |+++++|||+|+|++||++|            
T Consensus       296 ~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~~g~rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~  375 (1294)
T PRK11131        296 EREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQSHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTK  375 (1294)
T ss_pred             HHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcccCCeeEEEeccHHhhccccCcceEEEECCCccccccccccC
Confidence            99999999999988765   678999999866                99999999999999999996            


Q ss_pred             ---cC---CCHhHhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         135 ---LS---KSMENFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       135 ---~P---~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                         +|   .|..+|.||+||+||. .+|.|+.+|+..++...
T Consensus       376 ~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~~~~  416 (1294)
T PRK11131        376 VQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDFLSR  416 (1294)
T ss_pred             cccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHHHhh
Confidence               34   3557999999999999 78999999998877643

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.60  E-value=2e-14  Score=135.69  Aligned_cols=92  Identities=24%  Similarity=0.318  Sum_probs=83.2

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeec-
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCL-  135 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~-  135 (234)
                      .+.++||||+|++.++.++..|...|+++..+||++++.+                  |+.+++|+|+|++++||++|. 
T Consensus       445 ~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVii~d~e  524 (652)
T PRK05298        445 KGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDAD  524 (652)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEEEeCCc
Confidence            4678999999999999999999999999999999988632                  889999999999999999875 


Q ss_pred             ----CCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         136 ----SKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       136 ----P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                          |.+..+|+||+||+||. ..|.+++|++..+.
T Consensus       525 ifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~  559 (652)
T PRK05298        525 KEGFLRSERSLIQTIGRAARN-VNGKVILYADKITD  559 (652)
T ss_pred             ccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCH
Confidence                78999999999999996 68999999986443

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.58  E-value=5.6e-14  Score=133.44  Aligned_cols=99  Identities=20%  Similarity=0.467  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecc--------hHHHHHHHHHHHHc--CCceeeeccCCCchh-----------------
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTS--------IKECEDLREELRNR--GLRVSAYHAKLESNV-----------------  114 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t--------~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~-----------------  114 (234)
                      .+..+.+.+.   .+.+++|||++        ...++.+++.|.+.  ++++..+||+|++++                 
T Consensus       460 ~~~~i~~~~~---~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILV  536 (681)
T PRK10917        460 VYERIREEIA---KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILV  536 (681)
T ss_pred             HHHHHHHHHH---cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            3344444442   56789999985        44667788888876  578999999999877                 


Q ss_pred             -hhhcccCCCCCCccEEEEeecCC-CHhHhhhhhcccccCCCceEEEEEee
Q psy4494         115 -SIAFGLGIDKPNVRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       115 -T~~~~~Gid~~~v~~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                       |+++++|+|+|++++||+++.|. ....|.|++||+||.|.+|.|+++++
T Consensus       537 aT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~  587 (681)
T PRK10917        537 ATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYK  587 (681)
T ss_pred             ECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEEC
Confidence             99999999999999999999997 57788899999999999999999995

>KOG0329|consensus

Probab=99.58  E-value=3.6e-16  Score=128.21  Aligned_cols=144  Identities=15%  Similarity=0.245  Sum_probs=93.2

Q ss_pred             chHHHHHHHhhhccCchh--HHHHhhCCCCCcEEEEEe-eccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEE
Q psy4494           4 LLYTIAYLNLWRTSFYQV--SIAFGLGIDKPNVRFVIH-HCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGI   80 (234)
Q Consensus         4 ~~~~~a~l~l~~at~p~~--~i~~~~~~~~~~i~~~~~-~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~i   80 (234)
                      .+.+-.|..+|++|+++.  ++.....-||-.|-+.-. .-....+++||.- -+...+..++..|.+.+    .-..++
T Consensus       213 ~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~Yvk-Lke~eKNrkl~dLLd~L----eFNQVv  287 (387)
T KOG0329|consen  213 MTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVK-LKENEKNRKLNDLLDVL----EFNQVV  287 (387)
T ss_pred             cCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHh-hhhhhhhhhhhhhhhhh----hhccee
Confidence            334445556677777664  444444445544332211 1222344555543 22222333444454444    345699


Q ss_pred             EEecchHHHHHHHHHHHHcCCceeeeccCCCchhhhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEE
Q psy4494          81 IYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCIL  160 (234)
Q Consensus        81 If~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~  160 (234)
                      ||+.|.....     ++          ..  --.|+.+|||+|+..|+.|+|||+|.+.++|+||+|||||.|.+|.+|.
T Consensus       288 IFvKsv~Rl~-----f~----------kr--~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglait  350 (387)
T KOG0329|consen  288 IFVKSVQRLS-----FQ----------KR--LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAIT  350 (387)
T ss_pred             Eeeehhhhhh-----hh----------hh--hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceee
Confidence            9998877622     11          11  0129999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHH
Q psy4494         161 YYRLPDVFK  169 (234)
Q Consensus       161 ~~~~~d~~~  169 (234)
                      |++..+...
T Consensus       351 fvs~e~da~  359 (387)
T KOG0329|consen  351 FVSDENDAK  359 (387)
T ss_pred             hhcchhhHH
Confidence            998765443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.56  E-value=8.5e-14  Score=131.23  Aligned_cols=89  Identities=24%  Similarity=0.470  Sum_probs=78.6

Q ss_pred             CCCcEEEEecch--------HHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCC
Q psy4494          75 RNQSGIIYTTSI--------KECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPN  126 (234)
Q Consensus        75 ~~~~~iIf~~t~--------~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~  126 (234)
                      .+.+++|||++.        ..++.+++.|.+.  ++.+..+||+|++++                  |+++++|+|+|+
T Consensus       447 ~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~  526 (630)
T TIGR00643       447 KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN  526 (630)
T ss_pred             hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCC
Confidence            467899999875        5677888888764  778999999999876                  999999999999


Q ss_pred             ccEEEEeecCC-CHhHhhhhhcccccCCCceEEEEEee
Q psy4494         127 VRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       127 v~~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                      +++||+++.|. +...|.|++||+||.|++|.|++++.
T Consensus       527 v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~  564 (630)
T TIGR00643       527 ATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK  564 (630)
T ss_pred             CcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEEC
Confidence            99999999997 67788899999999999999999983

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

Probab=99.55  E-value=3.1e-14  Score=135.43  Aligned_cols=85  Identities=16%  Similarity=0.255  Sum_probs=71.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------------------------hhhccc
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------------------------SIAFGL  120 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------------------------T~~~~~  120 (234)
                      .++++||||||++.++.+++.|++.++  ..+||+|++.+                                  |+++++
T Consensus       271 ~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaer  348 (844)
T TIGR02621       271 SGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEV  348 (844)
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchhhh
Confidence            467899999999999999999998886  88999876521                                  788899


Q ss_pred             CCCCCCccEEEEeecCCCHhHhhhhhcccccCCCc-eEEEEEeec
Q psy4494         121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQI-AHCILYYRL  164 (234)
Q Consensus       121 Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~-~~~i~~~~~  164 (234)
                      |+|++. ++||++..|  .++|+||+||+||.|+. +.++.++..
T Consensus       349 GLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       349 GVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             cccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence            999996 899998776  68999999999999885 444555543

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.53  E-value=2e-14  Score=137.24  Aligned_cols=110  Identities=24%  Similarity=0.307  Sum_probs=94.6

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...|.+.+... ..+.|+||||+|++.++.++..|...|++...+|+.....+                |+.+|||
T Consensus       580 ~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLnakq~~REa~Iia~AG~~g~VtIATNMAGRG  659 (1025)
T PRK12900        580 RREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNAKQHDREAEIVAEAGQKGAVTIATNMAGRG  659 (1025)
T ss_pred             HHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecCCHHHhHHHHHHhcCCCCeEEEeccCcCCC
Confidence            456777888777532 35789999999999999999999999999999998654443                9999999


Q ss_pred             CCCC---Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         122 IDKP---NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       122 id~~---~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      +||+   +|.     +||++..|.+...|.|++||+||.|.+|.+++|++..|..
T Consensus       660 tDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~L  714 (1025)
T PRK12900        660 TDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDEL  714 (1025)
T ss_pred             CCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHHH
Confidence            9999   564     4599999999999999999999999999999999987654

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

Probab=99.51  E-value=2.2e-13  Score=121.07  Aligned_cols=107  Identities=18%  Similarity=0.267  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHhhc---CCCcEEEEecchHHHHHHHHHHHHcCCcee-eecc--------CCCchh---------------
Q psy4494          62 CLDELADLMSRRF---RNQSGIIYTTSIKECEDLREELRNRGLRVS-AYHA--------KLESNV---------------  114 (234)
Q Consensus        62 ~~~~l~~~l~~~~---~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~-~~h~--------~~~~~~---------------  114 (234)
                      |++.+.+++++.+   .+.++|||++.++.++.+++.|...+..+. .|-|        ||++.+               
T Consensus       349 Kl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nV  428 (542)
T COG1111         349 KLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNV  428 (542)
T ss_pred             cHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCceE
Confidence            4555555555443   467999999999999999999999988774 3433        577765               


Q ss_pred             ---hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         115 ---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                         |++...|+|+|+++.||.|++-.|.-.++||.||+||. ++|..++++..++...
T Consensus       429 LVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gtrde  485 (542)
T COG1111         429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGTRDE  485 (542)
T ss_pred             EEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCchHH
Confidence               99999999999999999999999999999999999998 7888999998874443

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.51  E-value=1.5e-13  Score=135.75  Aligned_cols=155  Identities=18%  Similarity=0.229  Sum_probs=107.0

Q ss_pred             HHhhhccCchhHHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCC--hHHHHHHHHHHHHh--hcCCCcEEEEecch
Q psy4494          11 LNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAA--QKDCLDELADLMSR--RFRNQSGIIYTTSI   86 (234)
Q Consensus        11 l~l~~at~p~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~--~~~~~~~l~~~l~~--~~~~~~~iIf~~t~   86 (234)
                      +-++|||+....+....+. .|.|.+.  . ....+..+|........  ..++...+.+.+..  ...++.+|||++++
T Consensus       214 lIlmSATld~~~fa~~F~~-apvI~V~--G-r~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~  289 (1283)
T TIGR01967       214 IIITSATIDPERFSRHFNN-APIIEVS--G-RTYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGE  289 (1283)
T ss_pred             EEEEeCCcCHHHHHHHhcC-CCEEEEC--C-CcccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCH
Confidence            4568888875544444432 3333321  1 12234555543221111  12233333333321  11457899999999


Q ss_pred             HHHHHHHHHHHHcC---CceeeeccCCCchh----------------hhhcccCCCCCCccEEEEeecCC----------
Q psy4494          87 KECEDLREELRNRG---LRVSAYHAKLESNV----------------SIAFGLGIDKPNVRFVIHHCLSK----------  137 (234)
Q Consensus        87 ~~~~~l~~~L~~~~---~~~~~~h~~~~~~~----------------T~~~~~Gid~~~v~~Vi~~~~P~----------  137 (234)
                      ++++.+++.|++.+   +.+.++||++++++                |+++++|||+|+|++||++|++.          
T Consensus       290 ~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~  369 (1283)
T TIGR01967       290 REIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKV  369 (1283)
T ss_pred             HHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCCCCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCc
Confidence            99999999999764   45889999999866                99999999999999999999543          


Q ss_pred             --------CHhHhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         138 --------SMENFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       138 --------~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                              |..+|.||.||+||.| +|.|+.+|+..++...
T Consensus       370 ~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~~~~  409 (1283)
T TIGR01967       370 QRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDFNSR  409 (1283)
T ss_pred             cccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHHHhh
Confidence                    5579999999999998 9999999998877543

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.51  E-value=3e-13  Score=130.48  Aligned_cols=106  Identities=18%  Similarity=0.282  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHhh---cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccC--------CCchh---------------
Q psy4494          61 DCLDELADLMSRR---FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAK--------LESNV---------------  114 (234)
Q Consensus        61 ~~~~~l~~~l~~~---~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~--------~~~~~---------------  114 (234)
                      .|+..|.+++.+.   ..+.++||||++++.++.+++.|...|+.+..+||.        +++.+               
T Consensus       347 pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~v  426 (773)
T PRK13766        347 PKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNV  426 (773)
T ss_pred             hHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCE
Confidence            3566666666542   357899999999999999999999999999999986        66543               


Q ss_pred             ---hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         115 ---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                         |+++++|+|+|++++||+||+|++...|+||+||+||.|. |.+++++.....
T Consensus       427 LvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~t~  481 (773)
T PRK13766        427 LVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKGTR  481 (773)
T ss_pred             EEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCCCh
Confidence               9999999999999999999999999999999999999876 666777765443

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.49  E-value=4.4e-13  Score=118.38  Aligned_cols=73  Identities=21%  Similarity=0.363  Sum_probs=65.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcC--CceeeeccCCCchh------------hhhcccCCCCCCccEEEEeecCCCHh
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRG--LRVSAYHAKLESNV------------SIAFGLGIDKPNVRFVIHHCLSKSME  140 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~--~~~~~~h~~~~~~~------------T~~~~~Gid~~~v~~Vi~~~~P~~~~  140 (234)
                      +++++||||||++.++.++..|++.+  +.+..+||.+++.+            |++++||+|++.+ .|| ++ |.+.+
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~  347 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERAMQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAA  347 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHhccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHH
Confidence            46789999999999999999999864  57888999998866            9999999999987 666 55 99999


Q ss_pred             Hhhhhhcccc
Q psy4494         141 NFYQESGRAG  150 (234)
Q Consensus       141 ~y~qr~GR~g  150 (234)
                      +|+||+||+|
T Consensus       348 ~yiqR~GR~g  357 (357)
T TIGR03158       348 AFWQRLGRLG  357 (357)
T ss_pred             HHhhhcccCC
Confidence            9999999997

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.

>PRK02362 ski2-like helicase; Provisional

Probab=99.48  E-value=1.3e-13  Score=132.17  Aligned_cols=101  Identities=19%  Similarity=0.274  Sum_probs=83.9

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcC------------------------------------Cceee
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRG------------------------------------LRVSA  105 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~------------------------------------~~~~~  105 (234)
                      .+..+.+.+.   .++++||||+|++.|+.++..|....                                    ..+.+
T Consensus       232 ~~~~~~~~~~---~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~  308 (737)
T PRK02362        232 TLNLVLDTLE---EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAF  308 (737)
T ss_pred             HHHHHHHHHH---cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEe
Confidence            4444444443   46789999999999999998886431                                    24788


Q ss_pred             eccCCCchh------------------hhhcccCCCCCCccEEEE----ee-----cCCCHhHhhhhhcccccCCCc--e
Q psy4494         106 YHAKLESNV------------------SIAFGLGIDKPNVRFVIH----HC-----LSKSMENFYQESGRAGRDGQI--A  156 (234)
Q Consensus       106 ~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~----~~-----~P~~~~~y~qr~GR~gR~g~~--~  156 (234)
                      +||++++++                  |+++++|+|+|.+++||+    ||     .|.+..+|+||+|||||.|..  |
T Consensus       309 hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G  388 (737)
T PRK02362        309 HHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYG  388 (737)
T ss_pred             ecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCc
Confidence            999999987                  999999999999999997    76     688999999999999998865  9


Q ss_pred             EEEEEeecc
Q psy4494         157 HCILYYRLP  165 (234)
Q Consensus       157 ~~i~~~~~~  165 (234)
                      .++++....
T Consensus       389 ~~ii~~~~~  397 (737)
T PRK02362        389 EAVLLAKSY  397 (737)
T ss_pred             eEEEEecCc
Confidence            999998764

>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=99.48  E-value=5.1e-14  Score=97.11  Aligned_cols=60  Identities=33%  Similarity=0.496  Sum_probs=56.3

Q ss_pred             HHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCC
Q psy4494          94 EELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDG  153 (234)
Q Consensus        94 ~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g  153 (234)
                      +.|+..++.+..+||++++++                  |+++++|+|+|++++||++++|++...|.|++||+||.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            367888999999999998877                  999999999999999999999999999999999999987

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 ....

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

Probab=99.47  E-value=2.3e-13  Score=129.01  Aligned_cols=102  Identities=25%  Similarity=0.425  Sum_probs=89.6

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcC-CceeeeccCCCchh------------------hhhccc
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRG-LRVSAYHAKLESNV------------------SIAFGL  120 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~------------------T~~~~~  120 (234)
                      ......+.++++   ....+|||+||+..+|.++..|++.+ ..+...||+++.+.                  |+.+..
T Consensus       240 ~~~~~~i~~~v~---~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLEL  316 (814)
T COG1201         240 AALYERIAELVK---KHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLEL  316 (814)
T ss_pred             HHHHHHHHHHHh---hcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhh
Confidence            345666777776   34589999999999999999999886 78999999999877                  999999


Q ss_pred             CCCCCCccEEEEeecCCCHhHhhhhhccccc-CCCceEEEEEeec
Q psy4494         121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGR-DGQIAHCILYYRL  164 (234)
Q Consensus       121 Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR-~g~~~~~i~~~~~  164 (234)
                      |||+.+|+.||+|+.|.++...+||+||+|. -|..+.++++...
T Consensus       317 GIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         317 GIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             ccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            9999999999999999999999999999996 6777888887765

>PRK14701 reverse gyrase; Provisional

Probab=99.45  E-value=1.5e-13  Score=139.32  Aligned_cols=110  Identities=18%  Similarity=0.276  Sum_probs=88.6

Q ss_pred             HHHHHHHHhhcCCCcEEEEecchHH---HHHHHHHHHHcCCceeeeccCCCchh-------------h----hhcccCCC
Q psy4494          64 DELADLMSRRFRNQSGIIYTTSIKE---CEDLREELRNRGLRVSAYHAKLESNV-------------S----IAFGLGID  123 (234)
Q Consensus        64 ~~l~~~l~~~~~~~~~iIf~~t~~~---~~~l~~~L~~~~~~~~~~h~~~~~~~-------------T----~~~~~Gid  123 (234)
                      ..+.+++.. . +..+||||+|++.   |+++++.|...|+++..+||+.....             |    +.++||||
T Consensus       320 ~~L~~ll~~-~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~R~~~l~~F~~G~~~VLVaT~s~~gvaaRGID  397 (1638)
T PRK14701        320 EHVRELLKK-L-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAKNKKGFDLFEEGEIDYLIGVATYYGTLVRGLD  397 (1638)
T ss_pred             HHHHHHHHh-C-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecchHHHHHHHHHcCCCCEEEEecCCCCeeEecCc
Confidence            456666653 2 5679999999886   48999999999999999999743322             6    46789999


Q ss_pred             CCC-ccEEEEeecCC---CHhHhhhhh-------------cccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         124 KPN-VRFVIHHCLSK---SMENFYQES-------------GRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       124 ~~~-v~~Vi~~~~P~---~~~~y~qr~-------------GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      +|+ |++|||||+|.   +++.|.|..             ||+||+|.++.+++.+..++...+..++.
T Consensus       398 iP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~~~~~~~~~~~l~  466 (1638)
T PRK14701        398 LPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFPEDVEFLRSILK  466 (1638)
T ss_pred             cCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHHhHHHHHHHHHHHhc
Confidence            999 99999999999   999888887             99999999988876666666665555543

>KOG0349|consensus

Probab=99.43  E-value=2.2e-13  Score=119.08  Aligned_cols=93  Identities=18%  Similarity=0.374  Sum_probs=85.1

Q ss_pred             cCCCcEEEEecchHHHHHHHHHHHHcC---CceeeeccCCCchh------------------hhhcccCCCCCCccEEEE
Q psy4494          74 FRNQSGIIYTTSIKECEDLREELRNRG---LRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIH  132 (234)
Q Consensus        74 ~~~~~~iIf~~t~~~~~~l~~~L~~~~---~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~  132 (234)
                      ....++||||.|+..|+.|-.++.++|   +.+..+||+..+.+                  |++++||+|+.++.++||
T Consensus       503 h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~in  582 (725)
T KOG0349|consen  503 HAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMIN  582 (725)
T ss_pred             hccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEE
Confidence            356789999999999999999999874   57999999997665                  999999999999999999


Q ss_pred             eecCCCHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         133 HCLSKSMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       133 ~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      ..+|.+-.+|+||+||.||+.+-|.+|.++....
T Consensus       583 vtlpd~k~nyvhrigrvgraermglaislvat~~  616 (725)
T KOG0349|consen  583 VTLPDDKTNYVHRIGRVGRAERMGLAISLVATVP  616 (725)
T ss_pred             EecCcccchhhhhhhccchhhhcceeEEEeeccc
Confidence            9999999999999999999999999999987643

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.42  E-value=1e-12  Score=120.92  Aligned_cols=92  Identities=21%  Similarity=0.185  Sum_probs=80.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------h-hhcccCCCCCCccEEEEeec
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------S-IAFGLGIDKPNVRFVIHHCL  135 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T-~~~~~Gid~~~v~~Vi~~~~  135 (234)
                      .+.+++|||+++++++.+++.|+..|.++..+||++++++                  | +.+++|+|+|++++||++.+
T Consensus       343 ~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p  422 (501)
T PHA02558        343 KGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHP  422 (501)
T ss_pred             cCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecC
Confidence            3567899999999999999999999999999999999775                  5 79999999999999999999


Q ss_pred             CCCHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         136 SKSMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       136 P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      |.+...|+||+||++|.+......++++.-|
T Consensus       423 ~~s~~~~~QriGR~~R~~~~K~~~~i~D~vD  453 (501)
T PHA02558        423 SKSKIIVLQSIGRVLRKHGSKSIATVWDIID  453 (501)
T ss_pred             CcchhhhhhhhhccccCCCCCceEEEEEeec
Confidence            9999999999999999776555555555433

>PRK09401 reverse gyrase; Reviewed

Probab=99.38  E-value=6e-13  Score=132.02  Aligned_cols=133  Identities=20%  Similarity=0.164  Sum_probs=89.7

Q ss_pred             HHHhhhccCchhHHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHH-
Q psy4494          10 YLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKE-   88 (234)
Q Consensus        10 ~l~l~~at~p~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~-   88 (234)
                      ++.+||||.+...+...+-.+.-.+.+........++.+.|....      ++...+.+++.. + +.++||||+|++. 
T Consensus       270 q~ilfSAT~~~~~~~~~l~~~ll~~~v~~~~~~~rnI~~~yi~~~------~k~~~L~~ll~~-l-~~~~LIFv~t~~~~  341 (1176)
T PRK09401        270 VLVVSSATGRPRGNRVKLFRELLGFEVGSPVFYLRNIVDSYIVDE------DSVEKLVELVKR-L-GDGGLIFVPSDKGK  341 (1176)
T ss_pred             eEEEEeCCCCccchHHHHhhccceEEecCcccccCCceEEEEEcc------cHHHHHHHHHHh-c-CCCEEEEEecccCh
Confidence            466889998743111100011111121111122334445554321      244455666643 2 3579999999877 


Q ss_pred             --HHHHHHHHHHcCCceeeeccCCCchh-----------------hhhcccCCCCCC-ccEEEEeecCC------CHhHh
Q psy4494          89 --CEDLREELRNRGLRVSAYHAKLESNV-----------------SIAFGLGIDKPN-VRFVIHHCLSK------SMENF  142 (234)
Q Consensus        89 --~~~l~~~L~~~~~~~~~~h~~~~~~~-----------------T~~~~~Gid~~~-v~~Vi~~~~P~------~~~~y  142 (234)
                        ++.+++.|+..|+++..+||+|...-                 |++++||||+|+ |++|||||+|.      ..+.|
T Consensus       342 ~~ae~l~~~L~~~gi~v~~~hg~l~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~  421 (1176)
T PRK09401        342 EYAEELAEYLEDLGINAELAISGFERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAP  421 (1176)
T ss_pred             HHHHHHHHHHHHCCCcEEEEeCcHHHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccC
Confidence              99999999999999999999982211                 588999999999 89999999998      67789


Q ss_pred             hhhhcccc
Q psy4494         143 YQESGRAG  150 (234)
Q Consensus       143 ~qr~GR~g  150 (234)
                      .||+||+-
T Consensus       422 ~~~~~r~~  429 (1176)
T PRK09401        422 PFLLLRLL  429 (1176)
T ss_pred             HHHHHHHH
Confidence            99999995

>PRK00254 ski2-like helicase; Provisional

Probab=99.35  E-value=3.2e-12  Score=122.35  Aligned_cols=99  Identities=20%  Similarity=0.318  Sum_probs=79.0

Q ss_pred             HHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc---------------------------------CCceeeeccCCC
Q psy4494          65 ELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR---------------------------------GLRVSAYHAKLE  111 (234)
Q Consensus        65 ~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~---------------------------------~~~~~~~h~~~~  111 (234)
                      .+.+.+.   .++++||||+|++.|+.++..|...                                 ...+.++||+|+
T Consensus       230 ~~~~~i~---~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~  306 (720)
T PRK00254        230 LVYDAVK---KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLG  306 (720)
T ss_pred             HHHHHHH---hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCC
Confidence            3444443   4678999999999999988777421                                 123889999999


Q ss_pred             chh------------------hhhcccCCCCCCccEEEE-------eecCC-CHhHhhhhhcccccCC--CceEEEEEee
Q psy4494         112 SNV------------------SIAFGLGIDKPNVRFVIH-------HCLSK-SMENFYQESGRAGRDG--QIAHCILYYR  163 (234)
Q Consensus       112 ~~~------------------T~~~~~Gid~~~v~~Vi~-------~~~P~-~~~~y~qr~GR~gR~g--~~~~~i~~~~  163 (234)
                      +++                  |+++++|+|+|.+++||.       ++.|. ...+|+||+|||||.|  ..|.++++..
T Consensus       307 ~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~  386 (720)
T PRK00254        307 RTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVAT  386 (720)
T ss_pred             HHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEec
Confidence            987                  999999999999999994       56554 5679999999999965  6799999987


Q ss_pred             ccc
Q psy4494         164 LPD  166 (234)
Q Consensus       164 ~~d  166 (234)
                      ..+
T Consensus       387 ~~~  389 (720)
T PRK00254        387 TEE  389 (720)
T ss_pred             Ccc
Confidence            654

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

Probab=99.33  E-value=1.9e-12  Score=116.65  Aligned_cols=152  Identities=24%  Similarity=0.366  Sum_probs=103.0

Q ss_pred             HHHHHHHhhhccCchh-HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhc-------CCC
Q psy4494           6 YTIAYLNLWRTSFYQV-SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRF-------RNQ   77 (234)
Q Consensus         6 ~~~a~l~l~~at~p~~-~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~-------~~~   77 (234)
                      |+-||+-.+|||.-+- ..+..++.     +.+....-|-.++-+....   .+..+|...+.++.+..+       ..+
T Consensus       370 ~~~AQ~i~LSATVgNp~elA~~l~a-----~lV~y~~RPVplErHlvf~---~~e~eK~~ii~~L~k~E~~~~sskg~rG  441 (830)
T COG1202         370 FPGAQFIYLSATVGNPEELAKKLGA-----KLVLYDERPVPLERHLVFA---RNESEKWDIIARLVKREFSTESSKGYRG  441 (830)
T ss_pred             CCCCeEEEEEeecCChHHHHHHhCC-----eeEeecCCCCChhHeeeee---cCchHHHHHHHHHHHHHHhhhhccCcCC
Confidence            3335555566665443 34444444     2333333333333333332   223456666666665332       135


Q ss_pred             cEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEE---eecC
Q psy4494          78 SGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIH---HCLS  136 (234)
Q Consensus        78 ~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~---~~~P  136 (234)
                      ++|||++|++.|+.++..|..+|+++.+||++++..+                  |-|++.|+|+|.-+.|+.   .+.-
T Consensus       442 QtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLaMG~~  521 (830)
T COG1202         442 QTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIE  521 (830)
T ss_pred             ceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHHcccc
Confidence            7999999999999999999999999999999999866                  889999999995544321   2333


Q ss_pred             C-CHhHhhhhhcccccCC--CceEEEEEeecc
Q psy4494         137 K-SMENFYQESGRAGRDG--QIAHCILYYRLP  165 (234)
Q Consensus       137 ~-~~~~y~qr~GR~gR~g--~~~~~i~~~~~~  165 (234)
                      | ++.+|.|+.|||||.+  ..|..++++.+.
T Consensus       522 WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg  553 (830)
T COG1202         522 WLSVREFQQMLGRAGRPDYHDRGKVYLLVEPG  553 (830)
T ss_pred             cCCHHHHHHHhcccCCCCcccCceEEEEecCC
Confidence            3 7789999999999976  458888888874

>PRK01172 ski2-like helicase; Provisional

Probab=99.27  E-value=2.4e-11  Score=115.69  Aligned_cols=99  Identities=24%  Similarity=0.260  Sum_probs=76.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcC-------------------------CceeeeccCCCchh---------------
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRG-------------------------LRVSAYHAKLESNV---------------  114 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~-------------------------~~~~~~h~~~~~~~---------------  114 (234)
                      .++++||||+|++.++.++..|....                         ..+.++||++++++               
T Consensus       235 ~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~V  314 (674)
T PRK01172        235 DGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKV  314 (674)
T ss_pred             CCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeE
Confidence            46789999999999999999987531                         12678999999977               


Q ss_pred             ---hhhcccCCCCCCccEEEEeec---------CCCHhHhhhhhcccccCCC--ceEEEEEeeccc-HHHhhhhH
Q psy4494         115 ---SIAFGLGIDKPNVRFVIHHCL---------SKSMENFYQESGRAGRDGQ--IAHCILYYRLPD-VFKLSSMV  174 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~~~~---------P~~~~~y~qr~GR~gR~g~--~~~~i~~~~~~d-~~~~~~~~  174 (234)
                         |+++++|+|+|.. .||+++.         |-+..+|.||+|||||.|.  .|.++++....+ ...+.+.+
T Consensus       315 LvaT~~la~Gvnipa~-~VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~~~~~~~~~l  388 (674)
T PRK01172        315 IVATPTLAAGVNLPAR-LVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKKYL  388 (674)
T ss_pred             EEecchhhccCCCcce-EEEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcccHHHHHHHH
Confidence               9999999999986 4555543         4577899999999999884  577887765433 44444443

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.25  E-value=1.1e-11  Score=85.19  Aligned_cols=63  Identities=35%  Similarity=0.493  Sum_probs=56.1

Q ss_pred             HHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccC
Q psy4494          91 DLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRD  152 (234)
Q Consensus        91 ~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~  152 (234)
                      .+.+.|+..++.+..+||++++++                  |.+++.|+|+++++.||.+++|.+...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            466777777888888888887765                  88999999999999999999999999999999999997


Q ss_pred             C
Q psy4494         153 G  153 (234)
Q Consensus       153 g  153 (234)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            6

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.23  E-value=4.5e-11  Score=112.92  Aligned_cols=101  Identities=14%  Similarity=0.043  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-------------------hhhcccC
Q psy4494          62 CLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-------------------SIAFGLG  121 (234)
Q Consensus        62 ~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-------------------T~~~~~G  121 (234)
                      |+..+..++... .++.++||||++.+.++.++..|.     +..+||++++.+                   |.+.++|
T Consensus       481 K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeG  555 (732)
T TIGR00603       481 KFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTS  555 (732)
T ss_pred             HHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccc
Confidence            445555555432 257799999999999999998883     566899999866                   7888999


Q ss_pred             CCCCCccEEEEeecC-CCHhHhhhhhcccccCCCceEE-------EEEeecccH
Q psy4494         122 IDKPNVRFVIHHCLS-KSMENFYQESGRAGRDGQIAHC-------ILYYRLPDV  167 (234)
Q Consensus       122 id~~~v~~Vi~~~~P-~~~~~y~qr~GR~gR~g~~~~~-------i~~~~~~d~  167 (234)
                      +|+|++++||+++.| .+...|+||+||++|.+..+.+       +.++++...
T Consensus       556 IDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~  609 (732)
T TIGR00603       556 IDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQ  609 (732)
T ss_pred             cCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCch
Confidence            999999999999998 5999999999999998765543       667766543

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).

>KOG0354|consensus

Probab=99.15  E-value=2.9e-10  Score=106.34  Aligned_cols=106  Identities=20%  Similarity=0.332  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHHHhhc---CCCcEEEEecchHHHHHHHHHHHH---cCCceeeecc--------CCCchh-----------
Q psy4494          60 KDCLDELADLMSRRF---RNQSGIIYTTSIKECEDLREELRN---RGLRVSAYHA--------KLESNV-----------  114 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~---~~~~~iIf~~t~~~~~~l~~~L~~---~~~~~~~~h~--------~~~~~~-----------  114 (234)
                      ..+++.+.+++.+.+   +..++||||.+|..|+.+..+|.+   .|+++..+-|        +|++++           
T Consensus       394 npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G  473 (746)
T KOG0354|consen  394 NPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDG  473 (746)
T ss_pred             ChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCC
Confidence            356777777776443   467899999999999999999983   2455555554        344443           


Q ss_pred             -------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         115 -------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       115 -------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                             |++...|+|++.+++||.||.-.++...+||.|| ||.- .|.++++++....
T Consensus       474 ~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t~~~~  531 (746)
T KOG0354|consen  474 EINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTTGSEV  531 (746)
T ss_pred             CccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEcchhH
Confidence                   9999999999999999999999999999999999 8974 4667777775433

>TIGR01054 rgy reverse gyrase

Probab=99.15  E-value=2.8e-10  Score=113.29  Aligned_cols=73  Identities=26%  Similarity=0.485  Sum_probs=62.0

Q ss_pred             HHHHHHHHhhcCCCcEEEEecch---HHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCC
Q psy4494          64 DELADLMSRRFRNQSGIIYTTSI---KECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGI  122 (234)
Q Consensus        64 ~~l~~~l~~~~~~~~~iIf~~t~---~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gi  122 (234)
                      ..|.+++.. + +.++||||+|+   +.|++++..|+..|+++..+||+++++.                  |++++|||
T Consensus       316 ~~L~~ll~~-l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~~~l~~Fr~G~~~vLVata~~tdv~aRGI  393 (1171)
T TIGR01054       316 ETLLEIVKK-L-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPKEDYEKFAEGEIDVLIGVASYYGTLVRGL  393 (1171)
T ss_pred             HHHHHHHHH-c-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCHHHHHHHHcCCCCEEEEeccccCcccccC
Confidence            345555543 2 45799999999   9999999999999999999999996543                  48899999


Q ss_pred             CCCC-ccEEEEeecCCC
Q psy4494         123 DKPN-VRFVIHHCLSKS  138 (234)
Q Consensus       123 d~~~-v~~Vi~~~~P~~  138 (234)
                      |+|+ |++|||||+|..
T Consensus       394 Dip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       394 DLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             CCCccccEEEEECCCCE
Confidence            9999 899999999975

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.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.13  E-value=3.3e-10  Score=107.99  Aligned_cols=109  Identities=25%  Similarity=0.263  Sum_probs=92.9

Q ss_pred             hHHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+.+.+ ...+.|+||||+|++.++.++..|...|++...+||.....+                |+.+|||
T Consensus       412 ~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnakq~eREa~Iia~Ag~~g~VtIATNmAGRG  491 (830)
T PRK12904        412 EKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAKNHEREAEIIAQAGRPGAVTIATNMAGRG  491 (830)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCchHHHHHHHHHhcCCCceEEEecccccCC
Confidence            45677778777754 235789999999999999999999999999999999744433                9999999


Q ss_pred             CCCCCc------------------------------c--------EEEEeecCCCHhHhhhhhcccccCCCceEEEEEee
Q psy4494         122 IDKPNV------------------------------R--------FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       122 id~~~v------------------------------~--------~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                      +|++-=                              .        +||--..|.|..---|-.||+||.|.+|.+-.|++
T Consensus       492 tDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~lS  571 (830)
T PRK12904        492 TDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLS  571 (830)
T ss_pred             cCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEEEE
Confidence            999832                              1        69988999999999999999999999999999999


Q ss_pred             cccH
Q psy4494         164 LPDV  167 (234)
Q Consensus       164 ~~d~  167 (234)
                      -+|-
T Consensus       572 leD~  575 (830)
T PRK12904        572 LEDD  575 (830)
T ss_pred             cCcH
Confidence            8764

>KOG4150|consensus

Probab=99.09  E-value=1.1e-09  Score=99.17  Aligned_cols=134  Identities=21%  Similarity=0.250  Sum_probs=96.5

Q ss_pred             CcEEEEEeeccCCCcceEEEEEEcC-----CChHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHc----C-
Q psy4494          32 PNVRFVIHHCLSKSMENFYQVRIKP-----AAQKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNR----G-  100 (234)
Q Consensus        32 ~~i~~~~~~~~~~~~~~~y~v~~~~-----~~~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~----~-  100 (234)
                      ..+.++-....|.+..++..+.+..     .+++.++.+..+++.+- ..+-++|-||.+++.||-+....++-    + 
T Consensus       475 ~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~  554 (1034)
T KOG4150|consen  475 SELELVTIDGSPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAP  554 (1034)
T ss_pred             cceEEEEecCCCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhH
Confidence            3455555566777777777766532     12333444433333221 25778999999999999887665532    1 


Q ss_pred             ---CceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEE
Q psy4494         101 ---LRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCI  159 (234)
Q Consensus       101 ---~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i  159 (234)
                         -.+..|.|+...++                  |+|+..|||+.+.+.|++.++|.++.++.|+.|||||..+++.++
T Consensus       555 ~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLav  634 (1034)
T KOG4150|consen  555 HLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAV  634 (1034)
T ss_pred             HHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccccCCCceEE
Confidence               01445666666554                  999999999999999999999999999999999999999998888


Q ss_pred             EEeecc
Q psy4494         160 LYYRLP  165 (234)
Q Consensus       160 ~~~~~~  165 (234)
                      ......
T Consensus       635 yva~~~  640 (1034)
T KOG4150|consen  635 YVAFLG  640 (1034)
T ss_pred             EEEecc
Confidence            877653

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=1.3e-09  Score=104.29  Aligned_cols=110  Identities=25%  Similarity=0.273  Sum_probs=93.0

Q ss_pred             hHHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..+|...+.+.+.+ ...+.|+||||+|++.++.++..|...|++...+||.+.+.+                |+.+|||
T Consensus       426 ~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~VtIATNmAGRG  505 (896)
T PRK13104        426 QADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGAVTIATNMAGRG  505 (896)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCcEEEeccCccCC
Confidence            44566666665543 236789999999999999999999999999999999998776                9999999


Q ss_pred             CCCCC---------------------------------cc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEee
Q psy4494         122 IDKPN---------------------------------VR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       122 id~~~---------------------------------v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                      +|+.-                                 |.     +||--..+.|..-=.|-.||+||.|.+|.+-.|++
T Consensus       506 tDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~lS  585 (896)
T PRK13104        506 TDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYLS  585 (896)
T ss_pred             cceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEE
Confidence            99971                                 21     68888888888888999999999999999999999


Q ss_pred             cccHH
Q psy4494         164 LPDVF  168 (234)
Q Consensus       164 ~~d~~  168 (234)
                      -+|-.
T Consensus       586 leD~l  590 (896)
T PRK13104        586 LEDNL  590 (896)
T ss_pred             cCcHH
Confidence            87643

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

Probab=99.02  E-value=5.3e-09  Score=94.10  Aligned_cols=115  Identities=26%  Similarity=0.349  Sum_probs=95.0

Q ss_pred             cceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-----------
Q psy4494          46 MENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-----------  114 (234)
Q Consensus        46 ~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------  114 (234)
                      ++--.+|.+.....++++.++.+...   .+.+++|-+-|++.+|.|.++|.+.|+++.++|++.+.-+           
T Consensus       419 lDP~ievRp~~~QvdDL~~EI~~r~~---~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G  495 (663)
T COG0556         419 LDPEIEVRPTKGQVDDLLSEIRKRVA---KNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLG  495 (663)
T ss_pred             CCCceeeecCCCcHHHHHHHHHHHHh---cCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcC
Confidence            34445666666777888888887765   5689999999999999999999999999999999998765           


Q ss_pred             -------hhhcccCCCCCCccEEEEeec-----CCCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         115 -------SIAFGLGIDKPNVRFVIHHCL-----SKSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       115 -------T~~~~~Gid~~~v~~Vi~~~~-----P~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                             -+.+-.|+|+|.|.+|..+|.     ..|-.+++|-+|||.|.-+ |.+|+|.+.
T Consensus       496 ~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~~-GkvIlYAD~  556 (663)
T COG0556         496 EFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN-GKVILYADK  556 (663)
T ss_pred             CccEEEeehhhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhccC-CeEEEEchh
Confidence                   556667999999999998865     4578899999999999753 677887654

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

Probab=99.01  E-value=2.4e-09  Score=104.06  Aligned_cols=155  Identities=20%  Similarity=0.209  Sum_probs=111.7

Q ss_pred             chHHHHHHHhhhccCchhHHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEe
Q psy4494           4 LLYTIAYLNLWRTSFYQVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYT   83 (234)
Q Consensus         4 ~~~~~a~l~l~~at~p~~~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~   83 (234)
                      +.-++.-|+|..+..|+..-++.+|+..=.+   +...+.++....=.|.  +.+..-..+.|..-+   .+++++..-+
T Consensus       739 Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSv---I~TPP~~R~pV~T~V~--~~d~~~ireAI~REl---~RgGQvfYv~  810 (1139)
T COG1197         739 LRANVDVLTLSATPIPRTLNMSLSGIRDLSV---IATPPEDRLPVKTFVS--EYDDLLIREAILREL---LRGGQVFYVH  810 (1139)
T ss_pred             HhccCcEEEeeCCCCcchHHHHHhcchhhhh---ccCCCCCCcceEEEEe--cCChHHHHHHHHHHH---hcCCEEEEEe
Confidence            3345566788888899988888888832111   1111222222222222  222222333444333   3678877778


Q ss_pred             cchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCC-CHhHh
Q psy4494          84 TSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSK-SMENF  142 (234)
Q Consensus        84 ~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~-~~~~y  142 (234)
                      |..+..++++..|++.  ..++.+-||.|+..+                  |.....|||+|+++.+|..+.-. .+.+.
T Consensus       811 NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGLsQL  890 (1139)
T COG1197         811 NRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGLAQL  890 (1139)
T ss_pred             cchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccHHHH
Confidence            9999999999999987  667999999999987                  88889999999999888766543 68899


Q ss_pred             hhhhcccccCCCceEEEEEeeccc
Q psy4494         143 YQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       143 ~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      +|-.||.||..+.+.|+++|++..
T Consensus       891 yQLRGRVGRS~~~AYAYfl~p~~k  914 (1139)
T COG1197         891 YQLRGRVGRSNKQAYAYFLYPPQK  914 (1139)
T ss_pred             HHhccccCCccceEEEEEeecCcc
Confidence            999999999999999999998754

>PRK09694 helicase Cas3; Provisional

Probab=99.01  E-value=3.6e-09  Score=102.44  Aligned_cols=88  Identities=14%  Similarity=0.289  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcC---CceeeeccCCCchh-----------------------
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRG---LRVSAYHAKLESNV-----------------------  114 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~---~~~~~~h~~~~~~~-----------------------  114 (234)
                      ..+..+.+.+.   .+++++|||||++.++++++.|++.+   ..+..+||.+...+                       
T Consensus       548 ~~l~~i~~~~~---~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~I  624 (878)
T PRK09694        548 TLLQRMIAAAN---AGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRI  624 (878)
T ss_pred             HHHHHHHHHHh---cCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeE
Confidence            34444444433   56789999999999999999999764   67999999987543                       


Q ss_pred             ---hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCC
Q psy4494         115 ---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQ  154 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~  154 (234)
                         |.++.+|+|+ +++.+|....|  ++.++||+||+||.++
T Consensus       625 LVaTQViE~GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        625 LVATQVVEQSLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             EEECcchhheeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence               8888999999 48999998888  6799999999999775

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.98  E-value=3.7e-09  Score=101.12  Aligned_cols=108  Identities=22%  Similarity=0.231  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccCC
Q psy4494          60 KDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLGI  122 (234)
Q Consensus        60 ~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~Gi  122 (234)
                      .+|...+.+-+.+ ...+.|+||||+|++.++.++..|...|++...+|+.+++.+                |+.+|||+
T Consensus       432 ~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~VtIATnmAGRGT  511 (908)
T PRK13107        432 DEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGAVTIATNMAGRGT  511 (908)
T ss_pred             HHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCcEEEecCCcCCCc
Confidence            4566666555442 235789999999999999999999999999999999998776                99999999


Q ss_pred             CCCC--------------------------------cc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         123 DKPN--------------------------------VR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       123 d~~~--------------------------------v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      |+.-                                |.     +||--..+.|..-=.|-.||+||.|.+|.+..|++.+
T Consensus       512 DIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~lSlE  591 (908)
T PRK13107        512 DIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYLSME  591 (908)
T ss_pred             ceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEEEeC
Confidence            9972                                21     7888888998888899999999999999999999987


Q ss_pred             cH
Q psy4494         166 DV  167 (234)
Q Consensus       166 d~  167 (234)
                      |-
T Consensus       592 D~  593 (908)
T PRK13107        592 DS  593 (908)
T ss_pred             cH
Confidence            74

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.84  E-value=3.7e-08  Score=96.63  Aligned_cols=104  Identities=20%  Similarity=0.163  Sum_probs=85.1

Q ss_pred             HHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhhcc
Q psy4494          62 CLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIAFG  119 (234)
Q Consensus        62 ~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~~~  119 (234)
                      ++..|.+++..- ..+.++|||+......+.|..+|...|+....++|+++.++                     |.+.|
T Consensus       472 Kl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGG  551 (1033)
T PLN03142        472 KMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGG  551 (1033)
T ss_pred             HHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccc
Confidence            444444444321 14679999999999999999999999999999999998654                     88999


Q ss_pred             cCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEE--EEEeecc
Q psy4494         120 LGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHC--ILYYRLP  165 (234)
Q Consensus       120 ~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~--i~~~~~~  165 (234)
                      .|||+...++||+||+|+++....|++||+-|.|+...+  +-|+...
T Consensus       552 lGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~g  599 (1033)
T PLN03142        552 LGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEY  599 (1033)
T ss_pred             cCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCC
Confidence            999999999999999999999999999999999977443  3344443

>KOG0948|consensus

Probab=98.77  E-value=7.5e-08  Score=89.66  Aligned_cols=99  Identities=25%  Similarity=0.426  Sum_probs=71.3

Q ss_pred             HHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCc---------------------------------------eee
Q psy4494          65 ELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR---------------------------------------VSA  105 (234)
Q Consensus        65 ~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~---------------------------------------~~~  105 (234)
                      .+++.+... +..++|||+=|+++||..|..+....++                                       +..
T Consensus       373 kiVkmi~~~-~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGI  451 (1041)
T KOG0948|consen  373 KIVKMIMER-NYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAIDQLSEEDRELPQIENILPLLRRGIGI  451 (1041)
T ss_pred             HHHHHHHhh-cCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHHHhcChhhccchHHHHHHHHHHhcccc
Confidence            444444332 4578999999999999999888643221                                       566


Q ss_pred             eccCCCchh------------------hhhcccCCCCCCccEEEEeecCC---------CHhHhhhhhcccccCCC--ce
Q psy4494         106 YHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSK---------SMENFYQESGRAGRDGQ--IA  156 (234)
Q Consensus       106 ~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~---------~~~~y~qr~GR~gR~g~--~~  156 (234)
                      .|||+-+--                  |..|++|+|.|. +.|+.-..-+         +.-.|+|+.|||||.|.  .|
T Consensus       452 HHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPA-kTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~DdrG  530 (1041)
T KOG0948|consen  452 HHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPA-KTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDDRG  530 (1041)
T ss_pred             ccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcc-eeEEEeeccccCCcceeeecccceEEecccccccCCCCCc
Confidence            777766521                  999999999994 4554432221         45699999999999875  59


Q ss_pred             EEEEEeecc
Q psy4494         157 HCILYYRLP  165 (234)
Q Consensus       157 ~~i~~~~~~  165 (234)
                      .+|++++..
T Consensus       531 ivIlmiDek  539 (1041)
T KOG0948|consen  531 IVILMIDEK  539 (1041)
T ss_pred             eEEEEecCc
Confidence            999998764

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

Probab=98.77  E-value=3.5e-08  Score=95.67  Aligned_cols=90  Identities=32%  Similarity=0.391  Sum_probs=78.7

Q ss_pred             CCCcEEEEecchHHHHHHH----HHHHHcC----CceeeeccCCCchh------------------hhhcccCCCCCCcc
Q psy4494          75 RNQSGIIYTTSIKECEDLR----EELRNRG----LRVSAYHAKLESNV------------------SIAFGLGIDKPNVR  128 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~----~~L~~~~----~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~  128 (234)
                      .+.++|+|+.+++.++.+.    ..+...+    ..+..|+|++..++                  |.++..|||+.+++
T Consensus       305 ~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~ld  384 (851)
T COG1205         305 NGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLD  384 (851)
T ss_pred             cCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehhhh
Confidence            5778999999999999997    3444444    56889999999877                  99999999999999


Q ss_pred             EEEEeecCC-CHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         129 FVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       129 ~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      .||+++.|. +..+++||.||+||.++.+..+..+..
T Consensus       385 avi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~~  421 (851)
T COG1205         385 AVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLRS  421 (851)
T ss_pred             hHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeCC
Confidence            999999999 899999999999999988877777764

>TIGR00595 priA primosomal protein N'

Probab=98.76  E-value=6e-08  Score=89.38  Aligned_cols=77  Identities=26%  Similarity=0.334  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHc--CCceeeeccCCCchh--------------------hhhcccCCCCCCccEEE--Eeec----CC---
Q psy4494          89 CEDLREELRNR--GLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVI--HHCL----SK---  137 (234)
Q Consensus        89 ~~~l~~~L~~~--~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi--~~~~----P~---  137 (234)
                      ++++.+.|++.  +.++..+|++++...                    |..+++|+|+|+|++|+  ++|.    |.   
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra  350 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA  350 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccch
Confidence            58888999876  788999999987542                    99999999999999985  5554    32   


Q ss_pred             ---CHhHhhhhhcccccCCCceEEEEE-eecc
Q psy4494         138 ---SMENFYQESGRAGRDGQIAHCILY-YRLP  165 (234)
Q Consensus       138 ---~~~~y~qr~GR~gR~g~~~~~i~~-~~~~  165 (234)
                         ....|+|.+||+||.++.|.+++. +.++
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~  382 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNPN  382 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCCC
Confidence               245789999999999999988853 3443

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).

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

Probab=98.73  E-value=7.5e-08  Score=95.75  Aligned_cols=77  Identities=17%  Similarity=0.175  Sum_probs=66.1

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc------CC---ceeeeccCCCchh-----------------hhhcccCCCCCCccE
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR------GL---RVSAYHAKLESNV-----------------SIAFGLGIDKPNVRF  129 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~------~~---~~~~~h~~~~~~~-----------------T~~~~~Gid~~~v~~  129 (234)
                      ++++||||.+++.|+.+++.|.+.      +.   .+..+||+.+..+                 ++.+++|+|+|.|..
T Consensus       698 ~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~  777 (1123)
T PRK11448        698 EGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSIDKPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICN  777 (1123)
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCccchHHHHHHHhCCCCCeEEEEecccccCCCcccccE
Confidence            478999999999999999988753      22   3566888876543                 788899999999999


Q ss_pred             EEEeecCCCHhHhhhhhcccccC
Q psy4494         130 VIHHCLSKSMENFYQESGRAGRD  152 (234)
Q Consensus       130 Vi~~~~P~~~~~y~qr~GR~gR~  152 (234)
                      ||.+.++.|...|+|++||+.|-
T Consensus       778 vVf~rpvkS~~lf~QmIGRgtR~  800 (1123)
T PRK11448        778 LVFLRRVRSRILYEQMLGRATRL  800 (1123)
T ss_pred             EEEecCCCCHHHHHHHHhhhccC
Confidence            99999999999999999999994

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.72  E-value=8.2e-08  Score=91.53  Aligned_cols=109  Identities=21%  Similarity=0.261  Sum_probs=90.4

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+-+... ..++|+||.|.|.+..+.++..|...|++...+++.....+                |+.+|||
T Consensus       408 ~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e~EA~IIa~AG~~GaVTIATNMAGRG  487 (925)
T PRK12903        408 KHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNAREAEIIAKAGQKGAITIATNMAGRG  487 (925)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchhhHHHHHHhCCCCCeEEEecccccCC
Confidence            345666666655432 36789999999999999999999999999888888655444                9999999


Q ss_pred             CCCCCcc--------EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         122 IDKPNVR--------FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       122 id~~~v~--------~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      .||.--.        +||....|.+..---|-.||+||.|.+|.+-.|++-.|-
T Consensus       488 TDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~  541 (925)
T PRK12903        488 TDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQ  541 (925)
T ss_pred             cCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecchH
Confidence            9997322        899999999988778999999999999999999988663

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.67  E-value=1.3e-07  Score=88.91  Aligned_cols=109  Identities=26%  Similarity=0.311  Sum_probs=91.3

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+-+.+. ..+.|+||.+.|.+..|.++..|.+.|++...+++.....+                |+.+|||
T Consensus       409 ~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~~gaVTIATNMAGRG  488 (764)
T PRK12326        409 AAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGKYGAVTVSTQMAGRG  488 (764)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCCCCcEEEEecCCCCc
Confidence            455666666555432 36889999999999999999999999999999988765544                9999999


Q ss_pred             CCCC----------Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         122 IDKP----------NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       122 id~~----------~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      .||.          .|.     +||-...|.|..--.|-.||+||.|.+|.+..|++-+|-
T Consensus       489 TDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        489 TDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             cCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcchh
Confidence            9997          222     799999999999999999999999999999999998764

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

Probab=98.67  E-value=1.7e-07  Score=85.15  Aligned_cols=88  Identities=20%  Similarity=0.322  Sum_probs=74.8

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLS  136 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P  136 (234)
                      ...+++||+.++..++.++..+...|+ +..+.|..+..+                  +..+..|+|+|+++.+|.....
T Consensus       282 ~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t  360 (442)
T COG1061         282 RGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPT  360 (442)
T ss_pred             CCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCC
Confidence            467899999999999999999998887 778888888776                  6678889999999999999999


Q ss_pred             CCHhHhhhhhccccc--CCCceEEEEEee
Q psy4494         137 KSMENFYQESGRAGR--DGQIAHCILYYR  163 (234)
Q Consensus       137 ~~~~~y~qr~GR~gR--~g~~~~~i~~~~  163 (234)
                      .+...|+||+||.-|  .|.....+++|.
T Consensus       361 ~S~~~~~Q~lGR~LR~~~~k~~~~~~~~~  389 (442)
T COG1061         361 GSRRLFIQRLGRGLRPAEGKEDTLALDYS  389 (442)
T ss_pred             CcHHHHHHHhhhhccCCCCCCceEEEEEE
Confidence            999999999999999  344444444443

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.61  E-value=5.3e-07  Score=86.57  Aligned_cols=100  Identities=22%  Similarity=0.305  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHH---c------------------C----------------Ccee
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRN---R------------------G----------------LRVS  104 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~---~------------------~----------------~~~~  104 (234)
                      .+..+.+.+.   .++++||||+|++.+...|..|+.   .                  +                .-+.
T Consensus       242 ~~~~v~~~~~---~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~Gva  318 (766)
T COG1204         242 ALELVLESLA---EGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVA  318 (766)
T ss_pred             HHHHHHHHHh---cCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCcc
Confidence            3344444443   578899999999999999999982   0                  0                0156


Q ss_pred             eeccCCCchh------------------hhhcccCCCCCCccEEE----Eee-----cCCCHhHhhhhhcccccCC--Cc
Q psy4494         105 AYHAKLESNV------------------SIAFGLGIDKPNVRFVI----HHC-----LSKSMENFYQESGRAGRDG--QI  155 (234)
Q Consensus       105 ~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi----~~~-----~P~~~~~y~qr~GR~gR~g--~~  155 (234)
                      ..|++++.+.                  |..++.|+|.|.=+.||    -|+     .+-+.-+|.|+.|||||.|  ..
T Consensus       319 fHhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~  398 (766)
T COG1204         319 FHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDY  398 (766)
T ss_pred             ccccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCC
Confidence            7788888766                  99999999999444443    245     4556779999999999976  34


Q ss_pred             eEEEEEeec
Q psy4494         156 AHCILYYRL  164 (234)
Q Consensus       156 ~~~i~~~~~  164 (234)
                      |.++++...
T Consensus       399 G~~~i~~~~  407 (766)
T COG1204         399 GEAIILATS  407 (766)
T ss_pred             CcEEEEecC
Confidence            667776633

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.61  E-value=2.8e-07  Score=87.83  Aligned_cols=76  Identities=25%  Similarity=0.241  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHc--CCceeeeccCCCchh--------------------hhhcccCCCCCCccEEEEe--ecCCC-----
Q psy4494          88 ECEDLREELRNR--GLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIHH--CLSKS-----  138 (234)
Q Consensus        88 ~~~~l~~~L~~~--~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~~--~~P~~-----  138 (234)
                      .++.+++.|++.  +.++..+|+++.+..                    |..+++|+|+|+|++|+.+  |.+-+     
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfr  517 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFR  517 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccc
Confidence            567888888876  788999999986421                    9999999999999999655  44433     


Q ss_pred             -----HhHhhhhhcccccCCCceEEEEEee
Q psy4494         139 -----MENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       139 -----~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                           ...|+|++||+||.+..|.+++.-.
T Consensus       518 a~Er~~~~l~q~~GRagR~~~~g~viiqT~  547 (679)
T PRK05580        518 ASERTFQLLTQVAGRAGRAEKPGEVLIQTY  547 (679)
T ss_pred             hHHHHHHHHHHHHhhccCCCCCCEEEEEeC
Confidence                 2579999999999999999986543

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

Probab=98.51  E-value=7.7e-07  Score=85.68  Aligned_cols=95  Identities=24%  Similarity=0.342  Sum_probs=81.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHH----cCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEE
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRN----RGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIH  132 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~  132 (234)
                      ..+..+||.+-.++.+++.+.|.+    ..+.+.++||.++.++                  |+.+..+|-|++|++||.
T Consensus       258 ~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VID  337 (845)
T COG1643         258 GSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVID  337 (845)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEec
Confidence            467899999999999999999998    3577999999999877                  999999999999999998


Q ss_pred             eecC------------------CCHhHhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         133 HCLS------------------KSMENFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       133 ~~~P------------------~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                      -+.-                  -|-.+-.||.|||||-+ +|.|+=+|+..++..+
T Consensus       338 sG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~~~~~  392 (845)
T COG1643         338 SGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEEDFLAF  392 (845)
T ss_pred             CCcccccccccccCceeeeEEEechhhhhhhccccccCC-CceEEEecCHHHHHhc
Confidence            7653                  34558899999999986 6999999998776643

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

Probab=98.47  E-value=2.4e-06  Score=79.55  Aligned_cols=104  Identities=21%  Similarity=0.455  Sum_probs=81.6

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchH--------HHHHHHHHHHHc--CCceeeeccCCCchh---------------
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIK--------ECEDLREELRNR--GLRVSAYHAKLESNV---------------  114 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~--------~~~~l~~~L~~~--~~~~~~~h~~~~~~~---------------  114 (234)
                      .+.++.+.+-+.   .+.++.+-|+-++        .++++++.|+..  +.++..+||.|..++               
T Consensus       460 ~~v~e~i~~ei~---~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~I  536 (677)
T COG1200         460 PEVYERIREEIA---KGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDI  536 (677)
T ss_pred             HHHHHHHHHHHH---cCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcE
Confidence            334444444443   4667888786544        566777888754  667999999999766               


Q ss_pred             ---hhhcccCCCCCCccEEEEeecCC-CHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         115 ---SIAFGLGIDKPNVRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                         |.+...|+|+|+....|..+.-. .+.+.=|-.||.||.+.++.|++++.+..
T Consensus       537 LVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~  592 (677)
T COG1200         537 LVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPL  592 (677)
T ss_pred             EEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCC
Confidence               99999999999999999887654 57788899999999999999999998754

>KOG0950|consensus

Probab=98.46  E-value=3.7e-07  Score=87.06  Aligned_cols=100  Identities=24%  Similarity=0.375  Sum_probs=77.7

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc--------------------------------------CCceeeeccCCCchh---
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR--------------------------------------GLRVSAYHAKLESNV---  114 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~--------------------------------------~~~~~~~h~~~~~~~---  114 (234)
                      +.++||||++++.|+.+|..+...                                      ..-+++.|++++.++   
T Consensus       460 ~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~  539 (1008)
T KOG0950|consen  460 GSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEEREI  539 (1008)
T ss_pred             CCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHHH
Confidence            456999999999999999666420                                      111778888888876   


Q ss_pred             ---------------hhhcccCCCCCCccEEEEe---ec-CCCHhHhhhhhcccccCCC--ceEEEEEeecccHHHhhhh
Q psy4494         115 ---------------SIAFGLGIDKPNVRFVIHH---CL-SKSMENFYQESGRAGRDGQ--IAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       115 ---------------T~~~~~Gid~~~v~~Vi~~---~~-P~~~~~y~qr~GR~gR~g~--~~~~i~~~~~~d~~~~~~~  173 (234)
                                     |+.++.|++.|..+++|-.   +. +.+...|.|++|||||.|-  .|.+|++..+.+......+
T Consensus       540 iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~~~~l  619 (1008)
T KOG0950|consen  540 IEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRVREL  619 (1008)
T ss_pred             HHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhHHHHH
Confidence                           8889999999988777754   22 2366699999999999874  5999999999997766655


Q ss_pred             HH
Q psy4494         174 VF  175 (234)
Q Consensus       174 ~~  175 (234)
                      +.
T Consensus       620 v~  621 (1008)
T KOG0950|consen  620 VN  621 (1008)
T ss_pred             Hh
Confidence            43

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.41  E-value=2e-06  Score=82.99  Aligned_cols=109  Identities=19%  Similarity=0.222  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccCC
Q psy4494          60 KDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLGI  122 (234)
Q Consensus        60 ~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~Gi  122 (234)
                      .++...+.+-+.+ ...+.|+||-|.|....+.++..|...|++...+++.....+                |+.+|||.
T Consensus       551 ~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~iia~AG~~g~VTIATNmAGRGT  630 (970)
T PRK12899        551 REKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAEIIAGAGKLGAVTVATNMAGRGT  630 (970)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHHHHHhcCCCCcEEEeeccccCCc
Confidence            4566655554432 235788999999999999999999999999888888755444                88999999


Q ss_pred             CCC---Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         123 DKP---NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       123 d~~---~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      ||.   .|.     +||.-..|.+..--.|-.||+||.|.+|.+..|++-+|-.
T Consensus       631 DIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlEDdL  684 (970)
T PRK12899        631 DIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFEDRL  684 (970)
T ss_pred             ccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcchHH
Confidence            986   222     7999999999999999999999999999999999987643

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.41  E-value=1.2e-06  Score=84.22  Aligned_cols=109  Identities=22%  Similarity=0.254  Sum_probs=89.4

Q ss_pred             HHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccCC
Q psy4494          60 KDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLGI  122 (234)
Q Consensus        60 ~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~Gi  122 (234)
                      .+|...+.+-+... ..+.|+||-+.|.+..|.++..|...|++...+++.....+                |+.+|||.
T Consensus       432 ~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa~AG~~GaVTIATNMAGRGT  511 (913)
T PRK13103        432 EEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIAQAGRPGALTIATNMAGRGT  511 (913)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhHHHHHHcCCCCCcEEEeccCCCCCC
Confidence            45666666555432 35889999999999999999999999998877777655544                99999999


Q ss_pred             CCC--------------------------------Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         123 DKP--------------------------------NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       123 d~~--------------------------------~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      ||.                                .|.     +||--..|.|..-=.|-.||+||.|.+|.+-.|++.+
T Consensus       512 DIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSlE  591 (913)
T PRK13103        512 DILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFYLSLE  591 (913)
T ss_pred             CEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEEEcC
Confidence            995                                232     7898889999888899999999999999999999987


Q ss_pred             cHH
Q psy4494         166 DVF  168 (234)
Q Consensus       166 d~~  168 (234)
                      |-.
T Consensus       592 D~L  594 (913)
T PRK13103        592 DSL  594 (913)
T ss_pred             cHH
Confidence            643

>KOG0952|consensus

Probab=98.37  E-value=7.6e-06  Score=79.01  Aligned_cols=157  Identities=15%  Similarity=0.194  Sum_probs=103.7

Q ss_pred             hhccCchh-HHHHhhCCCCC-cEEEEEeeccCCCcceEEEEEEcCC-------ChHHHHHHHHHHHHhhcCCCcEEEEec
Q psy4494          14 WRTSFYQV-SIAFGLGIDKP-NVRFVIHHCLSKSMENFYQVRIKPA-------AQKDCLDELADLMSRRFRNQSGIIYTT   84 (234)
Q Consensus        14 ~~at~p~~-~i~~~~~~~~~-~i~~~~~~~~~~~~~~~y~v~~~~~-------~~~~~~~~l~~~l~~~~~~~~~iIf~~   84 (234)
                      +|||.|+. +++-.++.+++ .+.+....--|-.+...+.-.+...       -..-+..++.+.++   .+.+++|||.
T Consensus       281 LSATlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~---~g~qVlvFvh  357 (1230)
T KOG0952|consen  281 LSATLPNYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQ---EGHQVLVFVH  357 (1230)
T ss_pred             eeccCCCHHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHH---cCCeEEEEEe
Confidence            68999996 77777888753 3433322222222333222222210       01224455666665   5778999999


Q ss_pred             chHHHHHHHHHHHHc----CCc-------------------eeeeccCCCchh------------------hhhcccCCC
Q psy4494          85 SIKECEDLREELRNR----GLR-------------------VSAYHAKLESNV------------------SIAFGLGID  123 (234)
Q Consensus        85 t~~~~~~l~~~L~~~----~~~-------------------~~~~h~~~~~~~------------------T~~~~~Gid  123 (234)
                      +++.+-+.|+.|.+.    |..                   ....|+||..+.                  |..++.|++
T Consensus       358 sR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGVN  437 (1230)
T KOG0952|consen  358 SRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGVN  437 (1230)
T ss_pred             cChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEecceeeeccC
Confidence            999999999999743    111                   456677776655                  889999999


Q ss_pred             CCCccEEEEeecCC-----------CHhHhhhhhcccccC--CCceEEEEEeecccHHHhhhhH
Q psy4494         124 KPNVRFVIHHCLSK-----------SMENFYQESGRAGRD--GQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       124 ~~~v~~Vi~~~~P~-----------~~~~y~qr~GR~gR~--g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      .| ..+||..+.+-           +..+.+|-.|||||.  +..|.++++-+..-+.....++
T Consensus       438 LP-A~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~~Y~sLl  500 (1230)
T KOG0952|consen  438 LP-AYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLDHYESLL  500 (1230)
T ss_pred             Cc-ceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHHHHHHHH
Confidence            99 67788776652           355889999999994  5679888887766666555554

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.35  E-value=2.8e-06  Score=82.51  Aligned_cols=109  Identities=24%  Similarity=0.271  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccCC
Q psy4494          60 KDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLGI  122 (234)
Q Consensus        60 ~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~Gi  122 (234)
                      .+|...+.+-+.+ ...++|+||-+.|.+..|.++..|...|++...+++.....+                |+-+|||.
T Consensus       611 ~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~GaVTIATNMAGRGT  690 (1112)
T PRK12901        611 REKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQPGTVTIATNMAGRGT  690 (1112)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCCCcEEEeccCcCCCc
Confidence            4566666555443 236889999999999999999999999999888877665544                88999999


Q ss_pred             CCC---Ccc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         123 DKP---NVR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       123 d~~---~v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                      ||.   .|.     +||--..|.|..---|-.||+||.|.+|.+-.|++-+|-.
T Consensus       691 DIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDdL  744 (1112)
T PRK12901        691 DIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDNL  744 (1112)
T ss_pred             CcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccHH
Confidence            997   232     7998899999999999999999999999999999987643

>KOG0922|consensus

Probab=98.35  E-value=2e-06  Score=79.44  Aligned_cols=124  Identities=20%  Similarity=0.224  Sum_probs=90.7

Q ss_pred             cceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc------CC--ceeeeccCCCchh---
Q psy4494          46 MENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR------GL--RVSAYHAKLESNV---  114 (234)
Q Consensus        46 ~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~------~~--~~~~~h~~~~~~~---  114 (234)
                      ++.+|.-.+.+.-..+.+..+.++-.. .+++-.+||-...++.+.+.+.|.+.      +.  -+.++||+++.++   
T Consensus       229 Vei~y~~~p~~dYv~a~~~tv~~Ih~~-E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~r  307 (674)
T KOG0922|consen  229 VEILYLKEPTADYVDAALITVIQIHLT-EPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSR  307 (674)
T ss_pred             eeEEeccCCchhhHHHHHHHHHHHHcc-CCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhc
Confidence            344554422222222333334444333 46677999999999999999999865      11  2468999999887   


Q ss_pred             ---------------hhhcccCCCCCCccEEEEeec------------------CCCHhHhhhhhcccccCCCceEEEEE
Q psy4494         115 ---------------SIAFGLGIDKPNVRFVIHHCL------------------SKSMENFYQESGRAGRDGQIAHCILY  161 (234)
Q Consensus       115 ---------------T~~~~~Gid~~~v~~Vi~~~~------------------P~~~~~y~qr~GR~gR~g~~~~~i~~  161 (234)
                                     |+.+...+-|++|.+||.-|.                  |-|-.+=.||.|||||.| +|.|+-+
T Consensus       308 vF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRL  386 (674)
T KOG0922|consen  308 VFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRL  386 (674)
T ss_pred             cccCCCCCcceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCC-CceEEEe
Confidence                           899999999999999997654                  446678899999999986 6899999


Q ss_pred             eecccHHHhh
Q psy4494         162 YRLPDVFKLS  171 (234)
Q Consensus       162 ~~~~d~~~~~  171 (234)
                      |+..++..+.
T Consensus       387 Yte~~~~~~~  396 (674)
T KOG0922|consen  387 YTESAYDKMP  396 (674)
T ss_pred             eeHHHHhhcc
Confidence            9998886544

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.34  E-value=1.4e-06  Score=83.81  Aligned_cols=87  Identities=17%  Similarity=0.353  Sum_probs=73.2

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------------hhhcccCCCCCCccEEEE
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------------SIAFGLGIDKPNVRFVIH  132 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------------T~~~~~Gid~~~v~~Vi~  132 (234)
                      .+.+++|-|||++.|.+++..|+..+..+..+||.+....                      |.+...|+|+. .+.+| 
T Consensus       439 ~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-fd~mI-  516 (733)
T COG1203         439 EGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-FDVLI-  516 (733)
T ss_pred             cCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-cCeee-
Confidence            4678999999999999999999998878999999998754                      88888899987 66655 


Q ss_pred             eecCCCHhHhhhhhcccccCC--CceEEEEEeec
Q psy4494         133 HCLSKSMENFYQESGRAGRDG--QIAHCILYYRL  164 (234)
Q Consensus       133 ~~~P~~~~~y~qr~GR~gR~g--~~~~~i~~~~~  164 (234)
                       .=+..+++.+||.||++|-|  ..|..+++...
T Consensus       517 -Te~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~  549 (733)
T COG1203         517 -TELAPIDSLIQRAGRVNRHGKKENGKIYVYNDE  549 (733)
T ss_pred             -ecCCCHHHHHHHHHHHhhcccccCCceeEeecc
Confidence             44778999999999999998  56776666544

>KOG0947|consensus

Probab=98.32  E-value=1.3e-06  Score=83.48  Aligned_cols=89  Identities=27%  Similarity=0.447  Sum_probs=66.3

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc---------------------------------------eeeeccCCCchh-
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR---------------------------------------VSAYHAKLESNV-  114 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~---------------------------------------~~~~h~~~~~~~-  114 (234)
                      .--|+||||=|++.|++-+++|....+.                                       +++.|||+-+=- 
T Consensus       566 ~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivK  645 (1248)
T KOG0947|consen  566 NLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVK  645 (1248)
T ss_pred             ccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHH
Confidence            4568999999999999999999742211                                       567788876622 


Q ss_pred             -----------------hhhcccCCCCCCccEEEEeecCC---------CHhHhhhhhcccccCCC--ceEEEEEeec
Q psy4494         115 -----------------SIAFGLGIDKPNVRFVIHHCLSK---------SMENFYQESGRAGRDGQ--IAHCILYYRL  164 (234)
Q Consensus       115 -----------------T~~~~~Gid~~~v~~Vi~~~~P~---------~~~~y~qr~GR~gR~g~--~~~~i~~~~~  164 (234)
                                       |..++||+|.|. +.||.-.+-+         .+..|.|++|||||-|-  .|+.|++-..
T Consensus       646 E~VE~LFqrGlVKVLFATETFAMGVNMPA-RtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD~tGTVii~~~~  722 (1248)
T KOG0947|consen  646 EVVELLFQRGLVKVLFATETFAMGVNMPA-RTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRGLDETGTVIIMCKD  722 (1248)
T ss_pred             HHHHHHHhcCceEEEeehhhhhhhcCCCc-eeEEeeehhhccCcceeecCChhHHhhhccccccccCcCceEEEEecC
Confidence                             999999999994 5555443332         46699999999999874  5777776544

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

Probab=98.20  E-value=2.1e-05  Score=67.89  Aligned_cols=98  Identities=15%  Similarity=0.288  Sum_probs=68.4

Q ss_pred             HHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHc-C-CceeeeccCCCchh----------------hhhcccCCCCC
Q psy4494          65 ELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNR-G-LRVSAYHAKLESNV----------------SIAFGLGIDKP  125 (234)
Q Consensus        65 ~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~-~-~~~~~~h~~~~~~~----------------T~~~~~Gid~~  125 (234)
                      .|...+.+.. .+.+++||+++++..+.+++.|+.. . .++...|+.-....                |..+.||+-+|
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~d~~R~EkV~~fR~G~~~lLiTTTILERGVTfp  372 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSEDQHRKEKVEAFRDGKITLLITTTILERGVTFP  372 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeeccCccHHHHHHHHHcCceEEEEEeehhhcccccc
Confidence            4555555332 4688999999999999999999654 2 34466676543322                99999999999


Q ss_pred             CccEEEE-eecC-CCHhHhhhhhcccccC-CCc-eEEEEEe
Q psy4494         126 NVRFVIH-HCLS-KSMENFYQESGRAGRD-GQI-AHCILYY  162 (234)
Q Consensus       126 ~v~~Vi~-~~~P-~~~~~y~qr~GR~gR~-g~~-~~~i~~~  162 (234)
                      +|+..|. -.-+ -+-..++|-+||+||. .++ |....|.
T Consensus       373 ~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH  413 (441)
T COG4098         373 NVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFH  413 (441)
T ss_pred             cceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEe
Confidence            9997653 2211 2566899999999994 444 4444443

>KOG0923|consensus

Probab=98.16  E-value=3.9e-06  Score=77.63  Aligned_cols=122  Identities=20%  Similarity=0.271  Sum_probs=85.7

Q ss_pred             CCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc---------CCceeeeccCCCchh
Q psy4494          44 KSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR---------GLRVSAYHAKLESNV  114 (234)
Q Consensus        44 ~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~---------~~~~~~~h~~~~~~~  114 (234)
                      -.++.+|...+.+.-.+..+..+.++-.. .+.+-.|||..-.++.+.+...|.+.         .+-+.++|+.++++.
T Consensus       442 yPVdi~Yt~~PEAdYldAai~tVlqIH~t-qp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPsel  520 (902)
T KOG0923|consen  442 YPVDIFYTKAPEADYLDAAIVTVLQIHLT-QPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSEL  520 (902)
T ss_pred             cceeeecccCCchhHHHHHHhhheeeEec-cCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHH
Confidence            34677777644432222222222222111 14566899999888888888888653         455899999998866


Q ss_pred             ------------------hhhcccCCCCCCccEEEEeecC------------------CCHhHhhhhhcccccCCCceEE
Q psy4494         115 ------------------SIAFGLGIDKPNVRFVIHHCLS------------------KSMENFYQESGRAGRDGQIAHC  158 (234)
Q Consensus       115 ------------------T~~~~~Gid~~~v~~Vi~~~~P------------------~~~~~y~qr~GR~gR~g~~~~~  158 (234)
                                        |+.+...+-|++|.+||.-|.-                  -+-.+-.||+|||||.| +|.|
T Consensus       521 QakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKC  599 (902)
T KOG0923|consen  521 QAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKC  599 (902)
T ss_pred             HHhhcCCCCCCceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCce
Confidence                              9999999999999999976553                  23456789999999987 7899


Q ss_pred             EEEeecccH
Q psy4494         159 ILYYRLPDV  167 (234)
Q Consensus       159 i~~~~~~d~  167 (234)
                      +-+|+.+..
T Consensus       600 fRLYt~~aY  608 (902)
T KOG0923|consen  600 FRLYTAWAY  608 (902)
T ss_pred             EEeechhhh
Confidence            999996543

>KOG0951|consensus

Probab=98.15  E-value=2.1e-05  Score=77.30  Aligned_cols=158  Identities=15%  Similarity=0.171  Sum_probs=101.1

Q ss_pred             hhccCchh-HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCCh-HHHHHHHHH-----HHHhhcCCCcEEEEecch
Q psy4494          14 WRTSFYQV-SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQ-KDCLDELAD-----LMSRRFRNQSGIIYTTSI   86 (234)
Q Consensus        14 ~~at~p~~-~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~-~~~~~~l~~-----~l~~~~~~~~~iIf~~t~   86 (234)
                      +|||+|+. ++...++.+++.+.+.-..--|-.+.  +++.+-..++ ...+..+.+     ++. .....++|||+.++
T Consensus       480 LSATLPNy~DV~~Fl~v~~~glf~fd~syRpvPL~--qq~Igi~ek~~~~~~qamNe~~yeKVm~-~agk~qVLVFVHsR  556 (1674)
T KOG0951|consen  480 LSATLPNYEDVASFLRVDPEGLFYFDSSYRPVPLK--QQYIGITEKKPLKRFQAMNEACYEKVLE-HAGKNQVLVFVHSR  556 (1674)
T ss_pred             ecccCCchhhhHHHhccCcccccccCcccCcCCcc--ceEeccccCCchHHHHHHHHHHHHHHHH-hCCCCcEEEEEEec
Confidence            58999996 78888888887665432221222222  3333322211 112333322     232 23447899999999


Q ss_pred             HHHHHHHHHHHHc-------------------------------------CCceeeeccCCCchh---------------
Q psy4494          87 KECEDLREELRNR-------------------------------------GLRVSAYHAKLESNV---------------  114 (234)
Q Consensus        87 ~~~~~l~~~L~~~-------------------------------------~~~~~~~h~~~~~~~---------------  114 (234)
                      +++-+.|..++..                                     ..-.+..|+||+..+               
T Consensus       557 kET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~EdLf~~g~iqv  636 (1674)
T KOG0951|consen  557 KETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVEDLFADGHIQV  636 (1674)
T ss_pred             hHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHHHHHHHHhcCceeE
Confidence            9999999888720                                     112678899998866               


Q ss_pred             ---hhhcccCCCCCCccEEEE----eec------CCCHhHhhhhhcccccCC--CceEEEEEeecccHHHhhhhH
Q psy4494         115 ---SIAFGLGIDKPNVRFVIH----HCL------SKSMENFYQESGRAGRDG--QIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~----~~~------P~~~~~y~qr~GR~gR~g--~~~~~i~~~~~~d~~~~~~~~  174 (234)
                         |-.+++|++.|.=..+|-    ||+      +-++-+-+|+.|||||.+  ..|..|++-+..++......+
T Consensus       637 lvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~gegiiit~~se~qyyls~m  711 (1674)
T KOG0951|consen  637 LVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGEGIIITDHSELQYYLSLM  711 (1674)
T ss_pred             EEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCceeeccCchHhhhhHHhh
Confidence               888899999996555542    443      235779999999999954  456677766666666655544

>KOG0953|consensus

Probab=98.04  E-value=2.1e-05  Score=71.65  Aligned_cols=99  Identities=20%  Similarity=0.275  Sum_probs=76.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCCchh--------------------hhhcccCCCCCCccEEEEe
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIHH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~~  133 (234)
                      .++-+||- =|++..-.+...+..+|.. +++++|+++++.                    |+|.|||+|.. |+.||.|
T Consensus       356 k~GDCvV~-FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL~-IrRiiF~  433 (700)
T KOG0953|consen  356 KPGDCVVA-FSKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNLN-IRRIIFY  433 (700)
T ss_pred             CCCCeEEE-eehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeecccccccccc-eeEEEEe
Confidence            34444443 3577889999999988765 999999999865                    99999999987 9999998


Q ss_pred             ecC---------CCHhHhhhhhcccccCCC---ceEEEEEeecccHHHhhhhHHh
Q psy4494         134 CLS---------KSMENFYQESGRAGRDGQ---IAHCILYYRLPDVFKLSSMVFD  176 (234)
Q Consensus       134 ~~P---------~~~~~y~qr~GR~gR~g~---~~~~i~~~~~~d~~~~~~~~~~  176 (234)
                      ++-         -+..+..|=+|||||.|.   .|.+. -+..+|+..+..+++.
T Consensus       434 sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vT-tl~~eDL~~L~~~l~~  487 (700)
T KOG0953|consen  434 SLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVT-TLHSEDLKLLKRILKR  487 (700)
T ss_pred             ecccCCcccceeccHHHHHHHhhcccccccCCcCceEE-EeeHhhHHHHHHHHhC
Confidence            764         356688999999999764   35444 4556788887777753

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.04  E-value=4.3e-05  Score=73.50  Aligned_cols=66  Identities=23%  Similarity=0.130  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHH-hhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCC-C-chh----------------hhhccc
Q psy4494          60 KDCLDELADLMS-RRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL-E-SNV----------------SIAFGL  120 (234)
Q Consensus        60 ~~~~~~l~~~l~-~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~-~-~~~----------------T~~~~~  120 (234)
                      .++...+.+-+. ....++|+||-+.|.+..|.++..|...|++...+++.. . ..+                |+.+||
T Consensus       407 ~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~AG~~G~VTIATNMAGR  486 (870)
T CHL00122        407 LSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQAGRKGSITIATNMAGR  486 (870)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHhcCCCCcEEEeccccCC
Confidence            445555555443 233578999999999999999999999999999999863 1 222                999999


Q ss_pred             CCCCC
Q psy4494         121 GIDKP  125 (234)
Q Consensus       121 Gid~~  125 (234)
                      |.||.
T Consensus       487 GTDI~  491 (870)
T CHL00122        487 GTDII  491 (870)
T ss_pred             CcCee
Confidence            99985

>KOG0390|consensus

Probab=97.73  E-value=0.00023  Score=67.91  Aligned_cols=104  Identities=24%  Similarity=0.151  Sum_probs=79.8

Q ss_pred             ChHHHHHHHHHHHHh-hcCCCcEEEEecchHHHHHHHHHHHH-cCCceeeeccCCCchh---------------------
Q psy4494          58 AQKDCLDELADLMSR-RFRNQSGIIYTTSIKECEDLREELRN-RGLRVSAYHAKLESNV---------------------  114 (234)
Q Consensus        58 ~~~~~~~~l~~~l~~-~~~~~~~iIf~~t~~~~~~l~~~L~~-~~~~~~~~h~~~~~~~---------------------  114 (234)
                      ....++..|..++.. .....--.|++.+.....++.+.+.. +|..+..+||.++..+                     
T Consensus       575 ~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlS  654 (776)
T KOG0390|consen  575 SKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLS  654 (776)
T ss_pred             hhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEe
Confidence            345566666666521 11222235556666677776666654 4999999999999877                     


Q ss_pred             hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEE
Q psy4494         115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY  161 (234)
Q Consensus       115 T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~  161 (234)
                      +.|-|.||+.-+...||.||+.+++..=.|.++|+-|+|++-.+.+|
T Consensus       655 sKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iY  701 (776)
T KOG0390|consen  655 SKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIY  701 (776)
T ss_pred             cccccCceeecccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEE
Confidence            88899999999999999999999999999999999999987655554

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.68  E-value=0.00029  Score=68.07  Aligned_cols=67  Identities=19%  Similarity=0.174  Sum_probs=52.2

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccC-CC-chh----------------hhhcc
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAK-LE-SNV----------------SIAFG  119 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~-~~-~~~----------------T~~~~  119 (234)
                      ..++...+.+-+.+. ..+.|+||-+.|.+..|.++..|...|++...+++. .. ..+                |+.+|
T Consensus       421 ~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~AG~~GaVTIATNMAG  500 (939)
T PRK12902        421 EIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQAGRKGAVTIATNMAG  500 (939)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHhcCCCCcEEEeccCCC
Confidence            345666666555432 368899999999999999999999999998888886 22 222                88999


Q ss_pred             cCCCCC
Q psy4494         120 LGIDKP  125 (234)
Q Consensus       120 ~Gid~~  125 (234)
                      ||.||.
T Consensus       501 RGTDIk  506 (939)
T PRK12902        501 RGTDII  506 (939)
T ss_pred             CCcCEe
Confidence            999985

>KOG0920|consensus

Probab=97.63  E-value=0.00021  Score=69.41  Aligned_cols=108  Identities=24%  Similarity=0.304  Sum_probs=82.8

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc-------CCceeeeccCCCchh------------------h
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR-------GLRVSAYHAKLESNV------------------S  115 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~-------~~~~~~~h~~~~~~~------------------T  115 (234)
                      +.+..+...+-+....+..|||-+...+...+.+.|..+       .+-+.++|+.|+..+                  |
T Consensus       398 ~Li~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaT  477 (924)
T KOG0920|consen  398 DLIEDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILAT  477 (924)
T ss_pred             HHHHHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhh
Confidence            344455544444445678999999999999999999753       256899999999866                  9


Q ss_pred             hhcccCCCCCCccEEEEeecCC------------------CHhHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         116 IAFGLGIDKPNVRFVIHHCLSK------------------SMENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       116 ~~~~~Gid~~~v~~Vi~~~~P~------------------~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                      +.+...|-|++|-+||..+.-+                  +-.+-.||.|||||. ++|.|+-+|+...+..
T Consensus       478 NIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~~~~~  548 (924)
T KOG0920|consen  478 NIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRSRYEK  548 (924)
T ss_pred             hhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechhhhhh
Confidence            9999999999999999875422                  223557999999997 4688999998765544

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

Probab=97.63  E-value=0.00018  Score=68.53  Aligned_cols=76  Identities=24%  Similarity=0.299  Sum_probs=62.0

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc-----CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEE
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR-----GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIH  132 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~  132 (234)
                      .+++||||.+..+|+.+...|...     |--+..+.|+-.+.+                  .+.+..|||+|.|..+|.
T Consensus       426 ~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~~q~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF  505 (875)
T COG4096         426 IGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQAQALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVF  505 (875)
T ss_pred             cCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchhhHHHHHHHHhcCCCCceEEehhhhhcCCCchheeeeee
Confidence            578999999999999999999864     222455555544433                  566777999999999999


Q ss_pred             eecCCCHhHhhhhhccccc
Q psy4494         133 HCLSKSMENFYQESGRAGR  151 (234)
Q Consensus       133 ~~~P~~~~~y~qr~GR~gR  151 (234)
                      +..=.|...|.|++||+-|
T Consensus       506 ~r~VrSktkF~QMvGRGTR  524 (875)
T COG4096         506 DRKVRSKTKFKQMVGRGTR  524 (875)
T ss_pred             hhhhhhHHHHHHHhcCccc
Confidence            9888999999999999988

>KOG0924|consensus

Probab=97.61  E-value=0.00024  Score=66.37  Aligned_cols=89  Identities=24%  Similarity=0.353  Sum_probs=71.0

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc----------CCceeeeccCCCchh------------------hhhcccCCCCCCc
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR----------GLRVSAYHAKLESNV------------------SIAFGLGIDKPNV  127 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~----------~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v  127 (234)
                      ++-.+||..-.+..|.....+.+.          ++.+.++++.++..-                  |+.+...+-+|+|
T Consensus       563 ~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI  642 (1042)
T KOG0924|consen  563 PGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGI  642 (1042)
T ss_pred             CCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecce
Confidence            456799998888777766666532          567899999988654                  9999999999999


Q ss_pred             cEEEEeec------------------CCCHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         128 RFVIHHCL------------------SKSMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       128 ~~Vi~~~~------------------P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      .+||..+.                  |-+-.+-.||.|||||.| +|.|+-+|+..
T Consensus       643 ~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~  697 (1042)
T KOG0924|consen  643 RYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTED  697 (1042)
T ss_pred             EEEEecCceeeeecccccccceeEEEechhccchhhccccCCCC-Ccceeeehhhh
Confidence            99998754                  445557789999999987 78999999873

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

Probab=97.41  E-value=0.00032  Score=68.88  Aligned_cols=89  Identities=30%  Similarity=0.435  Sum_probs=67.4

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHc----------------------------CCc-------------eeeeccCCCch
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNR----------------------------GLR-------------VSAYHAKLESN  113 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~----------------------------~~~-------------~~~~h~~~~~~  113 (234)
                      +.-++|+|+=|++.|+..+..+...                            +++             +.+.|++|-+.
T Consensus       378 ~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~  457 (1041)
T COG4581         378 NLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPA  457 (1041)
T ss_pred             cCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchH
Confidence            4568999999999999999887511                            121             44677887775


Q ss_pred             h------------------hhhcccCCCCCCccEEEEeecC---------CCHhHhhhhhcccccCCCc--eEEEEEeec
Q psy4494         114 V------------------SIAFGLGIDKPNVRFVIHHCLS---------KSMENFYQESGRAGRDGQI--AHCILYYRL  164 (234)
Q Consensus       114 ~------------------T~~~~~Gid~~~v~~Vi~~~~P---------~~~~~y~qr~GR~gR~g~~--~~~i~~~~~  164 (234)
                      .                  |..+++|+|.| ++.|+...+-         -+...|.|..|||||.|..  |++|+...+
T Consensus       458 ~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmP-artvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~G~vI~~~~~  536 (1041)
T COG4581         458 IKELVEELFQEGLVKVVFATETFAIGINMP-ARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVLGTVIVIEPP  536 (1041)
T ss_pred             HHHHHHHHHhccceeEEeehhhhhhhcCCc-ccceeeeeeEEecCCceeecChhHHHHhhhhhccccccccceEEEecCC
Confidence            4                  99999999999 6666665442         3677999999999998754  777777444

>KOG0384|consensus

Probab=97.37  E-value=0.00077  Score=66.50  Aligned_cols=91  Identities=23%  Similarity=0.220  Sum_probs=78.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhhcccCCCCCCccEEEEe
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIAFGLGIDKPNVRFVIHH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~~~~Gid~~~v~~Vi~~  133 (234)
                      .+.++|||..-.+..+-|+++|..++++..-+-|.+..+.                     |-|-|.|||....+.||.|
T Consensus       698 ~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLatADTVIIF  777 (1373)
T KOG0384|consen  698 GGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLATADTVIIF  777 (1373)
T ss_pred             CCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccccceEEEe
Confidence            3679999999999999999999999999888888876543                     9999999999999999999


Q ss_pred             ecCCCHhHhhhhhcccccCCCceE--EEEEeecc
Q psy4494         134 CLSKSMENFYQESGRAGRDGQIAH--CILYYRLP  165 (234)
Q Consensus       134 ~~P~~~~~y~qr~GR~gR~g~~~~--~i~~~~~~  165 (234)
                      |--+++-.=+|-..||-|-|++..  .+-|++.+
T Consensus       778 DSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~  811 (1373)
T KOG0384|consen  778 DSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKN  811 (1373)
T ss_pred             CCCCCcchHHHHHHHHHhhcccceEEEEEEecCC
Confidence            999999999999999999998644  34445544

>KOG0387|consensus

Probab=97.26  E-value=0.0011  Score=62.88  Aligned_cols=100  Identities=20%  Similarity=0.198  Sum_probs=82.4

Q ss_pred             HHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHH-HcCCceeeeccCCCchh--------------------hhhcc
Q psy4494          62 CLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELR-NRGLRVSAYHAKLESNV--------------------SIAFG  119 (234)
Q Consensus        62 ~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~-~~~~~~~~~h~~~~~~~--------------------T~~~~  119 (234)
                      ++..+.+++.... .+.++|+|..|+....-+-..|. ..|+...-+-|..+...                    |-+-|
T Consensus       531 Km~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTrvGG  610 (923)
T KOG0387|consen  531 KMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTRVGG  610 (923)
T ss_pred             hHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEecccc
Confidence            5555666665332 46799999999999999999998 57888888888766544                    88899


Q ss_pred             cCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEE
Q psy4494         120 LGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY  161 (234)
Q Consensus       120 ~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~  161 (234)
                      .|++.-+.+.||.||+-+++..=.|-.-||-|-|++-..++|
T Consensus       611 LGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VY  652 (923)
T KOG0387|consen  611 LGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVY  652 (923)
T ss_pred             cccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEE
Confidence            999999999999999999999999999999999987544443

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

Probab=97.18  E-value=0.00071  Score=64.99  Aligned_cols=108  Identities=26%  Similarity=0.264  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHHH-hhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccCC
Q psy4494          60 KDCLDELADLMS-RRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLGI  122 (234)
Q Consensus        60 ~~~~~~l~~~l~-~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~Gi  122 (234)
                      .+|...+++-+. ....++|+||-+.+.+..|.+++.|++.|++-..+.+....++                |+-+|||-
T Consensus       412 ~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~EA~Iia~AG~~gaVTiATNMAGRGT  491 (822)
T COG0653         412 EEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAREAEIIAQAGQPGAVTIATNMAGRGT  491 (822)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHHHHHHhhcCCCCccccccccccCCc
Confidence            456666655554 3346899999999999999999999999998766666555444                88899999


Q ss_pred             CCCCcc-----------EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         123 DKPNVR-----------FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       123 d~~~v~-----------~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      |+.--.           +||--.--++-.-=-|-.||+||.|.+|.+..|++-.|.
T Consensus       492 DIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSleD~  547 (822)
T COG0653         492 DIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDD  547 (822)
T ss_pred             ccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhHHH
Confidence            986222           355443333433335888999999999999999887654

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

Probab=97.11  E-value=0.0015  Score=63.72  Aligned_cols=72  Identities=24%  Similarity=0.480  Sum_probs=57.0

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecc---hHHHHHHHHHHHHcCCceeeeccCCCchh-----------------hhhcccCC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTS---IKECEDLREELRNRGLRVSAYHAKLESNV-----------------SIAFGLGI  122 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t---~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------------T~~~~~Gi  122 (234)
                      .+.+.++++.  -+.-+|||++.   ++.+++++++|+++|+.+..+|+.-...-                 ..++-||+
T Consensus       324 ~e~~~elvk~--lG~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~~~~~le~F~~GeidvLVGvAsyYG~lVRGl  401 (1187)
T COG1110         324 LEKVVELVKK--LGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKEEALEDFEEGEVDVLVGVASYYGVLVRGL  401 (1187)
T ss_pred             HHHHHHHHHH--hCCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeeccchhhhhhhccCceeEEEEecccccceeecC
Confidence            4444455543  24458999999   99999999999999999999998642111                 67788999


Q ss_pred             CCC-CccEEEEeecC
Q psy4494         123 DKP-NVRFVIHHCLS  136 (234)
Q Consensus       123 d~~-~v~~Vi~~~~P  136 (234)
                      |.| .|+++|.||.|
T Consensus       402 DLP~rirYaIF~GvP  416 (1187)
T COG1110         402 DLPHRIRYAVFYGVP  416 (1187)
T ss_pred             CchhheeEEEEecCC
Confidence            999 56999999999

>KOG0385|consensus

Probab=97.08  E-value=0.0051  Score=58.45  Aligned_cols=103  Identities=19%  Similarity=0.125  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhhccc
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIAFGL  120 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~~~~  120 (234)
                      .++.|+.-|++  .+.+++||..-....+-+-++..-+++...-+-|+++-++                     |-|-|.
T Consensus       475 vLDkLL~~Lk~--~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRAGGL  552 (971)
T KOG0385|consen  475 VLDKLLPKLKE--QGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRAGGL  552 (971)
T ss_pred             hHHHHHHHHHh--CCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecccccc
Confidence            34444444443  5789999998888888888888888999888999988766                     999999


Q ss_pred             CCCCCCccEEEEeecCCCHhHhhhhhcccccCCCce--EEEEEeeccc
Q psy4494         121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIA--HCILYYRLPD  166 (234)
Q Consensus       121 Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~--~~i~~~~~~d  166 (234)
                      |||....+.||.||.-+++-.=+|..-||-|-|+..  .++-+++.+.
T Consensus       553 GINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitent  600 (971)
T KOG0385|consen  553 GINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENT  600 (971)
T ss_pred             ccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccch
Confidence            999999999999999999999999999999988764  4444455543

>KOG0926|consensus

Probab=96.97  E-value=0.0035  Score=59.82  Aligned_cols=49  Identities=27%  Similarity=0.474  Sum_probs=40.2

Q ss_pred             hhhcccCCCCCCccEEEEeecCC--------CH----------hHhhhhhcccccCCCceEEEEEeec
Q psy4494         115 SIAFGLGIDKPNVRFVIHHCLSK--------SM----------ENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       115 T~~~~~Gid~~~v~~Vi~~~~P~--------~~----------~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      |+++...+-||+|++||..|.-+        .+          .+=-||+|||||.| +|+|+-+|+.
T Consensus       637 TNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg-pGHcYRLYSS  703 (1172)
T KOG0926|consen  637 TNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG-PGHCYRLYSS  703 (1172)
T ss_pred             ccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC-CCceeehhhh
Confidence            99999999999999999876543        12          24469999999987 6899999986

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

Probab=96.89  E-value=0.01  Score=58.05  Aligned_cols=83  Identities=19%  Similarity=0.115  Sum_probs=73.8

Q ss_pred             cEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------------hhhcccCCCCCCccEEEEeecCC
Q psy4494          78 SGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIHHCLSK  137 (234)
Q Consensus        78 ~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~~~~P~  137 (234)
                      +++||.......+-+...|...++....++|+++.+.                    +.+.|.|++...-++||+||..+
T Consensus       713 kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~w  792 (866)
T COG0553         713 KVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWW  792 (866)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEecccc
Confidence            8999999999999999999999988999999886443                    67999999999999999999999


Q ss_pred             CHhHhhhhhcccccCCCceEEEE
Q psy4494         138 SMENFYQESGRAGRDGQIAHCIL  160 (234)
Q Consensus       138 ~~~~y~qr~GR~gR~g~~~~~i~  160 (234)
                      ++....|...|+-|.|+....-+
T Consensus       793 np~~~~Qa~dRa~RigQ~~~v~v  815 (866)
T COG0553         793 NPAVELQAIDRAHRIGQKRPVKV  815 (866)
T ss_pred             ChHHHHHHHHHHHHhcCcceeEE
Confidence            99999999999999887654433

>KOG0925|consensus

Probab=96.38  E-value=0.016  Score=52.62  Aligned_cols=91  Identities=20%  Similarity=0.278  Sum_probs=67.6

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc---------CCceeeeccCCCchh-------------------hhhcccCCCCCCc
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR---------GLRVSAYHAKLESNV-------------------SIAFGLGIDKPNV  127 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~---------~~~~~~~h~~~~~~~-------------------T~~~~~Gid~~~v  127 (234)
                      ++-.+||....++.+...+.+...         .+.+.++|-...+.-                   |+.+...+-+++|
T Consensus       253 ~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLyP~~qq~iFep~p~~~~~~~~RkvVvstniaetsltidgi  332 (699)
T KOG0925|consen  253 PGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLYPAQQQRIFEPAPEKRNGAYGRKVVVSTNIAETSLTIDGI  332 (699)
T ss_pred             CCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecCchhhccccCCCCcccCCCccceEEEEecchheeeeeccE
Confidence            566899999999988888877632         345777774333221                   7777788899999


Q ss_pred             cEEEEeec------------------CCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         128 RFVIHHCL------------------SKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       128 ~~Vi~~~~------------------P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      .+||.-|+                  |-|-.+--||.||+||. ++|.|.-+|+.+-+
T Consensus       333 v~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~~~  389 (699)
T KOG0925|consen  333 VFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  389 (699)
T ss_pred             EEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHHhh
Confidence            99997665                  44555778899999886 57889999987544

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

Probab=96.32  E-value=0.047  Score=53.90  Aligned_cols=90  Identities=18%  Similarity=0.115  Sum_probs=59.5

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHH----cCCceeeeccCCCchh---------------hhhcccCCCCCCcc--EEEEe
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRN----RGLRVSAYHAKLESNV---------------SIAFGLGIDKPNVR--FVIHH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~---------------T~~~~~Gid~~~v~--~Vi~~  133 (234)
                      .+++++||++|.+..+.++..|..    .++.+..-+.+.+...               |+.+.+|||+++..  .||..
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~q~~~~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~  752 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEVLAQGINGSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIP  752 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhhhccccCceEEecCCCccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEe
Confidence            457899999999999999999975    2444322111111211               88999999999876  45666


Q ss_pred             ecCC----C--------------------------HhHhhhhhcccccCCCceEEEEEeec
Q psy4494         134 CLSK----S--------------------------MENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       134 ~~P~----~--------------------------~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      ++|-    +                          +..+.|-+||.=|..+..-++++.+.
T Consensus       753 ~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~ilD~  813 (850)
T TIGR01407       753 RLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVILDR  813 (850)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEEcc
Confidence            6662    1                          22456788999887655334555544

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.

>KOG1000|consensus

Probab=96.28  E-value=0.015  Score=52.91  Aligned_cols=83  Identities=17%  Similarity=0.171  Sum_probs=73.5

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------------hhhcccCCCCCCccEEEEee
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIHHC  134 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~~~  134 (234)
                      ++.+.+||+......+.+...+.++++...-+.|..++..                    -.|.|+|+++...+.||...
T Consensus       491 ~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaE  570 (689)
T KOG1000|consen  491 PPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAE  570 (689)
T ss_pred             CCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEE
Confidence            4668999999999999999999999998888888887765                    56889999999999999999


Q ss_pred             cCCCHhHhhhhhcccccCCCceE
Q psy4494         135 LSKSMENFYQESGRAGRDGQIAH  157 (234)
Q Consensus       135 ~P~~~~~y~qr~GR~gR~g~~~~  157 (234)
                      +|+++.-++|--.|+-|-|+++.
T Consensus       571 L~wnPgvLlQAEDRaHRiGQkss  593 (689)
T KOG1000|consen  571 LHWNPGVLLQAEDRAHRIGQKSS  593 (689)
T ss_pred             ecCCCceEEechhhhhhccccce
Confidence            99999999998888888887643

>COG4889 Predicted helicase [General function prediction only]

Probab=96.27  E-value=0.0019  Score=62.16  Aligned_cols=87  Identities=23%  Similarity=0.353  Sum_probs=65.2

Q ss_pred             CcEEEEecchHHHHHHHHHHHH-------------cCCc--eeeeccCCCchh---------------------hhhccc
Q psy4494          77 QSGIIYTTSIKECEDLREELRN-------------RGLR--VSAYHAKLESNV---------------------SIAFGL  120 (234)
Q Consensus        77 ~~~iIf~~t~~~~~~l~~~L~~-------------~~~~--~~~~h~~~~~~~---------------------T~~~~~  120 (234)
                      +++|-||.+++....+++.+..             .++.  +.+..|.|+..+                     --.++.
T Consensus       461 ~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcLSE  540 (1518)
T COG4889         461 QRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCLSE  540 (1518)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhhhc
Confidence            5789999999988888876642             2344  444446666543                     334677


Q ss_pred             CCCCCCccEEEEeecCCCHhHhhhhhccccc--CCC-ceEEEEEee
Q psy4494         121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGR--DGQ-IAHCILYYR  163 (234)
Q Consensus       121 Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR--~g~-~~~~i~~~~  163 (234)
                      |+|+|..+.||.|++-.++.+.+|-+||.-|  -|+ -|..|+-+.
T Consensus       541 GVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIa  586 (1518)
T COG4889         541 GVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIA  586 (1518)
T ss_pred             CCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEec
Confidence            9999999999999999999999999999999  243 376666553

>KOG0949|consensus

Probab=96.16  E-value=0.0059  Score=59.46  Aligned_cols=58  Identities=29%  Similarity=0.461  Sum_probs=43.5

Q ss_pred             eeeeccCCCchh------------------hhhcccCCCCCCccEEEEeec--CCCHhHhhhhhcccccCCC--ceEEEE
Q psy4494         103 VSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCL--SKSMENFYQESGRAGRDGQ--IAHCIL  160 (234)
Q Consensus       103 ~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~--P~~~~~y~qr~GR~gR~g~--~~~~i~  160 (234)
                      +.+.|++++..+                  |..++.|||.| .+.|+..+-  --++-.|-|++|||||.|=  -|..+.
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMP-CrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~F 1043 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMP-CRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVF 1043 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCC-ceeEEEeccccccCchhHHhhhccccccccccccceEE
Confidence            567788888766                  99999999999 566665433  2367799999999999763  455554


Q ss_pred             E
Q psy4494         161 Y  161 (234)
Q Consensus       161 ~  161 (234)
                      +
T Consensus      1044 m 1044 (1330)
T KOG0949|consen 1044 M 1044 (1330)
T ss_pred             E
Confidence            4

>KOG0391|consensus

Probab=96.05  E-value=0.057  Score=53.92  Aligned_cols=103  Identities=15%  Similarity=0.115  Sum_probs=78.9

Q ss_pred             ChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------------hhh
Q psy4494          58 AQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------------SIA  117 (234)
Q Consensus        58 ~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------------T~~  117 (234)
                      .+-+.+..|++-|+.  .+.++|||+.-.+..+-|-.+|..+|+.-.-+.|....++                    |-.
T Consensus      1260 GKLQtLAiLLqQLk~--eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrS 1337 (1958)
T KOG0391|consen 1260 GKLQTLAILLQQLKS--EGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRS 1337 (1958)
T ss_pred             chHHHHHHHHHHHHh--cCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccC
Confidence            344556666665553  5789999999999999999999999998888888877665                    777


Q ss_pred             cccCCCCCCccEEEEeecCCCHh------HhhhhhcccccCCCceEEEEEeeccc
Q psy4494         118 FGLGIDKPNVRFVIHHCLSKSME------NFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       118 ~~~Gid~~~v~~Vi~~~~P~~~~------~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      -|.|||.-+.+.||.||--+++.      +.-||||++ |   .-+.+-|++...
T Consensus      1338 ggvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqt-R---DVHIYRLISe~T 1388 (1958)
T KOG0391|consen 1338 GGVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQT-R---DVHIYRLISERT 1388 (1958)
T ss_pred             CccccccccCceEEEecCCCCchhhhHHHHHHHhhcCc-c---ceEEEEeeccch
Confidence            78899999999999999988755      666777776 3   344555555543

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

Probab=96.04  E-value=0.027  Score=44.36  Aligned_cols=89  Identities=22%  Similarity=0.235  Sum_probs=51.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcC----CceeeeccCCCchh---------------hh--hcccCCCCCC--ccEEE
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRG----LRVSAYHAKLESNV---------------SI--AFGLGIDKPN--VRFVI  131 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~----~~~~~~h~~~~~~~---------------T~--~~~~Gid~~~--v~~Vi  131 (234)
                      .++.++||++|.+..+.+.+.+....    +.+.. .++.+.+.               +.  .+..|||+++  .+.||
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~-q~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~vi   86 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFV-QGSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAVI   86 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEE-STCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeee-cCcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhheee
Confidence            46789999999999999999998653    22222 22222211               33  6788999995  77899


Q ss_pred             EeecCC----CH--------------------------hHhhhhhcccccCCCceEEEEEeec
Q psy4494         132 HHCLSK----SM--------------------------ENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       132 ~~~~P~----~~--------------------------~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      ..++|-    ++                          ....|-+||+=|..+.--++++.+.
T Consensus        87 i~glPfp~~~d~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~Qa~GR~iR~~~D~g~i~llD~  149 (167)
T PF13307_consen   87 IVGLPFPPPSDPLVQAKREYLDKQGKNPFRDWYLPPAIRKLKQAIGRLIRSEDDYGVIILLDS  149 (167)
T ss_dssp             EES-----TTCHHHHHHHHHHHHCCTTCHHHHTHHHHHHHHHHHHHCC--STT-EEEEEEESG
T ss_pred             ecCCCCCCCCCHHHHHHHHHHHHHhccchhhHhhHHHHHHHhhhcCcceeccCCcEEEEEEcC
Confidence            998883    21                          1235678999997766445555543

>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=95.99  E-value=0.13  Score=46.75  Aligned_cols=104  Identities=13%  Similarity=0.127  Sum_probs=79.3

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hh--hcccCCCCCCccEEEEee
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SI--AFGLGIDKPNVRFVIHHC  134 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~--~~~~Gid~~~v~~Vi~~~  134 (234)
                      ..+.+|||++|--+=-+|-++|++.++....+|--.+..+                  |.  -+=+=..+.+|++||.|+
T Consensus       299 ~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~irGi~~viFY~  378 (442)
T PF06862_consen  299 KMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIRGIRHVIFYG  378 (442)
T ss_pred             CCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceecCCcEEEEEC
Confidence            4567999999999999999999998888777776666555                  11  112245678899999999


Q ss_pred             cCCCHhHhhhhhcccccCC------CceEEEEEeecccHHHhhhhHHhhh
Q psy4494         135 LSKSMENFYQESGRAGRDG------QIAHCILYYRLPDVFKLSSMVFDQQ  178 (234)
Q Consensus       135 ~P~~~~~y~qr~GR~gR~g------~~~~~i~~~~~~d~~~~~~~~~~~~  178 (234)
                      +|..+.=|..-+.-.+...      ....+.++|+..|...+..++..++
T Consensus       379 ~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIVGt~r  428 (442)
T PF06862_consen  379 PPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIVGTER  428 (442)
T ss_pred             CCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHhCHHH
Confidence            9999887766665444433      3689999999999998888875543

; GO: 0005634 nucleus

>KOG0388|consensus

Probab=95.87  E-value=0.055  Score=51.42  Aligned_cols=82  Identities=22%  Similarity=0.149  Sum_probs=72.2

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-------------------hhhcccCCCCCCccEEEEeec
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-------------------SIAFGLGIDKPNVRFVIHHCL  135 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-------------------T~~~~~Gid~~~v~~Vi~~~~  135 (234)
                      .+.++++|+.-.+..+-+-++|...+++-.-+.|+.....                   |-|-|.||+....+.||.||.
T Consensus      1043 egHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViFYdS 1122 (1185)
T KOG0388|consen 1043 EGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIFYDS 1122 (1185)
T ss_pred             CCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEEecC
Confidence            4678999999999999999999999988888888765544                   889999999999999999999


Q ss_pred             CCCHhHhhhhhcccccCCCce
Q psy4494         136 SKSMENFYQESGRAGRDGQIA  156 (234)
Q Consensus       136 P~~~~~y~qr~GR~gR~g~~~  156 (234)
                      -+++.-=.|...||-|-|+.-
T Consensus      1123 DWNPT~D~QAMDRAHRLGQTr 1143 (1185)
T KOG0388|consen 1123 DWNPTADQQAMDRAHRLGQTR 1143 (1185)
T ss_pred             CCCcchhhHHHHHHHhccCcc
Confidence            999999999999999988653

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

Probab=95.61  E-value=0.11  Score=49.93  Aligned_cols=75  Identities=13%  Similarity=0.153  Sum_probs=55.6

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc-----CCceeeeccCCCch------------------------h------------
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR-----GLRVSAYHAKLESN------------------------V------------  114 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~------------------------~------------  114 (234)
                      ..+++|||.++..|..+.+.|.+.     +..+..+++..+.+                        .            
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            478999999999999999998654     23455555543221                        0            


Q ss_pred             ----hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccccc
Q psy4494         115 ----SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR  151 (234)
Q Consensus       115 ----T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR  151 (234)
                          ++-+..|.|.|.+..++... |-..-.++|.+||+-|
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldK-plk~h~LlQai~R~nR  633 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDK-PLKYHGLLQAIARTNR  633 (667)
T ss_pred             EEEEEcccccccCCCccceEEEec-cccccHHHHHHHHhcc
Confidence                66667799999998877554 5444568999999999

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

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=95.57  E-value=0.38  Score=46.52  Aligned_cols=60  Identities=15%  Similarity=0.219  Sum_probs=43.4

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc-CCceeeeccCCCchh-------------------hhhcccCCCCCC--ccEEEEe
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR-GLRVSAYHAKLESNV-------------------SIAFGLGIDKPN--VRFVIHH  133 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~-------------------T~~~~~Gid~~~--v~~Vi~~  133 (234)
                      ++.++||++|.+..+.++..|... +.+ ...+|..+...                   |..+..|||+|+  .+.||..
T Consensus       534 ~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~~~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~vII~  612 (697)
T PRK11747        534 HKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGDQPRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQVIIT  612 (697)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCCchHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEEEEE
Confidence            445899999999999999999743 333 33355433211                   667778999986  6889888


Q ss_pred             ecC
Q psy4494         134 CLS  136 (234)
Q Consensus       134 ~~P  136 (234)
                      .+|
T Consensus       613 kLP  615 (697)
T PRK11747        613 KIP  615 (697)
T ss_pred             cCC
Confidence            777

>KOG0389|consensus

Probab=95.57  E-value=0.11  Score=49.81  Aligned_cols=113  Identities=17%  Similarity=0.117  Sum_probs=86.6

Q ss_pred             CCChHHHHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------------
Q psy4494          56 PAAQKDCLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------------  114 (234)
Q Consensus        56 ~~~~~~~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------------  114 (234)
                      +.-...|+..|..+|.+-- .+.+++||..-....+-|-..|...++.-.-+-|...-..                    
T Consensus       756 ~~mdSgK~r~L~~LLp~~k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLS  835 (941)
T KOG0389|consen  756 LWMDSGKCRKLKELLPKIKKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLS  835 (941)
T ss_pred             hhhhhhhHhHHHHHHHHHhhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEe
Confidence            3334456666666665321 4689999998888888888889888888888877765443                    


Q ss_pred             hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCC--ceEEEEEeecccHH
Q psy4494         115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQ--IAHCILYYRLPDVF  168 (234)
Q Consensus       115 T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~--~~~~i~~~~~~d~~  168 (234)
                      |.|-|.||+....+.||.||+--++-+=.|.--|+-|.|+  +-+.+-+++...+.
T Consensus       836 TKAGG~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIE  891 (941)
T KOG0389|consen  836 TKAGGFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIE  891 (941)
T ss_pred             eccCcceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecCcHH
Confidence            9999999999999999999998887777888888888775  56677777776544

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

Probab=94.98  E-value=0.18  Score=48.60  Aligned_cols=76  Identities=25%  Similarity=0.330  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHc--CCceeeeccCCCchh--------------------hhhcccCCCCCCccEEEEeecCC--------
Q psy4494          88 ECEDLREELRNR--GLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIHHCLSK--------  137 (234)
Q Consensus        88 ~~~~l~~~L~~~--~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~~~~P~--------  137 (234)
                      -+|++.+.|+..  +.++..+-++.+...                    |-.+.-|.|+|+|..|...|.-.        
T Consensus       492 GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfR  571 (730)
T COG1198         492 GTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFR  571 (730)
T ss_pred             cHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcc
Confidence            356666666554  556666666655533                    77778899999999987765432        


Q ss_pred             C----HhHhhhhhcccccCCCceEEEEEee
Q psy4494         138 S----MENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       138 ~----~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                      .    .-.+.|=.|||||.+.+|..++=--
T Consensus       572 A~Er~fqll~QvaGRAgR~~~~G~VvIQT~  601 (730)
T COG1198         572 ASERTFQLLMQVAGRAGRAGKPGEVVIQTY  601 (730)
T ss_pred             hHHHHHHHHHHHHhhhccCCCCCeEEEEeC
Confidence            2    3367889999999988877666443

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

Probab=94.56  E-value=0.005  Score=57.53  Aligned_cols=36  Identities=53%  Similarity=0.869  Sum_probs=33.2

Q ss_pred             HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCC
Q psy4494          22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPA   57 (234)
Q Consensus        22 ~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~   57 (234)
                      +++|+||||+|+||+++|..+|.++..||+..++.+
T Consensus       287 T~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAG  322 (590)
T COG0514         287 TNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAG  322 (590)
T ss_pred             eccccCccCCCCceEEEEecCCCCHHHHHHHHhhcc
Confidence            689999999999999999999999999999888653

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

Probab=94.52  E-value=0.5  Score=45.20  Aligned_cols=97  Identities=18%  Similarity=0.156  Sum_probs=66.7

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCC-ceeeeccCCCchh----------------hhhcccCCCCC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGL-RVSAYHAKLESNV----------------SIAFGLGIDKP  125 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~-~~~~~h~~~~~~~----------------T~~~~~Gid~~  125 (234)
                      ...+..++..  .+++++||++|.+..+.+++.+..... .....+|..+..+                +..+..|+|++
T Consensus       468 ~~~i~~~~~~--~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~  545 (654)
T COG1199         468 AAYLREILKA--SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDEREELLEKFKASGEGLILVGGGSFWEGVDFP  545 (654)
T ss_pred             HHHHHHHHhh--cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcHHHHHHHHHHhcCCeEEEeeccccCcccCC
Confidence            3344444432  456899999999999999999987664 2445566655543                66677899999


Q ss_pred             Cc--cEEEEeecCCC------------------------------HhHhhhhhcccccCCCc-eEEEEE
Q psy4494         126 NV--RFVIHHCLSKS------------------------------MENFYQESGRAGRDGQI-AHCILY  161 (234)
Q Consensus       126 ~v--~~Vi~~~~P~~------------------------------~~~y~qr~GR~gR~g~~-~~~i~~  161 (234)
                      +=  +.||..++|--                              +....|-+||.=|.-.. |..+++
T Consensus       546 g~~l~~vvI~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivll  614 (654)
T COG1199         546 GDALRLVVIVGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLL  614 (654)
T ss_pred             CCCeeEEEEEecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEe
Confidence            54  67888877632                              34668889999885443 544443

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

Probab=94.38  E-value=1.3  Score=44.29  Aligned_cols=61  Identities=18%  Similarity=0.152  Sum_probs=42.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcC----CceeeeccC--CCchh---------------hhhcccCCCCCC--ccEEE
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRG----LRVSAYHAK--LESNV---------------SIAFGLGIDKPN--VRFVI  131 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~----~~~~~~h~~--~~~~~---------------T~~~~~Gid~~~--v~~Vi  131 (234)
                      .+++++|+++|.+..+.+++.|....    +.+.. .|.  .+...               |..+..|||+|+  .+.||
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~-Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~vi  829 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLA-QGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLV  829 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEe-cCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEE
Confidence            45789999999999999999997542    22222 221  12211               777888999996  47788


Q ss_pred             EeecC
Q psy4494         132 HHCLS  136 (234)
Q Consensus       132 ~~~~P  136 (234)
                      ...+|
T Consensus       830 I~kLP  834 (928)
T PRK08074        830 IVRLP  834 (928)
T ss_pred             EecCC
Confidence            87766

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=93.75  E-value=1.1  Score=44.11  Aligned_cols=24  Identities=21%  Similarity=0.340  Sum_probs=21.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHH
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRN   98 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~   98 (234)
                      .+.++||||+..+.|..|.++|..
T Consensus       294 ~~~~iLI~~~d~~T~~qL~~~L~~  317 (814)
T TIGR00596       294 GPGKVLIMCSDNRTCLQLRDYLTT  317 (814)
T ss_pred             CCCcEEEEEcchHHHHHHHHHHHh
Confidence            356799999999999999998865

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

>KOG0351|consensus

Probab=93.71  E-value=0.015  Score=57.30  Aligned_cols=35  Identities=57%  Similarity=1.000  Sum_probs=33.5

Q ss_pred             HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcC
Q psy4494          22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKP   56 (234)
Q Consensus        22 ~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~   56 (234)
                      +++|+||||+|+||+++|+..|++++.|||..++.
T Consensus       542 TVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRA  576 (941)
T KOG0351|consen  542 TVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRA  576 (941)
T ss_pred             EeeccCCCCCCceeEEEECCCchhHHHHHHhcccc
Confidence            78999999999999999999999999999998875

>KOG0353|consensus

Probab=93.20  E-value=0.014  Score=51.46  Aligned_cols=31  Identities=71%  Similarity=1.307  Sum_probs=29.1

Q ss_pred             HHHHhhCCCCCcEEEEEeeccCCCcceEEEE
Q psy4494          22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQV   52 (234)
Q Consensus        22 ~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v   52 (234)
                      +++|+||+|+|+||+++|+.++++++.||+.
T Consensus       374 tvafgmgidkpdvrfvihhsl~ksienyyqa  404 (695)
T KOG0353|consen  374 TVAFGMGIDKPDVRFVIHHSLPKSIENYYQA  404 (695)
T ss_pred             EeeecccCCCCCeeEEEecccchhHHHHHHH
Confidence            5789999999999999999999999999974

>KOG0392|consensus

Probab=92.98  E-value=0.37  Score=48.58  Aligned_cols=97  Identities=18%  Similarity=0.118  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHhhc---------------CCCcEEEEecchHHHHHHHHHHHHcCCc-ee--eeccCCCchh--------
Q psy4494          61 DCLDELADLMSRRF---------------RNQSGIIYTTSIKECEDLREELRNRGLR-VS--AYHAKLESNV--------  114 (234)
Q Consensus        61 ~~~~~l~~~l~~~~---------------~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~--~~h~~~~~~~--------  114 (234)
                      -|+..|.+++.+-.               ...+++|||.-+...+-+-+-|.+.-.+ +.  .+-|+.++.+        
T Consensus      1310 pKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~F 1389 (1549)
T KOG0392|consen 1310 PKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERF 1389 (1549)
T ss_pred             hhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHh
Confidence            46777777776311               2358999999999999999888765333 33  5668887766        


Q ss_pred             ------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceE
Q psy4494         115 ------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAH  157 (234)
Q Consensus       115 ------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~  157 (234)
                                  |-+-|.|+|..+.+.||.++=-|++..=+|-+-||-|-|++-+
T Consensus      1390 N~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDRAHRIGQKrv 1444 (1549)
T KOG0392|consen 1390 NEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDRAHRIGQKRV 1444 (1549)
T ss_pred             cCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHHHHhhcCcee
Confidence                        7788999999999999999999999999999999999998754

>KOG0386|consensus

Probab=92.79  E-value=0.51  Score=46.58  Aligned_cols=90  Identities=17%  Similarity=0.141  Sum_probs=74.8

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhhcccCCCCCCccEEEEe
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIAFGLGIDKPNVRFVIHH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~~~~Gid~~~v~~Vi~~  133 (234)
                      .+.+++.|+.-.....-+..+|.-.++.-.-+-|....++                     |.|-|.|+|....+.||.|
T Consensus       725 tgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviif  804 (1157)
T KOG0386|consen  725 TGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIF  804 (1157)
T ss_pred             cCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEe
Confidence            4778999998888888888889877777666666655544                     8899999999999999999


Q ss_pred             ecCCCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         134 CLSKSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       134 ~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      |.-+++....|+--||-|-|+...+-++.--
T Consensus       805 dsdwnp~~d~qaqdrahrigq~~evRv~rl~  835 (1157)
T KOG0386|consen  805 DSDWNPHQDLQAQDRAHRIGQKKEVRVLRLI  835 (1157)
T ss_pred             cCCCCchhHHHHHHHHHHhhchhheeeeeee
Confidence            9999999999999999999887666555543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=92.46  E-value=3.5  Score=39.97  Aligned_cols=63  Identities=16%  Similarity=0.107  Sum_probs=41.8

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCC--------ceeeeccCC-Cchh-------------------h--hhcccCCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGL--------RVSAYHAKL-ESNV-------------------S--IAFGLGIDK  124 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~--------~~~~~h~~~-~~~~-------------------T--~~~~~Gid~  124 (234)
                      .++.++||++|....+.+.+.+...++        .+..=..++ +.+.                   +  ..++.|||+
T Consensus       521 ~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGIDf  600 (705)
T TIGR00604       521 IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDF  600 (705)
T ss_pred             CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeCCCcchHHHHHHHHHHHHhcCCceEEEEecCCcccCcccc
Confidence            357799999999999999998875432        111111111 1111                   1  345679999


Q ss_pred             CC--ccEEEEeecCC
Q psy4494         125 PN--VRFVIHHCLSK  137 (234)
Q Consensus       125 ~~--v~~Vi~~~~P~  137 (234)
                      ++  .+.||..++|-
T Consensus       601 ~~~~~r~ViivGlPf  615 (705)
T TIGR00604       601 CDDLGRAVIMVGIPY  615 (705)
T ss_pred             CCCCCcEEEEEccCC
Confidence            96  68999999985

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).

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

Probab=92.24  E-value=2  Score=42.39  Aligned_cols=88  Identities=15%  Similarity=0.060  Sum_probs=58.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeecc-CCCchh---------------hhhcccCCCCCC--ccEEEEeecC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA-KLESNV---------------SIAFGLGIDKPN--VRFVIHHCLS  136 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~-~~~~~~---------------T~~~~~Gid~~~--v~~Vi~~~~P  136 (234)
                      .+++++|+++|.+..+.+++.|......+ ...| +++...               |..+..|+|+|+  ...||...+|
T Consensus       646 ~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~kLP  724 (820)
T PRK07246        646 LQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNGTAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVITRLP  724 (820)
T ss_pred             cCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCccHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEecCC
Confidence            46789999999999999999997655444 3334 233322               778888999973  4556666665


Q ss_pred             ----CC--------------------------HhHhhhhhcccccCCC-ceEEEEEeec
Q psy4494         137 ----KS--------------------------MENFYQESGRAGRDGQ-IAHCILYYRL  164 (234)
Q Consensus       137 ----~~--------------------------~~~y~qr~GR~gR~g~-~~~~i~~~~~  164 (234)
                          .+                          +..+.|-+||.=|... .|. +++.++
T Consensus       725 F~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gv-v~ilD~  782 (820)
T PRK07246        725 FDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSA-VLILDR  782 (820)
T ss_pred             CCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEE-EEEECC
Confidence                22                          2245677888888654 454 444444

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=92.04  E-value=1.4  Score=43.01  Aligned_cols=99  Identities=12%  Similarity=0.104  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------hhhcccCCCCCCc--
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------SIAFGLGIDKPNV--  127 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------T~~~~~Gid~~~v--  127 (234)
                      ....|..-|.   .++..-||++|...++.+++.....+-.+..++|.-...+            |.+...|+++...  
T Consensus       271 F~~~L~~~L~---~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv~~W~~~~VviYT~~itvG~Sf~~~HF  347 (824)
T PF02399_consen  271 FFSELLARLN---AGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDVESWKKYDVVIYTPVITVGLSFEEKHF  347 (824)
T ss_pred             HHHHHHHHHh---CCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccccccccceeEEEEeceEEEEeccchhhc
Confidence            3444444443   4667789999999999999999888888888888665544            7777778877644  


Q ss_pred             cEEEEeecC----CCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         128 RFVIHHCLS----KSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       128 ~~Vi~~~~P----~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      +-+.-|=-|    .++.+.+|.+||. |.=.....+++++.
T Consensus       348 ~~~f~yvk~~~~gpd~~s~~Q~lgRv-R~l~~~ei~v~~d~  387 (824)
T PF02399_consen  348 DSMFAYVKPMSYGPDMVSVYQMLGRV-RSLLDNEIYVYIDA  387 (824)
T ss_pred             eEEEEEecCCCCCCcHHHHHHHHHHH-HhhccCeEEEEEec
Confidence            444444223    3677899999999 65445556666665

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>KOG1002|consensus

Probab=91.61  E-value=0.29  Score=44.95  Aligned_cols=90  Identities=14%  Similarity=0.117  Sum_probs=69.3

Q ss_pred             hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------------hhhcccCCCCCCccEEEE
Q psy4494          73 RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIH  132 (234)
Q Consensus        73 ~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~  132 (234)
                      ....-++|||..-....+-+.-.|.+.|+.+.-+-|+|++..                    ..|-|..++.-...+|+.
T Consensus       635 rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFm  714 (791)
T KOG1002|consen  635 RDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFM  714 (791)
T ss_pred             cccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEe
Confidence            335567899999888888888999999999999999999977                    344566777778889999


Q ss_pred             eecCCCHhHhhhhhcccccCCC--ceEEEEEe
Q psy4494         133 HCLSKSMENFYQESGRAGRDGQ--IAHCILYY  162 (234)
Q Consensus       133 ~~~P~~~~~y~qr~GR~gR~g~--~~~~i~~~  162 (234)
                      .|+=+++.--+|-..|.-|-|+  +-..+.|.
T Consensus       715 mDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~  746 (791)
T KOG1002|consen  715 MDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFC  746 (791)
T ss_pred             ecccccHHHHhhhhhhHHhhcCccceeEEEee
Confidence            9987888766676666666554  44444444

>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=90.07  E-value=2.7  Score=35.10  Aligned_cols=88  Identities=13%  Similarity=0.118  Sum_probs=64.0

Q ss_pred             CCceeeeccCCCchh-----------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccc-cCCCceEEEEE
Q psy4494         100 GLRVSAYHAKLESNV-----------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG-RDGQIAHCILY  161 (234)
Q Consensus       100 ~~~~~~~h~~~~~~~-----------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~g-R~g~~~~~i~~  161 (234)
                      ++.+...+++.+...                 -+.++||+-+++........-|...++++|+.=.-| |.|-...+-+|
T Consensus       110 ~~~v~~vNS~~~~~~ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~QmgRwFGYR~gY~dl~Ri~  189 (239)
T PF10593_consen  110 GIEVVVVNSGSSDDSLDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQMGRWFGYRPGYEDLCRIY  189 (239)
T ss_pred             CceEEEEeCCCccccccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHHHhhcccCCcccccceEEe
Confidence            577888886654432                 457899999999988888888889999999966666 77778888888


Q ss_pred             eecccHHHhhhhHHhhhhhhHhHHHH
Q psy4494         162 YRLPDVFKLSSMVFDQQTGLANLYNI  187 (234)
Q Consensus       162 ~~~~d~~~~~~~~~~~~~~~~~l~~~  187 (234)
                      .++.-...+..+...+..-++.++.|
T Consensus       190 ~~~~l~~~f~~i~~~~e~lr~~i~~~  215 (239)
T PF10593_consen  190 MPEELYDWFRHIAEAEEELREEIKEM  215 (239)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            87766666666665444444444444

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

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=88.89  E-value=1.4  Score=30.34  Aligned_cols=37  Identities=14%  Similarity=0.161  Sum_probs=32.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      +..++++||.+-..+...+..|+..|+++..+.|+++
T Consensus        50 ~~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          50 KDKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             CCCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence            4568999999877888999999999999999999875

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=86.98  E-value=1.2  Score=44.74  Aligned_cols=73  Identities=22%  Similarity=0.246  Sum_probs=53.4

Q ss_pred             EEEEecchHHHHHHHHHHHHc------CCceeeeccCCCchh--------------------------------------
Q psy4494          79 GIIYTTSIKECEDLREELRNR------GLRVSAYHAKLESNV--------------------------------------  114 (234)
Q Consensus        79 ~iIf~~t~~~~~~l~~~L~~~------~~~~~~~h~~~~~~~--------------------------------------  114 (234)
                      ++|=+++++.+-.++..|-..      .+....||+......                                      
T Consensus       759 GliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~  838 (1110)
T TIGR02562       759 GLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNH  838 (1110)
T ss_pred             EEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCC
Confidence            578888999999999888754      234778999872211                                      


Q ss_pred             ------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCC
Q psy4494         115 ------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQ  154 (234)
Q Consensus       115 ------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~  154 (234)
                            |.+...|+|+. .+.+  +--|.++.+.+|++||..|.|.
T Consensus       839 ~~i~v~Tqv~E~g~D~d-fd~~--~~~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       839 LFIVLATPVEEVGRDHD-YDWA--IADPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             CeEEEEeeeEEEEeccc-CCee--eeccCcHHHHHHHhhccccccc
Confidence                  66667787765 3333  3458899999999999999664

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.

>KOG1015|consensus

Probab=86.64  E-value=1.3  Score=43.82  Aligned_cols=99  Identities=17%  Similarity=0.037  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHc----------------------CCceeeeccCCCchh----
Q psy4494          62 CLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNR----------------------GLRVSAYHAKLESNV----  114 (234)
Q Consensus        62 ~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~----------------------~~~~~~~h~~~~~~~----  114 (234)
                      ++-.|+++|+.- .-+.+.|||..|.....-+-.+|...                      |..-..+-|..+..+    
T Consensus      1127 KmiLLleIL~mceeIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~ 1206 (1567)
T KOG1015|consen 1127 KMILLLEILRMCEEIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKW 1206 (1567)
T ss_pred             ceehHHHHHHHHHHhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHH
Confidence            344455555421 23788999999998888888888631                      222223334433332    


Q ss_pred             ------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEE
Q psy4494         115 ------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCIL  160 (234)
Q Consensus       115 ------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~  160 (234)
                                        |-|-+.|||.-..+.||.||..|++.-=.|-+=|+-|.|+.--+++
T Consensus      1207 ~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyi 1270 (1567)
T KOG1015|consen 1207 AEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYI 1270 (1567)
T ss_pred             HHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceee
Confidence                              8888999999999999999999999999999999999887544433

>KOG0352|consensus

Probab=86.25  E-value=0.15  Score=45.95  Aligned_cols=35  Identities=43%  Similarity=0.902  Sum_probs=31.4

Q ss_pred             HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcC
Q psy4494          22 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKP   56 (234)
Q Consensus        22 ~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~   56 (234)
                      ++.|+||.|+|+||+++|+.+++++--||+.-++.
T Consensus       312 T~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRA  346 (641)
T KOG0352|consen  312 TVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRA  346 (641)
T ss_pred             EeccccccCCcceeEEEecCchhhhHHHHHhcccc
Confidence            67899999999999999999999998898876653

>PRK14701 reverse gyrase; Provisional

Probab=84.96  E-value=1.5  Score=46.40  Aligned_cols=29  Identities=28%  Similarity=0.513  Sum_probs=24.5

Q ss_pred             CHhHhhhhhccccc--CC--CceEEEEEeeccc
Q psy4494         138 SMENFYQESGRAGR--DG--QIAHCILYYRLPD  166 (234)
Q Consensus       138 ~~~~y~qr~GR~gR--~g--~~~~~i~~~~~~d  166 (234)
                      ++.+|+|-.||+.|  +|  .+|.++++++...
T Consensus       495 d~~tyiqasgrtsrl~~gg~tkgls~~~~d~~~  527 (1638)
T PRK14701        495 DVRTYIQASGRTSRLFAGGITKGASVLIVDDPE  527 (1638)
T ss_pred             CcccceeccchhhhccCCCcCCceEEEEecCHH
Confidence            78899999999999  34  4699999998754

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=84.73  E-value=2.3  Score=29.79  Aligned_cols=37  Identities=16%  Similarity=0.171  Sum_probs=31.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      ..++.++||.+=..+...+..|+..|+++..+.|++.
T Consensus        60 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~   96 (100)
T cd01523          60 DDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMK   96 (100)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHH
Confidence            4578999999877889999999999999888888874

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>KOG2340|consensus

Probab=84.28  E-value=3  Score=38.85  Aligned_cols=101  Identities=14%  Similarity=0.124  Sum_probs=71.9

Q ss_pred             cEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hh--hcccCCCCCCccEEEEeecCC
Q psy4494          78 SGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SI--AFGLGIDKPNVRFVIHHCLSK  137 (234)
Q Consensus        78 ~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~--~~~~Gid~~~v~~Vi~~~~P~  137 (234)
                      -++||.++--.--++-.++++.++....+|-=.+.+.                  |.  -+-+--++.+|+.||.|.+|.
T Consensus       554 ~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfYqpP~  633 (698)
T KOG2340|consen  554 GILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFYQPPN  633 (698)
T ss_pred             ceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEecCCC
Confidence            4699999999999999999887665444432222211                  11  223467889999999999999


Q ss_pred             CHh---Hhhhhhccccc----CCCceEEEEEeecccHHHhhhhHHhhh
Q psy4494         138 SME---NFYQESGRAGR----DGQIAHCILYYRLPDVFKLSSMVFDQQ  178 (234)
Q Consensus       138 ~~~---~y~qr~GR~gR----~g~~~~~i~~~~~~d~~~~~~~~~~~~  178 (234)
                      .+.   ..+-+.+|+--    ++....+.++|+..|...+..++..++
T Consensus       634 ~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~Le~ivGter  681 (698)
T KOG2340|consen  634 NPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRLENIVGTER  681 (698)
T ss_pred             CcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHHHHhhhHHH
Confidence            876   44556666532    445688999999999988888776544

>KOG0701|consensus

Probab=83.44  E-value=1.4  Score=46.11  Aligned_cols=76  Identities=22%  Similarity=0.219  Sum_probs=61.7

Q ss_pred             CcEEEEecchHHHHHHHHHHHHcC-CceeeeccCCCchh-----------------------------hhhcccCCCCCC
Q psy4494          77 QSGIIYTTSIKECEDLREELRNRG-LRVSAYHAKLESNV-----------------------------SIAFGLGIDKPN  126 (234)
Q Consensus        77 ~~~iIf~~t~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~-----------------------------T~~~~~Gid~~~  126 (234)
                      -.+|+|++.+..+..+.+.+++.. .+...+-|.+.+..                             |+++-.|+|.+.
T Consensus       293 l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~  372 (1606)
T KOG0701|consen  293 LSGIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPK  372 (1606)
T ss_pred             hhheeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhh
Confidence            468999999999999998888652 23444555554433                             888888999999


Q ss_pred             ccEEEEeecCCCHhHhhhhhcccccC
Q psy4494         127 VRFVIHHCLSKSMENFYQESGRAGRD  152 (234)
Q Consensus       127 v~~Vi~~~~P~~~~~y~qr~GR~gR~  152 (234)
                      +..|+.++.|....+|+|+.||+-+.
T Consensus       373 ~~~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  373 CNLVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hhhheeccCcchHHHHHHhhcccccc
Confidence            99999999999999999999999654

>KOG1123|consensus

Probab=82.88  E-value=7.3  Score=36.22  Aligned_cols=73  Identities=19%  Similarity=0.148  Sum_probs=53.4

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-------------------hhhcccCCCCCCccEEEEeec
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-------------------SIAFGLGIDKPNVRFVIHHCL  135 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-------------------T~~~~~Gid~~~v~~Vi~~~~  135 (234)
                      ++.+.|||..+.-...+.|-.|.     --.++|..++.+                   +.+....+|+|..++.|+...
T Consensus       542 RgDKiIVFsDnvfALk~YAikl~-----KpfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQISS  616 (776)
T KOG1123|consen  542 RGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQISS  616 (776)
T ss_pred             cCCeEEEEeccHHHHHHHHHHcC-----CceEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEEcc
Confidence            67899999988776666665553     335667777766                   445567999999999998754


Q ss_pred             CC-CHhHhhhhhcccccC
Q psy4494         136 SK-SMENFYQESGRAGRD  152 (234)
Q Consensus       136 P~-~~~~y~qr~GR~gR~  152 (234)
                      -. +-.+=.||.||.-|+
T Consensus       617 H~GSRRQEAQRLGRILRA  634 (776)
T KOG1123|consen  617 HGGSRRQEAQRLGRILRA  634 (776)
T ss_pred             cccchHHHHHHHHHHHHH
Confidence            43 455778899988875

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=82.13  E-value=3.1  Score=28.97  Aligned_cols=37  Identities=14%  Similarity=0.002  Sum_probs=31.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCC-ceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGL-RVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~-~~~~~h~~~~  111 (234)
                      +..++|+||++-..+...+..|+..|+ ++..+.|++.
T Consensus        55 ~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          55 RATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            467899999998888999999999998 5788888874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>smart00450 RHOD Rhodanese Homology Domain

Probab=81.90  E-value=2  Score=29.35  Aligned_cols=37  Identities=16%  Similarity=0.249  Sum_probs=32.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~  111 (234)
                      ...+.||||.+-..+..++..|+..|++ +..+.|++.
T Consensus        55 ~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       55 KDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence            4578999999988999999999999987 888888874

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

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

Probab=81.13  E-value=9.3  Score=36.65  Aligned_cols=72  Identities=11%  Similarity=0.088  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc-CCceeeeccCCCc-hh-------------------hhhccc
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR-GLRVSAYHAKLES-NV-------------------SIAFGL  120 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~-~~-------------------T~~~~~  120 (234)
                      ....+..++..  ..++++|.+.|.+..+.+++.|... .++ ....|..+. .+                   |..+..
T Consensus       458 ~~~~~~~~~~~--~~G~~lvLfTS~~~~~~~~~~l~~~l~~~-~l~qg~~~~~~~l~~~f~~~~~~~~~~vL~gt~sfwe  534 (636)
T TIGR03117       458 VSLSTAAILRK--AQGGTLVLTTAFSHISAIGQLVELGIPAE-IVIQSEKNRLASAEQQFLALYANGIQPVLIAAGGAWT  534 (636)
T ss_pred             HHHHHHHHHHH--cCCCEEEEechHHHHHHHHHHHHhhcCCC-EEEeCCCccHHHHHHHHHHhhcCCCCcEEEeCCcccc
Confidence            44566666653  4678999999999999999999764 333 445565532 21                   778888


Q ss_pred             CCCC----------CCccEEEEeecC
Q psy4494         121 GIDK----------PNVRFVIHHCLS  136 (234)
Q Consensus       121 Gid~----------~~v~~Vi~~~~P  136 (234)
                      |+|+          ..++.||...+|
T Consensus       535 GvDv~~~~~~p~~G~~Ls~ViI~kLP  560 (636)
T TIGR03117       535 GIDLTHKPVSPDKDNLLTDLIITCAP  560 (636)
T ss_pred             ccccCCccCCCCCCCcccEEEEEeCC
Confidence            9999          247889988777

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.

>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1

Probab=80.21  E-value=4.2  Score=29.67  Aligned_cols=38  Identities=13%  Similarity=0.142  Sum_probs=31.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCCc
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLES  112 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~~  112 (234)
                      +..++|+||.+-..+...+..|+..|++ +..+.|+++.
T Consensus        63 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~v~~l~gG~~~  101 (117)
T cd01522          63 KDRPVLLLCRSGNRSIAAAEAAAQAGFTNVYNVLEGFEG  101 (117)
T ss_pred             CCCeEEEEcCCCccHHHHHHHHHHCCCCeEEECcCceec
Confidence            4677999999988889999999999985 6668888864

This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	234
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		4e-49
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		2e-25
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		2e-23

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

Iteration: 1
 Score =  191 bits (484), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 89/192 (46%), Positives = 124/192 (64%), Gaps = 18/192 (9%)
Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KP+  +D ++++  L++ R++ QSGIIY  S K+ E +   L+N G+   AYHA
Sbjct: 240 YYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHA 299
Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE                     ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 300 NLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 359
Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RD   A CILYY   D+F++SSMV  +  G   LY +VSYC + ++CRR ++A +FDE W
Sbjct: 360 RDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVW 419
Query: 211 SDTECRGMCDHC 222
           +   C  MCD+C
Sbjct: 420 NSEACNKMCDNC 431

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

Iteration: 1
 Score =  112 bits (279), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 74/216 (34%), Positives = 116/216 (53%), Gaps = 44/216 (20%)
Query: 30  DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC 89
           D+PN+R+++       ME F     KP      LD+L   +  + R +SGIIY  S  + 
Sbjct: 209 DRPNIRYML-------MEKF-----KP------LDQLMRYVQEQ-RGKSGIIYCNSRAKV 249
Query: 90  EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVI 131
           ED    L+++G+  +AYHA LE+NV                  ++AFG+GI+KPNVRFV+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV 309
Query: 132 HHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTG-LANL----YN 186
           H  + +++E++YQE+GRAGRDG  A  +L+Y   D+  L   + ++  G L ++     N
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLN 369
Query: 187 IVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
            +    +   CRR ++ +YF E   +  C G CD C
Sbjct: 370 AMGAFAEAQTCRRLVLLNYFGEGRQEP-C-GNCDIC 403

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

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 72/218 (33%), Positives = 110/218 (50%), Gaps = 48/218 (22%)
Query: 30  DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC 89
           D+PN+R+ +              + KP      LD+L   +  + R +SGIIY  S  + 
Sbjct: 209 DRPNIRYXLXE------------KFKP------LDQLXRYVQEQ-RGKSGIIYCNSRAKV 249
Query: 90  EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVI 131
           ED    L+++G+  +AYHA LE+NV                  ++AFG GI+KPNVRFV+
Sbjct: 250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVV 309
Query: 132 HHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYC 191
           H  + +++E++YQE+GRAGRDG  A   L+Y   D   L   + ++  G   L +I  + 
Sbjct: 310 HFDIPRNIESYYQETGRAGRDGLPAEAXLFYDPADXAWLRRCLEEKPQG--QLQDIERHK 367
Query: 192 L-------DQTRCRRAIIASYFDEAWSDTECRGMCDHC 222
           L       +   CRR ++ +YF E   +  C G CD C
Sbjct: 368 LNAXGAFAEAQTCRRLVLLNYFGEGRQEP-C-GNCDIC 403

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	234
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-86
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-16
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	6e-52
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	4e-13
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	7e-06
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-05
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	3e-04
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	3e-04
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-04
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-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 =  266 bits (682), Expect = 2e-86
 Identities = 90/204 (44%), Positives = 128/204 (62%), Gaps = 19/204 (9%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           +Y+VR KP+  +D ++++  L++ R++ QSGIIY  S K+ E +   L+N G+   AYHA
Sbjct: 240 YYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHA 299

Query: 109 KLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE                     ++AFG+GIDKP+VRFVIHH +SKSMEN+YQESGRAG
Sbjct: 300 NLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAG 359

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAW 210
           RD   A CILYY   D+F++SSMV  +  G   LY +VSYC + ++CRR ++A +FDE W
Sbjct: 360 RDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVW 419

Query: 211 SDTECRGMCDHCRGGRRDAKRVDV 234
           +   C  MCD+C       +R ++
Sbjct: 420 NSEACNKMCDNCCKD-SAFERKNI 442

>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 = 76.6 bits (189), Expect = 2e-16
 Identities = 23/29 (79%), Positives = 28/29 (96%)

Query: 23  IAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
           +AFG+GIDKP+VRFVIHH +SKSMEN+YQ
Sbjct: 325 VAFGMGIDKPDVRFVIHHSMSKSMENYYQ 353

>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 =  174 bits (444), Expect = 6e-52
 Identities = 68/210 (32%), Positives = 105/210 (50%), Gaps = 35/210 (16%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
            Y +  K       LD+L   +  + R +SGIIY  S  + ED    L+++G+  +AYHA
Sbjct: 214 RYMLMEK----FKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHA 268

Query: 109 KLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE+NV                  ++AFG+GI+KPNVRFV+H  + +++E++YQE+GRAG
Sbjct: 269 GLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAG 328

Query: 151 RDGQIAHCILYYRLPDVFKLSSMVFD------QQTGLANLYNIVSYCLDQTRCRRAIIAS 204
           RDG  A  +L+Y   D+  L   + +      Q      L  + ++  +   CRR ++ +
Sbjct: 329 RDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFA-EAQTCRRLVLLN 387

Query: 205 YFDEAWSDTECRGMCDHCRGGRRDAKRVDV 234
           YF E      C G CD C       K+ D 
Sbjct: 388 YFGEG-RQEPC-GNCDICLDPP---KQYDG 412

>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 = 67.2 bits (165), Expect = 4e-13
 Identities = 16/29 (55%), Positives = 26/29 (89%)

Query: 23  IAFGLGIDKPNVRFVIHHCLSKSMENFYQ 51
           +AFG+GI+KPNVRFV+H  + +++E++YQ
Sbjct: 294 VAFGMGINKPNVRFVVHFDIPRNIESYYQ 322

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 44.1 bits (105), Expect = 7e-06
 Identities = 34/123 (27%), Positives = 53/123 (43%), Gaps = 22/123 (17%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY V ++    K   + L DL       Q+ +I+  + ++ E+L  +LRN    VSA ++
Sbjct: 7   FY-VNVEEEEYK--YECLTDLYDSISVTQA-VIFCNTRRKVEELTTKLRNDKFTVSAIYS 62

Query: 109 KLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            L                S + I+      GID   V  VI++ L  + EN+    GR G
Sbjct: 63  DLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGG 122

Query: 151 RDG 153
           R G
Sbjct: 123 RFG 125

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 23/109 (21%), Positives = 41/109 (37%), Gaps = 19/109 (17%)

Query: 63  LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE----------- 111
             +L DL+     NQ  +I+  S++ C  L + L  +     A H  +            
Sbjct: 19  NRKLFDLLDVLEFNQV-VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF 77

Query: 112 ----SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDG 153
                 + +A   FG G+D   V    ++ + +  + +     RAGR G
Sbjct: 78  KDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 126

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 28/113 (24%), Positives = 41/113 (36%), Gaps = 24/113 (21%)

Query: 63  LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL------------ 110
           L  L  L S+   NQ+ II+  S    E L +++ + G      HA++            
Sbjct: 246 LHCLNTLFSKLQINQA-IIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEF 304

Query: 111 ---ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFY----QESGRAGRDG 153
              +    +       GID   V  VI+    K+ E  Y      SGR G  G
Sbjct: 305 RQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAET-YLHRIGRSGRFGHLG 356

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.0 bits (95), Expect = 2e-04
 Identities = 27/208 (12%), Positives = 56/208 (26%), Gaps = 61/208 (29%)

Query: 42  LSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGI-IYTTSI-------KECEDLR 93
           L+  +E+   V ++PA  +   D L+      F   + I     S+        +   + 
Sbjct: 355 LTTIIESSLNV-LEPAEYRKMFDRLS-----VFPPSAHIPTILLSLIWFDVIKSDVMVVV 408

Query: 94  EELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHC---LSKSMENFYQESGRAG 150
            +L    L                  +          I      L   +EN Y       
Sbjct: 409 NKLHKYSL------------------VEKQPKESTISIPSIYLELKVKLENEYA------ 444

Query: 151 RDGQIAH--CILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTR------CRRAII 202
                 H   + +Y +P  F    ++          Y+ + + L            R + 
Sbjct: 445 -----LHRSIVDHYNIPKTFDSDDLIPPYLDQY--FYSHIGHHLKNIEHPERMTLFRMV- 496

Query: 203 ASYFDEAWSDTECR--GMCDHCRGGRRD 228
             + D  + + + R      +  G   +
Sbjct: 497 --FLDFRFLEQKIRHDSTAWNASGSILN 522

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 40.2 bits (95), Expect = 3e-04
 Identities = 35/127 (27%), Positives = 52/127 (40%), Gaps = 27/127 (21%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY + ++    K  LD L DL       Q+ +I+  + ++ + L E++  R   VSA H 
Sbjct: 257 FY-INVEREEWK--LDTLCDLYETLTITQA-VIFINTRRKVDWLTEKMHARDFTVSAMHG 312

Query: 109 KLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ----ES 146
            ++               S V I       GID   V  VI++ L  + EN Y       
Sbjct: 313 DMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNREN-YIHRIGRG 371

Query: 147 GRAGRDG 153
           GR GR G
Sbjct: 372 GRFGRKG 378

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 32/127 (25%), Positives = 53/127 (41%), Gaps = 27/127 (21%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           F+ V ++    K   D L DL       Q+ +I+  + ++ + L E++R     VS+ H 
Sbjct: 253 FF-VAVEREEWK--FDTLCDLYDTLTITQA-VIFCNTKRKVDWLTEKMREANFTVSSMHG 308

Query: 109 KLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ----ES 146
            +                S V I+   +  G+D P V  +I++ L  + E  Y      S
Sbjct: 309 DMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL-YIHRIGRS 367

Query: 147 GRAGRDG 153
           GR GR G
Sbjct: 368 GRYGRKG 374

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 23/109 (21%), Positives = 42/109 (38%), Gaps = 19/109 (17%)

Query: 63  LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL------------ 110
             +L DL+     NQ  +I+  S++ C  L + L  +     A H  +            
Sbjct: 238 NRKLFDLLDVLEFNQV-VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF 296

Query: 111 ---ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDG 153
              +  + +A   FG G+D   V    ++ + +  + +     RAGR G
Sbjct: 297 KDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFG 345

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 39.4 bits (93), Expect = 6e-04
 Identities = 35/127 (27%), Positives = 53/127 (41%), Gaps = 27/127 (21%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
           FY V ++    K   + L DL       Q+ +I+  + ++ E+L  +LRN    VSA ++
Sbjct: 236 FY-VNVEEEEYK--YECLTDLYDSISVTQA-VIFCNTRRKVEELTTKLRNDKFTVSAIYS 291

Query: 109 KLE---------------SNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ----ES 146
            L                S + I+      GID   V  VI++ L  + EN Y       
Sbjct: 292 DLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKEN-YIHRIGRG 350

Query: 147 GRAGRDG 153
           GR GR G
Sbjct: 351 GRFGRKG 357

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	234
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.92
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.92
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.91
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.91
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.91
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.91
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.9
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.89
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.89
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.88
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.88
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.88
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.78
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.86
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.85
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.84
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.84
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.84
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.83
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.83
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.82
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.79
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.79
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.79
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.78
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.76
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.75
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.75
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.74
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.73
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.73
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.72
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.71
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.71
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.7
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.7
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.7
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.69
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.69
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.66
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.66
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.66
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.65
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.64
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.64
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.62
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.61
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.6
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.6
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.57
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.57
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.57
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.56
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.55
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.55
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.54
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.54
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.53
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.5
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.49
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.47
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.46
3h1t_A	590	Type I site-specific restriction-modification syst	99.46
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.44
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.41
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.4
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.28
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.7
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.31
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.23
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	96.23
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	92.95
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	89.49
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	86.81
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	86.14
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	85.35
2jtq_A	85	Phage shock protein E; solution structure rhodanes	84.57
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	84.52
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	84.45
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	83.78
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	83.2
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	82.38
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	82.01

>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=100.00  E-value=9.6e-37  Score=283.19  Aligned_cols=217  Identities=43%  Similarity=0.788  Sum_probs=181.0

Q ss_pred             hhhccCchh---HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHH
Q psy4494          13 LWRTSFYQV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC   89 (234)
Q Consensus        13 l~~at~p~~---~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~   89 (234)
                      +++||.+..   .+...++...+. .+   .....+.+.+|.+..++....+++..|.+++.....+.++||||+|++.+
T Consensus       205 ~lSAT~~~~v~~~i~~~l~~~~~~-~~---~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~  280 (591)
T 2v1x_A          205 GLTATATNHVLTDAQKILCIEKCF-TF---TASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDS  280 (591)
T ss_dssp             EEESSCCHHHHHHHHHHTTCCSCE-EE---ECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHH
T ss_pred             EEecCCCHHHHHHHHHHhCCCCcE-EE---ecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHH
Confidence            466777664   233344443322 11   22344567889998887777778888988887655678999999999999


Q ss_pred             HHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccccc
Q psy4494          90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR  151 (234)
Q Consensus        90 ~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR  151 (234)
                      +.++..|+..|+.+..|||+|++++                  |++++||||+|+|++||||++|.++++|+||+||+||
T Consensus       281 e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR  360 (591)
T 2v1x_A          281 EQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGR  360 (591)
T ss_dssp             HHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCT
T ss_pred             HHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCc
Confidence            9999999999999999999999876                  9999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEeecccHHHhhhhHHhhhhhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCCCCCCccc
Q psy4494         152 DGQIAHCILYYRLPDVFKLSSMVFDQQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGGRRDAKR  231 (234)
Q Consensus       152 ~g~~~~~i~~~~~~d~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~~~~~~~~  231 (234)
                      +|++|.++++|++.|...+..++..+....+.+++|..|++++..|||..++.||||...+..|.++||||.... ..+.
T Consensus       361 ~G~~g~~i~l~~~~D~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Crr~~ll~~f~e~~~~~~c~~~Cd~C~~~~-~~~~  439 (591)
T 2v1x_A          361 DDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDS-AFER  439 (591)
T ss_dssp             TSSCEEEEEEECHHHHHHHHHHTTTSTTHHHHHHHHHHHHTCSSSCHHHHHHHHHTCCC---CCCSCBHHHHCCC-CEEE
T ss_pred             CCCCceEEEEEChHHHHHHHHHHhhhhhhHHHHHHHHHHHhcccccHHHHHHHHcCCCCCccccCCCCCCCCCCC-cccc
Confidence            999999999999999999988887777778899999999987889999999999999877677977899999886 4555


Q ss_pred             ccC
Q psy4494         232 VDV  234 (234)
Q Consensus       232 ~~~  234 (234)
                      .|+
T Consensus       440 ~d~  442 (591)
T 2v1x_A          440 KNI  442 (591)
T ss_dssp             EEC
T ss_pred             cch
Confidence            553

>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=100.00  E-value=2.5e-33  Score=257.05  Aligned_cols=202  Identities=35%  Similarity=0.605  Sum_probs=164.8

Q ss_pred             hhhccCchh---HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHH
Q psy4494          13 LWRTSFYQV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC   89 (234)
Q Consensus        13 l~~at~p~~---~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~   89 (234)
                      +++||.+..   .+...+++..+.+..    ....+.+.+|.+..+.    ++...+.+++... .+.++||||+|++.+
T Consensus       179 ~lSAT~~~~~~~~i~~~l~~~~~~~~~----~~~~r~~l~~~v~~~~----~~~~~l~~~l~~~-~~~~~IVf~~sr~~~  249 (523)
T 1oyw_A          179 ALTATADDTTRQDIVRLLGLNDPLIQI----SSFDRPNIRYMLMEKF----KPLDQLMRYVQEQ-RGKSGIIYCNSRAKV  249 (523)
T ss_dssp             EEESCCCHHHHHHHHHHHTCCSCEEEE----CCCCCTTEEEEEEECS----SHHHHHHHHHHHT-TTCCEEEECSSHHHH
T ss_pred             EEeCCCCHHHHHHHHHHhCCCCCeEEe----CCCCCCceEEEEEeCC----CHHHHHHHHHHhc-CCCcEEEEeCCHHHH
Confidence            456776654   345556666554332    2334557778876653    3455666666543 567899999999999


Q ss_pred             HHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccccc
Q psy4494          90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR  151 (234)
Q Consensus        90 ~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR  151 (234)
                      +.+++.|+..|+.+..|||++++++                  |++++||||+|+|++||||++|.++++|+||+||+||
T Consensus       250 e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR  329 (523)
T 1oyw_A          250 EDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGR  329 (523)
T ss_dssp             HHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCT
T ss_pred             HHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccC
Confidence            9999999999999999999999866                  9999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEeecccHHHhhhhHHh------hhhhhHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCCC
Q psy4494         152 DGQIAHCILYYRLPDVFKLSSMVFD------QQTGLANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRGG  225 (234)
Q Consensus       152 ~g~~~~~i~~~~~~d~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~~  225 (234)
                      +|.+|.+++++++.|......++..      ......++++|..|++ +..|||+.|+.||||... .+| +.||||...
T Consensus       330 ~g~~~~~~l~~~~~d~~~~~~~~~~~~~~~~~~~~~~~l~~m~~~~~-~~~crr~~l~~~f~e~~~-~~c-~~cd~c~~~  406 (523)
T 1oyw_A          330 DGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFAE-AQTCRRLVLLNYFGEGRQ-EPC-GNCDICLDP  406 (523)
T ss_dssp             TSSCEEEEEEECHHHHHHHHHHHHTSCCSHHHHHHHHHHHHHHHHHT-CSSCHHHHHHHHTTCCCC-SCC-SCBHHHHSC
T ss_pred             CCCCceEEEEeCHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHh-ccccHhhhhHhhcCCCCC-CCC-CCCCCCCCC
Confidence            9999999999999998888777753      2334568999999996 689999999999999864 468 689999987


Q ss_pred             C
Q psy4494         226 R  226 (234)
Q Consensus       226 ~  226 (234)
                      +
T Consensus       407 ~  407 (523)
T 1oyw_A          407 P  407 (523)
T ss_dssp             C
T ss_pred             c
Confidence            6

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

Probab=99.92  E-value=2.2e-24  Score=168.67  Aligned_cols=126  Identities=21%  Similarity=0.303  Sum_probs=108.8

Q ss_pred             CCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------
Q psy4494          44 KSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------  114 (234)
Q Consensus        44 ~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------  114 (234)
                      ..+.++|....    ..+|+..|.+++... .+.++||||+|++.++.++..|...|+.+..+||+|++.+         
T Consensus         8 ~~i~~~~~~~~----~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~   82 (163)
T 2hjv_A            8 RNIEHAVIQVR----EENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFK   82 (163)
T ss_dssp             CCEEEEEEECC----GGGHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             ccceEEEEECC----hHHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHH
Confidence            34555555532    356788888888753 6778999999999999999999999999999999998866         


Q ss_pred             ---------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhH
Q psy4494         115 ---------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       115 ---------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                               |+++++|+|+|++++||+||+|.+..+|+||+||+||.|++|.+++|+.+.|...+..+.
T Consensus        83 ~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~  151 (163)
T 2hjv_A           83 RGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIE  151 (163)
T ss_dssp             TTSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHH
T ss_pred             cCCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHH
Confidence                     999999999999999999999999999999999999999999999999988876655443

>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=99.92  E-value=2.5e-24  Score=172.04  Aligned_cols=129  Identities=18%  Similarity=0.287  Sum_probs=98.9

Q ss_pred             CCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------
Q psy4494          43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------  114 (234)
Q Consensus        43 ~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------  114 (234)
                      +..+.++|..+.    ..+|+..|.+++.....+.++||||+|++.++.++..|+..|+.+..+||++++.+        
T Consensus        17 ~~~i~q~~~~v~----~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f   92 (185)
T 2jgn_A           17 SENITQKVVWVE----ESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQF   92 (185)
T ss_dssp             CTTEEEEEEECC----GGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHH
T ss_pred             CCCceEEEEEeC----cHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHH
Confidence            445556665532    34678888888875435788999999999999999999999999999999998766        


Q ss_pred             ----------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         115 ----------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       115 ----------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                                |+++++|+|+|++++||+||+|+++.+|+||+||+||.|++|.+++|+++.|...+..+..
T Consensus        93 ~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~  163 (185)
T 2jgn_A           93 RSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLD  163 (185)
T ss_dssp             HHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHH
T ss_pred             HcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHH
Confidence                      9999999999999999999999999999999999999999999999999988766655543

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

Probab=99.91  E-value=3.3e-24  Score=172.21  Aligned_cols=124  Identities=17%  Similarity=0.251  Sum_probs=102.0

Q ss_pred             ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------
Q psy4494          41 CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------  114 (234)
Q Consensus        41 ~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------  114 (234)
                      .....+.++|....    ..+|+..|.+++..  .+.++||||++++.++.++..|+..|+.+..+||++++++      
T Consensus        25 ~~~~~i~q~~~~~~----~~~K~~~L~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~   98 (191)
T 2p6n_A           25 AASLDVIQEVEYVK----EEAKMVYLLECLQK--TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIE   98 (191)
T ss_dssp             ---CCSEEEEEECC----GGGHHHHHHHHHTT--SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHH
T ss_pred             CCCcCceEEEEEcC----hHHHHHHHHHHHHh--CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHH
Confidence            34455666665532    34688888888874  3568999999999999999999999999999999999866      


Q ss_pred             ------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecc-cHHHh
Q psy4494         115 ------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLP-DVFKL  170 (234)
Q Consensus       115 ------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~-d~~~~  170 (234)
                                  |+++++|+|+|++++||+||+|.+..+|+||+||+||.|++|.+++|+++. +....
T Consensus        99 ~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~  167 (191)
T 2p6n_A           99 AFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL  167 (191)
T ss_dssp             HHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHH
T ss_pred             HHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHH
Confidence                        999999999999999999999999999999999999999999999999876 44433

>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=99.91  E-value=9.6e-24  Score=166.81  Aligned_cols=127  Identities=20%  Similarity=0.311  Sum_probs=105.3

Q ss_pred             CCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------
Q psy4494          43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------  114 (234)
Q Consensus        43 ~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------  114 (234)
                      +..+.++|....   ...+|+..|.+++.. ..++++||||++++.++.++..|...|+.+..+||++++.+        
T Consensus         5 ~~~i~q~~~~~~---~~~~K~~~L~~ll~~-~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f   80 (175)
T 2rb4_A            5 LNNIRQYYVLCE---HRKDKYQALCNIYGS-ITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRF   80 (175)
T ss_dssp             BCCEEEEEEECS---SHHHHHHHHHHHHTT-SCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHH
T ss_pred             cCCceEEEEEcC---ChHhHHHHHHHHHHh-CCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHH
Confidence            345566666532   234588888888864 36789999999999999999999999999999999999876        


Q ss_pred             ----------hhhcccCCCCCCccEEEEeecC------CCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         115 ----------SIAFGLGIDKPNVRFVIHHCLS------KSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       115 ----------T~~~~~Gid~~~v~~Vi~~~~P------~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                                |+++++|+|+|++++||+||+|      .+..+|+||+||+||.|+.|.+++++++.+...+..+
T Consensus        81 ~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i  155 (175)
T 2rb4_A           81 RDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKI  155 (175)
T ss_dssp             HTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHH
T ss_pred             HcCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHH
Confidence                      9999999999999999999999      9999999999999999999999999998886655443

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

Probab=99.91  E-value=1.7e-23  Score=163.89  Aligned_cols=125  Identities=26%  Similarity=0.363  Sum_probs=102.4

Q ss_pred             CcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------
Q psy4494          45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------  114 (234)
Q Consensus        45 ~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------  114 (234)
                      .+.++|......   ..|+..|.+++.. ..++++||||+|++.++.++..|...++.+..+||++++.+          
T Consensus         3 ~i~~~~~~~~~~---~~K~~~l~~ll~~-~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~   78 (165)
T 1fuk_A            3 GIKQFYVNVEEE---EYKYECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRS   78 (165)
T ss_dssp             -CEEEEEEEESG---GGHHHHHHHHHHH-TTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CcEEEEEECCcc---hhHHHHHHHHHHh-CCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHc
Confidence            355666665432   2377777777764 36788999999999999999999999999999999999866          


Q ss_pred             --------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         115 --------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       115 --------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                              |+++++|+|+|++++||+||+|.+..+|+||+||+||.|++|.+++++++.+...+..+
T Consensus        79 g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~  145 (165)
T 1fuk_A           79 GSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMREL  145 (165)
T ss_dssp             TSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHH
T ss_pred             CCCEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHH
Confidence                    99999999999999999999999999999999999999999999999998887655443

>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=99.91  E-value=6.5e-24  Score=167.60  Aligned_cols=118  Identities=19%  Similarity=0.336  Sum_probs=103.9

Q ss_pred             CCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------
Q psy4494          44 KSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------  114 (234)
Q Consensus        44 ~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------  114 (234)
                      ..+.++|....    ..+|+..|.+++.. ..+.++||||++++.++.++..|...|+.+..+||+|++.+         
T Consensus         4 ~~i~q~~~~~~----~~~K~~~L~~ll~~-~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~   78 (172)
T 1t5i_A            4 HGLQQYYVKLK----DNEKNRKLFDLLDV-LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFK   78 (172)
T ss_dssp             -CCEEEEEECC----GGGHHHHHHHHHHH-SCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEEECC----hHHHHHHHHHHHHh-CCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHH
Confidence            45566666532    34678888888874 36778999999999999999999999999999999999866         


Q ss_pred             ---------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         115 ---------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       115 ---------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                               |+++++|+|+|++++||+||+|++..+|+||+||+||.|+.|.+++|+++.+
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                     9999999999999999999999999999999999999999999999998764

>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=99.90  E-value=1.3e-23  Score=171.18  Aligned_cols=114  Identities=25%  Similarity=0.412  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      .+++..|.+++... .++++||||+|++.++.++..|...|+.+..+||++++++                  |+++++|
T Consensus        16 ~~k~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~G   94 (212)
T 3eaq_A           16 RGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARG   94 (212)
T ss_dssp             TSHHHHHHHHHHHH-CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCS
T ss_pred             HHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcC
Confidence            45777788877643 6789999999999999999999999999999999999876                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhH
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      +|+|+|++|||||+|.+..+|+||+||+||.|++|.+++++++.+...+..+.
T Consensus        95 idi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~  147 (212)
T 3eaq_A           95 LDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALE  147 (212)
T ss_dssp             SSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHH
T ss_pred             CCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999998876665543

>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=99.89  E-value=1.1e-22  Score=182.33  Aligned_cols=149  Identities=13%  Similarity=0.205  Sum_probs=113.3

Q ss_pred             HHhhhccCchhHHHHhhCCCCCcEEEEEee--ccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          11 LNLWRTSFYQVSIAFGLGIDKPNVRFVIHH--CLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        11 l~l~~at~p~~~i~~~~~~~~~~i~~~~~~--~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      .-+|+||+|..........-...+.+.+..  .....+.+.+...    ....+...|.+++...  ..++||||+|++.
T Consensus       239 ~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~----~~~~k~~~l~~~l~~~--~~~~lVF~~t~~~  312 (434)
T 2db3_A          239 TLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEV----NKYAKRSKLIEILSEQ--ADGTIVFVETKRG  312 (434)
T ss_dssp             EEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEEC----CGGGHHHHHHHHHHHC--CTTEEEECSSHHH
T ss_pred             EEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEe----CcHHHHHHHHHHHHhC--CCCEEEEEeCcHH
Confidence            346889998753322222212223333322  2223333443332    2345677777777653  3459999999999


Q ss_pred             HHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccc
Q psy4494          89 CEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG  150 (234)
Q Consensus        89 ~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~g  150 (234)
                      ++.+++.|...|+.+..+||++++++                  |+++++|+|+|+|++|||||+|.+..+|+||+||+|
T Consensus       313 a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~g  392 (434)
T 2db3_A          313 ADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTG  392 (434)
T ss_dssp             HHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSS
T ss_pred             HHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccc
Confidence            99999999999999999999999876                  999999999999999999999999999999999999


Q ss_pred             cCCCceEEEEEeecc
Q psy4494         151 RDGQIAHCILYYRLP  165 (234)
Q Consensus       151 R~g~~~~~i~~~~~~  165 (234)
                      |.|+.|.+++|+++.
T Consensus       393 R~g~~G~a~~~~~~~  407 (434)
T 2db3_A          393 RVGNNGRATSFFDPE  407 (434)
T ss_dssp             CTTCCEEEEEEECTT
T ss_pred             cCCCCCEEEEEEecc
Confidence            999999999999864

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

Probab=99.89  E-value=1.7e-22  Score=172.94  Aligned_cols=113  Identities=23%  Similarity=0.414  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      .+|+..|.+++... .++++||||+|++.++.++..|...|+.+..+||+|++++                  |+++++|
T Consensus        13 ~~K~~~L~~ll~~~-~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~G   91 (300)
T 3i32_A           13 RGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARG   91 (300)
T ss_dssp             SSHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCS
T ss_pred             HHHHHHHHHHHHhc-CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcC
Confidence            35777788877654 5789999999999999999999999999999999999876                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      +|+|+|++|||||+|.+..+|+||+||+||.|++|.+++|+++.+...+..+
T Consensus        92 idi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~i  143 (300)
T 3i32_A           92 LDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEAL  143 (300)
T ss_dssp             TTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHH
T ss_pred             ccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999886655443

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

Probab=99.88  E-value=4.2e-22  Score=176.07  Aligned_cols=116  Identities=19%  Similarity=0.331  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      .++...+.+++.......++||||+|++.++.+++.|...|+.+..+||++++++                  |+++++|
T Consensus       260 ~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~G  339 (417)
T 2i4i_A          260 SDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARG  339 (417)
T ss_dssp             GGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTT
T ss_pred             HhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcC
Confidence            4567777777775445778999999999999999999999999999999999765                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      +|+|++++||+||+|.+..+|+||+||+||.|+.|.+++|+++.|......+..
T Consensus       340 idip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~  393 (417)
T 2i4i_A          340 LDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLD  393 (417)
T ss_dssp             SCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHH
T ss_pred             CCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHH
Confidence            999999999999999999999999999999999999999999988776665553

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

Probab=99.88  E-value=9.7e-22  Score=181.93  Aligned_cols=114  Identities=21%  Similarity=0.336  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc---CCceeeeccCCCchh------------------hhhccc
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR---GLRVSAYHAKLESNV------------------SIAFGL  120 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~------------------T~~~~~  120 (234)
                      .+..+...+.....+.++||||+|++.++.++..|+..   ++.+..+||+|++++                  |+++++
T Consensus       274 ~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~  353 (579)
T 3sqw_A          274 AVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGAR  353 (579)
T ss_dssp             HHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhc
Confidence            34455555554345779999999999999999999987   899999999999876                  999999


Q ss_pred             CCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       121 Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      |+|+|+|++||+|++|.++.+|+||+||+||+|+.|.+++++.+.|...+..+..
T Consensus       354 GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~  408 (579)
T 3sqw_A          354 GMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELED  408 (579)
T ss_dssp             SCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHH
T ss_pred             CCCcccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999877766643

>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=99.88  E-value=6.4e-22  Score=182.09  Aligned_cols=113  Identities=21%  Similarity=0.337  Sum_probs=100.3

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc---CCceeeeccCCCchh------------------hhhcccC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR---GLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      +..+...+.....+.++||||+|++.++.++..|...   ++.+..+||+|++++                  |+++++|
T Consensus       326 ~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~G  405 (563)
T 3i5x_A          326 VEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARG  405 (563)
T ss_dssp             HHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSS
T ss_pred             HHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcC
Confidence            4444455544346779999999999999999999987   899999999999876                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      +|+|+|++||+||+|.++.+|+||+||+||.|+.|.+++++.+.|...+..+..
T Consensus       406 iDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~  459 (563)
T 3i5x_A          406 MDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELED  459 (563)
T ss_dssp             CCCTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHH
T ss_pred             CCcccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999887776653

>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=99.78  E-value=1.4e-23  Score=165.27  Aligned_cols=113  Identities=19%  Similarity=0.298  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      .+++..|.+++.. ..+.++||||++++.++.++..|+..|+.+..+||++++.+                  |+++++|
T Consensus        15 ~~k~~~l~~ll~~-~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G   93 (170)
T 2yjt_D           15 EHKTALLVHLLKQ-PEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARG   93 (170)
Confidence            3466677777764 35678999999999999999999999999999999998766                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      +|+|++++||+||+|.+..+|+||+||+||.|+.|.+++++.+.|...+..+
T Consensus        94 id~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~  145 (170)
T 2yjt_D           94 IDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKV  145 (170)
Confidence            9999999999999999999999999999999999999999988776654443

>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=99.86  E-value=6.3e-21  Score=168.43  Aligned_cols=112  Identities=23%  Similarity=0.390  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCC
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGI  122 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gi  122 (234)
                      .+...+.+++... ...++||||+|++.++.+++.|...|+.+..+||++++++                  |+++++|+
T Consensus       262 ~k~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi  340 (410)
T 2j0s_A          262 WKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGL  340 (410)
T ss_dssp             HHHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSC
T ss_pred             hHHHHHHHHHHhc-CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcC
Confidence            3566666666543 5678999999999999999999999999999999999765                  99999999


Q ss_pred             CCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         123 DKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       123 d~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      |+|++++||+||+|.+...|+||+||+||.|++|.+++|+++.|...+..+
T Consensus       341 di~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i  391 (410)
T 2j0s_A          341 DVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDI  391 (410)
T ss_dssp             CCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHH
T ss_pred             CcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999887665543

>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=99.85  E-value=9.1e-21  Score=166.74  Aligned_cols=115  Identities=26%  Similarity=0.374  Sum_probs=102.4

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      ..+...+..++.. ...+++||||++++.++.+++.|...|+.+..+||++++++                  |+++++|
T Consensus       243 ~~k~~~l~~~~~~-~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~G  321 (400)
T 1s2m_A          243 RQKLHCLNTLFSK-LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG  321 (400)
T ss_dssp             GGHHHHHHHHHHH-SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSS
T ss_pred             hhHHHHHHHHHhh-cCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccC
Confidence            4466666676654 36678999999999999999999999999999999999865                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      +|+|++++||+|++|.+..+|+||+||+||.|++|.+++++++.|...+..+.+
T Consensus       322 idip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~  375 (400)
T 1s2m_A          322 IDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQ  375 (400)
T ss_dssp             CCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHH
T ss_pred             CCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHH
Confidence            999999999999999999999999999999999999999999998776655543

>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=99.84  E-value=2.8e-20  Score=163.78  Aligned_cols=109  Identities=20%  Similarity=0.285  Sum_probs=97.5

Q ss_pred             CChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhc
Q psy4494          57 AAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAF  118 (234)
Q Consensus        57 ~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~  118 (234)
                      .....+...+.+++... ..+++||||+|++.++.++..|...++.+..+||++++++                  |+++
T Consensus       248 ~~~~~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~  326 (412)
T 3fht_A          248 SSRDEKFQALCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVC  326 (412)
T ss_dssp             SSHHHHHHHHHHHHHHH-SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGG
T ss_pred             CChHHHHHHHHHHHhhc-CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCcc
Confidence            33456777777777643 5678999999999999999999999999999999999866                  9999


Q ss_pred             ccCCCCCCccEEEEeecC------CCHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         119 GLGIDKPNVRFVIHHCLS------KSMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       119 ~~Gid~~~v~~Vi~~~~P------~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      ++|+|+|++++||+||+|      .+..+|+||+||+||.|+.|.+++++++.+
T Consensus       327 ~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~  380 (412)
T 3fht_A          327 ARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH  380 (412)
T ss_dssp             TSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHH
T ss_pred             ccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChh
Confidence            999999999999999999      567899999999999999999999998765

>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=99.84  E-value=1.3e-20  Score=166.13  Aligned_cols=158  Identities=22%  Similarity=0.304  Sum_probs=105.9

Q ss_pred             HhhhccCchhHHHHhhCCCCCcEEEEEe--eccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHH
Q psy4494          12 NLWRTSFYQVSIAFGLGIDKPNVRFVIH--HCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKEC   89 (234)
Q Consensus        12 ~l~~at~p~~~i~~~~~~~~~~i~~~~~--~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~   89 (234)
                      -+++||.|..........-...+.+...  ......+..+|....   ....++..+.+++.. ...+++||||++++.+
T Consensus       218 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~-~~~~~~lvf~~~~~~~  293 (414)
T 3eiq_A          218 VLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVE---REEWKLDTLCDLYET-LTITQAVIFINTRRKV  293 (414)
T ss_dssp             EEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECS---SSTTHHHHHHHHHHS-SCCSSCEEECSCHHHH
T ss_pred             EEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeC---hHHhHHHHHHHHHHh-CCCCcEEEEeCCHHHH
Confidence            3567887765332222222222222221  222333344443322   223466677777764 3567899999999999


Q ss_pred             HHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhccccc
Q psy4494          90 EDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR  151 (234)
Q Consensus        90 ~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR  151 (234)
                      +.+++.|...++.+..+||++++++                  |+++++|+|+|++++||+|++|.+..+|+||+||+||
T Consensus       294 ~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR  373 (414)
T 3eiq_A          294 DWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGR  373 (414)
T ss_dssp             HHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC--
T ss_pred             HHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccC
Confidence            9999999999999999999998765                  9999999999999999999999999999999999999


Q ss_pred             CCCceEEEEEeecccHHHhhhh
Q psy4494         152 DGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       152 ~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                      .|++|.+++++++.|...+..+
T Consensus       374 ~g~~g~~~~~~~~~~~~~~~~~  395 (414)
T 3eiq_A          374 FGRKGVAINMVTEEDKRTLRDI  395 (414)
T ss_dssp             -----CEEEEECSTHHHHHHHH
T ss_pred             CCCCceEEEEEcHHHHHHHHHH
Confidence            9999999999999887665544

>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=99.84  E-value=4.5e-20  Score=161.22  Aligned_cols=112  Identities=26%  Similarity=0.411  Sum_probs=98.6

Q ss_pred             ChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcc
Q psy4494          58 AQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFG  119 (234)
Q Consensus        58 ~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~  119 (234)
                      ....+...+..++.. ...+++||||++++.++.+++.|+..++.+..+||++++++                  |++++
T Consensus       226 ~~~~~~~~l~~~~~~-~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~  304 (395)
T 3pey_A          226 NEADKFDVLTELYGL-MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA  304 (395)
T ss_dssp             SHHHHHHHHHHHHTT-TTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGS
T ss_pred             chHHHHHHHHHHHHh-ccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhh
Confidence            345566666666653 35688999999999999999999999999999999999866                  99999


Q ss_pred             cCCCCCCccEEEEeecCC------CHhHhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         120 LGIDKPNVRFVIHHCLSK------SMENFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       120 ~Gid~~~v~~Vi~~~~P~------~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                      +|+|+|++++||+||+|.      +..+|+||+||+||.|+.|.+++++.+.+....
T Consensus       305 ~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~  361 (395)
T 3pey_A          305 RGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNI  361 (395)
T ss_dssp             SSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHH
T ss_pred             cCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHH
Confidence            999999999999999999      999999999999999999999999987654433

>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=99.83  E-value=1e-20  Score=178.14  Aligned_cols=141  Identities=17%  Similarity=0.191  Sum_probs=93.6

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHc------CCceeeeccC--------CCchh------------------hhhcccCCC
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNR------GLRVSAYHAK--------LESNV------------------SIAFGLGID  123 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~------~~~~~~~h~~--------~~~~~------------------T~~~~~Gid  123 (234)
                      +.++||||++++.++.+++.|...      |+++..+||+        |++++                  |+++++|||
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GID  479 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGLD  479 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTSC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCc
Confidence            689999999999999999999987      8999999999        88876                  999999999


Q ss_pred             CCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHh--------hhhHHh--------------hhhhh
Q psy4494         124 KPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKL--------SSMVFD--------------QQTGL  181 (234)
Q Consensus       124 ~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~--------~~~~~~--------------~~~~~  181 (234)
                      +|+|++|||||+|+++.+|+||+|||||.|  +..+++....+....        ..++..              .....
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~GRArr~g--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  557 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQARGRARADE--STYVLVAHSGSGVIERETVNDFREKMMYKAIHCVQNMKPEEYAHKILE  557 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHHTTSCSSS--CEEEEEEESSSCSHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHH
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcCCCCCCC--ceEEEEEeCCchHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHH
Confidence            999999999999999999999999988776  334444443321111        011000              01112


Q ss_pred             HhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCC
Q psy4494         182 ANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDH  221 (234)
Q Consensus       182 ~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~  221 (234)
                      ..++++..+.. ...|++..++.||++... ..| +.||+
T Consensus       558 ~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~c-~~c~~  594 (699)
T 4gl2_A          558 LQMQSIMEKKM-KTKRNIAKHYKNNPSLIT-FLC-KNCSV  594 (699)
T ss_dssp             HHHHHHHHCCS-CCC----------CCSEE-EEE-SSSCC
T ss_pred             HHHHHHHHHHH-HHhhhHHhhhhcCcceeE-EEC-CCCCc
Confidence            34567777774 678999999999998743 234 45553

>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=99.83  E-value=9.6e-20  Score=159.42  Aligned_cols=107  Identities=20%  Similarity=0.322  Sum_probs=96.9

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      .++...+.+++.. ...+++||||++++.++.+++.|...|+.+..+||++++++                  |+++++|
T Consensus       235 ~~~~~~l~~~l~~-~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~G  313 (391)
T 1xti_A          235 NEKNRKLFDLLDV-LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG  313 (391)
T ss_dssp             GGHHHHHHHHHHH-SCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSC
T ss_pred             hhHHHHHHHHHHh-cCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcC
Confidence            4466667777764 36789999999999999999999999999999999998765                  9999999


Q ss_pred             CCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         122 IDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      +|+|++++||+|++|.+..+|+||+||+||.|++|.+++++++.+.
T Consensus       314 idi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~  359 (391)
T 1xti_A          314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEND  359 (391)
T ss_dssp             BCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHH
T ss_pred             CCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccch
Confidence            9999999999999999999999999999999999999999987654

>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=99.82  E-value=6.6e-20  Score=158.66  Aligned_cols=114  Identities=22%  Similarity=0.418  Sum_probs=102.6

Q ss_pred             hHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhccc
Q psy4494          59 QKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGL  120 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~  120 (234)
                      ..+++..+.+++..  ...++||||+|++.++.+++.|+..++.+..+||++++++                  |+++++
T Consensus       223 ~~~~~~~l~~~l~~--~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~  300 (367)
T 1hv8_A          223 ENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSR  300 (367)
T ss_dssp             GGGHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHH
T ss_pred             hHHHHHHHHHHHhc--CCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhc
Confidence            34567777777763  5678999999999999999999999999999999998865                  999999


Q ss_pred             CCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhH
Q psy4494         121 GIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       121 Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      |+|+|++++||++++|.+..+|+||+||+||.|++|.+++++++.|...+..+.
T Consensus       301 Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~  354 (367)
T 1hv8_A          301 GIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIE  354 (367)
T ss_dssp             HCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHH
T ss_pred             CCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999998887665544

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

Probab=99.79  E-value=1.7e-19  Score=169.64  Aligned_cols=108  Identities=17%  Similarity=0.260  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHhhc---CCCcEEEEecchHHHHHHHHHHHHcC----Cceeeec--------cCCCchh-----------
Q psy4494          61 DCLDELADLMSRRF---RNQSGIIYTTSIKECEDLREELRNRG----LRVSAYH--------AKLESNV-----------  114 (234)
Q Consensus        61 ~~~~~l~~~l~~~~---~~~~~iIf~~t~~~~~~l~~~L~~~~----~~~~~~h--------~~~~~~~-----------  114 (234)
                      .++..|.+++...+   .+.++||||++++.++.+++.|+..+    +++..+|        |+|++++           
T Consensus       380 ~k~~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~  459 (696)
T 2ykg_A          380 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKAS  459 (696)
T ss_dssp             HHHHHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC----------------------------
T ss_pred             HHHHHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhc
Confidence            46777777776542   46789999999999999999999988    8899995        4887654           


Q ss_pred             --------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         115 --------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       115 --------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                              |+++++|||+|+|++||+||+|.+..+|+||+|| ||. ++|.++++++..+....
T Consensus       460 g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~  521 (696)
T 2ykg_A          460 GDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEK  521 (696)
T ss_dssp             -CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHHH
T ss_pred             CCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHH
Confidence                    9999999999999999999999999999999999 998 78999999998776443

>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=99.79  E-value=2.3e-19  Score=169.55  Aligned_cols=109  Identities=21%  Similarity=0.246  Sum_probs=98.1

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..+|...|.+.+... ..++++||||+|++.++.|+..|...|+++..+||++.+.+                |+.+|||
T Consensus       414 ~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g~VlIATdmAgRG  493 (844)
T 1tf5_A          414 MEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRG  493 (844)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTCEEEEETTSSTT
T ss_pred             HHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCCeEEEeCCccccC
Confidence            456777787777542 24678999999999999999999999999999999987665                9999999


Q ss_pred             CCCC--------CccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         122 IDKP--------NVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       122 id~~--------~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      +|++        ++.+||||+.|.+...|+||+||+||+|++|.+++|++..|.
T Consensus       494 ~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          494 TDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             CCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             cCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            9999        788999999999999999999999999999999999998764

>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=99.79  E-value=8.8e-21  Score=171.40  Aligned_cols=152  Identities=18%  Similarity=0.277  Sum_probs=11.6

Q ss_pred             HHhhhccCchhHHHHhhC-C-CCCcEEEEEeeccCCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHH
Q psy4494          11 LNLWRTSFYQVSIAFGLG-I-DKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKE   88 (234)
Q Consensus        11 l~l~~at~p~~~i~~~~~-~-~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~   88 (234)
                      +-+++||++.....+... . ++..+.+.........+..+|.....   ...+...+..++.. ....++||||+|++.
T Consensus       270 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~-~~~~~~lvF~~s~~~  345 (479)
T 3fmp_B          270 MLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSS---RDEKFQALCNLYGA-ITIAQAMIFCHTRKT  345 (479)
T ss_dssp             EEEEESCCCHHHHHHHHHHSSSEEEEEEC---------------------------------------------------
T ss_pred             EEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCC---HHHHHHHHHHHHhh-ccCCceEEEeCcHHH
Confidence            345788888753222221 2 22222222222223333344433222   22345555555543 246789999999999


Q ss_pred             HHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCC------CHhHhhh
Q psy4494          89 CEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSK------SMENFYQ  144 (234)
Q Consensus        89 ~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~------~~~~y~q  144 (234)
                      ++.++..|...++.+..+||++++++                  |+++++|+|+|+|++||+||+|.      +..+|+|
T Consensus       346 ~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Q  425 (479)
T 3fmp_B          346 ASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLH  425 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHH
Confidence            99999999999999999999998866                  99999999999999999999994      6689999


Q ss_pred             hhcccccCCCceEEEEEeeccc
Q psy4494         145 ESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       145 r~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      |+||+||.|+.|.+++|+++.+
T Consensus       426 r~GRagR~g~~G~~i~~~~~~~  447 (479)
T 3fmp_B          426 RIGRTGRFGKRGLAVNMVDSKH  447 (479)
T ss_dssp             ----------------------
T ss_pred             HhcccccCCCCceEEEEEcCcc
Confidence            9999999999999999998765

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.78  E-value=1.4e-20  Score=164.81  Aligned_cols=112  Identities=27%  Similarity=0.369  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCC
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGID  123 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid  123 (234)
                      +...+.+++.. ....++||||++++.++.+++.|+..++.+..+||++++++                  |+++++|+|
T Consensus       246 ~~~~l~~~~~~-~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gld  324 (394)
T 1fuu_A          246 KYECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGID  324 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhc-CCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCC
Confidence            34445555543 35678999999999999999999999999999999998765                  999999999


Q ss_pred             CCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhH
Q psy4494         124 KPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       124 ~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                      +|++++||+|++|.+..+|+||+||+||.|++|.+++++++.|...+..+.
T Consensus       325 i~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~  375 (394)
T 1fuu_A          325 VQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELE  375 (394)
T ss_dssp             ---------------------------------------------------
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHH
Confidence            999999999999999999999999999999999999999998876655443

>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=99.76  E-value=1.5e-18  Score=161.46  Aligned_cols=109  Identities=27%  Similarity=0.351  Sum_probs=97.2

Q ss_pred             hHHHHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..++...+.+.+.... .++++||||+|++.++.++..|...|+++..+||+..+.+                |+.+|||
T Consensus       456 ~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g~VtVATdmAgRG  535 (822)
T 3jux_A          456 QKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRG  535 (822)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTTCEEEEETTTTTT
T ss_pred             HHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCCeEEEEcchhhCC
Confidence            4567888888776432 4788999999999999999999999999999999966544                9999999


Q ss_pred             CCCC--------CccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         122 IDKP--------NVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       122 id~~--------~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      +|++        ++.+|||+++|.+...|.||+||+||+|.+|.+++|++..|.
T Consensus       536 tDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          536 TDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             CCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             cCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHH
Confidence            9998        666999999999999999999999999999999999999873

>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=99.75  E-value=1.1e-18  Score=169.71  Aligned_cols=107  Identities=18%  Similarity=0.241  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHHHhh---cCCCcEEEEecchHHHHHHHHHHHHc------------CCceeeeccCCCchh----------
Q psy4494          60 KDCLDELADLMSRR---FRNQSGIIYTTSIKECEDLREELRNR------------GLRVSAYHAKLESNV----------  114 (234)
Q Consensus        60 ~~~~~~l~~~l~~~---~~~~~~iIf~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~----------  114 (234)
                      ..++..|.+++.+.   ..+.++||||++++.++.++..|...            |.....+||+|++.+          
T Consensus       612 ~~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~  691 (936)
T 4a2w_A          612 NPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKT  691 (936)
T ss_dssp             CHHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC--------------------------
T ss_pred             CHHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhc
Confidence            44677777777653   24689999999999999999999986            555566688888765          


Q ss_pred             ---------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         115 ---------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       115 ---------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                               |+++++|||+|+|++|||||+|+++.+|+||+|| ||. ++|.++++++..+..
T Consensus       692 ~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~e  752 (936)
T 4a2w_A          692 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (936)
T ss_dssp             --CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHHH
T ss_pred             cCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCHH
Confidence                     9999999999999999999999999999999999 999 778899999886553

>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=99.74  E-value=3e-18  Score=146.67  Aligned_cols=92  Identities=17%  Similarity=0.302  Sum_probs=83.8

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLS  136 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P  136 (234)
                      .++++||||++++.++.+++.|.    .+..+||+++.++                  |+++++|+|+|++++||+|++|
T Consensus       219 ~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~  294 (337)
T 2z0m_A          219 KDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAP  294 (337)
T ss_dssp             CCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSCC
T ss_pred             CCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecCC
Confidence            57889999999999999999886    5889999998866                  9999999999999999999999


Q ss_pred             CCHhHhhhhhcccccCCCceEEEEEeecccHHHhh
Q psy4494         137 KSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLS  171 (234)
Q Consensus       137 ~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~  171 (234)
                      .+..+|+||+||+||.|++|.+++|+. .+.....
T Consensus       295 ~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~  328 (337)
T 2z0m_A          295 QDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEK  328 (337)
T ss_dssp             SSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHH
T ss_pred             CCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHH
Confidence            999999999999999999999999998 5554433

>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=99.73  E-value=7.2e-17  Score=151.60  Aligned_cols=98  Identities=21%  Similarity=0.280  Sum_probs=88.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeec-
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCL-  135 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~-  135 (234)
                      .+.++||||+|++.++.++..|...|+.+..+||++++.+                  |+++++|+|+|+|++||++|. 
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d  517 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDAD  517 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTT
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCc
Confidence            4679999999999999999999999999999999998655                  899999999999999999997 


Q ss_pred             ----CCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         136 ----SKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       136 ----P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                          |.+..+|+||+||+||.+ +|.+++|+++.+......+
T Consensus       518 ~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i  558 (664)
T 1c4o_A          518 KEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAI  558 (664)
T ss_dssp             SCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHH
T ss_pred             ccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHHHHH
Confidence                999999999999999995 7999999988776554443

>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=99.73  E-value=5.1e-17  Score=152.56  Aligned_cols=97  Identities=25%  Similarity=0.299  Sum_probs=88.4

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeec-
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCL-  135 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~-  135 (234)
                      .+.++||||+|++.++.++..|...|+++..+||++++.+                  |+++++|+|+|+|++||++|. 
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d  523 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDAD  523 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcc
Confidence            4678999999999999999999999999999999998655                  899999999999999999998 


Q ss_pred             ----CCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhh
Q psy4494         136 ----SKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSS  172 (234)
Q Consensus       136 ----P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~  172 (234)
                          |.+..+|+||+||+||. .+|.+++|+++.+......
T Consensus       524 ~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~~  563 (661)
T 2d7d_A          524 KEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEIA  563 (661)
T ss_dssp             CCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHHH
T ss_pred             cccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHHH
Confidence                99999999999999998 7899999999877654443

>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=99.72  E-value=1.7e-17  Score=156.61  Aligned_cols=110  Identities=24%  Similarity=0.317  Sum_probs=98.2

Q ss_pred             ChHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhccc
Q psy4494          58 AQKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGL  120 (234)
Q Consensus        58 ~~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~  120 (234)
                      ...+|...|.+.+... ..++++||||+|++.++.|+..|...|+++..+||.+.+.+                |+.+||
T Consensus       422 ~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G~VtIATnmAgR  501 (853)
T 2fsf_A          422 TEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPAAVTIATNMAGR  501 (853)
T ss_dssp             SHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTTCEEEEESCCSS
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCCeEEEecccccC
Confidence            3567888888877543 35678999999999999999999999999999999987655                999999


Q ss_pred             CCCCCC--------------------------------c-----cEEEEeecCCCHhHhhhhhcccccCCCceEEEEEee
Q psy4494         121 GIDKPN--------------------------------V-----RFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYR  163 (234)
Q Consensus       121 Gid~~~--------------------------------v-----~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~  163 (234)
                      |+|++.                                |     .+||||+.|.+...|.||+||+||.|.+|.+++|++
T Consensus       502 GtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls  581 (853)
T 2fsf_A          502 GTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLS  581 (853)
T ss_dssp             CSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEE
T ss_pred             CcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEec
Confidence            999997                                4     599999999999999999999999999999999999


Q ss_pred             cccH
Q psy4494         164 LPDV  167 (234)
Q Consensus       164 ~~d~  167 (234)
                      ..|.
T Consensus       582 ~eD~  585 (853)
T 2fsf_A          582 MEDA  585 (853)
T ss_dssp             TTSG
T ss_pred             ccHH
Confidence            8764

>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=99.71  E-value=3.7e-17  Score=145.49  Aligned_cols=109  Identities=19%  Similarity=0.267  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHhh---cCCCcEEEEecchHHHHHHHHHHHHcCCceeeecc--------CCCchh--------------
Q psy4494          60 KDCLDELADLMSRR---FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA--------KLESNV--------------  114 (234)
Q Consensus        60 ~~~~~~l~~~l~~~---~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~--------~~~~~~--------------  114 (234)
                      ..++..+.+++...   ..+.++||||++++.++.+++.|...|+.+..+||        +++.++              
T Consensus       342 ~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~  421 (494)
T 1wp9_A          342 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  421 (494)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             ChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCce
Confidence            34666777777653   35789999999999999999999999999999999        787765              


Q ss_pred             ----hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         115 ----SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       115 ----T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                          |+++++|+|+|++++||+||+|+++..|+||+||+||.|+ |.++.++.+.+...
T Consensus       422 vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~ee  479 (494)
T 1wp9_A          422 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTRDE  479 (494)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSHHH
T ss_pred             EEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCHHH
Confidence                9999999999999999999999999999999999999998 99999999887653

>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=99.71  E-value=2.9e-17  Score=149.90  Aligned_cols=108  Identities=18%  Similarity=0.243  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHhh---cCCCcEEEEecchHHHHHHHHHHHHc------------CCceeeeccCCCchh----------
Q psy4494          60 KDCLDELADLMSRR---FRNQSGIIYTTSIKECEDLREELRNR------------GLRVSAYHAKLESNV----------  114 (234)
Q Consensus        60 ~~~~~~l~~~l~~~---~~~~~~iIf~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~----------  114 (234)
                      ..++..|.+++.+.   ..+.++||||++++.++.++..|...            |.....+||+|++++          
T Consensus       371 ~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~  450 (556)
T 4a2p_A          371 NPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKT  450 (556)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC---------------------------
T ss_pred             ChHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcc
Confidence            34667777777543   35689999999999999999999875            444556677787765          


Q ss_pred             ---------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         115 ---------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       115 ---------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                               |+++++|+|+|+|++|||||+|+++..|+||+|| ||. ++|.++++++..+...
T Consensus       451 ~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~  512 (556)
T 4a2p_A          451 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVE  512 (556)
T ss_dssp             ---CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHHH
T ss_pred             cCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchHH
Confidence                     9999999999999999999999999999999999 999 8899999998876543

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

Probab=99.70  E-value=1.4e-17  Score=162.59  Aligned_cols=163  Identities=19%  Similarity=0.341  Sum_probs=110.3

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCC---------------------------------------
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGL---------------------------------------  101 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~---------------------------------------  101 (234)
                      .++..+.+.+... ...++||||+|++.|+.++..|...++                                       
T Consensus       322 ~~~~~li~~l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~  400 (997)
T 4a4z_A          322 KTWPEIVNYLRKR-ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLER  400 (997)
T ss_dssp             THHHHHHHHHHHT-TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhc
Confidence            4566677777643 567899999999999999999977655                                       


Q ss_pred             ceeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecCC---------CHhHhhhhhcccccCC-
Q psy4494         102 RVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLSK---------SMENFYQESGRAGRDG-  153 (234)
Q Consensus       102 ~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P~---------~~~~y~qr~GR~gR~g-  153 (234)
                      .+.++||+|++.+                  |+++++|||+|+ ..||+++.|.         +..+|+||+|||||.| 
T Consensus       401 gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~  479 (997)
T 4a4z_A          401 GIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGL  479 (997)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCTTT
T ss_pred             CeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccCCC
Confidence            3689999999866                  999999999999 6666655555         9999999999999998 


Q ss_pred             -CceEEEEEee--cccHHHhhhhHHhh-------------------hhhhHhHHHHHHHh-----hcCcccHHHHHHhHc
Q psy4494         154 -QIAHCILYYR--LPDVFKLSSMVFDQ-------------------QTGLANLYNIVSYC-----LDQTRCRRAIIASYF  206 (234)
Q Consensus       154 -~~~~~i~~~~--~~d~~~~~~~~~~~-------------------~~~~~~l~~~~~~~-----~~~~~Crr~~l~~~f  206 (234)
                       ..|.+++++.  ..+...+..++...                   +.....++.|+.+.     .+...|++...+.+|
T Consensus       480 ~~~G~vi~l~~~~~~~~~~~~~~i~~~~~~l~s~~~~~ynm~l~ll~~~~~~~~~~l~~sf~~~~~~~~~~~~~~~l~~l  559 (997)
T 4a4z_A          480 DSTGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVL  559 (997)
T ss_dssp             CSSEEEEEECCSSCCCHHHHHHHHHSCCCCCCCCCCCCHHHHHHHHHHCTTHHHHHHHTSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcceEEEEecCCCcchHHHHHHHhcCCCcccccccccchHHHHHHHhhccccHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence             5688888883  33444444442211                   11122345555432     235679999999999


Q ss_pred             CCCCCCCccCCCCCCCCCCC
Q psy4494         207 DEAWSDTECRGMCDHCRGGR  226 (234)
Q Consensus       207 ~e~~~~~~c~~~Cd~C~~~~  226 (234)
                      ++......| ..||+|....
T Consensus       560 ~~~~~~~~~-~~c~~c~~~~  578 (997)
T 4a4z_A          560 QEELQTIEY-KSCEICDNDI  578 (997)
T ss_dssp             HHHHHC--------------
T ss_pred             HHHHHHhhh-hccccccccH
Confidence            987655457 6799996543

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

Probab=99.70  E-value=3.7e-17  Score=144.79  Aligned_cols=99  Identities=18%  Similarity=0.272  Sum_probs=83.8

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCcee-eeccCCCc------------hh----hhhcccCCCCC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS-AYHAKLES------------NV----SIAFGLGIDKP  125 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~-~~h~~~~~------------~~----T~~~~~Gid~~  125 (234)
                      ...+.+++..  .+.++||||+|++.++.++..|+..|+.+. .+||....            -.    |+++++|+|+|
T Consensus       241 ~~~l~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~~r~~~~f~~g~~~vLvat~s~T~~~~~GiDip  318 (414)
T 3oiy_A          241 KEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLP  318 (414)
T ss_dssp             HHHHHHHHHH--HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCHHHHHHHHHTTSCSEEEEECCTTCCCCCCCCCT
T ss_pred             HHHHHHHHHH--cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCcchHHHHHhCCCCeEEEEecCcCchhhccCccc
Confidence            3445555554  357899999999999999999999999998 99985211            01    68899999999


Q ss_pred             C-ccEEEEeecC--CCHhHhhhhhcccccCC----CceEEEEEee
Q psy4494         126 N-VRFVIHHCLS--KSMENFYQESGRAGRDG----QIAHCILYYR  163 (234)
Q Consensus       126 ~-v~~Vi~~~~P--~~~~~y~qr~GR~gR~g----~~~~~i~~~~  163 (234)
                      + |++||+||+|  .+..+|+||+||+||.|    +.|.+++++.
T Consensus       319 ~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~~  363 (414)
T 3oiy_A          319 ERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEE  363 (414)
T ss_dssp             TTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEECC
T ss_pred             cccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEEc
Confidence            9 9999999999  99999999999999987    5899999994

>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=99.70  E-value=7.9e-17  Score=152.61  Aligned_cols=110  Identities=24%  Similarity=0.252  Sum_probs=97.6

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..+|...|.+.+... ..++++||||+|++.++.|+..|...|+++..+||.+.+.+                |+.+|||
T Consensus       442 ~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G~VtIATnmAgRG  521 (922)
T 1nkt_A          442 EEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRGGVTVATNMAGRG  521 (922)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTTCEEEEETTCSTT
T ss_pred             HHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCCeEEEecchhhcC
Confidence            456787787777543 25678999999999999999999999999999999987655                9999999


Q ss_pred             CCCCCc----------------------------------------------------cEEEEeecCCCHhHhhhhhccc
Q psy4494         122 IDKPNV----------------------------------------------------RFVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus       122 id~~~v----------------------------------------------------~~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      +||+.+                                                    .+||||+.|.+...|.||+||+
T Consensus       522 tDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRT  601 (922)
T 1nkt_A          522 TDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRS  601 (922)
T ss_dssp             CCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTS
T ss_pred             ccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhccc
Confidence            999975                                                    4999999999999999999999


Q ss_pred             ccCCCceEEEEEeecccHH
Q psy4494         150 GRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d~~  168 (234)
                      ||.|.+|.+++|++..|..
T Consensus       602 GRqGdpG~s~fflSleD~l  620 (922)
T 1nkt_A          602 GRQGDPGESRFYLSLGDEL  620 (922)
T ss_dssp             SGGGCCEEEEEEEETTSHH
T ss_pred             ccCCCCeeEEEEechhHHH
Confidence            9999999999999987753

>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=99.69  E-value=2.8e-17  Score=153.28  Aligned_cols=92  Identities=24%  Similarity=0.343  Sum_probs=85.2

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-----------hhhcccCCCCCCccEEE----------Ee
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-----------SIAFGLGIDKPNVRFVI----------HH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------T~~~~~Gid~~~v~~Vi----------~~  133 (234)
                      .++++||||+|++.++.+++.|++.++.+..+||++++++           |++++||||++ |++||          ||
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~er~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNy  473 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDF  473 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGGSCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEEC
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHHHHhCCCcEEEECChHHccCCCC-CcEEEecCccccccccc
Confidence            5788999999999999999999999999999999999876           99999999997 99988          67


Q ss_pred             e-----------cCCCHhHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         134 C-----------LSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       134 ~-----------~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                      |           .|.+.++|+||+||+|| |++|. +.|+++.|...
T Consensus       474 DydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~~  518 (666)
T 3o8b_A          474 SLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERPS  518 (666)
T ss_dssp             CCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBCS
T ss_pred             ccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhhc
Confidence            7           99999999999999999 99999 99998876543

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

Probab=99.69  E-value=4.8e-17  Score=148.14  Aligned_cols=108  Identities=18%  Similarity=0.238  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHHhh---cCCCcEEEEecchHHHHHHHHHHHHcC----Ccee--------eeccCCCchh-----------
Q psy4494          61 DCLDELADLMSRR---FRNQSGIIYTTSIKECEDLREELRNRG----LRVS--------AYHAKLESNV-----------  114 (234)
Q Consensus        61 ~~~~~l~~~l~~~---~~~~~~iIf~~t~~~~~~l~~~L~~~~----~~~~--------~~h~~~~~~~-----------  114 (234)
                      .++..|.+++...   ..+.++||||++++.++.++..|...+    +.+.        .+||+|++++           
T Consensus       371 ~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~  450 (555)
T 3tbk_A          371 PKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRAS  450 (555)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-------------------------
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcC
Confidence            4666666666542   246899999999999999999999864    3444        4455777765           


Q ss_pred             --------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHh
Q psy4494         115 --------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKL  170 (234)
Q Consensus       115 --------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~  170 (234)
                              |+++++|+|+|++++|||||+|+++.+|+||+|| ||. ++|.+++++++.+....
T Consensus       451 g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~  512 (555)
T 3tbk_A          451 GDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEK  512 (555)
T ss_dssp             -CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHH
T ss_pred             CCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHH
Confidence                    9999999999999999999999999999999999 999 89999999998766443

>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=99.66  E-value=1.5e-16  Score=143.19  Aligned_cols=88  Identities=20%  Similarity=0.194  Sum_probs=81.3

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEEEEee-------
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFVIHHC-------  134 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~Vi~~~-------  134 (234)
                      .+++||||+|++.++.+++.|+..|+.+..+||++..+.              |+++++|+|+|+ ++|||||       
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~  266 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVI  266 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTHHHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHHHHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccc
Confidence            568999999999999999999999999999999887543              999999999999 9999999       


Q ss_pred             -------------cCCCHhHhhhhhcccccCCC-ceEEEEEeec
Q psy4494         135 -------------LSKSMENFYQESGRAGRDGQ-IAHCILYYRL  164 (234)
Q Consensus       135 -------------~P~~~~~y~qr~GR~gR~g~-~~~~i~~~~~  164 (234)
                                   .|.+..+|+||+||+||.|. +|.+++|+..
T Consensus       267 d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~  310 (451)
T 2jlq_A          267 LTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGD  310 (451)
T ss_dssp             ECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSC
T ss_pred             cccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCC
Confidence                         99999999999999999998 8888888743

>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=99.66  E-value=2.1e-16  Score=141.84  Aligned_cols=94  Identities=19%  Similarity=0.205  Sum_probs=81.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEEEE--------
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFVIH--------  132 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~Vi~--------  132 (234)
                      .++++||||+|++.++.+++.|+..++++..+||+.-.+.              |+++++|+|+| +++||+        
T Consensus       176 ~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv  254 (440)
T 1yks_A          176 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPV  254 (440)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecchhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceee
Confidence            3678999999999999999999999999999999533222              99999999999 999996        


Q ss_pred             -----------eecCCCHhHhhhhhcccccC-CCceEEEEEe---ecccHHH
Q psy4494         133 -----------HCLSKSMENFYQESGRAGRD-GQIAHCILYY---RLPDVFK  169 (234)
Q Consensus       133 -----------~~~P~~~~~y~qr~GR~gR~-g~~~~~i~~~---~~~d~~~  169 (234)
                                 |+.|.+..+|+||+||+||. |++|.+++|+   ++.|...
T Consensus       255 ~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~  306 (440)
T 1yks_A          255 LVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHH  306 (440)
T ss_dssp             EETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTB
T ss_pred             ecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhh
Confidence                       99999999999999999997 7899999997   4555433

>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=99.66  E-value=1.4e-16  Score=151.84  Aligned_cols=104  Identities=16%  Similarity=0.219  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHH-----------cCCceeeeccCCCchh----------------
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRN-----------RGLRVSAYHAKLESNV----------------  114 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~-----------~~~~~~~~h~~~~~~~----------------  114 (234)
                      .+..+.++... ..++++||||++++.++.++..|..           .++.+.++||++++++                
T Consensus       290 ~l~~l~~~~~~-~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g  368 (773)
T 2xau_A          290 AIRTVLQIHAT-EEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRP  368 (773)
T ss_dssp             HHHHHHHHHHH-SCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSC
T ss_pred             HHHHHHHHHHh-cCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCC
Confidence            34444444432 2577899999999999999999985           5788999999997532                


Q ss_pred             -------hhhcccCCCCCCccEEEEeec------------------CCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         115 -------SIAFGLGIDKPNVRFVIHHCL------------------SKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       115 -------T~~~~~Gid~~~v~~Vi~~~~------------------P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                             |+++++|||+|+|++||++|+                  |.+..+|+||+|||||. .+|.|+.++++.++
T Consensus       369 ~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          369 GRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             CEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             ceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence                   899999999999999999888                  88999999999999999 89999999998776

>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=99.65  E-value=5.5e-16  Score=148.39  Aligned_cols=108  Identities=18%  Similarity=0.243  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHHHhh---cCCCcEEEEecchHHHHHHHHHHHHc------------CCceeeeccCCCchh----------
Q psy4494          60 KDCLDELADLMSRR---FRNQSGIIYTTSIKECEDLREELRNR------------GLRVSAYHAKLESNV----------  114 (234)
Q Consensus        60 ~~~~~~l~~~l~~~---~~~~~~iIf~~t~~~~~~l~~~L~~~------------~~~~~~~h~~~~~~~----------  114 (234)
                      ..++..|.+++.+.   ..+.++||||++++.++.++..|+..            |.....+||+|++++          
T Consensus       612 ~~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~  691 (797)
T 4a2q_A          612 NPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKT  691 (797)
T ss_dssp             CHHHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC--------------------------
T ss_pred             ChHHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhc
Confidence            34666677776542   35689999999999999999999874            455666788888765          


Q ss_pred             ---------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHH
Q psy4494         115 ---------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFK  169 (234)
Q Consensus       115 ---------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~  169 (234)
                               |+++++|||+|+|++|||||+|+++..|+||+|| ||. ++|.++++++..+...
T Consensus       692 ~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~ee  753 (797)
T 4a2q_A          692 SKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVE  753 (797)
T ss_dssp             --CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHHHH
T ss_pred             cCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHHH
Confidence                     9999999999999999999999999999999999 999 8899999998876543

>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=99.64  E-value=4.1e-16  Score=145.30  Aligned_cols=94  Identities=19%  Similarity=0.164  Sum_probs=82.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEE----------
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFV----------  130 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~V----------  130 (234)
                      ..+++||||+|++.++.+++.|+..++++..+||+...+.              |+++++|+|+| |++|          
T Consensus       354 ~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~  432 (618)
T 2whx_A          354 YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVIDPRRCLKPV  432 (618)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTTHHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEE
T ss_pred             CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChHHHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEEECcceecce
Confidence            3678999999999999999999999999999999633222              99999999997 9988          


Q ss_pred             ----------EEeecCCCHhHhhhhhcccccCCC-ceEEEEEee---cccHHH
Q psy4494         131 ----------IHHCLSKSMENFYQESGRAGRDGQ-IAHCILYYR---LPDVFK  169 (234)
Q Consensus       131 ----------i~~~~P~~~~~y~qr~GR~gR~g~-~~~~i~~~~---~~d~~~  169 (234)
                                |||+.|.+..+|+||+||+||.|. +|.+++|++   +.|...
T Consensus       433 ~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~  485 (618)
T 2whx_A          433 ILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDH  485 (618)
T ss_dssp             EECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTC
T ss_pred             ecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHH
Confidence                      888889999999999999999964 899999997   555443

>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=99.64  E-value=3.5e-16  Score=141.07  Aligned_cols=89  Identities=17%  Similarity=0.163  Sum_probs=78.3

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEEEE---------
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFVIH---------  132 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~Vi~---------  132 (234)
                      .+++||||+|++.++.+++.|+..++.+..+||..-.+.              |+++++|+|+|+ ++||+         
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~  268 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRKSYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTI  268 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTTCCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEE
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHHHHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCccccccc
Confidence            678999999999999999999999999999999633221              999999999999 99999         


Q ss_pred             -----------eecCCCHhHhhhhhcccccCCC-ceEEEEEeecc
Q psy4494         133 -----------HCLSKSMENFYQESGRAGRDGQ-IAHCILYYRLP  165 (234)
Q Consensus       133 -----------~~~P~~~~~y~qr~GR~gR~g~-~~~~i~~~~~~  165 (234)
                                 |+.|.+..+|+||+||+||.|. +|.+++|+.+.
T Consensus       269 ~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          269 LEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             ECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             ccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence                       7799999999999999999997 89999999875

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.62  E-value=7.6e-16  Score=129.82  Aligned_cols=107  Identities=16%  Similarity=0.107  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHc-CCceeeeccCCCchh--------------------hhh
Q psy4494          60 KDCLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNR-GLRVSAYHAKLESNV--------------------SIA  117 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~--------------------T~~  117 (234)
                      ..|+..|.+++.+.. .+.++||||+++..++.+...|... |+.+..+||++++++                    |++
T Consensus        95 s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~  174 (271)
T 1z5z_A           95 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  174 (271)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT
T ss_pred             CHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhh
Confidence            456777777665421 5679999999999999999999885 999999999998755                    889


Q ss_pred             cccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEE--EEEeeccc
Q psy4494         118 FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHC--ILYYRLPD  166 (234)
Q Consensus       118 ~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~--i~~~~~~d  166 (234)
                      .|+|+|++.+++||+||+|+++..|.|++||++|.|+.+.+  +.++....
T Consensus       175 ~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~T  225 (271)
T 1z5z_A          175 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  225 (271)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETTS
T ss_pred             hcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCCC
Confidence            99999999999999999999999999999999999987544  44555543

>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=99.61  E-value=1.1e-15  Score=150.39  Aligned_cols=103  Identities=20%  Similarity=0.380  Sum_probs=82.1

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCc---------------------------------------
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR---------------------------------------  102 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~---------------------------------------  102 (234)
                      .+..+...+... ...++||||+|++.|+.++..|...++.                                       
T Consensus       428 ~l~~li~~l~~~-~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~g  506 (1108)
T 3l9o_A          428 DIYKIVKMIWKK-KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRG  506 (1108)
T ss_dssp             HHHHHHHHHHHT-TCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHT
T ss_pred             HHHHHHHHHHhc-CCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcC
Confidence            344455554432 4678999999999999999998653332                                       


Q ss_pred             eeeeccCCCchh------------------hhhcccCCCCCCccEEEEeecC--------CCHhHhhhhhcccccCC--C
Q psy4494         103 VSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHCLS--------KSMENFYQESGRAGRDG--Q  154 (234)
Q Consensus       103 ~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~~P--------~~~~~y~qr~GR~gR~g--~  154 (234)
                      +..+||+|++.+                  |+++++|||+|++++||+++.|        .+..+|+||+|||||.|  .
T Consensus       507 V~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~  586 (1108)
T 3l9o_A          507 IGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDD  586 (1108)
T ss_dssp             EEEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCS
T ss_pred             eeeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCC
Confidence            688999999876                  9999999999999999977664        36678999999999999  6


Q ss_pred             ceEEEEEeecc
Q psy4494         155 IAHCILYYRLP  165 (234)
Q Consensus       155 ~~~~i~~~~~~  165 (234)
                      .|.+++++++.
T Consensus       587 ~G~~ill~~~~  597 (1108)
T 3l9o_A          587 RGIVIMMIDEK  597 (1108)
T ss_dssp             SEEEEEEECCC
T ss_pred             ceEEEEEecCC
Confidence            89999999875

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

Probab=99.60  E-value=1.7e-15  Score=142.35  Aligned_cols=92  Identities=21%  Similarity=0.201  Sum_probs=80.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEEEE--------
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFVIH--------  132 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~Vi~--------  132 (234)
                      .++++||||+|++.++.+++.|+..++.+..+||+.-.+.              |+++++|+|+| +++|||        
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~  487 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRKSYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRKSVKPT  487 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSSSHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCEECCEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChHHHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCCcccce
Confidence            4678999999999999999999999999999999522111              99999999999 999998        


Q ss_pred             ------------eecCCCHhHhhhhhcccccC-CCceEEEEEe---ecccH
Q psy4494         133 ------------HCLSKSMENFYQESGRAGRD-GQIAHCILYY---RLPDV  167 (234)
Q Consensus       133 ------------~~~P~~~~~y~qr~GR~gR~-g~~~~~i~~~---~~~d~  167 (234)
                                  |+.|.+..+|+||+||+||. |++|.+++|+   ++.|.
T Consensus       488 vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~  538 (673)
T 2wv9_A          488 ILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDT  538 (673)
T ss_dssp             EECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCT
T ss_pred             eeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHH
Confidence                        67899999999999999998 7899999996   45553

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

Probab=99.60  E-value=3.1e-16  Score=154.36  Aligned_cols=72  Identities=18%  Similarity=0.302  Sum_probs=60.2

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCcee-eeccCCCchh-----------------hhhcccCCCC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVS-AYHAKLESNV-----------------SIAFGLGIDK  124 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~-~~h~~~~~~~-----------------T~~~~~Gid~  124 (234)
                      ...|.+++..  .++++||||+|++.++.++..|+..|+.+. .+||.-.. .                 |++++||+|+
T Consensus       298 ~~~L~~ll~~--~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~rr~-l~~F~~G~~~VLVatas~TdvlarGIDi  374 (1104)
T 4ddu_A          298 KEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKN-FEDFKVGKINILIGVQAYYGKLTRGVDL  374 (1104)
T ss_dssp             HHHHHHHHHH--HCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSHHHH-HHHHHHTSCSEEEEETTTHHHHCCSCCC
T ss_pred             HHHHHHHHHh--cCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCcHHH-HHHHHCCCCCEEEEecCCCCeeEecCcC
Confidence            3444555554  347899999999999999999999999998 99994221 1                 6899999999


Q ss_pred             CC-ccEEEEeecCC
Q psy4494         125 PN-VRFVIHHCLSK  137 (234)
Q Consensus       125 ~~-v~~Vi~~~~P~  137 (234)
                      |+ |++|||||+|.
T Consensus       375 p~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          375 PERIKYVIFWGTPS  388 (1104)
T ss_dssp             TTTCCEEEEESCCE
T ss_pred             CCCCCEEEEECCCC
Confidence            99 99999999998

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

Probab=99.57  E-value=8.4e-15  Score=138.50  Aligned_cols=103  Identities=25%  Similarity=0.314  Sum_probs=84.2

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcC------------------------------------Ccee
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRG------------------------------------LRVS  104 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~------------------------------------~~~~  104 (234)
                      .+...+.+.+.   .++++||||+|++.++.++..|.+..                                    ..+.
T Consensus       240 ~~~~~~~~~~~---~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~  316 (715)
T 2va8_A          240 AIIAYTLDSLS---KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVA  316 (715)
T ss_dssp             HHHHHHHHHHT---TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEE
T ss_pred             HHHHHHHHHHh---cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEE
Confidence            34555555553   56889999999999999999998642                                    2388


Q ss_pred             eeccCCCchh------------------hhhcccCCCCCCccEEEE----ee-------cCCCHhHhhhhhcccccCC--
Q psy4494         105 AYHAKLESNV------------------SIAFGLGIDKPNVRFVIH----HC-------LSKSMENFYQESGRAGRDG--  153 (234)
Q Consensus       105 ~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~----~~-------~P~~~~~y~qr~GR~gR~g--  153 (234)
                      ++||++++++                  |+++++|+|+|++++||+    ||       .|.+..+|+||+|||||.|  
T Consensus       317 ~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~  396 (715)
T 2va8_A          317 YHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFD  396 (715)
T ss_dssp             EECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTC
T ss_pred             EECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCC
Confidence            9999999876                  999999999999999999    99       8999999999999999988  


Q ss_pred             CceEEEEEeeccc
Q psy4494         154 QIAHCILYYRLPD  166 (234)
Q Consensus       154 ~~~~~i~~~~~~d  166 (234)
                      .+|.++++++..+
T Consensus       397 ~~G~~~~l~~~~~  409 (715)
T 2va8_A          397 QIGESIVVVRDKE  409 (715)
T ss_dssp             SCEEEEEECSCGG
T ss_pred             CCceEEEEeCCch
Confidence            5799999998766

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

Probab=99.57  E-value=7e-15  Score=143.63  Aligned_cols=109  Identities=19%  Similarity=0.320  Sum_probs=89.4

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCc---------------------------------------e
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR---------------------------------------V  103 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~---------------------------------------~  103 (234)
                      +..+.+.+... ...++||||+|++.|+.++..|...++.                                       +
T Consensus       331 l~~l~~~l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI  409 (1010)
T 2xgj_A          331 IYKIVKMIWKK-KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGI  409 (1010)
T ss_dssp             HHHHHHHHHHH-TCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTE
T ss_pred             HHHHHHHHHhc-CCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCe
Confidence            34455555432 4568999999999999999999765442                                       6


Q ss_pred             eeeccCCCchh------------------hhhcccCCCCCCccEEEE----eec----CCCHhHhhhhhcccccCCC--c
Q psy4494         104 SAYHAKLESNV------------------SIAFGLGIDKPNVRFVIH----HCL----SKSMENFYQESGRAGRDGQ--I  155 (234)
Q Consensus       104 ~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~----~~~----P~~~~~y~qr~GR~gR~g~--~  155 (234)
                      ..+||+|++.+                  |+++++|+|+|++++||+    ||.    |.++.+|+||+|||||.|.  .
T Consensus       410 ~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~~  489 (1010)
T 2xgj_A          410 GIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDR  489 (1010)
T ss_dssp             EEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCSS
T ss_pred             eEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCCc
Confidence            78999999876                  999999999999999999    999    8999999999999999996  5


Q ss_pred             eEEEEEeecc-cHHHhhh
Q psy4494         156 AHCILYYRLP-DVFKLSS  172 (234)
Q Consensus       156 ~~~i~~~~~~-d~~~~~~  172 (234)
                      |.+++++++. +...+..
T Consensus       490 G~vi~l~~~~~e~~~~~~  507 (1010)
T 2xgj_A          490 GIVIMMIDEKMEPQVAKG  507 (1010)
T ss_dssp             EEEEEEECSCCCHHHHHH
T ss_pred             eEEEEEECCCCCHHHHHH
Confidence            9999999865 4333333

>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=99.57  E-value=6.6e-15  Score=143.50  Aligned_cols=103  Identities=17%  Similarity=0.173  Sum_probs=91.8

Q ss_pred             hHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHH-cCCceeeeccCCCchh--------------------hhh
Q psy4494          59 QKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRN-RGLRVSAYHAKLESNV--------------------SIA  117 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~-~~~~~~~~h~~~~~~~--------------------T~~  117 (234)
                      ...+...|.+++.. ..+.++||||++++.++.++..|.. .|+++..+||+|++.+                    |++
T Consensus       487 ~~~K~~~L~~ll~~-~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v  565 (968)
T 3dmq_A          487 FDPRVEWLMGYLTS-HRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEI  565 (968)
T ss_dssp             TSHHHHHHHHHHHH-TSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCC
T ss_pred             ccHHHHHHHHHHHh-CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecch
Confidence            34578888888875 4678999999999999999999995 5999999999999865                    899


Q ss_pred             cccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEe
Q psy4494         118 FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYY  162 (234)
Q Consensus       118 ~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~  162 (234)
                      +++|+|+|++++||+||+|+++..|.|++||+||.|+.+.+++++
T Consensus       566 ~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~  610 (968)
T 3dmq_A          566 GSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHV  610 (968)
T ss_dssp             TTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEE
T ss_pred             hhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEE
Confidence            999999999999999999999999999999999999988655554

>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=99.56  E-value=4.6e-15  Score=145.65  Aligned_cols=105  Identities=23%  Similarity=0.336  Sum_probs=80.8

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-----------------hhhcccCCCCC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-----------------SIAFGLGIDKP  125 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------------T~~~~~Gid~~  125 (234)
                      ...|.+++..  .+.++||||+|++.++.++..|+.. +.+..+||++....                 |+++++|+|+|
T Consensus       264 ~~~L~~ll~~--~~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip  340 (1054)
T 1gku_B          264 ISTLSSILEK--LGTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLP  340 (1054)
T ss_dssp             TTTTHHHHTT--SCSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSSHHHHHHHHTSCSEEEEECC------CCSCCT
T ss_pred             HHHHHHHHhh--cCCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHHHHHHHHHcCCCcEEEEecCCCCeeEeccccC
Confidence            3345555553  2578999999999999999999988 99999999996432                 38899999999


Q ss_pred             Cc-cEEEEeecC--------------------------------------------------------------------
Q psy4494         126 NV-RFVIHHCLS--------------------------------------------------------------------  136 (234)
Q Consensus       126 ~v-~~Vi~~~~P--------------------------------------------------------------------  136 (234)
                      +| ++|||||+|                                                                    
T Consensus       341 ~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  420 (1054)
T 1gku_B          341 ERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGE  420 (1054)
T ss_dssp             TTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSCSSSEEETTE
T ss_pred             CcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccceeEeecc
Confidence            95 999999999                                                                    


Q ss_pred             ---CCHhHhhhhhcccccCCCceE--EEEEeecccHHHh
Q psy4494         137 ---KSMENFYQESGRAGRDGQIAH--CILYYRLPDVFKL  170 (234)
Q Consensus       137 ---~~~~~y~qr~GR~gR~g~~~~--~i~~~~~~d~~~~  170 (234)
                         .+..+|+||+||+||.|..|.  ++.++...|...+
T Consensus       421 ~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~  459 (1054)
T 1gku_B          421 VIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELL  459 (1054)
T ss_dssp             EEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHH
T ss_pred             eecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHH
Confidence               789999999999999776653  5666655554443

>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=99.55  E-value=1.4e-14  Score=143.18  Aligned_cols=91  Identities=20%  Similarity=0.252  Sum_probs=84.5

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccCCCCCCccEEEEee
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLGIDKPNVRFVIHHC  134 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~Gid~~~v~~Vi~~~  134 (234)
                      .+++++|||++++.++.+++.|++.  +..+..+||+|++++                  |+++++|+|+|++++||+++
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VIi~~  890 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIER  890 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEEEeC
Confidence            5788999999999999999999987  889999999999866                  99999999999999999998


Q ss_pred             c-CCCHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         135 L-SKSMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       135 ~-P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      . +.++.+|+||+||+||.|+.|.+++++++.
T Consensus       891 ~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~  922 (1151)
T 2eyq_A          891 ADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  922 (1151)
T ss_dssp             TTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CCCCCHHHHHHHHhccCcCCCceEEEEEECCc
Confidence            8 468999999999999999999999999764

>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=99.55  E-value=1.3e-14  Score=136.94  Aligned_cols=104  Identities=17%  Similarity=0.253  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc------------------------------CCceeeeccCCC
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR------------------------------GLRVSAYHAKLE  111 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~------------------------------~~~~~~~h~~~~  111 (234)
                      +...+.+.+.   .++++||||+|++.++.++..|.+.                              +..+..+||+++
T Consensus       231 ~~~~~~~~~~---~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~  307 (702)
T 2p6r_A          231 FEELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLL  307 (702)
T ss_dssp             HHHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSC
T ss_pred             HHHHHHHHHh---cCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCC
Confidence            4445555554   5688999999999999999999753                              134788999999


Q ss_pred             chh------------------hhhcccCCCCCCccEEEE----ee---cCCCHhHhhhhhcccccCC--CceEEEEEeec
Q psy4494         112 SNV------------------SIAFGLGIDKPNVRFVIH----HC---LSKSMENFYQESGRAGRDG--QIAHCILYYRL  164 (234)
Q Consensus       112 ~~~------------------T~~~~~Gid~~~v~~Vi~----~~---~P~~~~~y~qr~GR~gR~g--~~~~~i~~~~~  164 (234)
                      +++                  |+++++|+|+|++++||+    ||   .|.+..+|+||+|||||.|  .+|.++++++.
T Consensus       308 ~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~  387 (702)
T 2p6r_A          308 NGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGK  387 (702)
T ss_dssp             HHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCG
T ss_pred             HHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecC
Confidence            876                  999999999999999999    66   7899999999999999988  58999999998


Q ss_pred             ccHH
Q psy4494         165 PDVF  168 (234)
Q Consensus       165 ~d~~  168 (234)
                      .+..
T Consensus       388 ~~~~  391 (702)
T 2p6r_A          388 RDRE  391 (702)
T ss_dssp             GGHH
T ss_pred             ccHH
Confidence            8754

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

Probab=99.54  E-value=1.9e-14  Score=135.10  Aligned_cols=96  Identities=21%  Similarity=0.276  Sum_probs=81.8

Q ss_pred             CcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------------hhhcccCCCCCCccEEEEeec-
Q psy4494          77 QSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------------SIAFGLGIDKPNVRFVIHHCL-  135 (234)
Q Consensus        77 ~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------------T~~~~~Gid~~~v~~Vi~~~~-  135 (234)
                      ...||||+|++.++.++..|...++.+..+||+|++++                    |+++++|+|+ +|++||++|+ 
T Consensus       321 ~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~  399 (677)
T 3rc3_A          321 PGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLI  399 (677)
T ss_dssp             TTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSB
T ss_pred             CCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCcc
Confidence            44699999999999999999999999999999999873                    9999999999 8999999999 


Q ss_pred             -------------CCCHhHhhhhhcccccCCCc---eEEEEEeecccHHHhhhhH
Q psy4494         136 -------------SKSMENFYQESGRAGRDGQI---AHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       136 -------------P~~~~~y~qr~GR~gR~g~~---~~~i~~~~~~d~~~~~~~~  174 (234)
                                   |.+..+|+||+|||||.|..   |.+++++ +.+...+..+.
T Consensus       400 k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~-~~d~~~~~~~~  453 (677)
T 3rc3_A          400 KPSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMN-HEDLSLLKEIL  453 (677)
T ss_dssp             C-----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESS-TTHHHHHHHHH
T ss_pred             ccccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEe-cchHHHHHHHH
Confidence                         77999999999999999864   7666654 44444444443

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

Probab=99.54  E-value=1.4e-14  Score=129.66  Aligned_cols=86  Identities=16%  Similarity=0.204  Sum_probs=74.5

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccE------------
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRF------------  129 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~------------  129 (234)
                      .+++||||+|++.++.+++.|+..++++..+||++..+.              |+++++|+|+| +..            
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~  249 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRKTFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPIL  249 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTTTHHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCccHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCcccccee
Confidence            568999999999999999999999999999999854322              99999999999 655            


Q ss_pred             -----EEEeecCCCHhHhhhhhcccccCCC-ceEEEEEe
Q psy4494         130 -----VIHHCLSKSMENFYQESGRAGRDGQ-IAHCILYY  162 (234)
Q Consensus       130 -----Vi~~~~P~~~~~y~qr~GR~gR~g~-~~~~i~~~  162 (234)
                           ||+++.|.+..+|+||+||+||.|. .+.++++.
T Consensus       250 d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~  288 (431)
T 2v6i_A          250 LDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYS  288 (431)
T ss_dssp             ETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEEC
T ss_pred             cccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEc
Confidence                 6889999999999999999999985 45555554

>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=99.53  E-value=1.4e-14  Score=137.08  Aligned_cols=104  Identities=21%  Similarity=0.290  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc------------------C---------------Cceeeecc
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR------------------G---------------LRVSAYHA  108 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~------------------~---------------~~~~~~h~  108 (234)
                      +...+.+.+.   .++++||||+|++.++.++..|.+.                  +               ..+.++||
T Consensus       226 ~~~~~~~~~~---~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~  302 (720)
T 2zj8_A          226 WEELVYDAIR---KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHA  302 (720)
T ss_dssp             TTHHHHHHHH---TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECT
T ss_pred             HHHHHHHHHh---CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecC
Confidence            3444555554   4688999999999999999999753                  1               13889999


Q ss_pred             CCCchh------------------hhhcccCCCCCCccEEEE----ee----cCCCHhHhhhhhcccccCC--CceEEEE
Q psy4494         109 KLESNV------------------SIAFGLGIDKPNVRFVIH----HC----LSKSMENFYQESGRAGRDG--QIAHCIL  160 (234)
Q Consensus       109 ~~~~~~------------------T~~~~~Gid~~~v~~Vi~----~~----~P~~~~~y~qr~GR~gR~g--~~~~~i~  160 (234)
                      ++++++                  |+++++|+|+|++++||+    ||    .|.+..+|+||+|||||.|  ..|.+++
T Consensus       303 ~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~  382 (720)
T 2zj8_A          303 GLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGII  382 (720)
T ss_dssp             TSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEE
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEE
Confidence            999877                  999999999999999999    77    6899999999999999988  5899999


Q ss_pred             EeecccHH
Q psy4494         161 YYRLPDVF  168 (234)
Q Consensus       161 ~~~~~d~~  168 (234)
                      +++..+..
T Consensus       383 l~~~~~~~  390 (720)
T 2zj8_A          383 VSTSDDPR  390 (720)
T ss_dssp             ECSSSCHH
T ss_pred             EecCccHH
Confidence            99987743

>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=2.1e-14  Score=136.74  Aligned_cols=90  Identities=24%  Similarity=0.392  Sum_probs=78.3

Q ss_pred             CCCcEEEEecch--------HHHHHHHHHHHH---cCCceeeeccCCCchh------------------hhhcccCCCCC
Q psy4494          75 RNQSGIIYTTSI--------KECEDLREELRN---RGLRVSAYHAKLESNV------------------SIAFGLGIDKP  125 (234)
Q Consensus        75 ~~~~~iIf~~t~--------~~~~~l~~~L~~---~~~~~~~~h~~~~~~~------------------T~~~~~Gid~~  125 (234)
                      .+.+++|||++.        +.++.+++.|.+   .++.+..+||+|++++                  |+++++|+|+|
T Consensus       577 ~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDiP  656 (780)
T 1gm5_A          577 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVP  656 (780)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCT
T ss_pred             cCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccCC
Confidence            467899999965        457888999987   4788999999998866                  99999999999


Q ss_pred             CccEEEEeecCC-CHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         126 NVRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       126 ~v~~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      ++++||+++.|. +...|.||+||+||.|++|.|++++++
T Consensus       657 ~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~  696 (780)
T 1gm5_A          657 RANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGD  696 (780)
T ss_dssp             TCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCS
T ss_pred             CCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECC
Confidence            999999999996 688899999999999999999999984

>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=99.49  E-value=3.5e-14  Score=127.75  Aligned_cols=99  Identities=19%  Similarity=0.199  Sum_probs=83.5

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCC
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGI  122 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gi  122 (234)
                      .++..+.+++.. ..+.++||||++++.++.+++.|.     +..+||+++.++                  |+++++|+
T Consensus       335 ~k~~~l~~~l~~-~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gl  408 (472)
T 2fwr_A          335 NKIRKLREILER-HRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  408 (472)
T ss_dssp             HHHHHHHHHHHH-TSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHHh-CCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCc
Confidence            456677777765 467899999999999999999984     678999998765                  99999999


Q ss_pred             CCCCccEEEEeecCCCHhHhhhhhcccccCCCc---eEEEEEeecc
Q psy4494         123 DKPNVRFVIHHCLSKSMENFYQESGRAGRDGQI---AHCILYYRLP  165 (234)
Q Consensus       123 d~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~---~~~i~~~~~~  165 (234)
                      |+|++++||+++.|+++..|+||+||+||.|+.   ...+.+++..
T Consensus       409 dlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          409 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             ccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            999999999999999999999999999998844   4444455544

>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=99.47  E-value=3.7e-13  Score=137.17  Aligned_cols=162  Identities=14%  Similarity=0.094  Sum_probs=111.7

Q ss_pred             HhhhccCchh-HHHHhhCCCCCcEEEEEeeccCCCcceEEEEEEcCCChHHHH----HHHHHHHHhhcCCCcEEEEecch
Q psy4494          12 NLWRTSFYQV-SIAFGLGIDKPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCL----DELADLMSRRFRNQSGIIYTTSI   86 (234)
Q Consensus        12 ~l~~at~p~~-~i~~~~~~~~~~i~~~~~~~~~~~~~~~y~v~~~~~~~~~~~----~~l~~~l~~~~~~~~~iIf~~t~   86 (234)
                      -.+|||.++. .++.-++.++..+.......-|-.++.+....... .....+    ..+...+......+++||||+|+
T Consensus      1087 I~lSATl~N~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~-~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~sR 1165 (1724)
T 4f92_B         1087 VALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNIS-HTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSR 1165 (1724)
T ss_dssp             EEEESCBTTHHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCC-SHHHHHHTTHHHHHHHHHHHCSSSCEEEEESSH
T ss_pred             EEEeCCCCCHHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCC-CchhhhhhhcchHHHHHHHhcCCCCeeeeCCCH
Confidence            3478898886 55556777666554332222222333333322221 222222    22334444444678999999999


Q ss_pred             HHHHHHHHHHHHc----------------------------------CCceeeeccCCCchh------------------
Q psy4494          87 KECEDLREELRNR----------------------------------GLRVSAYHAKLESNV------------------  114 (234)
Q Consensus        87 ~~~~~l~~~L~~~----------------------------------~~~~~~~h~~~~~~~------------------  114 (234)
                      +.|+.++..|...                                  ..-+.++||+|++++                  
T Consensus      1166 ~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~~G~i~VLva 1245 (1724)
T 4f92_B         1166 KQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVA 1245 (1724)
T ss_dssp             HHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHHHTSBCEEEE
T ss_pred             HHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHHCCCCeEEEE
Confidence            9999998877421                                  112788999999977                  


Q ss_pred             hhhcccCCCCCCccEEEE----------eecCCCHhHhhhhhcccccCCC--ceEEEEEeecccHHHhhhhH
Q psy4494         115 SIAFGLGIDKPNVRFVIH----------HCLSKSMENFYQESGRAGRDGQ--IAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       115 T~~~~~Gid~~~v~~Vi~----------~~~P~~~~~y~qr~GR~gR~g~--~~~~i~~~~~~d~~~~~~~~  174 (234)
                      |+.+++|+|+|.+.+||.          ...|.++.+|+||+|||||.|.  .|.++++..+.+...+..++
T Consensus      1246 T~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~avll~~~~~~~~~~~ll 1317 (1724)
T 4f92_B         1246 SRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFL 1317 (1724)
T ss_dssp             EGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEEEEEEEGGGHHHHHHHT
T ss_pred             ChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEEEEEecchHHHHHHHHh
Confidence            999999999999999883          3346789999999999999986  79999999988777666554

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.46  E-value=6.7e-14  Score=127.07  Aligned_cols=88  Identities=17%  Similarity=0.180  Sum_probs=77.8

Q ss_pred             CCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------h-hhcccCCCCCCccEEEEeecC
Q psy4494          76 NQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------S-IAFGLGIDKPNVRFVIHHCLS  136 (234)
Q Consensus        76 ~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T-~~~~~Gid~~~v~~Vi~~~~P  136 (234)
                      ..+.|||++ .+.++.+++.|.+.+.++..+||++++++                  | +++++|+|+|++++||+++.|
T Consensus       348 ~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~~  426 (510)
T 2oca_A          348 ENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHGV  426 (510)
T ss_dssp             CEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSCC
T ss_pred             CCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCCC
Confidence            445666666 88899999999998889999999999765                  8 999999999999999999999


Q ss_pred             CCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         137 KSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       137 ~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      .+...|+|++||+||.|..+..+++++.
T Consensus       427 ~s~~~~~Q~~GR~gR~g~~~~~v~i~~~  454 (510)
T 2oca_A          427 KSKIIVLQTIGRVLRKHGSKTIATVWDL  454 (510)
T ss_dssp             CSCCHHHHHHHHHHTTTCCCCCCEEEEE
T ss_pred             CCHHHHHHHHhcccccCCCCceEEEEEe
Confidence            9999999999999999988766666663

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.46  E-value=1.5e-13  Score=127.17  Aligned_cols=90  Identities=24%  Similarity=0.347  Sum_probs=74.7

Q ss_pred             HHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCc--------eeeeccCCCc-hh-------------------hh
Q psy4494          65 ELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR--------VSAYHAKLES-NV-------------------SI  116 (234)
Q Consensus        65 ~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~--------~~~~h~~~~~-~~-------------------T~  116 (234)
                      .+.+.+....+..++||||++++.++.++..|...+..        +..+||++++ .+                   |+
T Consensus       428 ~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~~r~~~l~~F~~~~~~~~~ilvtt~  507 (590)
T 3h1t_A          428 HLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGKIGKGHLSRFQELETSTPVILTTSQ  507 (590)
T ss_dssp             HHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHHHHHHHHHHHHCTTCCCCCEEEESS
T ss_pred             HHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChHHHHHHHHHHhCCCCCCCEEEEECC
Confidence            34444444334578999999999999999999876433        6788999875 11                   67


Q ss_pred             hcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCC
Q psy4494         117 AFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQ  154 (234)
Q Consensus       117 ~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~  154 (234)
                      ++++|+|+|++++||++++|.+...|+||+||+||.+.
T Consensus       508 ~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          508 LLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             TTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             hhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            99999999999999999999999999999999999764

>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=99.44  E-value=3e-13  Score=122.47  Aligned_cols=106  Identities=16%  Similarity=0.107  Sum_probs=84.1

Q ss_pred             HHHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHc-CCceeeeccCCCchh--------------------hhhc
Q psy4494          61 DCLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNR-GLRVSAYHAKLESNV--------------------SIAF  118 (234)
Q Consensus        61 ~~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~--------------------T~~~  118 (234)
                      .|+..+.+++.+.. .+.++||||++++.++.+...|... |+.+..+||++++++                    |++.
T Consensus       325 ~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~  404 (500)
T 1z63_A          325 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAG  404 (500)
T ss_dssp             HHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC
T ss_pred             hhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccc
Confidence            45555666665332 4678999999999999999999885 999999999998655                    7899


Q ss_pred             ccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEE--EEEeeccc
Q psy4494         119 GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHC--ILYYRLPD  166 (234)
Q Consensus       119 ~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~--i~~~~~~d  166 (234)
                      ++|+|++.+++||+||+|+++..|.|++||++|.|+...+  +.++....
T Consensus       405 ~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~t  454 (500)
T 1z63_A          405 GFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGT  454 (500)
T ss_dssp             -CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETTS
T ss_pred             cCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCCC
Confidence            9999999999999999999999999999999998876544  44555543

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=99.41  E-value=1.2e-12  Score=122.64  Aligned_cols=92  Identities=15%  Similarity=0.059  Sum_probs=82.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhhcccCCCCCCccEEEEe
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIAFGLGIDKPNVRFVIHH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~~~~Gid~~~v~~Vi~~  133 (234)
                      .+.++|||+++++.++.+...|...|+.+..+||+++.++                     |.+.|+|+|++++++||+|
T Consensus       415 ~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~  494 (644)
T 1z3i_X          415 TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMF  494 (644)
T ss_dssp             CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEEC
T ss_pred             CCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEE
Confidence            4679999999999999999999999999999999998765                     8899999999999999999


Q ss_pred             ecCCCHhHhhhhhcccccCCCce--EEEEEeeccc
Q psy4494         134 CLSKSMENFYQESGRAGRDGQIA--HCILYYRLPD  166 (234)
Q Consensus       134 ~~P~~~~~y~qr~GR~gR~g~~~--~~i~~~~~~d  166 (234)
                      |+|+++..|.|++||++|.|+..  ..+-++....
T Consensus       495 d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~t  529 (644)
T 1z3i_X          495 DPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGT  529 (644)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETTS
T ss_pred             CCCCCccHHHHHHHhhhhcCCCCceEEEEEEECCC
Confidence            99999999999999999998764  4444555543

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.40  E-value=7.5e-13  Score=134.96  Aligned_cols=161  Identities=15%  Similarity=0.158  Sum_probs=106.6

Q ss_pred             hhhccCchh-HHHHhhCCCCCcEEEEEeeccC-CCcceEEEEEEcCCChHHHHHHH----HHHHHhhcCCCcEEEEecch
Q psy4494          13 LWRTSFYQV-SIAFGLGIDKPNVRFVIHHCLS-KSMENFYQVRIKPAAQKDCLDEL----ADLMSRRFRNQSGIIYTTSI   86 (234)
Q Consensus        13 l~~at~p~~-~i~~~~~~~~~~i~~~~~~~~~-~~~~~~y~v~~~~~~~~~~~~~l----~~~l~~~~~~~~~iIf~~t~   86 (234)
                      .+|||.|+. .++..++.+++.-.+.+....+ -.+..++... ...........+    ...+.+.....++||||+|+
T Consensus       249 ~LSATl~N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~-~~~~~~~~~~~~~~~~~~~v~~~~~~~~~LVF~~sR  327 (1724)
T 4f92_B          249 GLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGI-TEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSR  327 (1724)
T ss_dssp             EEECSCTTHHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEE-CCCCHHHHHHHHHHHHHHHHTTCCSSCCEEEECSST
T ss_pred             EEecccCCHHHHHHHhCCCCCCCeEEECCCCccCccEEEEecc-CCcchhhhhHHHHHHHHHHHHHHhcCCcEEEECCCH
Confidence            468999886 4555566554332222222221 1223222221 222222222222    33333334567899999999


Q ss_pred             HHHHHHHHHHHHc-------------------------------------CCceeeeccCCCchh---------------
Q psy4494          87 KECEDLREELRNR-------------------------------------GLRVSAYHAKLESNV---------------  114 (234)
Q Consensus        87 ~~~~~l~~~L~~~-------------------------------------~~~~~~~h~~~~~~~---------------  114 (234)
                      +.|+.+|..|.+.                                     ..-+.++||+|++++               
T Consensus       328 ~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~~vE~~F~~G~i~v  407 (1724)
T 4f92_B          328 KETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQV  407 (1724)
T ss_dssp             TTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHHHHHHHHHTTCCCE
T ss_pred             HHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHHHHHHHHHCCCCeE
Confidence            9999999988631                                     112678999999977               


Q ss_pred             ---hhhcccCCCCCCccEEEE----eec------CCCHhHhhhhhcccccCC--CceEEEEEeecccHHHhhhhH
Q psy4494         115 ---SIAFGLGIDKPNVRFVIH----HCL------SKSMENFYQESGRAGRDG--QIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       115 ---T~~~~~Gid~~~v~~Vi~----~~~------P~~~~~y~qr~GR~gR~g--~~~~~i~~~~~~d~~~~~~~~  174 (234)
                         |+++++|+|+|.++.||.    |+.      |-++.+|+||+|||||.|  ..|.++++.++.+......++
T Consensus       408 lvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~~ii~~~~~~~~~~~~ll  482 (1724)
T 4f92_B          408 LVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLL  482 (1724)
T ss_dssp             EEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEEEEEEEESTTCCHHHHHT
T ss_pred             EEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccEEEEEecchhHHHHHHHH
Confidence               999999999999999985    543      458899999999999976  479999999988766555443

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.28  E-value=1.4e-11  Score=117.96  Aligned_cols=105  Identities=19%  Similarity=0.155  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHhhc-CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhhcc
Q psy4494          62 CLDELADLMSRRF-RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIAFG  119 (234)
Q Consensus        62 ~~~~l~~~l~~~~-~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~~~  119 (234)
                      |+..|.+++.... .+.++|||+.....++.+...|...|+++..+||+++.++                     |.+.|
T Consensus       557 K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg  636 (800)
T 3mwy_W          557 KMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGG  636 (800)
T ss_dssp             HHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHT
T ss_pred             HHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEeccccc
Confidence            5555666665322 4679999999999999999999999999999999998765                     88999


Q ss_pred             cCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCc--eEEEEEeeccc
Q psy4494         120 LGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQI--AHCILYYRLPD  166 (234)
Q Consensus       120 ~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~--~~~i~~~~~~d  166 (234)
                      .|+|++.+++||+||+|+++..+.|++||+.|.|+.  ...+.|+....
T Consensus       637 ~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~T  685 (800)
T 3mwy_W          637 LGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDT  685 (800)
T ss_dssp             TTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETTS
T ss_pred             CCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCCC
Confidence            999999999999999999999999999999998875  44455566543

>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=98.70  E-value=6.2e-08  Score=94.82  Aligned_cols=49  Identities=16%  Similarity=0.156  Sum_probs=43.8

Q ss_pred             hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCc----eEEEEEeec
Q psy4494         115 SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQI----AHCILYYRL  164 (234)
Q Consensus       115 T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~----~~~i~~~~~  164 (234)
                      |+.+.+|+|+|.+ .|+++|.|.+...|+|++||++|.+..    |.++.|.+.
T Consensus       656 vd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~~~K~~G~IVdf~~~  708 (1038)
T 2w00_A          656 VGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDL  708 (1038)
T ss_dssp             SSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCCTTCCSEEEEESSCC
T ss_pred             cchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCCCCCCcEEEEEcccc
Confidence            8889999999999 789999999999999999999997653    888887764

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.31  E-value=5.1e-06  Score=79.35  Aligned_cols=39  Identities=31%  Similarity=0.337  Sum_probs=35.8

Q ss_pred             EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccH
Q psy4494         129 FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       129 ~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      +||--..+.|..-=.|-.||+||.|.+|.+.+|++-.|-
T Consensus       662 hVIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeDd  700 (997)
T 2ipc_A          662 FIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDD  700 (997)
T ss_dssp             CEEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSSH
T ss_pred             EEEeccCCchHHHHHHHhcccccCCCCCCeEEEEECChH
Confidence            799888999999889999999999999999999998763

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.23  E-value=0.00057  Score=62.40  Aligned_cols=70  Identities=13%  Similarity=0.091  Sum_probs=39.6

Q ss_pred             HHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCch-h----------------hhhcccCCCCC
Q psy4494          63 LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESN-V----------------SIAFGLGIDKP  125 (234)
Q Consensus        63 ~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~-~----------------T~~~~~Gid~~  125 (234)
                      ...|.+++..  .++.++||++|.+..+.+++.|..  .+ ...+|..... +                |..+..|||+|
T Consensus       373 ~~~l~~~~~~--~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~~~~~~~l~~f~~~~~il~~V~~~~~~EGiD~~  447 (540)
T 2vl7_A          373 SILLKRIYEN--SSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKKTRHEEVLELMKTGKYLVMLVMRAKESEGVEFR  447 (540)
T ss_dssp             HHHHHHHHHT--CSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTTCCHHHHHHHHHTSCCEEEEEC-----------
T ss_pred             HHHHHHHHHh--CCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCCCcHHHHHHHHhcCCeEEEEEecCceecceecC
Confidence            3344444432  467899999999999999998864  22 3445543222 1                67788999999


Q ss_pred             C----ccEEEEeecCC
Q psy4494         126 N----VRFVIHHCLSK  137 (234)
Q Consensus       126 ~----v~~Vi~~~~P~  137 (234)
                      +    +++||++++|-
T Consensus       448 ~~~~~~~~Vii~~lPf  463 (540)
T 2vl7_A          448 EKENLFESLVLAGLPY  463 (540)
T ss_dssp             ----CEEEEEEESCCC
T ss_pred             CCcccccEEEEECCCC
Confidence            7    89999999993

>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=96.23  E-value=0.036  Score=47.24  Aligned_cols=106  Identities=12%  Similarity=0.030  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-------------hhhcccCCC-----
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-------------SIAFGLGID-----  123 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-------------T~~~~~Gid-----  123 (234)
                      .+..|...+++  .+.+++||++..+..+-+-.+|...++...-+-|....++             |.+-|-|++     
T Consensus       113 ~L~~LL~~l~~--~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~k~~~~~~~i~Lltsag~~gin~~~~n  190 (328)
T 3hgt_A          113 VLRDLINLVQE--YETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAAAANDFSCTVHLFSSEGINFTKYPIKS  190 (328)
T ss_dssp             HHHHHHHHHTT--SCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC-------CCSEEEEEEESSCCCTTTSCCCC
T ss_pred             HHHHHHHHHHh--CCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhhhcccCCceEEEEECCCCCCcCccccc
Confidence            34444444433  4679999999999999999999999988888887744322             555566776     


Q ss_pred             CCCccEEEEeecCCCHhH-hhhhhcccccC----CCceEEEEEeecccHHH
Q psy4494         124 KPNVRFVIHHCLSKSMEN-FYQESGRAGRD----GQIAHCILYYRLPDVFK  169 (234)
Q Consensus       124 ~~~v~~Vi~~~~P~~~~~-y~qr~GR~gR~----g~~~~~i~~~~~~d~~~  169 (234)
                      ....+.||-||.-+++.. .+|.+-|+-|.    +++...+-+++.+..+.
T Consensus       191 l~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~TiEh  241 (328)
T 3hgt_A          191 KARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDH  241 (328)
T ss_dssp             CSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSHHH
T ss_pred             CCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCHHH
Confidence            567899999999988885 58877777775    34667777777765554

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=92.95  E-value=0.67  Score=42.83  Aligned_cols=115  Identities=13%  Similarity=0.142  Sum_probs=60.8

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-----------------h--hhcccCCCCCC--ccEEEEe
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-----------------S--IAFGLGIDKPN--VRFVIHH  133 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------------T--~~~~~Gid~~~--v~~Vi~~  133 (234)
                      .++.++||++|.+..+.+++.|+.  +... ...+++...                 +  ..+..|||+++  .+.||..
T Consensus       447 ~~g~~lvlF~Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~~~~~vL~~v~~gsf~EGiD~~g~~l~~viI~  523 (620)
T 4a15_A          447 VKKNTIVYFPSYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFRRDHGTIFAVSGGRLSEGINFPGNELEMIILA  523 (620)
T ss_dssp             HCSCEEEEESCHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHTTSCCEEEEETTSCC--------CCCCEEEES
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhccCCcEEEEEecCceeccccCCCCceEEEEEE
Confidence            367799999999999999988862  2111 222332111                 2  36778999985  5789998


Q ss_pred             ecCCC-----------------------------HhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHHhhhhhhHhH
Q psy4494         134 CLSKS-----------------------------MENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQTGLANL  184 (234)
Q Consensus       134 ~~P~~-----------------------------~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~~~~~~~l  184 (234)
                      ++|-.                             +....|-+||.=|....--++++.+..= ..+...+-.-+.....+
T Consensus       524 ~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~llD~R~-~~~~~~LP~~~~~~~~~  602 (620)
T 4a15_A          524 GLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRA-GQFRKFIPDMKKTSDPA  602 (620)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEECGGG-GGGGGGSTTCEEESCHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEEccch-HHHHHhCCchhhhcCcH
Confidence            88732                             1122588999999655433444444322 22222221112223447


Q ss_pred             HHHHHHhhc
Q psy4494         185 YNIVSYCLD  193 (234)
Q Consensus       185 ~~~~~~~~~  193 (234)
                      +++.+|+.+
T Consensus       603 ~~~~~f~~~  611 (620)
T 4a15_A          603 SDIYNFFIS  611 (620)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhC
Confidence            788888753

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=89.49  E-value=0.51  Score=32.90  Aligned_cols=37  Identities=14%  Similarity=0.157  Sum_probs=32.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      +..++++||.+-..+...+..|+..|+++..+.||+.
T Consensus        54 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           54 RDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             TTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             CCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHH
Confidence            4568999999988999999999999999999988875

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=86.81  E-value=0.91  Score=32.36  Aligned_cols=35  Identities=14%  Similarity=0.179  Sum_probs=30.6

Q ss_pred             CcEEEEe-cchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          77 QSGIIYT-TSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        77 ~~~iIf~-~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      .++|+|| .+-..+..++..|+..|+++..+.|++.
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~  125 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYK  125 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHH
Confidence            7899999 5777888999999999999999988874

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=86.14  E-value=5.8  Score=35.76  Aligned_cols=60  Identities=8%  Similarity=-0.032  Sum_probs=41.1

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------h--hhcccCCCCC-----CccEEEE
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------S--IAFGLGIDKP-----NVRFVIH  132 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------T--~~~~~Gid~~-----~v~~Vi~  132 (234)
                      .++.++||++|.+..+.+++.   .+.++..-..+++..+               +  ..+..|||+|     ..+.||.
T Consensus       392 ~~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~~~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~~viI  468 (551)
T 3crv_A          392 AKANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSSVEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVVI  468 (551)
T ss_dssp             CSSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCCHHHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEEEEEE
T ss_pred             CCCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCCHHHHHHHHHhcCCeEEEEEecceecccccccccCCcceeEEEE
Confidence            467899999999999999873   3444333222333211               2  4678899999     3788998


Q ss_pred             eecCC
Q psy4494         133 HCLSK  137 (234)
Q Consensus       133 ~~~P~  137 (234)
                      .++|-
T Consensus       469 ~~lPf  473 (551)
T 3crv_A          469 VGIPY  473 (551)
T ss_dssp             ESCCC
T ss_pred             EcCCC
Confidence            88773

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=85.35  E-value=0.89  Score=30.60  Aligned_cols=35  Identities=9%  Similarity=0.007  Sum_probs=31.3

Q ss_pred             CcEEEEecchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          77 QSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        77 ~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      .+.++||.+-..+...+..|+..|+++..+.|++.
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   88 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEGYEAMSLEGGLQ   88 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHTCCEEEETTGGG
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcCCcEEEEcccHH
Confidence            77999999988899999999999999888888875

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=84.57  E-value=2.6  Score=27.54  Aligned_cols=36  Identities=19%  Similarity=0.308  Sum_probs=29.6

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~  111 (234)
                      +..+.++||.+-..+...+..|+..|++ +..+ |++.
T Consensus        40 ~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           40 KNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             TTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             CCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            4678999999988899999999999986 5555 7764

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=84.52  E-value=1.3  Score=30.57  Aligned_cols=37  Identities=11%  Similarity=0.107  Sum_probs=31.5

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~  111 (234)
                      +..+++|||.+-..+..++..|+..|++ +..+.|++.
T Consensus        57 ~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           57 FDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             TTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             CCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHH
Confidence            4678999999988899999999999995 778888764

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=84.45  E-value=0.81  Score=31.22  Aligned_cols=37  Identities=11%  Similarity=0.161  Sum_probs=32.4

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      +..+.++||.+-..+...+..|+..|+++..+.|++.
T Consensus        55 ~~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~   91 (100)
T 3foj_A           55 DNETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMD   91 (100)
T ss_dssp             TTSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CCCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHH
Confidence            4568999999999999999999999998888888764

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=83.78  E-value=0.88  Score=32.45  Aligned_cols=37  Identities=14%  Similarity=0.105  Sum_probs=31.3

Q ss_pred             CCCcEEEEecchHH--HHHHHHHHHHcCCceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKE--CEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~--~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      +..+++|||.+-..  +..++..|+..|+++..+.||+.
T Consensus        70 ~~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~~  108 (124)
T 3flh_A           70 PAKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGALE  108 (124)
T ss_dssp             TTSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHHH
T ss_pred             CCCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcHH
Confidence            45679999998776  78999999999999888888874

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=82.38  E-value=0.9  Score=31.53  Aligned_cols=37  Identities=14%  Similarity=0.135  Sum_probs=31.8

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~  111 (234)
                      +.++.++||.+-..+...+..|+..|+++..+.||+.
T Consensus        55 ~~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~~   91 (103)
T 3iwh_A           55 KNEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGMH   91 (103)
T ss_dssp             TTSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHHH
T ss_pred             CCCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChHH
Confidence            4567999999988899999999999999888888764

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=82.01  E-value=1.5  Score=30.30  Aligned_cols=37  Identities=19%  Similarity=0.302  Sum_probs=31.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~  111 (234)
                      +..++++||.+-..+...+..|+..|++ +..+.|++.
T Consensus        51 ~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   88 (106)
T 3hix_A           51 KSRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLA   88 (106)
T ss_dssp             TTSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHHH
T ss_pred             CCCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCHH
Confidence            4567999999998999999999999995 888888764

---

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	234
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	4e-12
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	9e-12
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	7e-10
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	7e-09
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-08
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	1e-07
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	2e-07
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-07
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	4e-05
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	1e-04
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	0.001
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	0.002

>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 = 62.2 bits (151), Expect = 4e-12
 Identities = 20/128 (15%), Positives = 36/128 (28%), Gaps = 34/128 (26%)

Query: 72  RRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE-------------------- 111
              +    +I+  S K+C++L  +L   G+   AY+  L+                    
Sbjct: 32  EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMT 91

Query: 112 -----------SNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGR--DGQIAHC 158
                       N  +   +         +    L +   +  Q  GR GR   G I   
Sbjct: 92  GFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPG-IYRF 150

Query: 159 ILYYRLPD 166
           +     P 
Sbjct: 151 VAPGERPS 158

>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 = 60.1 bits (144), Expect = 9e-12
 Identities = 65/199 (32%), Positives = 100/199 (50%), Gaps = 32/199 (16%)

Query: 49  FYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 108
            Y +  K       LD+L   +  + R +SGIIY  S  + ED    L+++G+  +AYHA
Sbjct: 8   RYMLMEK----FKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHA 62

Query: 109 KLESN------------------VSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAG 150
            LE+N                   ++AFG+GI+KPNVRFV+H  + +++E++YQE+GRAG
Sbjct: 63  GLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAG 122

Query: 151 RDGQIAHCILYYRLPDVFKLSSMV------FDQQTGLANLYNIVSYCLDQTRCRRAIIAS 204
           RDG  A  +L+Y   D+  L   +        Q      L  + ++  +   CRR ++ +
Sbjct: 123 RDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIERHKLNAMGAFA-EAQTCRRLVLLN 181

Query: 205 YFDEAWSDTECRGMCDHCR 223
           YF E     E  G CD C 
Sbjct: 182 YFGEGRQ--EPCGNCDICL 198

>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 = 53.6 bits (128), Expect = 7e-10
 Identities = 20/119 (16%), Positives = 39/119 (32%), Gaps = 16/119 (13%)

Query: 47  ENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAY 106
            N  +V +    +     +   L     +    +I+  S K+C++L  +L   G+   AY
Sbjct: 8   PNIEEVALSTTGEIPFYGKAIPL--EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAY 65

Query: 107 HAKLESN-----------VSIAFGLGIDKPN---VRFVIHHCLSKSMENFYQESGRAGR 151
           +  L+ +            + A   G        +         +   +  Q  GR GR
Sbjct: 66  YRGLDVSVIPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR 124

>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 = 52.6 bits (125), Expect = 7e-09
 Identities = 23/129 (17%), Positives = 39/129 (30%), Gaps = 26/129 (20%)

Query: 61  DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSI---- 116
           D L E+     +R +N   I++T   +  + +  EL   G++   +  +           
Sbjct: 146 DKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQ 205

Query: 117 ----------------------AFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQ 154
                                     G+D P V  V+ +    S     Q  GR GR   
Sbjct: 206 REQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP 265

Query: 155 IAHCILYYR 163
               IL  +
Sbjct: 266 GRVIILMAK 274

>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 = 50.3 bits (119), Expect = 4e-08
 Identities = 19/121 (15%), Positives = 32/121 (26%), Gaps = 33/121 (27%)

Query: 75  RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL----------------------ES 112
                + +  SIK   D+   LR  G +V     K                       E 
Sbjct: 177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIKTRTNDWDFVVTTDISEM 236

Query: 113 NVSIAFGLGIDK-----------PNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILY 161
             +      ID               R ++   +  +  +  Q  GR GR+ +  +    
Sbjct: 237 GANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYI 296

Query: 162 Y 162
           Y
Sbjct: 297 Y 297

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 48.6 bits (115), Expect = 1e-07
 Identities = 23/145 (15%), Positives = 49/145 (33%), Gaps = 27/145 (18%)

Query: 47  ENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRG------ 100
            N   V +      + +  L+ ++ +      GIIY  + +E E++ E L+N+       
Sbjct: 2   RNVEDVAVN----DESISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKNKFRIGIVT 55

Query: 101 -LRVSAYHAKLESNVSI---------AFGLGIDKP-NVRFVIHHCLSKSMENFYQESGRA 149
             +   Y   +E  +               G+D P  +RF +         +F       
Sbjct: 56  ATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFV----GCPSFRVTIEDI 111

Query: 150 GRDGQIAHCILYYRLPDVFKLSSMV 174
                    +L Y   +V ++  ++
Sbjct: 112 DSLSPQMVKLLAYLYRNVDEIERLL 136

>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 = 47.6 bits (112), Expect = 2e-07
 Identities = 24/140 (17%), Positives = 42/140 (30%), Gaps = 14/140 (10%)

Query: 38  IHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECE------- 90
                 +++  + + R      K+ + +L +++  R R    II+T   +          
Sbjct: 56  YDERAYEALRAWEEARRIAFNSKNKIRKLREIL-ERHRKDKIIIFTRHNELVYRISKVFL 114

Query: 91  ------DLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 144
                     E R   L             S     GID P+    +    S S   + Q
Sbjct: 115 IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQ 174

Query: 145 ESGRAGRDGQIAHCILYYRL 164
             GR  R  +     + Y L
Sbjct: 175 RLGRILRPSKGKKEAVLYEL 194

>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 = 45.3 bits (106), Expect = 7e-07
 Identities = 30/129 (23%), Positives = 49/129 (37%), Gaps = 19/129 (14%)

Query: 63  LDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLE----------- 111
            + L DL          +I+  + ++ E+L  +LRN    VSA ++ L            
Sbjct: 15  YECLTDLY-DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEF 73

Query: 112 -------SNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRL 164
                     +     GID   V  VI++ L  + EN+    GR GR G+    I +   
Sbjct: 74  RSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTN 133

Query: 165 PDVFKLSSM 173
            DV  +  +
Sbjct: 134 EDVGAMREL 142

>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 = 40.3 bits (93), Expect = 4e-05
 Identities = 27/114 (23%), Positives = 47/114 (41%), Gaps = 8/114 (7%)

Query: 60  KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNVSIAFG 119
           K  +D L + M       S +      KE E + +E R+   RV           +  + 
Sbjct: 44  KRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVL--------ISTDVWA 95

Query: 120 LGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM 173
            G+D P V  +I++ L  + E +    GR+GR G+    I + +  D+  L  +
Sbjct: 96  RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDI 149

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.5 bits (91), Expect = 1e-04
 Identities = 21/139 (15%), Positives = 49/139 (35%), Gaps = 4/139 (2%)

Query: 31  KPNVRFVIHHCLSKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECE 90
           +           + + +      ++ A  ++   E++  ++   R  +   +   +    
Sbjct: 50  RRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQR 109

Query: 91  DLREELRNRG-LRVSAYHAKLESNVSIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRA 149
            + E+   RG ++V      L + V++     I +   RF  +      +  + Q +GRA
Sbjct: 110 RVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSK-RIKVSEYKQMAGRA 168

Query: 150 GRDGQ--IAHCILYYRLPD 166
           GR G       I+     D
Sbjct: 169 GRPGMDERGEAIIIVGKRD 187

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 20/118 (16%), Positives = 30/118 (25%), Gaps = 32/118 (27%)

Query: 80  IIYTTSIKECEDLREELRNRGLRVSAYHAKL----------------------ESNVSIA 117
             +  SI+    +   LR  G  V   + K                       E   ++ 
Sbjct: 40  AWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANLC 99

Query: 118 FGLGID----------KPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLP 165
               +D              +  I   L  S  +  Q  GR GR+        YY  P
Sbjct: 100 VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEP 157

>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 = 35.7 bits (81), Expect = 0.002
 Identities = 15/57 (26%), Positives = 26/57 (45%)

Query: 117 AFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM 173
               GID  ++  VI++ L ++ E++    GR GR G+    I      +  KL  +
Sbjct: 87  VMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYI 143

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	234
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	100.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.95
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.95
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.95
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.95
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.94
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.93
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.9
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.9
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.89
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.75
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.75
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.7
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.7
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.56
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.51
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.49
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.35
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.3
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.28
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.17
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.1
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.78
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	88.17
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	87.45
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	87.16
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	85.02
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	84.55

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.5e-40  Score=266.20  Aligned_cols=172  Identities=38%  Similarity=0.674  Sum_probs=147.9

Q ss_pred             CcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------
Q psy4494          45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------  114 (234)
Q Consensus        45 ~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------  114 (234)
                      +.|++|.|+.+.    +++..|.+++.. ..+.++||||+|++.++.++..|...|+.+..+||++++++          
T Consensus         4 RpNi~y~v~~~~----~k~~~L~~~l~~-~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~   78 (200)
T d1oywa3           4 RPNIRYMLMEKF----KPLDQLMRYVQE-QRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQR   78 (200)
T ss_dssp             CTTEEEEEEECS----SHHHHHHHHHHH-TTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CCCcEEEEEcCC----cHHHHHHHHHHh-cCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhc
Confidence            345557775543    356777887764 36778999999999999999999999999999999999877          


Q ss_pred             --------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHHhhh------hh
Q psy4494         115 --------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVFDQQ------TG  180 (234)
Q Consensus       115 --------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~~~~------~~  180 (234)
                              |+++|||||+|+|++|||||+|.++.+|+||+||+||+|++|.|++|+++.|...+..+++...      ..
T Consensus        79 g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i~~~~~~~~~~~~  158 (200)
T d1oywa3          79 DDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPQGQLQDIE  158 (200)
T ss_dssp             TSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHHTSCCSHHHHHH
T ss_pred             ccceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhhhccccccchhhh
Confidence                    9999999999999999999999999999999999999999999999999999988887765432      23


Q ss_pred             hHhHHHHHHHhhcCcccHHHHHHhHcCCCCCCCccCCCCCCCCC
Q psy4494         181 LANLYNIVSYCLDQTRCRRAIIASYFDEAWSDTECRGMCDHCRG  224 (234)
Q Consensus       181 ~~~l~~~~~~~~~~~~Crr~~l~~~f~e~~~~~~c~~~Cd~C~~  224 (234)
                      .+.+++|..|++ +..|||..|+.||||... .+| ++||+|..
T Consensus       159 ~~~~~~m~~~~~-~~~Crr~~ll~~fge~~~-~~C-~~CD~C~~  199 (200)
T d1oywa3         159 RHKLNAMGAFAE-AQTCRRLVLLNYFGEGRQ-EPC-GNCDICLD  199 (200)
T ss_dssp             HHHHHHHHHHHT-CSSCHHHHHHHHTTCCCC-SCC-SCBHHHHS
T ss_pred             HHHHHHHHHHHh-chhhHHHHHHHHcCCCCC-CCC-CCCCCCCC
Confidence            456799999995 789999999999999765 357 78999964

>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=99.95  E-value=1e-27  Score=187.09  Aligned_cols=127  Identities=21%  Similarity=0.390  Sum_probs=111.7

Q ss_pred             CCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------
Q psy4494          43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------  114 (234)
Q Consensus        43 ~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------  114 (234)
                      .+++.++|..+.+.   ..|+..|.+++.. ....++||||++++.++.++..|+..++.+..+||++++++        
T Consensus         5 l~~i~q~~v~v~~~---~~K~~~L~~ll~~-~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f   80 (168)
T d2j0sa2           5 LEGIKQFFVAVERE---EWKFDTLCDLYDT-LTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEF   80 (168)
T ss_dssp             CTTEEEEEEEESST---THHHHHHHHHHHH-HTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHH
T ss_pred             CCCcEEEEEEecCh---HHHHHHHHHHHHh-CCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHH
Confidence            35667777665432   4577788888764 46789999999999999999999999999999999999987        


Q ss_pred             ----------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         115 ----------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       115 ----------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                                |++++||+|+|+|++|||||+|++...|+||+||+||.|+.|.+++|+++.|...+..+
T Consensus        81 k~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i  149 (168)
T d2j0sa2          81 RSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDI  149 (168)
T ss_dssp             HHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHH
T ss_pred             hcCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHH
Confidence                      99999999999999999999999999999999999999999999999999987665543

>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=99.95  E-value=1.2e-27  Score=185.68  Aligned_cols=123  Identities=26%  Similarity=0.367  Sum_probs=103.0

Q ss_pred             ceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------
Q psy4494          47 ENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------  114 (234)
Q Consensus        47 ~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------  114 (234)
                      +++|..+..   .+.|+..|.+++.. .+..++||||+|++.++.++..|...++.+..+||++++++            
T Consensus         2 ~q~~~~v~~---~e~K~~~L~~ll~~-~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~   77 (162)
T d1fuka_           2 KQFYVNVEE---EEYKYECLTDLYDS-ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGS   77 (162)
T ss_dssp             EEEEEEEES---GGGHHHHHHHHHHH-TTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             EEEEEEeCC---cHHHHHHHHHHHHh-CCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcc
Confidence            455554433   34577788887764 46789999999999999999999999999999999999987            


Q ss_pred             ------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         115 ------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       115 ------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                            |++++||+|+|+|++|||||+|++++.|+||+||+||.|+.|.+++++++.|...+..+
T Consensus        78 ~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i  142 (162)
T d1fuka_          78 SRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMREL  142 (162)
T ss_dssp             CSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHH
T ss_pred             cceeeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHH
Confidence                  99999999999999999999999999999999999999999999999999887665543

>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=99.95  E-value=1.6e-27  Score=186.53  Aligned_cols=127  Identities=25%  Similarity=0.383  Sum_probs=112.9

Q ss_pred             CCCcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------
Q psy4494          43 SKSMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------  114 (234)
Q Consensus        43 ~~~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------  114 (234)
                      .+++.+||.++.    ..+|+..|.+++.. .+..++||||+|++.++.++..|...|+.+..+||++++++        
T Consensus         4 l~~i~q~yi~v~----~~~K~~~L~~ll~~-~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f   78 (171)
T d1s2ma2           4 LKGITQYYAFVE----ERQKLHCLNTLFSK-LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEF   78 (171)
T ss_dssp             CTTEEEEEEECC----GGGHHHHHHHHHHH-SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHH
T ss_pred             ccceEEEEEEcC----HHHHHHHHHHHHHh-CCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhc
Confidence            456778888743    34688888888875 46789999999999999999999999999999999999876        


Q ss_pred             ----------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhH
Q psy4494         115 ----------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMV  174 (234)
Q Consensus       115 ----------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~  174 (234)
                                |+++++|+|+|++++|||||+|+++.+|+||+||+||.|+.|.+++|+++.|...+..+.
T Consensus        79 ~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~  148 (171)
T d1s2ma2          79 RQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIE  148 (171)
T ss_dssp             HTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHH
T ss_pred             ccCccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHH
Confidence                      999999999999999999999999999999999999999999999999998876665543

>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=99.95  E-value=7.6e-28  Score=185.44  Aligned_cols=123  Identities=22%  Similarity=0.412  Sum_probs=108.7

Q ss_pred             CcceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------
Q psy4494          45 SMENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------  114 (234)
Q Consensus        45 ~~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------  114 (234)
                      ++.++|..+    +..+|+..|.+++..  .+.++||||+|++.++.++..|+..|+.+..+||++++.+          
T Consensus         3 nI~~~~i~v----~~~~K~~~L~~ll~~--~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~   76 (155)
T d1hv8a2           3 NIEQSYVEV----NENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQ   76 (155)
T ss_dssp             SSEEEEEEC----CGGGHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHT
T ss_pred             CeEEEEEEe----ChHHHHHHHHHHHcc--CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhc
Confidence            455666653    235688999998864  4668999999999999999999999999999999998876          


Q ss_pred             --------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhh
Q psy4494         115 --------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSM  173 (234)
Q Consensus       115 --------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~  173 (234)
                              |+++++|+|+|+|++|||||+|+++.+|+||+||+||.|++|.+++++++.|...+..+
T Consensus        77 ~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i  143 (155)
T d1hv8a2          77 KKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYI  143 (155)
T ss_dssp             TSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHH
T ss_pred             ccceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHH
Confidence                    99999999999999999999999999999999999999999999999999887665543

>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=99.93  E-value=1.7e-25  Score=174.44  Aligned_cols=116  Identities=19%  Similarity=0.343  Sum_probs=104.1

Q ss_pred             cceEEEEEEcCCChHHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-----------
Q psy4494          46 MENFYQVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-----------  114 (234)
Q Consensus        46 ~~~~y~v~~~~~~~~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------  114 (234)
                      +.+||...    ..++|+..|.+++.. ....++||||++++.++.+++.|...|+.+..+||+|++++           
T Consensus         2 l~q~~v~~----~~~~K~~~L~~ll~~-~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g   76 (168)
T d1t5ia_           2 LQQYYVKL----KDNEKNRKLFDLLDV-LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDF   76 (168)
T ss_dssp             CEEEEEEC----CGGGHHHHHHHHHHH-SCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             cEEEEEEe----ChHHHHHHHHHHHHh-CCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccc
Confidence            45666653    346788889998864 36778999999999999999999999999999999999987           


Q ss_pred             -------hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         115 -------SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       115 -------T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                             |+++++|+|+|++++|||||+|.++.+|+||+||+||.|++|.+++|+++.+
T Consensus        77 ~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~  135 (168)
T d1t5ia_          77 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEN  135 (168)
T ss_dssp             SCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHH
T ss_pred             cceeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchH
Confidence                   9999999999999999999999999999999999999999999999998754

>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=99.90  E-value=1.8e-24  Score=162.98  Aligned_cols=89  Identities=24%  Similarity=0.346  Sum_probs=82.3

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh-----------hhhcccCCCCCCccEEEEee----cCCCH
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV-----------SIAFGLGIDKPNVRFVIHHC----LSKSM  139 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~-----------T~~~~~Gid~~~v~~Vi~~~----~P~~~  139 (234)
                      +++++||||+|++.|+.|++.|+..|+++..|||+++.++           |++++||+| ++|+.|||++    +|.++
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~P~~~  112 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSDGKPQDA  112 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCCCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEETTEECCH
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhhhhhhhcceeehhHHHHhccc-cccceEEEEEecCCCCCCH
Confidence            5789999999999999999999999999999999999877           999999999 9999999965    69999


Q ss_pred             hHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         140 ENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       140 ~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      ++|+||+||+|| |++|. +.|+.++|
T Consensus       113 ~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         113 VSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             HHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             HHHHhHhccccC-CCCcE-EEEEcCCC
Confidence            999999999999 99995 66777765

>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=99.90  E-value=2.7e-23  Score=161.63  Aligned_cols=101  Identities=23%  Similarity=0.341  Sum_probs=85.5

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      ++++.++.+.+.   .+.++||||+|++.++.++..|...|+++.++||+|++.+                  |++++||
T Consensus        18 ~dll~~i~~~~~---~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~G   94 (174)
T d1c4oa2          18 LDLMEGIRERAA---RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREG   94 (174)
T ss_dssp             HHHHHHHHHHHH---TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTT
T ss_pred             HHHHHHHHHHHh---cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeee
Confidence            344444444433   5789999999999999999999999999999999999877                  9999999


Q ss_pred             CCCCCccEEEEeecCC-----CHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         122 IDKPNVRFVIHHCLSK-----SMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~-----~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      +|+|+|++||||++|.     +..+|+||+||+||+|+ |.+++++..
T Consensus        95 iDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~  141 (174)
T d1c4oa2          95 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADR  141 (174)
T ss_dssp             CCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSS
T ss_pred             ccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecC
Confidence            9999999999999776     45789999999999887 556655543

>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=99.89  E-value=4.3e-23  Score=162.21  Aligned_cols=98  Identities=26%  Similarity=0.369  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccC
Q psy4494          60 KDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        60 ~~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      ++++.++.+.+.   .+.++||||+|++.++.++..|+..|+++..+||+|++++                  |++++||
T Consensus        18 d~ll~~i~~~~~---~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rG   94 (181)
T d1t5la2          18 DDLIGEIRERVE---RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG   94 (181)
T ss_dssp             HHHHHHHHHHHH---TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSS
T ss_pred             HHHHHHHHHHHh---cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHcc
Confidence            444555444433   5678999999999999999999999999999999999977                  9999999


Q ss_pred             CCCCCccEEEEeecCC-----CHhHhhhhhcccccCCCceEEEE
Q psy4494         122 IDKPNVRFVIHHCLSK-----SMENFYQESGRAGRDGQIAHCIL  160 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~-----~~~~y~qr~GR~gR~g~~~~~i~  160 (234)
                      +|+|+|++|||||+|.     +..+|+||+||+||.|.....++
T Consensus        95 iDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~~  138 (181)
T d1t5la2          95 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIMY  138 (181)
T ss_dssp             CCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEE
T ss_pred             CCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCceeEee
Confidence            9999999999999996     67899999999999997554433

>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=99.75  E-value=3.1e-18  Score=143.18  Aligned_cols=106  Identities=20%  Similarity=0.265  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHh---hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCc--------hh----------------
Q psy4494          62 CLDELADLMSR---RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES--------NV----------------  114 (234)
Q Consensus        62 ~~~~l~~~l~~---~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~--------~~----------------  114 (234)
                      |+..+.+++.+   ...+.++||||++++.++.+++.|...++++..+||....        .+                
T Consensus       144 K~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vL  223 (286)
T d1wp9a2         144 KMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVL  223 (286)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEE
T ss_pred             HHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEE
Confidence            44444444432   2357789999999999999999999999999999875443        22                


Q ss_pred             --hhhcccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHH
Q psy4494         115 --SIAFGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVF  168 (234)
Q Consensus       115 --T~~~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~  168 (234)
                        |+++++|+|+|++++||+||+|+++..|+||+||+||.+ +|.+++|+.+....
T Consensus       224 v~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~e  278 (286)
T d1wp9a2         224 VATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTRD  278 (286)
T ss_dssp             EECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSHH
T ss_pred             EEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCHH
Confidence              999999999999999999999999999999999999975 67788888876544

>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=99.75  E-value=6.8e-19  Score=145.88  Aligned_cols=89  Identities=20%  Similarity=0.251  Sum_probs=78.7

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------------------hhhccc---CCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------------------SIAFGL---GID  123 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------------------T~~~~~---Gid  123 (234)
                      +++++||||+|++.|++++..|++.|+++..+||+++++.                            |+++.+   |+|
T Consensus        35 kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giD  114 (299)
T d1a1va2          35 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFS  114 (299)
T ss_dssp             HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECC
T ss_pred             cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCC
Confidence            4678999999999999999999999999999999998753                            666655   778


Q ss_pred             CCCccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         124 KPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       124 ~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                      ++.|.+||+|++|.++++|+||+||+|| |++|...++...
T Consensus       115 id~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~~  154 (299)
T d1a1va2         115 LDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAPG  154 (299)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCSC
T ss_pred             CCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEecC
Confidence            8888899999999999999999999999 999987665543

>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=99.70  E-value=1.8e-17  Score=132.02  Aligned_cols=102  Identities=18%  Similarity=0.265  Sum_probs=84.3

Q ss_pred             HHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcC------------------------------CceeeeccCCCch
Q psy4494          64 DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRG------------------------------LRVSAYHAKLESN  113 (234)
Q Consensus        64 ~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~------------------------------~~~~~~h~~~~~~  113 (234)
                      ..+.+++.   .+.++||||+|++.|+.+|..|.+..                              .-+..+||+|+++
T Consensus        31 ~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~  107 (201)
T d2p6ra4          31 ELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNG  107 (201)
T ss_dssp             HHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHH
T ss_pred             HHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhh
Confidence            33455555   46789999999999999998887420                              1178899999987


Q ss_pred             h------------------hhhcccCCCCCCccEEEE-------eecCCCHhHhhhhhcccccCCC--ceEEEEEeeccc
Q psy4494         114 V------------------SIAFGLGIDKPNVRFVIH-------HCLSKSMENFYQESGRAGRDGQ--IAHCILYYRLPD  166 (234)
Q Consensus       114 ~------------------T~~~~~Gid~~~v~~Vi~-------~~~P~~~~~y~qr~GR~gR~g~--~~~~i~~~~~~d  166 (234)
                      +                  |+++++|+|+|.++.||+       ++.|.+..+|+||+|||||.|.  .|.++++..+.+
T Consensus       108 ~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~  187 (201)
T d2p6ra4         108 QRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  187 (201)
T ss_dssp             HHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             hHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCC
Confidence            7                  999999999999999996       7888999999999999999884  799999887765


Q ss_pred             HH
Q psy4494         167 VF  168 (234)
Q Consensus       167 ~~  168 (234)
                      ..
T Consensus       188 ~~  189 (201)
T d2p6ra4         188 RE  189 (201)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=99.70  E-value=2.3e-19  Score=147.38  Aligned_cols=103  Identities=18%  Similarity=0.346  Sum_probs=83.6

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------h----hhc
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------S----IAF  118 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T----~~~  118 (234)
                      +++..|..++.. + +.++||||+|++.++.++++|+.      .+||++++++                  |    +++
T Consensus        12 ~~~~~l~~~l~~-~-~~~~iif~~~~~~~~~l~~~l~~------~~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~   83 (248)
T d1gkub2          12 ESISTLSSILEK-L-GTGGIIYARTGEEAEEIYESLKN------KFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTL   83 (248)
T ss_dssp             CCTTTTHHHHTT-S-CSCEEEEESSHHHHHHHHHTTTT------SSCEEECTTSSSHHHHHHHHTSCSEEEEECC-----
T ss_pred             hHHHHHHHHHHH-h-CCCEEEEECCHHHHHHHHHHHHH------hccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchh
Confidence            356667777763 2 46799999999999999999974      3899999876                  6    678


Q ss_pred             ccCCCCCC-ccEEEEeecCCCHhHhhhhhcccccCCCceEEEEEeecccHHHhhhhHH
Q psy4494         119 GLGIDKPN-VRFVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPDVFKLSSMVF  175 (234)
Q Consensus       119 ~~Gid~~~-v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d~~~~~~~~~  175 (234)
                      +||||+|+ |++|||||+|+    |.||+||+||+|+.+.+++++...+......+..
T Consensus        84 ~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~~~~l~~  137 (248)
T d1gkub2          84 VRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLP  137 (248)
T ss_dssp             -CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCT
T ss_pred             hhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHHHHHHHH
Confidence            99999996 99999999994    9999999999999999999998888776655443

>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=99.56  E-value=2e-15  Score=119.52  Aligned_cols=89  Identities=20%  Similarity=0.256  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh------------------hhhcccCC
Q psy4494          61 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGI  122 (234)
Q Consensus        61 ~~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~------------------T~~~~~Gi  122 (234)
                      .|+..|.+++.+ .++.++||||++++.++.+++.|.     +..+||+++.++                  |.++++|+
T Consensus        79 ~K~~~l~~ll~~-~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gi  152 (200)
T d2fwra1          79 NKIRKLREILER-HRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGI  152 (200)
T ss_dssp             HHHHHHHHHHHH-TSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSS
T ss_pred             HHHHHHHHHHHh-CCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhccc
Confidence            467788888875 467899999999999999988773     567899998875                  89999999


Q ss_pred             CCCCccEEEEeecCCCHhHhhhhhcccccCCCc
Q psy4494         123 DKPNVRFVIHHCLSKSMENFYQESGRAGRDGQI  155 (234)
Q Consensus       123 d~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~  155 (234)
                      |+|.+++||++++|+++..|+||+||++|.|+.
T Consensus       153 dl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~  185 (200)
T d2fwra1         153 DVPDANVGVIMSGSGSAREYIQRLGRILRPSKG  185 (200)
T ss_dssp             CSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTT
T ss_pred             CCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCC
Confidence            999999999999999999999999999998753

>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=99.51  E-value=6.5e-15  Score=117.00  Aligned_cols=104  Identities=22%  Similarity=0.405  Sum_probs=76.2

Q ss_pred             HHHHHHHHHhhc-CCCcEEEEecchHHHH--------HHHHHHHHc---CCceeeeccCCCchh----------------
Q psy4494          63 LDELADLMSRRF-RNQSGIIYTTSIKECE--------DLREELRNR---GLRVSAYHAKLESNV----------------  114 (234)
Q Consensus        63 ~~~l~~~l~~~~-~~~~~iIf~~t~~~~~--------~l~~~L~~~---~~~~~~~h~~~~~~~----------------  114 (234)
                      ...+.+.+++.. ++.++.+.|+.++..+        +..+.|.+.   ++++..+||.|++++                
T Consensus        15 ~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iL   94 (206)
T d1gm5a4          15 VNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDIL   94 (206)
T ss_dssp             HHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBC
T ss_pred             HHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEE
Confidence            344555554433 4566777787665444        334444332   667899999999987                


Q ss_pred             --hhhcccCCCCCCccEEEEeecCC-CHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         115 --SIAFGLGIDKPNVRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       115 --T~~~~~Gid~~~v~~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                        |+++++|||+|++++||+++.|. .+..|.|.+||+||.|++|.|++++++.+
T Consensus        95 VaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~  149 (206)
T d1gm5a4          95 VSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVG  149 (206)
T ss_dssp             CCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCC
T ss_pred             EEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeecccc
Confidence              99999999999999999999998 56677777999999999999999997654

>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=99.49  E-value=2.9e-14  Score=118.76  Aligned_cols=90  Identities=20%  Similarity=0.182  Sum_probs=76.9

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEEE---------
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFVI---------  131 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~Vi---------  131 (234)
                      ..+++||||+++++++.+++.|+..++.+..+||++.++.              |+++++|+|++ ++.||         
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~~~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~  255 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYIKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPV  255 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHHGGGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEE
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHHHhhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeee
Confidence            4678999999999999999999999999999999987755              99999999994 55554         


Q ss_pred             -Eee----------cCCCHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         132 -HHC----------LSKSMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       132 -~~~----------~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                       +++          .|-|..+|+||+||+||.|+.+..+++|...
T Consensus       256 ~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         256 ILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             EECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             EecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence             233          4567889999999999999999888887654

>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=99.35  E-value=5.9e-12  Score=99.35  Aligned_cols=101  Identities=18%  Similarity=0.241  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHc--CCceeeeccCCCchh------------------hhhcccC
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNR--GLRVSAYHAKLESNV------------------SIAFGLG  121 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~------------------T~~~~~G  121 (234)
                      ....+..-+.   ++.++.+.||..+..+.++..|.+.  ++++..+||.|++++                  |.+...|
T Consensus        20 i~~~I~~El~---rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvG   96 (211)
T d2eyqa5          20 VREAILREIL---RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETG   96 (211)
T ss_dssp             HHHHHHHHHT---TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGG
T ss_pred             HHHHHHHHHH---cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhc
Confidence            3444444443   5788999999999999999999875  778999999999987                  9999999


Q ss_pred             CCCCCccEEEEeecCC-CHhHhhhhhcccccCCCceEEEEEeecc
Q psy4494         122 IDKPNVRFVIHHCLSK-SMENFYQESGRAGRDGQIAHCILYYRLP  165 (234)
Q Consensus       122 id~~~v~~Vi~~~~P~-~~~~y~qr~GR~gR~g~~~~~i~~~~~~  165 (234)
                      ||+|+++.+|..+.+. .+.++.|-.||+||.+.++.|+++++..
T Consensus        97 iDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5          97 IDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             SCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             cCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecCC
Confidence            9999999999999886 8889999999999999999999999653

>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=99.30  E-value=1.3e-12  Score=109.03  Aligned_cols=89  Identities=20%  Similarity=0.208  Sum_probs=74.5

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh--------------hhhcccCCCCCCccEEEEeecC----
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV--------------SIAFGLGIDKPNVRFVIHHCLS----  136 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~--------------T~~~~~Gid~~~v~~Vi~~~~P----  136 (234)
                      ..++++|||++++++++++..|+..|..+..+||.+..++              |+++++|+++ +|.+||+.+.+    
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~~~~  113 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANL-CVERVLDCRTAFKPV  113 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC--------CCCSEEEESSSTTCCTTC-CCSEEEECCEEEEEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHhhhhcCCcCEEEEechhhhceec-CceEEEecCceecee
Confidence            3678999999999999999999999999999999988766              9999999999 59999977653    


Q ss_pred             ---------------CCHhHhhhhhcccccCCCceEEEEEeec
Q psy4494         137 ---------------KSMENFYQESGRAGRDGQIAHCILYYRL  164 (234)
Q Consensus       137 ---------------~~~~~y~qr~GR~gR~g~~~~~i~~~~~  164 (234)
                                     -+..+-.||.||+||.+..+.++.+|+.
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~~  156 (299)
T d1yksa2         114 LVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSE  156 (299)
T ss_dssp             EETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECS
T ss_pred             eecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeCC
Confidence                           2456778999999998766666666653

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.28  E-value=1.3e-11  Score=94.41  Aligned_cols=108  Identities=22%  Similarity=0.279  Sum_probs=92.5

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..+|+..+.+.+... ..++|+||++.|++..|.++..|...+++...+++....++                |+.+|||
T Consensus        16 ~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~g~VtIATNmAGRG   95 (175)
T d1tf5a4          16 MEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRG   95 (175)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTCEEEEETTSSTT
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCCCceeehhhHHHcC
Confidence            456777776665432 25789999999999999999999999999999998876655                9999999


Q ss_pred             CCCCC---cc-----EEEEeecCCCHhHhhhhhcccccCCCceEEEEEeeccc
Q psy4494         122 IDKPN---VR-----FVIHHCLSKSMENFYQESGRAGRDGQIAHCILYYRLPD  166 (234)
Q Consensus       122 id~~~---v~-----~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~i~~~~~~d  166 (234)
                      .|+.-   |.     +||.-..|.+..-..|-.||+||.|.+|.+.+|++.+|
T Consensus        96 tDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          96 TDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             CCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             CCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            99852   32     79999999999999999999999999999999998877

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.17  E-value=1.2e-10  Score=99.23  Aligned_cols=105  Identities=15%  Similarity=0.091  Sum_probs=86.8

Q ss_pred             HHHHHHHHHHHh--hcCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh---------------------hhh
Q psy4494          61 DCLDELADLMSR--RFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV---------------------SIA  117 (234)
Q Consensus        61 ~~~~~l~~~l~~--~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~---------------------T~~  117 (234)
                      .|+..|.+++..  ..++.++|||++.....+.+...|...|+....++|+++..+                     |.+
T Consensus       101 ~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~a  180 (346)
T d1z3ix1         101 GKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKA  180 (346)
T ss_dssp             HHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGG
T ss_pred             HHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchh
Confidence            455555555532  125679999999999999999999999999999999998754                     788


Q ss_pred             cccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCceEE--EEEeecc
Q psy4494         118 FGLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQIAHC--ILYYRLP  165 (234)
Q Consensus       118 ~~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~~~~--i~~~~~~  165 (234)
                      .|.|+|+...++||+||+++++..+.|++||+-|.|+...+  +-++..+
T Consensus       181 gg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~  230 (346)
T d1z3ix1         181 GGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  230 (346)
T ss_dssp             SCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             hhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCC
Confidence            89999999999999999999999999999999999976433  3344443

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.10  E-value=1e-10  Score=94.63  Aligned_cols=105  Identities=16%  Similarity=0.079  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHc-CCceeeeccCCCchh--------------------hhhc
Q psy4494          61 DCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNR-GLRVSAYHAKLESNV--------------------SIAF  118 (234)
Q Consensus        61 ~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~--------------------T~~~  118 (234)
                      .|+..+.+++.+. ..+.++||||+.....+.+...|... +..+..+||+++.++                    +.+.
T Consensus        69 ~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~  148 (244)
T d1z5za1          69 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAG  148 (244)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTT
T ss_pred             hHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhcccccccc
Confidence            4666666666532 25778999999999999999988755 888999999998865                    6788


Q ss_pred             ccCCCCCCccEEEEeecCCCHhHhhhhhcccccCCCc--eEEEEEeecc
Q psy4494         119 GLGIDKPNVRFVIHHCLSKSMENFYQESGRAGRDGQI--AHCILYYRLP  165 (234)
Q Consensus       119 ~~Gid~~~v~~Vi~~~~P~~~~~y~qr~GR~gR~g~~--~~~i~~~~~~  165 (234)
                      |.|+|+...++||+|++|+++..+.|+.||+-|.|+.  -..+.++...
T Consensus       149 g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~  197 (244)
T d1z5za1         149 GFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  197 (244)
T ss_dssp             CCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             ccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCC
Confidence            9999999999999999999999999999999998864  3444444544

>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=98.78  E-value=3.6e-08  Score=76.71  Aligned_cols=109  Identities=25%  Similarity=0.268  Sum_probs=90.6

Q ss_pred             hHHHHHHHHHHHHhh-cCCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCchh----------------hhhcccC
Q psy4494          59 QKDCLDELADLMSRR-FRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV----------------SIAFGLG  121 (234)
Q Consensus        59 ~~~~~~~l~~~l~~~-~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~~~----------------T~~~~~G  121 (234)
                      ..+|+..+.+-+... ..++|+||.+.|.+..|.++..|...|++...+++....++                |+-+|||
T Consensus        16 ~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAqAG~~GaVTIATNMAGRG   95 (219)
T d1nkta4          16 EEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRGGVTVATNMAGRG   95 (219)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTTCEEEEETTCSTT
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHhcccCCcEEeeccccCCC
Confidence            456777776655532 35889999999999999999999999999999999876555                8999999


Q ss_pred             CCCCC-----------------------------------------------cc-----EEEEeecCCCHhHhhhhhccc
Q psy4494         122 IDKPN-----------------------------------------------VR-----FVIHHCLSKSMENFYQESGRA  149 (234)
Q Consensus       122 id~~~-----------------------------------------------v~-----~Vi~~~~P~~~~~y~qr~GR~  149 (234)
                      .||.-                                               |.     +||-...-.|..-=-|-.||+
T Consensus        96 TDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLRGRs  175 (219)
T d1nkta4          96 TDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRS  175 (219)
T ss_dssp             CCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTS
T ss_pred             CceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEeccccccccccccccccc
Confidence            99942                                               11     688888788877778999999


Q ss_pred             ccCCCceEEEEEeecccH
Q psy4494         150 GRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       150 gR~g~~~~~i~~~~~~d~  167 (234)
                      ||.|.+|.+.+|++-+|-
T Consensus       176 GRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         176 GRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             SGGGCCEEEEEEEETTSH
T ss_pred             cccCCCccceeEEeccHH
Confidence            999999999999998875

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=88.17  E-value=0.3  Score=32.45  Aligned_cols=45  Identities=11%  Similarity=0.101  Sum_probs=35.3

Q ss_pred             HHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCc-eeeeccCCC
Q psy4494          67 ADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLR-VSAYHAKLE  111 (234)
Q Consensus        67 ~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~-~~~~h~~~~  111 (234)
                      ...+.+..+..+.|+||.+-..+..++..|...|++ +..+.||+.
T Consensus        49 ~~~~~~~~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          49 GAFMRDNDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHSCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             HHHhhhccccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            333333335678999999999999999999999995 778888874

>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=87.45  E-value=0.11  Score=38.41  Aligned_cols=27  Identities=11%  Similarity=-0.013  Sum_probs=23.0

Q ss_pred             HhhhhhcccccCCCceEEEEEeecccH
Q psy4494         141 NFYQESGRAGRDGQIAHCILYYRLPDV  167 (234)
Q Consensus       141 ~y~qr~GR~gR~g~~~~~i~~~~~~d~  167 (234)
                      ++.|.+||+||+|+.|.+.+++.....
T Consensus       116 s~~~yi~R~GRagR~g~~~~~~~~~~~  142 (181)
T d1t5la2         116 SERSLIQTIGRAARNANGHVIMYADTI  142 (181)
T ss_dssp             SHHHHHHHHGGGTTSTTCEEEEECSSC
T ss_pred             cHHHHHHHHHhhccccCceeEeecchh
Confidence            467889999999999999999887543

>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=87.16  E-value=0.39  Score=32.60  Aligned_cols=45  Identities=18%  Similarity=0.097  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHhhcCCCcEEEEecchHHHHHHHHHHHHcCCceeeecc
Q psy4494          62 CLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA  108 (234)
Q Consensus        62 ~~~~l~~~l~~~~~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~  108 (234)
                      -+..|..++.+  ...++||.|.|....+.+.+.|+.+++.+....+
T Consensus        22 p~~~L~~~i~~--~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~   66 (117)
T d2eyqa2          22 PLDALRKFLET--FDGPVVFSVESEGRREALGELLARIKIAPQRIMR   66 (117)
T ss_dssp             TTHHHHHHHTT--CCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSS
T ss_pred             HHHHHHHHHHh--CCCeEEEEECCccHHHHHHHHHHHcCCCceEecC
Confidence            35567777653  3567889999999999999999999988655443

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.02  E-value=0.45  Score=32.71  Aligned_cols=38  Identities=13%  Similarity=0.066  Sum_probs=34.0

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCCceeeeccCCCc
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLES  112 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~~~~~~h~~~~~  112 (234)
                      +.++.++||.+-..+...+..|+..|+++..+.|++..
T Consensus        79 ~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~a  116 (130)
T d1yt8a4          79 RGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSEA  116 (130)
T ss_dssp             BTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCGG
T ss_pred             ccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchHH
Confidence            56789999999889999999999999999999998864

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.55  E-value=0.37  Score=32.59  Aligned_cols=37  Identities=14%  Similarity=0.079  Sum_probs=32.2

Q ss_pred             CCCcEEEEecchHHHHHHHHHHHHcCC-ceeeeccCCC
Q psy4494          75 RNQSGIIYTTSIKECEDLREELRNRGL-RVSAYHAKLE  111 (234)
Q Consensus        75 ~~~~~iIf~~t~~~~~~l~~~L~~~~~-~~~~~h~~~~  111 (234)
                      +..++|+||++-..+..++..|...|+ .+..+.||+.
T Consensus        71 ~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~  108 (119)
T d1tq1a_          71 QSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  108 (119)
T ss_dssp             TTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHH
Confidence            467899999998889999999999998 4888889874