Psyllid ID: psy437

---

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----
Protein Sequence
FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGREDIREGETMEGE
Secondary Structure (PSIPRED)
ccccccccccEEEEEEcccHHHHHHHHHHHHccccccEEEEccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHccccEEEEEccccccccccccccccccccEEEEEccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEEEcccHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHcccEEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHccccHHHcccccccccc
Coil and Loop (DISEMBL)
fissfnranlkyeilpkKNVLKEVISLIKAkysgqsgivycLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVlikpdylppildlrlgrediregetmege
Flexible Loop (DISEMBL)
fissfnranlkyeilpkknVLKEVISLIKakysgqsgIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPdylppildlrlgrediregetmege
Low Complexity Region (SEG)
FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGREDIREGETMEGE
Disordered region (IsUnstruct)
*******ANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLG*************
Disordered Region (DISOPRED)
FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLP*********************
Disordered Region (DISEMBL)
FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGREDIR********
Disordered Region (DISPRO)
**SSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGR*D**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGREDIREGETMEGE
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	184	2.2.26 [Sep-21-2011]
Q9DEY9	1364	Bloom syndrome protein ho	N/A	N/A	0.445	0.060	0.523	8e-19
O18017	988	Bloom syndrome protein ho	yes	N/A	0.472	0.088	0.522	2e-18
Q9VGI8	1487	Bloom syndrome protein ho	yes	N/A	0.472	0.058	0.460	3e-18
O88700	1416	Bloom syndrome protein ho	yes	N/A	0.445	0.057	0.5	5e-18
Q9I920	1142	Bloom syndrome protein ho	no	N/A	0.456	0.073	0.488	7e-18
P54132	1417	Bloom syndrome protein OS	yes	N/A	0.445	0.057	0.488	1e-17
Q9FT74	606	ATP-dependent DNA helicas	yes	N/A	0.456	0.138	0.430	1e-13
Q9FT73	705	Mediator of RNA polymeras	no	N/A	0.5	0.130	0.422	2e-13
P46063	649	ATP-dependent DNA helicas	no	N/A	0.5	0.141	0.375	6e-13
Q5RF63	649	ATP-dependent DNA helicas	no	N/A	0.5	0.141	0.375	7e-13

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

 Score = 93.2 bits (230), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/84 (52%), Positives = 58/84 (69%), Gaps = 2/84 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F  SFNR NLKYE+LPKK   V  + +  IK  +   SGI+YCL+R ECD++A  L +E 
Sbjct: 805 FTMSFNRDNLKYEVLPKKPKRVALDCVEWIKKHHPNDSGIIYCLSRHECDTMADTLQKEG 864

Query: 59  INAISYHAGLADKLRNEVQMKWIS 82
           + A++YHAGLAD  R+ VQ KWI+
Sbjct: 865 LAALAYHAGLADSNRDYVQHKWIN 888

Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.
Xenopus laevis (taxid: 8355)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

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

 Score = 92.4 bits (228), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 46/88 (52%), Positives = 59/88 (67%), Gaps = 1/88 (1%)

Query: 1   FISSFNRANLKYEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
           FISSF R NLKY+++PK    L  V+  +K  Y G+SGIVYCL+RKEC++V   L +  +
Sbjct: 435 FISSFVRDNLKYDLIPKAARSLINVVEKMKQLYPGKSGIVYCLSRKECETVQMMLTKAGL 494

Query: 60  NAISYHAGLADKLRNEVQMKWISNKVHV 87
           +A  YHAGL D LR  VQ  WI+NK  V
Sbjct: 495 SAEVYHAGLNDNLRVSVQRSWIANKFDV 522

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

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 91.7 bits (226), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/89 (46%), Positives = 60/89 (67%), Gaps = 2/89 (2%)

Query: 1    FISSFNRANLKYEILPKKNV--LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
            F+SSFNR+NL+Y +LPKK V  L ++   I++K    SGI+YCL+RKECD  +  + ++ 
Sbjct: 923  FLSSFNRSNLRYRVLPKKGVSTLDDISRYIRSKPQHFSGIIYCLSRKECDETSKKMCKDG 982

Query: 59   INAISYHAGLADKLRNEVQMKWISNKVHV 87
            + A+SYHAGL D  R   Q  W++ K+ V
Sbjct: 983  VRAVSYHAGLTDTDRESRQKDWLTGKMRV 1011

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 = 90.5 bits (223), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 42/84 (50%), Positives = 59/84 (70%), Gaps = 2/84 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F  SFNR NLKY +LPKK   V  + +  I+  +   SGI+YCL+R+ECD++A  L +E 
Sbjct: 861 FSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQREG 920

Query: 59  INAISYHAGLADKLRNEVQMKWIS 82
           + A++YHAGL+D  R+EVQ KWI+
Sbjct: 921 LAALAYHAGLSDSARDEVQHKWIN 944

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

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 90.1 bits (222), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 42/86 (48%), Positives = 58/86 (67%), Gaps = 2/86 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F  SFNR NLKY++LPKK   V  + +  IK  +   SGI+YCL+R ECD+ AA L +E 
Sbjct: 583 FTMSFNRHNLKYDVLPKKPKKVAMDCLEWIKKYHPHDSGIIYCLSRHECDTTAAILQKEG 642

Query: 59  INAISYHAGLADKLRNEVQMKWISNK 84
           + A++YHAGL D  R+ VQ KW++ +
Sbjct: 643 LAALAYHAGLTDSNRDLVQKKWVNQE 668

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

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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

 Score = 89.4 bits (220), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/84 (48%), Positives = 59/84 (70%), Gaps = 2/84 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F  SFNR NLKY +LPKK   V  + +  I+  +   SGI+YCL+R+ECD++A  L ++ 
Sbjct: 853 FSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQRDG 912

Query: 59  INAISYHAGLADKLRNEVQMKWIS 82
           + A++YHAGL+D  R+EVQ KWI+
Sbjct: 913 LAALAYHAGLSDSARDEVQQKWIN 936

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

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q9FT74|RQL1_ARATH ATP-dependent DNA helicase Q-like 1 OS=Arabidopsis thaliana GN=RECQL1 PE=2 SV=1

 Score = 76.3 bits (186), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 37/86 (43%), Positives = 58/86 (67%), Gaps = 2/86 (2%)

Query: 4   SFNRANLKYEILPK-KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE-RINA 61
           SF+R NLKYE++ K K  LK++  L++ ++  QSGIVYCL++ EC  VA  L ++ ++  
Sbjct: 396 SFDRINLKYEVIVKTKEPLKQLQELLRDRFKDQSGIVYCLSKSECVDVAKFLNEKCKVKT 455

Query: 62  ISYHAGLADKLRNEVQMKWISNKVHV 87
           + YHAG+  K R +VQ KW + +V +
Sbjct: 456 VYYHAGVPAKQRVDVQRKWQTGEVRI 481

3'-5' DNA helicase that may play a role in the repair of DNA.

Arabidopsis thaliana (taxid: 3702)

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 = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/97 (42%), Positives = 57/97 (58%), Gaps = 5/97 (5%)

Query: 1   FISSFNRANLKYEILPK----KNVLKEVISLIKAKYSG-QSGIVYCLTRKECDSVAAALA 55
           F+SS NR NL Y +  K    K V+ E+   I+  YS  +SGIVYC +RKEC+ +A  L 
Sbjct: 275 FVSSVNRPNLFYSVREKSAVGKLVVDEIAEFIRESYSNNESGIVYCFSRKECEQIAGDLR 334

Query: 56  QERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV 92
           +  I+A  YHA +   +R +V M+W  NK+ V   TV
Sbjct: 335 ERGISADYYHADMDANMREKVHMRWSKNKLQVIVGTV 371

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

 Score = 73.9 bits (180), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 59/96 (61%), Gaps = 4/96 (4%)

Query: 1   FISSFNRANLKYEILPK----KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ 56
           F +SFNR NL YE+  K    ++ +++++ LI  +Y GQSGI+YC ++K+ + V  +L  
Sbjct: 277 FTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQN 336

Query: 57  ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV 92
             I+A +YHA L  + +  V  KW +N++ V   TV
Sbjct: 337 LGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV 372

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

 Score = 73.6 bits (179), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 59/96 (61%), Gaps = 4/96 (4%)

Query: 1   FISSFNRANLKYEILPK----KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ 56
           F +SFNR NL YE+  K    ++ +++++ LI  +Y GQSGI+YC ++K+ + V  +L  
Sbjct: 277 FTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLRN 336

Query: 57  ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV 92
             I+A +YHA L  + +  V  KW +N++ V   TV
Sbjct: 337 LGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV 372

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

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	184
328697674	1185	PREDICTED: Bloom syndrome protein homolo	0.472	0.073	0.606	2e-24
328725542	1185	PREDICTED: Bloom syndrome protein homolo	0.472	0.073	0.606	2e-24
328707887	1128	PREDICTED: Bloom syndrome protein homolo	0.472	0.077	0.584	7e-23
321478461	1276	DNA helicase bloom's syndrome protein A	0.472	0.068	0.588	7e-23
443726019	579	hypothetical protein CAPTEDRAFT_91032 [C	0.445	0.141	0.535	7e-20
330932861	1750	hypothetical protein PTT_16345 [Pyrenoph	0.472	0.049	0.522	4e-19
324502420	1090	Bloom syndrome protein [Ascaris suum]	0.472	0.079	0.534	5e-19
312373074	1384	hypothetical protein AND_18334 [Anophele	0.472	0.062	0.516	6e-19
307195272	1091	Bloom syndrome protein-like protein [Har	0.472	0.079	0.528	6e-19
195112008	1409	GI22449 [Drosophila mojavensis] gi|19391	0.472	0.061	0.516	8e-19

>gi|328697674|ref|XP_001952385.2| PREDICTED: Bloom syndrome protein homolog [Acyrthosiphon pisum]

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/89 (60%), Positives = 70/89 (78%), Gaps = 2/89 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+SSFNR NL Y+++PKK  + + E+ +LIK KY  QSGIVYCL+RKECD+ A  +  E 
Sbjct: 640 FLSSFNRPNLLYKVVPKKGKSAMAEIANLIKEKYKNQSGIVYCLSRKECDNTATYMCNEG 699

Query: 59  INAISYHAGLADKLRNEVQMKWISNKVHV 87
           I AISYHAGL+D  RN+VQMKWI+NKV++
Sbjct: 700 IKAISYHAGLSDPKRNDVQMKWITNKVNL 728

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328725542|ref|XP_001947924.2| PREDICTED: Bloom syndrome protein homolog [Acyrthosiphon pisum]

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/89 (60%), Positives = 70/89 (78%), Gaps = 2/89 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+SSFNR NL Y+++PKK  + + E+ +LIK KY  QSGIVYCL+RKECD+ A  +  E 
Sbjct: 640 FLSSFNRPNLLYKVVPKKGKSAMAEIANLIKEKYKNQSGIVYCLSRKECDNTATYMCNEG 699

Query: 59  INAISYHAGLADKLRNEVQMKWISNKVHV 87
           I AISYHAGL+D  RN+VQMKWI+NKV++
Sbjct: 700 IKAISYHAGLSDPKRNDVQMKWITNKVNL 728

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328707887|ref|XP_001947908.2| PREDICTED: Bloom syndrome protein homolog [Acyrthosiphon pisum]

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 52/89 (58%), Positives = 70/89 (78%), Gaps = 2/89 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+SSFNR NL YE++PKK  + L E+  LIK+K++ QSGI+YC+T+KECD+ A  ++ E 
Sbjct: 584 FVSSFNRPNLVYEVIPKKGKSSLLEIAKLIKSKFARQSGIIYCMTKKECDNTAIFMSGEG 643

Query: 59  INAISYHAGLADKLRNEVQMKWISNKVHV 87
           I A+SYHAGL DK RN+VQM+W SNK +V
Sbjct: 644 IKAVSYHAGLTDKKRNDVQMQWTSNKSNV 672

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321478461|gb|EFX89418.1| DNA helicase bloom's syndrome protein A [Daphnia pulex]

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 53/90 (58%), Positives = 67/90 (74%), Gaps = 3/90 (3%)

Query: 1   FISSFNRANLKYEILPKK---NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE 57
           F+SSFNR NLKY +LPKK    VL E+  LI  ++  +SGIVYCL+R+ECD VA +L   
Sbjct: 700 FLSSFNRPNLKYCVLPKKMKAGVLTEIAELITKRFDRKSGIVYCLSRRECDEVAQSLQSS 759

Query: 58  RINAISYHAGLADKLRNEVQMKWISNKVHV 87
           RI AISYHAGL+D+LR+E Q+KWI+  V V
Sbjct: 760 RIKAISYHAGLSDELRSESQLKWINGTVQV 789

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443726019|gb|ELU13361.1| hypothetical protein CAPTEDRAFT_91032 [Capitella teleta]

 Score =  102 bits (254), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 45/84 (53%), Positives = 64/84 (76%), Gaps = 2/84 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+ SFNR NLKYE+LPKK  ++  +VI++I +++S QSGIVYCL+R+ECD+V+  L +  
Sbjct: 199 FMQSFNRVNLKYEVLPKKPKSLTSDVINMIHSRFSNQSGIVYCLSRRECDTVSTDLTKAG 258

Query: 59  INAISYHAGLADKLRNEVQMKWIS 82
           I A +YHAGL D  R+ VQ KW++
Sbjct: 259 IQAKAYHAGLTDAQRSSVQQKWLN 282

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|330932861|ref|XP_003303943.1| hypothetical protein PTT_16345 [Pyrenophora teres f. teres 0-1] gi|311319743|gb|EFQ87962.1| hypothetical protein PTT_16345 [Pyrenophora teres f. teres 0-1]

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 46/88 (52%), Positives = 60/88 (68%), Gaps = 1/88 (1%)

Query: 1    FISSFNRANLKYEILPK-KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
            +  SFNR NL YE+LPK K V+  +  LIK KY+G+SGI+YCL+RK C+ VA  L++  I
Sbjct: 1041 YSQSFNRPNLSYEVLPKGKGVINSIADLIKEKYTGKSGIIYCLSRKTCEQVAQKLSETGI 1100

Query: 60   NAISYHAGLADKLRNEVQMKWISNKVHV 87
             A  YHAG+    R+EVQ KW  N+ HV
Sbjct: 1101 RAYHYHAGMDSADRSEVQRKWQKNEYHV 1128

Source: Pyrenophora teres f. teres 0-1

Species: Pyrenophora teres

Genus: Pyrenophora

Family: Pleosporaceae

Order: Pleosporales

Class: Dothideomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|324502420|gb|ADY41066.1| Bloom syndrome protein [Ascaris suum]

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 47/88 (53%), Positives = 65/88 (73%), Gaps = 1/88 (1%)

Query: 1   FISSFNRANLKYEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
           FISSF R+NLKY+++ K+   L  V+  +KA Y G+SGIVYCL+RKEC++V+ +L  + I
Sbjct: 505 FISSFVRSNLKYDVIAKRPKSLSAVMERMKALYPGKSGIVYCLSRKECETVSKSLQNQGI 564

Query: 60  NAISYHAGLADKLRNEVQMKWISNKVHV 87
           +A  YHAGL DK R  VQ KWI+N ++V
Sbjct: 565 SADVYHAGLPDKQRQNVQAKWINNHINV 592

Source: Ascaris suum

Species: Ascaris suum

Genus: Ascaris

Family: Ascarididae

Order: Ascaridida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

>gi|312373074|gb|EFR20899.1| hypothetical protein AND_18334 [Anopheles darlingi]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 46/89 (51%), Positives = 63/89 (70%), Gaps = 2/89 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+SSFNR NLKY +LPKK  +   E+I+LIKAK++  +GIVYCL++KECD +A    +  
Sbjct: 790 FLSSFNRPNLKYLVLPKKGASTKGEMINLIKAKFARDTGIVYCLSKKECDQLATDFRKAG 849

Query: 59  INAISYHAGLADKLRNEVQMKWISNKVHV 87
           I A SYHAGL D +R   Q +WI +++ V
Sbjct: 850 IKAKSYHAGLTDTIREATQKEWIGDRIKV 878

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307195272|gb|EFN77228.1| Bloom syndrome protein-like protein [Harpegnathos saltator]

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 62/89 (69%), Gaps = 2/89 (2%)

Query: 1   FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+SSFNR NL+Y I+ KK  N   EV+++IK K+    GIVYCL+RK+C+  AA L +  
Sbjct: 595 FMSSFNRPNLRYSIISKKGKNCSDEVVAMIKTKFKNVCGIVYCLSRKDCEDYAAHLKKNC 654

Query: 59  INAISYHAGLADKLRNEVQMKWISNKVHV 87
           I A+SYHAGL D  RN  Q KWI +++HV
Sbjct: 655 IKALSYHAGLTDNQRNNCQGKWILDEIHV 683

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195112008|ref|XP_002000568.1| GI22449 [Drosophila mojavensis] gi|193917162|gb|EDW16029.1| GI22449 [Drosophila mojavensis]

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 46/89 (51%), Positives = 63/89 (70%), Gaps = 2/89 (2%)

Query: 1   FISSFNRANLKYEILPKKNV--LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
           F+SSFNR NL+Y++LPKK V  L ++ + I+++ +  SGI+YCL+RKECD VA  +    
Sbjct: 836 FLSSFNRRNLRYQVLPKKGVSTLDDMRNFIQSRPATASGIIYCLSRKECDEVAKKMCAVG 895

Query: 59  INAISYHAGLADKLRNEVQMKWISNKVHV 87
           I A+SYHAGL D +R   Q  WI+NKV V
Sbjct: 896 IRALSYHAGLTDVVRESRQKDWITNKVRV 924

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	184
WB|WBGene00001865	988	him-6 [Caenorhabditis elegans	0.472	0.088	0.522	5.8e-17
UNIPROTKB|Q9DEY9	1364	blm "Bloom syndrome protein ho	0.445	0.060	0.523	7e-17
RGD|1308810	999	Blm "Bloom syndrome, RecQ heli	0.445	0.082	0.511	9.6e-17
FB|FBgn0002906	1487	Blm "Bloom syndrome helicase o	0.472	0.058	0.460	1e-16
UNIPROTKB|F1ND40	1142	BLM "Bloom syndrome protein ho	0.456	0.073	0.488	2.4e-16
UNIPROTKB|Q9I920	1142	BLM "Bloom syndrome protein ho	0.456	0.073	0.488	2.4e-16
UNIPROTKB|F1P3V1	1380	BLM "Bloom syndrome protein ho	0.456	0.060	0.488	3.1e-16
MGI|MGI:1328362	1416	Blm "Bloom syndrome, RecQ heli	0.445	0.057	0.5	4.1e-16
UNIPROTKB|H0YNU5	1286	BLM "Bloom syndrome protein" [	0.445	0.063	0.488	4.6e-16
UNIPROTKB|P54132	1417	BLM "Bloom syndrome protein" [	0.445	0.057	0.488	5.2e-16

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

 Score = 221 (82.9 bits), Expect = 5.8e-17, P = 5.8e-17
 Identities = 46/88 (52%), Positives = 59/88 (67%)

Query:     1 FISSFNRANLKYEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
             FISSF R NLKY+++PK    L  V+  +K  Y G+SGIVYCL+RKEC++V   L +  +
Sbjct:   435 FISSFVRDNLKYDLIPKAARSLINVVEKMKQLYPGKSGIVYCLSRKECETVQMMLTKAGL 494

Query:    60 NAISYHAGLADKLRNEVQMKWISNKVHV 87
             +A  YHAGL D LR  VQ  WI+NK  V
Sbjct:   495 SAEVYHAGLNDNLRVSVQRSWIANKFDV 522

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

GO:0051307 "meiotic chromosome separation" evidence=IMP

GO:0051276 "chromosome organization" evidence=IGI

GO:0007059 "chromosome segregation" evidence=IGI

GO:0007126 "meiosis" evidence=IGI

GO:0007067 "mitosis" evidence=IGI

GO:0007131 "reciprocal meiotic recombination" evidence=IMP

GO:0000077 "DNA damage checkpoint" evidence=IMP

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

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

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

GO:0019899 "enzyme binding" evidence=IPI

UNIPROTKB|Q9DEY9 blm "Bloom syndrome protein homolog" [Xenopus laevis (taxid:8355)]

 Score = 222 (83.2 bits), Expect = 7.0e-17, P = 7.0e-17
 Identities = 44/84 (52%), Positives = 58/84 (69%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKYE+LPKK   V  + +  IK  +   SGI+YCL+R ECD++A  L +E 
Sbjct:   805 FTMSFNRDNLKYEVLPKKPKRVALDCVEWIKKHHPNDSGIIYCLSRHECDTMADTLQKEG 864

Query:    59 INAISYHAGLADKLRNEVQMKWIS 82
             + A++YHAGLAD  R+ VQ KWI+
Sbjct:   865 LAALAYHAGLADSNRDYVQHKWIN 888

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

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

RGD|1308810 Blm "Bloom syndrome, RecQ helicase-like" [Rattus norvegicus (taxid:10116)]

 Score = 219 (82.2 bits), Expect = 9.6e-17, P = 9.6e-17
 Identities = 43/84 (51%), Positives = 59/84 (70%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY +LPKK   V  + +  I+  +   SGI+YCL+RKECD++A  L +E 
Sbjct:   844 FSMSFNRHNLKYYVLPKKPKKVALDCLEWIRKHHPYDSGIIYCLSRKECDTMADTLQREG 903

Query:    59 INAISYHAGLADKLRNEVQMKWIS 82
             + A++YHAGL+D  R+EVQ KWI+
Sbjct:   904 LAALAYHAGLSDSARDEVQHKWIN 927

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

GO:0000405 "bubble DNA binding" evidence=ISO

GO:0000723 "telomere maintenance" evidence=ISO

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

GO:0000733 "DNA strand renaturation" evidence=ISO

GO:0000800 "lateral element" evidence=ISO

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

GO:0002039 "p53 binding" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0004386 "helicase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA;ISO

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005657 "replication fork" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=ISO

GO:0006310 "DNA recombination" evidence=IEA

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

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

GO:0008150 "biological_process" evidence=ND

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

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

GO:0016363 "nuclear matrix" evidence=ISO

GO:0016605 "PML body" evidence=ISO

GO:0016887 "ATPase activity" evidence=ISO

GO:0031297 "replication fork processing" evidence=ISO

GO:0036310 "annealing helicase activity" evidence=ISO

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

GO:0045120 "pronucleus" evidence=ISO

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

GO:0045910 "negative regulation of DNA recombination" evidence=ISO

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

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

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

GO:0051098 "regulation of binding" evidence=ISO

GO:0051259 "protein oligomerization" evidence=ISO

GO:0051276 "chromosome organization" evidence=ISO

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

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

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

FB|FBgn0002906 Blm "Bloom syndrome helicase ortholog" [Drosophila melanogaster (taxid:7227)]

 Score = 221 (82.9 bits), Expect = 1.0e-16, P = 1.0e-16
 Identities = 41/89 (46%), Positives = 60/89 (67%)

Query:     1 FISSFNRANLKYEILPKKNV--LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F+SSFNR+NL+Y +LPKK V  L ++   I++K    SGI+YCL+RKECD  +  + ++ 
Sbjct:   923 FLSSFNRSNLRYRVLPKKGVSTLDDISRYIRSKPQHFSGIIYCLSRKECDETSKKMCKDG 982

Query:    59 INAISYHAGLADKLRNEVQMKWISNKVHV 87
             + A+SYHAGL D  R   Q  W++ K+ V
Sbjct:   983 VRAVSYHAGLTDTDRESRQKDWLTGKMRV 1011

GO:0006302 "double-strand break repair" evidence=IMP

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

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

GO:0004386 "helicase activity" evidence=ISS

GO:0003678 "DNA helicase activity" evidence=ISS

GO:0000731 "DNA synthesis involved in DNA repair" evidence=IMP

GO:0005524 "ATP binding" evidence=IEA

GO:0006260 "DNA replication" evidence=IEA

GO:0045003 "double-strand break repair via synthesis-dependent strand annealing" evidence=IMP

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0000732 "strand displacement" evidence=IDA

GO:0008094 "DNA-dependent ATPase activity" evidence=IDA

GO:0000403 "Y-form DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0000733 "DNA strand renaturation" evidence=IDA

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

GO:0000724 "double-strand break repair via homologous recombination" evidence=IMP

GO:0007131 "reciprocal meiotic recombination" evidence=IMP

GO:1901291 "negative regulation of double-strand break repair via single-strand annealing" evidence=IMP

UNIPROTKB|F1ND40 BLM "Bloom syndrome protein homolog" [Gallus gallus (taxid:9031)]

 Score = 216 (81.1 bits), Expect = 2.4e-16, P = 2.4e-16
 Identities = 42/86 (48%), Positives = 58/86 (67%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY++LPKK   V  + +  IK  +   SGI+YCL+R ECD+ AA L +E 
Sbjct:   583 FTMSFNRHNLKYDVLPKKPKKVAMDCLEWIKKYHPHDSGIIYCLSRHECDTTAAILQKEG 642

Query:    59 INAISYHAGLADKLRNEVQMKWISNK 84
             + A++YHAGL D  R+ VQ KW++ +
Sbjct:   643 LAALAYHAGLTDSNRDLVQKKWVNQE 668

GO:0006310 "DNA recombination" evidence=IEA

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

GO:0000405 "bubble DNA binding" evidence=IEA

GO:0000723 "telomere maintenance" evidence=IEA

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

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

GO:0000800 "lateral element" evidence=IEA

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

GO:0002039 "p53 binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005657 "replication fork" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0016363 "nuclear matrix" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

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

GO:0045120 "pronucleus" evidence=IEA

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

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

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

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

GO:0051098 "regulation of binding" evidence=IEA

GO:0051259 "protein oligomerization" evidence=IEA

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

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

UNIPROTKB|Q9I920 BLM "Bloom syndrome protein homolog" [Gallus gallus (taxid:9031)]

 Score = 216 (81.1 bits), Expect = 2.4e-16, P = 2.4e-16
 Identities = 42/86 (48%), Positives = 58/86 (67%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY++LPKK   V  + +  IK  +   SGI+YCL+R ECD+ AA L +E 
Sbjct:   583 FTMSFNRHNLKYDVLPKKPKKVAMDCLEWIKKYHPHDSGIIYCLSRHECDTTAAILQKEG 642

Query:    59 INAISYHAGLADKLRNEVQMKWISNK 84
             + A++YHAGL D  R+ VQ KW++ +
Sbjct:   643 LAALAYHAGLTDSNRDLVQKKWVNQE 668

GO:0006260 "DNA replication" 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:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|F1P3V1 BLM "Bloom syndrome protein homolog" [Gallus gallus (taxid:9031)]

 Score = 216 (81.1 bits), Expect = 3.1e-16, P = 3.1e-16
 Identities = 42/86 (48%), Positives = 58/86 (67%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY++LPKK   V  + +  IK  +   SGI+YCL+R ECD+ AA L +E 
Sbjct:   821 FTMSFNRHNLKYDVLPKKPKKVAMDCLEWIKKYHPHDSGIIYCLSRHECDTTAAILQKEG 880

Query:    59 INAISYHAGLADKLRNEVQMKWISNK 84
             + A++YHAGL D  R+ VQ KW++ +
Sbjct:   881 LAALAYHAGLTDSNRDLVQKKWVNQE 906

GO:0006310 "DNA recombination" evidence=IEA

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

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

GO:0000405 "bubble DNA binding" evidence=IEA

GO:0000723 "telomere maintenance" evidence=IEA

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

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

GO:0000800 "lateral element" evidence=IEA

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

GO:0002039 "p53 binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005657 "replication fork" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

GO:0016363 "nuclear matrix" evidence=IEA

GO:0016605 "PML body" evidence=IEA

GO:0031297 "replication fork processing" evidence=IEA

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

GO:0045120 "pronucleus" evidence=IEA

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

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

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

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

GO:0051098 "regulation of binding" evidence=IEA

GO:0051259 "protein oligomerization" evidence=IEA

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

MGI|MGI:1328362 Blm "Bloom syndrome, RecQ helicase-like" [Mus musculus (taxid:10090)]

 Score = 215 (80.7 bits), Expect = 4.1e-16, P = 4.1e-16
 Identities = 42/84 (50%), Positives = 59/84 (70%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY +LPKK   V  + +  I+  +   SGI+YCL+R+ECD++A  L +E 
Sbjct:   861 FSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQREG 920

Query:    59 INAISYHAGLADKLRNEVQMKWIS 82
             + A++YHAGL+D  R+EVQ KWI+
Sbjct:   921 LAALAYHAGLSDSARDEVQHKWIN 944

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000405 "bubble DNA binding" evidence=ISO

GO:0000723 "telomere maintenance" evidence=IGI

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

GO:0000733 "DNA strand renaturation" evidence=ISO

GO:0000800 "lateral element" evidence=ISO

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

GO:0002039 "p53 binding" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0004386 "helicase activity" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=ISO

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005657 "replication fork" evidence=IDA

GO:0005730 "nucleolus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=ISO;IDA

GO:0006260 "DNA replication" evidence=IEA

GO:0006281 "DNA repair" evidence=IDA

GO:0006310 "DNA recombination" evidence=IEA

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

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

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

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

GO:0016363 "nuclear matrix" evidence=ISO

GO:0016605 "PML body" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

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

GO:0016887 "ATPase activity" evidence=ISO

GO:0031297 "replication fork processing" evidence=ISO

GO:0036310 "annealing helicase activity" evidence=ISO

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

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0045120 "pronucleus" evidence=IDA

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

GO:0045910 "negative regulation of DNA recombination" evidence=ISO

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

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

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

GO:0051098 "regulation of binding" evidence=IDA

GO:0051259 "protein oligomerization" evidence=ISO

GO:0051276 "chromosome organization" evidence=IMP

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

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

UNIPROTKB|H0YNU5 BLM "Bloom syndrome protein" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 4.6e-16, P = 4.6e-16
 Identities = 41/84 (48%), Positives = 59/84 (70%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY +LPKK   V  + +  I+  +   SGI+YCL+R+ECD++A  L ++ 
Sbjct:   853 FSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQRDG 912

Query:    59 INAISYHAGLADKLRNEVQMKWIS 82
             + A++YHAGL+D  R+EVQ KWI+
Sbjct:   913 LAALAYHAGLSDSARDEVQQKWIN 936

GO:0003677 "DNA 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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|P54132 BLM "Bloom syndrome protein" [Homo sapiens (taxid:9606)]

 Score = 214 (80.4 bits), Expect = 5.2e-16, P = 5.2e-16
 Identities = 41/84 (48%), Positives = 59/84 (70%)

Query:     1 FISSFNRANLKYEILPKK--NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER 58
             F  SFNR NLKY +LPKK   V  + +  I+  +   SGI+YCL+R+ECD++A  L ++ 
Sbjct:   853 FSMSFNRHNLKYYVLPKKPKKVAFDCLEWIRKHHPYDSGIIYCLSRRECDTMADTLQRDG 912

Query:    59 INAISYHAGLADKLRNEVQMKWIS 82
             + A++YHAGL+D  R+EVQ KWI+
Sbjct:   913 LAALAYHAGLSDSARDEVQQKWIN 936

GO:0000723 "telomere maintenance" evidence=IEA

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

GO:0005657 "replication fork" evidence=IEA

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

GO:0045120 "pronucleus" evidence=IEA

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

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

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

GO:0051098 "regulation of binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0031297 "replication fork processing" evidence=IDA

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

GO:0005730 "nucleolus" evidence=IDA

GO:0016605 "PML body" evidence=IDA

GO:0048478 "replication fork protection" evidence=NAS

GO:0000800 "lateral element" evidence=IDA

GO:0006310 "DNA recombination" evidence=NAS

GO:0051259 "protein oligomerization" evidence=IDA

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

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

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

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

GO:0000405 "bubble DNA binding" evidence=IDA

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

GO:0002039 "p53 binding" evidence=IPI

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

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

GO:0000085 "G2 phase of mitotic cell cycle" evidence=NAS

GO:0000724 "double-strand break repair via homologous recombination" evidence=NAS

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

GO:0016363 "nuclear matrix" evidence=IDA

GO:0031572 "G2 DNA damage checkpoint" evidence=NAS

GO:0004386 "helicase activity" evidence=IDA

GO:0045910 "negative regulation of DNA recombination" evidence=IMP

GO:0006281 "DNA repair" evidence=NAS

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IMP;IDA

GO:0036310 "annealing helicase activity" evidence=IDA

GO:0005524 "ATP binding" evidence=IDA

GO:0016887 "ATPase activity" evidence=IDA

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

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

GO:0000733 "DNA strand renaturation" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O18017	BLM_CAEEL	3, ., 6, ., 4, ., 1, 2	0.5227	0.4728	0.0880	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	184
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	6e-25
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-20
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	4e-20
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	4e-12
PLN03137	1195	PLN03137, PLN03137, ATP-dependent DNA helicase; Q4	4e-11
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	7e-07
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	6e-04
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	0.004

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

 Score = 99.8 bits (249), Expect = 6e-25
 Identities = 33/88 (37%), Positives = 57/88 (64%), Gaps = 1/88 (1%)

Query: 1   FISSFNRANLKYEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
           F +SF+R NL YE+  K   +L++++  I+ ++ G+SGI+YC +RK+ + V A+L    I
Sbjct: 192 FCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGI 251

Query: 60  NAISYHAGLADKLRNEVQMKWISNKVHV 87
            A +YHAGL    R++V  K+  +++ V
Sbjct: 252 AAGAYHAGLEISARDDVHHKFQRDEIQV 279

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

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

 Score = 87.1 bits (216), Expect = 2e-20
 Identities = 35/87 (40%), Positives = 60/87 (68%), Gaps = 1/87 (1%)

Query: 1   FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN 60
           FI+SF+R NL++ ++ K N  K ++  +K K+ GQSGI+Y  +RK+ + +A  L  + I+
Sbjct: 192 FITSFDRPNLRFSVVKKNNKQKFLLDYLK-KHRGQSGIIYASSRKKVEELAERLESQGIS 250

Query: 61  AISYHAGLADKLRNEVQMKWISNKVHV 87
           A++YHAGL++K+R E Q  ++ + V V
Sbjct: 251 ALAYHAGLSNKVRAENQEDFLYDDVKV 277

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

 Score = 86.6 bits (215), Expect = 4e-20
 Identities = 30/88 (34%), Positives = 53/88 (60%), Gaps = 1/88 (1%)

Query: 1   FISSFNRANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERI 59
           F  SF+R NL  +++ K     ++  L        +SGI+YCLTRK+ + +A  L +  I
Sbjct: 196 FRGSFDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGI 255

Query: 60  NAISYHAGLADKLRNEVQMKWISNKVHV 87
           +A +YHAGL+++ R  VQ  ++++++ V
Sbjct: 256 SAGAYHAGLSNEERERVQQAFLNDEIKV 283

Length = 590

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

 Score = 63.6 bits (155), Expect = 4e-12
 Identities = 29/76 (38%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 2   ISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINA 61
           ISSF+R N++Y ++ K   L +++  ++ +  G+SGI+YC +R + +  AA L    I+A
Sbjct: 205 ISSFDRPNIRYTLVEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSRGISA 263

Query: 62  ISYHAGLADKLRNEVQ 77
            +YHAGL + +R +VQ
Sbjct: 264 AAYHAGLDNDVRADVQ 279

Length = 607

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

 Score = 60.7 bits (147), Expect = 4e-11
 Identities = 31/88 (35%), Positives = 50/88 (56%), Gaps = 1/88 (1%)

Query: 1   FISSFNRANLKYEILPK-KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
           F  SFNR NL Y ++PK K  L+++   IK  +  + GI+YCL+R +C+ VA  L +   
Sbjct: 646 FRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGH 705

Query: 60  NAISYHAGLADKLRNEVQMKWISNKVHV 87
            A  YH  +    R  VQ +W  +++++
Sbjct: 706 KAAFYHGSMDPAQRAFVQKQWSKDEINI 733

Length = 1195

>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 = 46.1 bits (110), Expect = 7e-07
 Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 9  NLKYEILPKKNV-LKEVISLIK-AKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHA 66
           +K  +LP ++  L+ ++ L+K     G   +++C ++K  D +A  L +  I   + H 
Sbjct: 1  PIKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60

Query: 67 GLADKLRNEVQMKWISNKVHV 87
            + + R EV   +   ++ V
Sbjct: 61 DGSQEEREEVLKDFREGEIVV 81

Length = 131

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

 Score = 39.4 bits (93), Expect = 6e-04
 Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 12  YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADK 71
           YE+ P +  L  +  L+   +  +S +V+C T+KEC  VA AL  +  +A++ H  L  +
Sbjct: 222 YEVSPDER-LPALQRLLL-HHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQR 279

Query: 72  LRNEV 76
            R++V
Sbjct: 280 DRDQV 284

Length = 460

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

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 29  KAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV 87
              Y GQ+ IV+  +R+ C  +A AL  + + A  YHAGL  K R  V+  + + ++  
Sbjct: 436 SKGYRGQT-IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAA 493

Length = 830

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	184
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.97
KOG0351|consensus	941		99.94
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.91
KOG0352|consensus	641		99.9
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.89
KOG0331|consensus	519		99.89
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.88
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.88
KOG0353|consensus	695		99.88
KOG0328|consensus	400		99.87
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.85
KOG0333|consensus	673		99.85
KOG0330|consensus	476		99.83
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.83
KOG0331|consensus	519		99.82
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.82
PTZ00110	545	helicase; Provisional	99.8
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.8
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.8
KOG0332|consensus	477		99.79
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.79
KOG0341|consensus	610		99.78
KOG0333|consensus	673		99.78
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.78
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.77
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.77
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.77
KOG0340|consensus	442		99.77
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.77
KOG0326|consensus	459		99.77
KOG0335|consensus	482		99.75
KOG0330|consensus	476		99.75
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.75
KOG0342|consensus	543		99.75
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.75
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.74
KOG0336|consensus	629		99.73
KOG0353|consensus	695		99.72
KOG0341|consensus	610		99.71
KOG0338|consensus	691		99.7
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.7
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.69
KOG0347|consensus	731		99.69
PTZ00424	401	helicase 45; Provisional	99.68
KOG0340|consensus	442		99.68
KOG0345|consensus	567		99.68
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.68
KOG0343|consensus	758		99.67
KOG0328|consensus	400		99.67
KOG0327|consensus	397		99.66
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.66
PTZ00110	545	helicase; Provisional	99.66
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.63
KOG0334|consensus	997		99.63
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.63
PRK13767	876	ATP-dependent helicase; Provisional	99.63
KOG0344|consensus	593		99.62
KOG0336|consensus	629		99.62
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.58
KOG0335|consensus	482		99.58
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.58
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.57
PRK04914	956	ATP-dependent helicase HepA; Validated	99.57
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.56
KOG0338|consensus	691		99.55
PRK14701	1638	reverse gyrase; Provisional	99.55
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.54
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.54
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.53
KOG4284|consensus	980		99.53
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.53
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.52
KOG0339|consensus	731		99.52
KOG0339|consensus	731		99.52
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.5
PRK05298	652	excinuclease ABC subunit B; Provisional	99.49
KOG0350|consensus	620		99.49
KOG0349|consensus	725		99.49
PRK09401	1176	reverse gyrase; Reviewed	99.47
KOG0342|consensus	543		99.47
PRK10689	1147	transcription-repair coupling factor; Provisional	99.46
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.46
KOG0326|consensus	459		99.45
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.45
PTZ00424	401	helicase 45; Provisional	99.44
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.43
KOG0348|consensus	708		99.42
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.42
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.42
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.42
KOG0346|consensus	569		99.41
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.41
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.4
PRK10689	1147	transcription-repair coupling factor; Provisional	99.39
PRK13767	876	ATP-dependent helicase; Provisional	99.39
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.39
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.39
PRK02362	737	ski2-like helicase; Provisional	99.38
PHA02653	675	RNA helicase NPH-II; Provisional	99.37
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.36
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.35
PRK13766	773	Hef nuclease; Provisional	99.35
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.34
KOG0334|consensus	997		99.32
KOG0327|consensus	397		99.32
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.31
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.3
PHA02558	501	uvsW UvsW helicase; Provisional	99.29
KOG0345|consensus	567		99.28
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.28
PRK00254	720	ski2-like helicase; Provisional	99.27
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.26
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.26
KOG0337|consensus	529		99.26
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.25
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.25
PRK05298	652	excinuclease ABC subunit B; Provisional	99.24
KOG4284|consensus	980		99.24
PRK04914	956	ATP-dependent helicase HepA; Validated	99.23
PHA02653	675	RNA helicase NPH-II; Provisional	99.2
KOG0344|consensus	593		99.2
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.18
KOG0354|consensus	746		99.17
PRK01172	674	ski2-like helicase; Provisional	99.16
PRK02362	737	ski2-like helicase; Provisional	99.16
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.15
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.13
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.13
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.09
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.09
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.08
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.08
KOG0352|consensus	641		99.07
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.06
COG1202	830	Superfamily II helicase, archaea-specific [General	99.02
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.01
KOG0346|consensus	569		99.01
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.0
PHA02558	501	uvsW UvsW helicase; Provisional	98.97
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.97
KOG0343|consensus	758		98.94
KOG0349|consensus	725		98.92
PRK00254	720	ski2-like helicase; Provisional	98.92
PRK01172	674	ski2-like helicase; Provisional	98.9
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.88
KOG0350|consensus	620		98.88
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.87
PRK09401	1176	reverse gyrase; Reviewed	98.85
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.85
PRK13766	773	Hef nuclease; Provisional	98.82
smart00490	82	HELICc helicase superfamily c-terminal domain.	98.82
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.81
PRK09694	878	helicase Cas3; Provisional	98.8
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.8
KOG0332|consensus	477		98.77
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.77
KOG0351|consensus	941		98.77
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.75
COG1201	814	Lhr Lhr-like helicases [General function predictio	98.73
COG1202	830	Superfamily II helicase, archaea-specific [General	98.72
PRK05580	679	primosome assembly protein PriA; Validated	98.66
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.65
KOG4150|consensus	1034		98.62
KOG0348|consensus	708		98.62
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.62
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.62
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.6
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.6
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.6
KOG0329|consensus	387		98.59
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.59
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.59
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.57
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.54
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.5
KOG0337|consensus	529		98.47
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.47
COG1204	766	Superfamily II helicase [General function predicti	98.47
COG1205	851	Distinct helicase family with a unique C-terminal	98.44
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.36
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.23
COG1205	851	Distinct helicase family with a unique C-terminal	98.23
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.15
KOG0354|consensus	746		98.13
PRK05580	679	primosome assembly protein PriA; Validated	98.07
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.06
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.06
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.06
KOG0347|consensus	731		98.06
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.05
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	97.98
PRK09694	878	helicase Cas3; Provisional	97.96
KOG0950|consensus	1008		97.94
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.92
KOG0948|consensus	1041		97.8
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.57
KOG0329|consensus	387		97.57
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.53
KOG0947|consensus	1248		97.52
KOG0951|consensus	1674		97.52
PRK14701	1638	reverse gyrase; Provisional	97.41
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	97.25
KOG0952|consensus	1230		97.17
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.15
PRK12904	830	preprotein translocase subunit SecA; Reviewed	97.04
PRK12326	764	preprotein translocase subunit SecA; Reviewed	96.98
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	96.97
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	96.87
PRK13107	908	preprotein translocase subunit SecA; Reviewed	96.8
PRK14873	665	primosome assembly protein PriA; Provisional	96.75
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.72
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	96.66
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	96.62
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.44
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	96.34
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	96.26
KOG0922|consensus	674		96.23
KOG0953|consensus	700		95.97
COG1204	766	Superfamily II helicase [General function predicti	95.86
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	95.82
CHL00122	870	secA preprotein translocase subunit SecA; Validate	95.8
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	95.76
KOG1000|consensus	689		95.73
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	95.68
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	95.57
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	95.52
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	95.48
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	95.31
KOG0391|consensus	1958		95.26
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	95.2
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	95.04
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	95.02
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	94.65
KOG0385|consensus	971		94.4
KOG1002|consensus	791		93.72
KOG0952|consensus	1230		93.69
KOG0923|consensus	902		93.66
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	93.17
KOG0384|consensus	1373		93.06
KOG0390|consensus	776		93.05
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	93.0
KOG0924|consensus	1042		92.93
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	92.76
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	92.3
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	92.0
KOG0950|consensus	1008		92.0
COG1198	730	PriA Primosomal protein N' (replication factor Y)	91.98
KOG4150|consensus	1034		91.84
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	91.78
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	91.69
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	91.6
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	91.37
KOG0920|consensus	924		90.55
KOG0953|consensus	700		90.05
KOG0949|consensus	1330		89.42
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	89.01
KOG0924|consensus	1042		88.4
KOG0392|consensus	1549		88.18
KOG1123|consensus	776		87.64
KOG0387|consensus	923		87.58
KOG0388|consensus	1185		87.34
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	87.21
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	86.89
KOG0389|consensus	941		86.87
KOG2340|consensus	698		86.74
KOG0949|consensus	1330		86.51
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	86.35
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	86.33
KOG0384|consensus	1373		86.05
cd06281	269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	85.97
KOG0922|consensus	674		85.85
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	85.71
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	85.62
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	84.5
cd01532	92	4RHOD_Repeat_1 Member of the Rhodanese Homology Do	83.87
KOG0389|consensus	941		83.54
cd01535	145	4RHOD_Repeat_4 Member of the Rhodanese Homology Do	83.39
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	83.24
cd01521	110	RHOD_PspE2 Member of the Rhodanese Homology Domain	83.19
COG4096	875	HsdR Type I site-specific restriction-modification	83.08
cd01528	101	RHOD_2 Member of the Rhodanese Homology Domain sup	83.06
cd06267	264	PBP1_LacI_sugar_binding_like Ligand binding domain	83.05
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	83.02
cd06282	266	PBP1_GntR_like_2 Ligand-binding domain of putative	82.91
PRK09189	240	uroporphyrinogen-III synthase; Validated	82.9
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	82.2
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	81.98
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	81.95
PF01751	100	Toprim: Toprim domain; InterPro: IPR006171 This is	81.49
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	81.4
COG1856	275	Uncharacterized homolog of biotin synthetase [Func	81.3
cd01519	106	RHOD_HSP67B2 Member of the Rhodanese Homology Doma	80.97
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	80.83
KOG0923|consensus	902		80.61
cd06309	273	PBP1_YtfQ_like Periplasmic binding domain of ABC-t	80.29
PRK12326	764	preprotein translocase subunit SecA; Reviewed	80.24

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

Probab=99.97  E-value=4e-31  Score=227.15  Aligned_cols=132  Identities=28%  Similarity=0.413  Sum_probs=114.5

Q ss_pred             CCCCCCCCCeEEEEEEccChHHHHHHHHHh--hcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHH
Q psy437            1 FISSFNRANLKYEILPKKNVLKEVISLIKA--KYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQM   78 (184)
Q Consensus         1 ~~~s~~R~Nl~y~v~~~~~k~~~L~~~l~~--~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~   78 (184)
                      |++||+||||+|.+.++.+-...+. +|.+  .....++||||.||+.+|.++++|+..|+++..|||||+.++|..+++
T Consensus       196 ~~~sfdRpNi~~~v~~~~~~~~q~~-fi~~~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~  274 (590)
T COG0514         196 FRGSFDRPNLALKVVEKGEPSDQLA-FLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQ  274 (590)
T ss_pred             EEecCCCchhhhhhhhcccHHHHHH-HHHhhccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHH
Confidence            5789999999999999764333333 4542  336778999999999999999999999999999999999999999999


Q ss_pred             HHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCc
Q psy437           79 KWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIK  158 (184)
Q Consensus        79 ~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~  158 (184)
                      +|.+++.+|||||.+|        ||   ||                                ||||||||+|+++|.+.
T Consensus       275 ~f~~~~~~iiVAT~AF--------GM---GI--------------------------------dKpdVRfViH~~lP~s~  311 (590)
T COG0514         275 AFLNDEIKVMVATNAF--------GM---GI--------------------------------DKPDVRFVIHYDLPGSI  311 (590)
T ss_pred             HHhcCCCcEEEEeccc--------cC---cc--------------------------------CCCCceEEEEecCCCCH
Confidence            9999999999999955        44   33                                89999999999999999


Q ss_pred             cccccccccccCCccccccc
Q psy437          159 PDYLPPILDLRLGREDIREG  178 (184)
Q Consensus       159 e~y~~~i~~~~~~r~~~~~~  178 (184)
                      |+|+||+  +|+|||+++.-
T Consensus       312 EsYyQE~--GRAGRDG~~a~  329 (590)
T COG0514         312 ESYYQET--GRAGRDGLPAE  329 (590)
T ss_pred             HHHHHHH--hhccCCCCcce
Confidence            9999999  59999987754

>KOG0351|consensus

Probab=99.94  E-value=7.3e-27  Score=210.44  Aligned_cols=132  Identities=40%  Similarity=0.563  Sum_probs=115.9

Q ss_pred             CCCCCCCCCeEEEEEEccC--hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHH
Q psy437            1 FISSFNRANLKYEILPKKN--VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQM   78 (184)
Q Consensus         1 ~~~s~~R~Nl~y~v~~~~~--k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~   78 (184)
                      |..||+||||+|+|.++.+  ..-.+...++..++..++||||.+|+.|+.++..|+..|+++++||+||+..+|..++.
T Consensus       450 ~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~  529 (941)
T KOG0351|consen  450 FKSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQK  529 (941)
T ss_pred             ecccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHH
Confidence            5689999999999999873  44555666666678889999999999999999999999999999999999999999999


Q ss_pred             HHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCc
Q psy437           79 KWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIK  158 (184)
Q Consensus        79 ~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~  158 (184)
                      +|..++.+|+|||-+||        |   ||                                |+||||+||||++|++.
T Consensus       530 ~w~~~~~~VivATVAFG--------M---GI--------------------------------dK~DVR~ViH~~lPks~  566 (941)
T KOG0351|consen  530 AWMSDKIRVIVATVAFG--------M---GI--------------------------------DKPDVRFVIHYSLPKSF  566 (941)
T ss_pred             HHhcCCCeEEEEEeecc--------C---CC--------------------------------CCCceeEEEECCCchhH
Confidence            99999999999999554        4   32                                78999999999999999


Q ss_pred             cccccccccccCCcccccc
Q psy437          159 PDYLPPILDLRLGREDIRE  177 (184)
Q Consensus       159 e~y~~~i~~~~~~r~~~~~  177 (184)
                      |.|||++  +|+||++++.
T Consensus       567 E~YYQE~--GRAGRDG~~s  583 (941)
T KOG0351|consen  567 EGYYQEA--GRAGRDGLPS  583 (941)
T ss_pred             HHHHHhc--cccCcCCCcc
Confidence            9999998  5999987664

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

Probab=99.91  E-value=2.6e-24  Score=195.14  Aligned_cols=127  Identities=28%  Similarity=0.473  Sum_probs=113.8

Q ss_pred             CCCCCCCCCeEEEEEEccCh-HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHH
Q psy437            1 FISSFNRANLKYEILPKKNV-LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMK   79 (184)
Q Consensus         1 ~~~s~~R~Nl~y~v~~~~~k-~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~   79 (184)
                      |..||+||||+|.|.++..+ ...|..++.......++||||+|++.|+.++..|...|+++..|||||++++|..++++
T Consensus       646 fr~Sf~RpNL~y~Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~  725 (1195)
T PLN03137        646 FRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQ  725 (1195)
T ss_pred             eecccCccceEEEEeccchhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHH
Confidence            46799999999999987643 56777777654446789999999999999999999999999999999999999999999


Q ss_pred             HhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           80 WISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        80 f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |.+|+++|||||+      ..++|+|+++|+ +|||+++|.+.+.|+||.+|.|.
T Consensus       726 F~~Gei~VLVATd------AFGMGIDkPDVR-~VIHydlPkSiEsYyQriGRAGR  773 (1195)
T PLN03137        726 WSKDEINIICATV------AFGMGINKPDVR-FVIHHSLPKSIEGYHQECGRAGR  773 (1195)
T ss_pred             HhcCCCcEEEEec------hhhcCCCccCCc-EEEEcCCCCCHHHHHhhhcccCC
Confidence            9999999999999      446799999999 99999999999999999977664

>KOG0352|consensus

Probab=99.90  E-value=1.3e-24  Score=178.48  Aligned_cols=131  Identities=34%  Similarity=0.421  Sum_probs=106.9

Q ss_pred             CCCCCCCCCeEEEEEEcc---ChHHHHHHHHHhhc------------CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEec
Q psy437            1 FISSFNRANLKYEILPKK---NVLKEVISLIKAKY------------SGQSGIVYCLTRKECDSVAAALAQERINAISYH   65 (184)
Q Consensus         1 ~~~s~~R~Nl~y~v~~~~---~k~~~L~~~l~~~~------------~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~h   65 (184)
                      |.++.+|.||+|.+..++   +.+..|.++-....            ..+.+||||.||..||++|-.|...|+++.+||
T Consensus       207 FkTP~FR~NLFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYH  286 (641)
T KOG0352|consen  207 FKTPTFRDNLFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYH  286 (641)
T ss_pred             ccCcchhhhhhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHh
Confidence            788999999999998765   45666666543221            235689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCC
Q psy437           66 AGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQW  145 (184)
Q Consensus        66 g~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~  145 (184)
                      +||...+|.+++++|.+++++||+||.++++      |.                                     |+|+
T Consensus       287 AGLK~~ERTeVQe~WM~~~~PvI~AT~SFGM------GV-------------------------------------DKp~  323 (641)
T KOG0352|consen  287 AGLKKKERTEVQEKWMNNEIPVIAATVSFGM------GV-------------------------------------DKPD  323 (641)
T ss_pred             cccccchhHHHHHHHhcCCCCEEEEEecccc------cc-------------------------------------CCcc
Confidence            9999999999999999999999999997755      22                                     6777


Q ss_pred             ccEEEecCCCCCccccccccccccCCccccc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDLRLGREDIR  176 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~~~~r~~~~  176 (184)
                      ||||+|+++|++.-.|||+-  +|+||++++
T Consensus       324 VRFViHW~~~qn~AgYYQES--GRAGRDGk~  352 (641)
T KOG0352|consen  324 VRFVIHWSPSQNLAGYYQES--GRAGRDGKR  352 (641)
T ss_pred             eeEEEecCchhhhHHHHHhc--cccccCCCc
Confidence            77777777777777777775  577777554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.89  E-value=1e-22  Score=174.63  Aligned_cols=126  Identities=29%  Similarity=0.521  Sum_probs=114.5

Q ss_pred             CCCCCCCCeEEEEEEcc-ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHH
Q psy437            2 ISSFNRANLKYEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKW   80 (184)
Q Consensus         2 ~~s~~R~Nl~y~v~~~~-~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f   80 (184)
                      ..|++|||++|.+.+.. .....+..++.+...+.++||||+|++.|+.++..|...|+++..|||+|++++|..+++.|
T Consensus       193 ~~s~~r~nl~~~v~~~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F  272 (470)
T TIGR00614       193 CTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKF  272 (470)
T ss_pred             eCCCCCCCcEEEEEeCCccHHHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHH
Confidence            46899999999998876 56778888886544666789999999999999999999999999999999999999999999


Q ss_pred             hccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           81 ISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        81 ~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++|+++|||||+      .+++|+|.++++ .|||+++|.+.+.|+|+.+|.|.
T Consensus       273 ~~g~~~vLVaT~------~~~~GID~p~V~-~VI~~~~P~s~~~y~Qr~GRaGR  319 (470)
T TIGR00614       273 QRDEIQVVVATV------AFGMGINKPDVR-FVIHYSLPKSMESYYQESGRAGR  319 (470)
T ss_pred             HcCCCcEEEEec------hhhccCCcccce-EEEEeCCCCCHHHHHhhhcCcCC
Confidence            999999999999      678899999999 99999999999999999977654

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

>KOG0331|consensus

Probab=99.89  E-value=3.3e-23  Score=175.81  Aligned_cols=109  Identities=18%  Similarity=0.237  Sum_probs=100.1

Q ss_pred             ChHHHHHHHHHhhc--CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeeccc
Q psy437           19 NVLKEVISLIKAKY--SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKE   96 (184)
Q Consensus        19 ~k~~~L~~~l~~~~--~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~   96 (184)
                      .|.+.|..+|.+..  ..+++||||+|++.|+.++..|+..++++..+||+++|.+|..+++.|++|..+|||||+    
T Consensus       324 ~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd----  399 (519)
T KOG0331|consen  324 AKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD----  399 (519)
T ss_pred             HHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEcc----
Confidence            46666777776542  566899999999999999999999999999999999999999999999999999999999    


Q ss_pred             HHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           97 CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        97 ~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                        ++|||||.++|+ +||||++|++.++|+||..++|+
T Consensus       400 --VAaRGLDi~dV~-lVInydfP~~vEdYVHRiGRTGR  434 (519)
T KOG0331|consen  400 --VAARGLDVPDVD-LVINYDFPNNVEDYVHRIGRTGR  434 (519)
T ss_pred             --cccccCCCcccc-EEEeCCCCCCHHHHHhhcCcccc
Confidence              999999999999 99999999999999999987765

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.88  E-value=2.5e-22  Score=176.94  Aligned_cols=125  Identities=26%  Similarity=0.501  Sum_probs=115.1

Q ss_pred             CCCCCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHh
Q psy437            2 ISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus         2 ~~s~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~   81 (184)
                      ..+++|||+.|.+.....+...|..++... .+.++||||+|++.|+.++..|...|+++..|||+|++++|..+++.|.
T Consensus       205 ~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~-~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~  283 (607)
T PRK11057        205 ISSFDRPNIRYTLVEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQ  283 (607)
T ss_pred             ECCCCCCcceeeeeeccchHHHHHHHHHhc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHH
Confidence            468999999999988777788888888653 6789999999999999999999999999999999999999999999999


Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +|+.+|||||+      .+++|+|+++++ +|||+++|.+.++|+|+..|.|.
T Consensus       284 ~g~~~VLVaT~------a~~~GIDip~V~-~VI~~d~P~s~~~y~Qr~GRaGR  329 (607)
T PRK11057        284 RDDLQIVVATV------AFGMGINKPNVR-FVVHFDIPRNIESYYQETGRAGR  329 (607)
T ss_pred             CCCCCEEEEec------hhhccCCCCCcC-EEEEeCCCCCHHHHHHHhhhccC
Confidence            99999999999      668899999999 99999999999999999977664

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.88  E-value=3.4e-22  Score=175.79  Aligned_cols=126  Identities=30%  Similarity=0.508  Sum_probs=116.0

Q ss_pred             CCCCCCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHH
Q psy437            1 FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKW   80 (184)
Q Consensus         1 ~~~s~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f   80 (184)
                      |..+++|||+.|.+.....+...+.+++... .+.++||||+|++.|+.+++.|...|+++..|||+|++++|..+++.|
T Consensus       192 ~~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~-~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F  270 (591)
T TIGR01389       192 FITSFDRPNLRFSVVKKNNKQKFLLDYLKKH-RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDF  270 (591)
T ss_pred             EecCCCCCCcEEEEEeCCCHHHHHHHHHHhc-CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHH
Confidence            3578999999999998888888999988764 567899999999999999999999999999999999999999999999


Q ss_pred             hccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           81 ISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        81 ~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+|+.+|||||+      .++.|+|+++++ .|+|+++|.+.+.|+|+..+.|.
T Consensus       271 ~~g~~~vlVaT~------a~~~GID~p~v~-~VI~~~~p~s~~~y~Q~~GRaGR  317 (591)
T TIGR01389       271 LYDDVKVMVATN------AFGMGIDKPNVR-FVIHYDMPGNLESYYQEAGRAGR  317 (591)
T ss_pred             HcCCCcEEEEec------hhhccCcCCCCC-EEEEcCCCCCHHHHhhhhccccC
Confidence            999999999999      557799999999 99999999999999999977653

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.

>KOG0353|consensus

Probab=99.88  E-value=1.6e-22  Score=164.60  Aligned_cols=122  Identities=34%  Similarity=0.604  Sum_probs=112.8

Q ss_pred             CCCCCCCCCeEEEEEEccC----hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHH
Q psy437            1 FISSFNRANLKYEILPKKN----VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEV   76 (184)
Q Consensus         1 ~~~s~~R~Nl~y~v~~~~~----k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~   76 (184)
                      |+++|+||||+|.|..+..    -.+.+..+|+..+.+.++||||-++++||.++..|+..|+.+..||+.|.+++|..+
T Consensus       280 f~a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~  359 (695)
T KOG0353|consen  280 FRAGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGA  359 (695)
T ss_pred             eecccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccc
Confidence            7899999999999997653    567788888777788999999999999999999999999999999999999999999


Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHH
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMK  129 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~  129 (184)
                      .+.|..|+++|+|||-++++      |+|+|+++ +|||..||++.++|+|.+
T Consensus       360 hq~w~a~eiqvivatvafgm------gidkpdvr-fvihhsl~ksienyyqas  405 (695)
T KOG0353|consen  360 HQGWIAGEIQVIVATVAFGM------GIDKPDVR-FVIHHSLPKSIENYYQAS  405 (695)
T ss_pred             cccccccceEEEEEEeeecc------cCCCCCee-EEEecccchhHHHHHHHH
Confidence            99999999999999997766      77999999 999999999999999965

>KOG0328|consensus

Probab=99.87  E-value=3.5e-22  Score=156.82  Aligned_cols=117  Identities=14%  Similarity=0.199  Sum_probs=106.3

Q ss_pred             eEEEEEEccC-hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEE
Q psy437           10 LKYEILPKKN-VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVG   88 (184)
Q Consensus        10 l~y~v~~~~~-k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vl   88 (184)
                      .+|.....++ |++.|+++.... .-.+++|||+|++.++++.+.|++.++.+...||+|++++|++++.+|++|+.+||
T Consensus       242 qf~v~ve~EewKfdtLcdLYd~L-tItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvL  320 (400)
T KOG0328|consen  242 QFFVAVEKEEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVL  320 (400)
T ss_pred             hheeeechhhhhHhHHHHHhhhh-ehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEE
Confidence            3555555554 999999988553 67899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           89 HWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        89 VaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++|+      .+|+|||.+.++ +|+|||+|...+.|+||..++|.
T Consensus       321 itTD------VwaRGiDv~qVs-lviNYDLP~nre~YIHRIGRSGR  359 (400)
T KOG0328|consen  321 ITTD------VWARGIDVQQVS-LVINYDLPNNRELYIHRIGRSGR  359 (400)
T ss_pred             EEec------hhhccCCcceeE-EEEecCCCccHHHHhhhhccccc
Confidence            9999      999999999999 99999999999999999988875

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

Probab=99.85  E-value=2.7e-21  Score=167.31  Aligned_cols=107  Identities=17%  Similarity=0.173  Sum_probs=99.3

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .|+..|..++... ...++||||+|+..++.++..|...|+++..+||+|+|++|.++++.|++|+.+|||||+      
T Consensus       259 ~k~~~L~~ll~~~-~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTD------  331 (513)
T COG0513         259 EKLELLLKLLKDE-DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATD------  331 (513)
T ss_pred             HHHHHHHHHHhcC-CCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEec------
Confidence            3999999988754 556799999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      .+|||||+++++ +|+|||+|.+.+.|+||.++.|
T Consensus       332 vaaRGiDi~~v~-~VinyD~p~~~e~yvHRiGRTg  365 (513)
T COG0513         332 VAARGLDIPDVS-HVINYDLPLDPEDYVHRIGRTG  365 (513)
T ss_pred             hhhccCCccccc-eeEEccCCCCHHHheeccCccc
Confidence            899999999999 9999999999999999986654

>KOG0333|consensus

Probab=99.85  E-value=4.4e-21  Score=160.84  Aligned_cols=110  Identities=12%  Similarity=0.176  Sum_probs=102.1

Q ss_pred             EccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           16 PKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        16 ~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ..+.|...|..+|.+. ..+++|||+|+++.|+.+|+.|.+.|+++..||||.++++|+.+++.|++|...|||||+   
T Consensus       500 ~ed~k~kkL~eil~~~-~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD---  575 (673)
T KOG0333|consen  500 SEDEKRKKLIEILESN-FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATD---  575 (673)
T ss_pred             cchHHHHHHHHHHHhC-CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec---
Confidence            3345889999999764 568999999999999999999999999999999999999999999999999999999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                         .+++|+|+++|+ +|+||+|+++.++|+||..+.|
T Consensus       576 ---vAgRGIDIpnVS-lVinydmaksieDYtHRIGRTg  609 (673)
T KOG0333|consen  576 ---VAGRGIDIPNVS-LVINYDMAKSIEDYTHRIGRTG  609 (673)
T ss_pred             ---ccccCCCCCccc-eeeecchhhhHHHHHHHhcccc
Confidence               889999999999 9999999999999999997654

>KOG0330|consensus

Probab=99.83  E-value=1.5e-20  Score=152.83  Aligned_cols=115  Identities=17%  Similarity=0.198  Sum_probs=106.2

Q ss_pred             EEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           11 KYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        11 ~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      +|.+.+...|...|+.+|++. .+.+.||||+|+.++..++-.|+..|+.+..+||.|++..|...+++|++|...||||
T Consensus       278 ~ylfv~~k~K~~yLV~ll~e~-~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~  356 (476)
T KOG0330|consen  278 TYLFVPGKDKDTYLVYLLNEL-AGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVC  356 (476)
T ss_pred             heEeccccccchhHHHHHHhh-cCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEe
Confidence            466666667888999988764 7789999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      |+      ..+||||+++++ +|+|||+|....+|+||..+.+
T Consensus       357 TD------VaSRGLDip~Vd-~VVNyDiP~~skDYIHRvGRta  392 (476)
T KOG0330|consen  357 TD------VASRGLDIPHVD-VVVNYDIPTHSKDYIHRVGRTA  392 (476)
T ss_pred             cc------hhcccCCCCCce-EEEecCCCCcHHHHHHHccccc
Confidence            99      899999999999 9999999999999999996543

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

Probab=99.83  E-value=1.9e-19  Score=155.81  Aligned_cols=134  Identities=17%  Similarity=0.168  Sum_probs=118.6

Q ss_pred             EEEEeccHHHHHHHHHHHHh----C-CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec-----------------
Q psy437           37 GIVYCLTRKECDSVAAALAQ----E-RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS-----------------   94 (184)
Q Consensus        37 ~IIf~~tr~~~e~la~~L~~----~-gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr-----------------   94 (184)
                      +||.+|||+.|.++++.+..    . ++.+..+.||++...+...+   ..| .+|||+|+.|                 
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l---~~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL---KRG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHH---hcC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            89999999999999998874    2 57789999998876655444   445 8899999998                 


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       178 lVlDEADrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~  257 (513)
T COG0513         178 LVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESE  257 (513)
T ss_pred             EEeccHhhhhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCH
Confidence                                                                                            


Q ss_pred             --------------------------ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           95 --------------------------KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        95 --------------------------~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                                                ..|+.++..|...|+++.++||++||..|..+...|++|++.|+||       +
T Consensus       258 ~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGi  337 (513)
T COG0513         258 EEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGL  337 (513)
T ss_pred             HHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccC
Confidence                                      4688899999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCcccccccccc-ccCCccc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILD-LRLGRED  174 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~-~~~~r~~  174 (184)
                      |+|+|.+|+|||+|.+.|.|+|||++ +|+||.+
T Consensus       338 Di~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G  371 (513)
T COG0513         338 DIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKG  371 (513)
T ss_pred             CccccceeEEccCCCCHHHheeccCccccCCCCC
Confidence            99999999999999999999999987 3777653

>KOG0331|consensus

Probab=99.82  E-value=9.8e-20  Score=154.75  Aligned_cols=165  Identities=13%  Similarity=0.159  Sum_probs=120.0

Q ss_pred             CeEEEEEEccCh------HHHHHHHHHhh-cCCCcEEEEeccH-HHHHHHHHHHHhCCCeeEEecCC-------------
Q psy437            9 NLKYEILPKKNV------LKEVISLIKAK-YSGQSGIVYCLTR-KECDSVAAALAQERINAISYHAG-------------   67 (184)
Q Consensus         9 Nl~y~v~~~~~k------~~~L~~~l~~~-~~~~~~IIf~~tr-~~~e~la~~L~~~gi~~~~~hg~-------------   67 (184)
                      .+.|.|..+.+.      ...+..+|.+. .+..++|.|..|- +.+..+|..+...-+.+...+-.             
T Consensus       239 ~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive  318 (519)
T KOG0331|consen  239 RVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVE  318 (519)
T ss_pred             ceeEEEeccHHhhhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhh
Confidence            466777765431      23444455442 1233688887774 46777887776532222222110             


Q ss_pred             -CCHHHHH----HHHHHHh-ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-
Q psy437           68 -LADKLRN----EVQMKWI-SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-  140 (184)
Q Consensus        68 -l~~~~R~----~~~~~f~-~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-  140 (184)
                       .+..++.    .+++... ..+.++||+|.+++.|+.+++.|...+++|.+||+|.+|+.|+.++..|++|+..|+|| 
T Consensus       319 ~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVAT  398 (519)
T KOG0331|consen  319 VCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVAT  398 (519)
T ss_pred             hcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEc
Confidence             1122222    3344444 23458999999999999999999999999999999999999999999999999999999 


Q ss_pred             ------EecCCccEEEecCCCCCccccccccccc-cCCcc
Q psy437          141 ------WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       141 ------~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                            +|+|+|++|||||+|.+.|+|+||++++ |+|+.
T Consensus       399 dVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~  438 (519)
T KOG0331|consen  399 DVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKK  438 (519)
T ss_pred             ccccccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCC
Confidence                  6999999999999999999999999763 55543

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

Probab=99.82  E-value=3.4e-19  Score=162.23  Aligned_cols=87  Identities=23%  Similarity=0.296  Sum_probs=80.4

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccc
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPD  160 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~  160 (184)
                      ||||.+|++||.+|..|...|+.+..||+||++..|..+|+.|..|++.|+||       +|+|+||+||||++|++.++
T Consensus       684 IIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEs  763 (1195)
T PLN03137        684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEG  763 (1195)
T ss_pred             eeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHH
Confidence            56666668899999999999999999999999999999999999999999999       59999999999999999999


Q ss_pred             cccccccccCCccccc
Q psy437          161 YLPPILDLRLGREDIR  176 (184)
Q Consensus       161 y~~~i~~~~~~r~~~~  176 (184)
                      |+||+  +|+||++.+
T Consensus       764 YyQri--GRAGRDG~~  777 (1195)
T PLN03137        764 YHQEC--GRAGRDGQR  777 (1195)
T ss_pred             HHhhh--cccCCCCCC
Confidence            99999  588887544

>PTZ00110 helicase; Provisional

Probab=99.80  E-value=4.7e-19  Score=154.47  Aligned_cols=115  Identities=12%  Similarity=0.137  Sum_probs=102.7

Q ss_pred             EEEEccChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           13 EILPKKNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        13 ~v~~~~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      .+.....|...|.+++.... ...++||||+|++.|+.++..|...|+++..+||++++++|..++++|++|+.+|||||
T Consensus       355 ~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaT  434 (545)
T PTZ00110        355 FVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIAT  434 (545)
T ss_pred             EEEechhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEc
Confidence            33444457788888776543 46789999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +      .+++|||.++++ +|||+|+|.+..+|+||..|.|.
T Consensus       435 d------v~~rGIDi~~v~-~VI~~d~P~s~~~yvqRiGRtGR  470 (545)
T PTZ00110        435 D------VASRGLDVKDVK-YVINFDFPNQIEDYVHRIGRTGR  470 (545)
T ss_pred             c------hhhcCCCcccCC-EEEEeCCCCCHHHHHHHhccccc
Confidence            9      889999999999 99999999999999999976543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.80  E-value=3.8e-19  Score=152.25  Aligned_cols=109  Identities=23%  Similarity=0.305  Sum_probs=100.5

Q ss_pred             cChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccH
Q psy437           18 KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKEC   97 (184)
Q Consensus        18 ~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~   97 (184)
                      ..|...|..++... .+.++||||+|++.++.+++.|...|+.+..+||+|++.+|..+++.|++|+.++||||+     
T Consensus       227 ~~k~~~l~~ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTd-----  300 (460)
T PRK11776        227 DERLPALQRLLLHH-QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATD-----  300 (460)
T ss_pred             HHHHHHHHHHHHhc-CCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEec-----
Confidence            34788888888653 667899999999999999999999999999999999999999999999999999999999     


Q ss_pred             HHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           98 DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        98 e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                       .+++|+|.++++ +|||+|+|.+...|+||..|.|.
T Consensus       301 -v~~rGiDi~~v~-~VI~~d~p~~~~~yiqR~GRtGR  335 (460)
T PRK11776        301 -VAARGLDIKALE-AVINYELARDPEVHVHRIGRTGR  335 (460)
T ss_pred             -ccccccchhcCC-eEEEecCCCCHhHhhhhcccccC
Confidence             889999999999 99999999999999999866543

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.80  E-value=2.1e-19  Score=152.40  Aligned_cols=108  Identities=15%  Similarity=0.187  Sum_probs=99.7

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .|...|..++... ...++||||+|+..|+.++..|...|+++..+||+|++++|..++++|++|+++|||||+      
T Consensus       241 ~k~~~l~~ll~~~-~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd------  313 (423)
T PRK04837        241 EKMRLLQTLIEEE-WPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD------  313 (423)
T ss_pred             HHHHHHHHHHHhc-CCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec------
Confidence            4777888887653 567899999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+++|+|.++++ +|||+|+|.+..+|+||..+.|.
T Consensus       314 v~~rGiDip~v~-~VI~~d~P~s~~~yiqR~GR~gR  348 (423)
T PRK04837        314 VAARGLHIPAVT-HVFNYDLPDDCEDYVHRIGRTGR  348 (423)
T ss_pred             hhhcCCCccccC-EEEEeCCCCchhheEeccccccC
Confidence            889999999999 99999999999999999976543

>KOG0332|consensus

Probab=99.79  E-value=2.6e-19  Score=145.16  Aligned_cols=115  Identities=12%  Similarity=0.142  Sum_probs=102.2

Q ss_pred             EEEEEcc-ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           12 YEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        12 y~v~~~~-~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      |..+..+ +|++.|.+++.- ..-+++||||.|++.+.+++..|.+.|..+..+||+|.-++|..+++.|+.|..+|||+
T Consensus       308 yv~C~~~~~K~~~l~~lyg~-~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLit  386 (477)
T KOG0332|consen  308 YVLCACRDDKYQALVNLYGL-LTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLIT  386 (477)
T ss_pred             eeeccchhhHHHHHHHHHhh-hhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEE
Confidence            5555544 599999997643 36789999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCCh------HHHHHHHHHhhCCC
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLAD------KLRNEVQMKWISNK  134 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~------~~r~~~~~~f~~~~  134 (184)
                      |+      ++|||+|.+.++ .|+|||+|-      +.+.|+||..+.|.
T Consensus       387 Tn------V~ARGiDv~qVs-~VvNydlP~~~~~~pD~etYlHRiGRtGR  429 (477)
T KOG0332|consen  387 TN------VCARGIDVAQVS-VVVNYDLPVKYTGEPDYETYLHRIGRTGR  429 (477)
T ss_pred             ec------hhhcccccceEE-EEEecCCccccCCCCCHHHHHHHhccccc
Confidence            99      899999999999 999999995      56788888877664

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.79  E-value=7.5e-19  Score=150.34  Aligned_cols=108  Identities=16%  Similarity=0.120  Sum_probs=97.6

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .+...|..++.. ....++||||+|+..++.+++.|...++++..+||+|++++|..++++|++|+++|||||+      
T Consensus       231 ~k~~~l~~l~~~-~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd------  303 (456)
T PRK10590        231 RKRELLSQMIGK-GNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD------  303 (456)
T ss_pred             HHHHHHHHHHHc-CCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc------
Confidence            455566665644 2557899999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+++|+|.++++ +|||+++|.+..+|+|+..+.|.
T Consensus       304 v~~rGiDip~v~-~VI~~~~P~~~~~yvqR~GRaGR  338 (456)
T PRK10590        304 IAARGLDIEELP-HVVNYELPNVPEDYVHRIGRTGR  338 (456)
T ss_pred             HHhcCCCcccCC-EEEEeCCCCCHHHhhhhcccccc
Confidence            889999999999 99999999999999999977653

>KOG0341|consensus

Probab=99.78  E-value=3.8e-19  Score=145.05  Aligned_cols=106  Identities=12%  Similarity=0.157  Sum_probs=97.8

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      |+-.|++.|.+  ..+|.+|||..+.+++.+.++|--.|+.++++|||.+|++|...++.|+.|+-.|||||+      .
T Consensus       409 KiVylLeCLQK--T~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATD------V  480 (610)
T KOG0341|consen  409 KIVYLLECLQK--TSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATD------V  480 (610)
T ss_pred             hhhhHHHHhcc--CCCceEEEeccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEec------c
Confidence            55566677755  678999999999999999999999999999999999999999999999999999999999      8


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++.|||.++|. +|||||||.+.++|+||..+.|.
T Consensus       481 ASKGLDFp~iq-HVINyDMP~eIENYVHRIGRTGR  514 (610)
T KOG0341|consen  481 ASKGLDFPDIQ-HVINYDMPEEIENYVHRIGRTGR  514 (610)
T ss_pred             hhccCCCccch-hhccCCChHHHHHHHHHhcccCC
Confidence            89999999999 99999999999999999976553

>KOG0333|consensus

Probab=99.78  E-value=8.9e-19  Score=147.13  Aligned_cols=103  Identities=16%  Similarity=0.145  Sum_probs=93.9

Q ss_pred             HHHHHHHHHHhcc-CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Ee
Q psy437           71 KLRNEVQMKWISN-KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WK  142 (184)
Q Consensus        71 ~~R~~~~~~f~~g-~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D  142 (184)
                      +++.++++-..++ +-++||+.++++.||.+|.+|++.|+.++.+|++-.++.|.++++.|++|...|+||       +|
T Consensus       503 ~k~kkL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGID  582 (673)
T KOG0333|consen  503 EKRKKLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGID  582 (673)
T ss_pred             HHHHHHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCC
Confidence            4477777777665 779999999999999999999999999999999999999999999999999999999       69


Q ss_pred             cCCccEEEecCCCCCcccccccccc-ccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      +|||++|+|||+++++++|+|||++ +|+|-.
T Consensus       583 IpnVSlVinydmaksieDYtHRIGRTgRAGk~  614 (673)
T KOG0333|consen  583 IPNVSLVINYDMAKSIEDYTHRIGRTGRAGKS  614 (673)
T ss_pred             CCccceeeecchhhhHHHHHHHhccccccccC
Confidence            9999999999999999999999976 366654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.78  E-value=1.3e-18  Score=152.32  Aligned_cols=109  Identities=14%  Similarity=0.153  Sum_probs=100.1

Q ss_pred             cChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccH
Q psy437           18 KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKEC   97 (184)
Q Consensus        18 ~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~   97 (184)
                      ..|...|..++... ...++||||+|+..|+.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+     
T Consensus       242 ~~k~~~L~~ll~~~-~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTd-----  315 (572)
T PRK04537        242 EEKQTLLLGLLSRS-EGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD-----  315 (572)
T ss_pred             HHHHHHHHHHHhcc-cCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEeh-----
Confidence            34777788877653 667899999999999999999999999999999999999999999999999999999999     


Q ss_pred             HHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           98 DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        98 e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                       .+++|||.++++ +|||+++|.+..+|+||..+.|.
T Consensus       316 -v~arGIDip~V~-~VInyd~P~s~~~yvqRiGRaGR  350 (572)
T PRK04537        316 -VAARGLHIDGVK-YVYNYDLPFDAEDYVHRIGRTAR  350 (572)
T ss_pred             -hhhcCCCccCCC-EEEEcCCCCCHHHHhhhhccccc
Confidence             899999999999 99999999999999999976543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.77  E-value=2.9e-18  Score=145.78  Aligned_cols=121  Identities=15%  Similarity=0.133  Sum_probs=104.0

Q ss_pred             CCCCeEEEEEEc---cChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc
Q psy437            6 NRANLKYEILPK---KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS   82 (184)
Q Consensus         6 ~R~Nl~y~v~~~---~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~   82 (184)
                      .+.++.......   ..|...|..++... ...++||||+|++.++.++..|...|+++..+||+|++.+|..+++.|++
T Consensus       215 ~~~~i~~~~~~~~~~~~k~~~l~~l~~~~-~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~  293 (434)
T PRK11192        215 ERKKIHQWYYRADDLEHKTALLCHLLKQP-EVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTD  293 (434)
T ss_pred             cccCceEEEEEeCCHHHHHHHHHHHHhcC-CCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhC
Confidence            345554333332   24777777777542 56789999999999999999999999999999999999999999999999


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+++|||||+      .+++|+|.++++ +|||+++|.+...|+||..|.|.
T Consensus       294 G~~~vLVaTd------~~~~GiDip~v~-~VI~~d~p~s~~~yiqr~GR~gR  338 (434)
T PRK11192        294 GRVNVLVATD------VAARGIDIDDVS-HVINFDMPRSADTYLHRIGRTGR  338 (434)
T ss_pred             CCCcEEEEcc------ccccCccCCCCC-EEEEECCCCCHHHHhhccccccc
Confidence            9999999999      889999999999 99999999999999999976543

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.77  E-value=1.2e-17  Score=143.32  Aligned_cols=86  Identities=24%  Similarity=0.276  Sum_probs=81.0

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccc
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPD  160 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~  160 (184)
                      ||+|+++++|+.++..|...|+++..||+++|+..|..+++.|++|++.|+||       +|+|+|++|||+++|++.++
T Consensus       230 IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~  309 (470)
T TIGR00614       230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMES  309 (470)
T ss_pred             EEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHH
Confidence            88888889999999999999999999999999999999999999999999999       59999999999999999999


Q ss_pred             cccccccccCCcccc
Q psy437          161 YLPPILDLRLGREDI  175 (184)
Q Consensus       161 y~~~i~~~~~~r~~~  175 (184)
                      |+|++  +|+||++.
T Consensus       310 y~Qr~--GRaGR~G~  322 (470)
T TIGR00614       310 YYQES--GRAGRDGL  322 (470)
T ss_pred             HHhhh--cCcCCCCC
Confidence            99999  58888653

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

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.77  E-value=3.3e-18  Score=151.06  Aligned_cols=120  Identities=16%  Similarity=0.189  Sum_probs=105.4

Q ss_pred             CCCCeE--EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437            6 NRANLK--YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus         6 ~R~Nl~--y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      .++++.  |.......|...|..+|... ...++||||+|+..++.+++.|...|+.+..+||+|++.+|..++++|++|
T Consensus       216 ~~~~i~q~~~~v~~~~k~~~L~~~L~~~-~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G  294 (629)
T PRK11634        216 TRPDISQSYWTVWGMRKNEALVRFLEAE-DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDG  294 (629)
T ss_pred             cCCceEEEEEEechhhHHHHHHHHHHhc-CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCC
Confidence            355654  33333345788888888653 567899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +.+|||||+      .+++|+|.++++ +|||+++|.+.+.|+|+..+.|
T Consensus       295 ~~~ILVATd------v~arGIDip~V~-~VI~~d~P~~~e~yvqRiGRtG  337 (629)
T PRK11634        295 RLDILIATD------VAARGLDVERIS-LVVNYDIPMDSESYVHRIGRTG  337 (629)
T ss_pred             CCCEEEEcc------hHhcCCCcccCC-EEEEeCCCCCHHHHHHHhcccc
Confidence            999999999      999999999999 9999999999999999997654

>KOG0340|consensus

Probab=99.77  E-value=2.1e-18  Score=139.12  Aligned_cols=113  Identities=13%  Similarity=0.176  Sum_probs=99.5

Q ss_pred             EEEEEccChHHHHHHHHHhhc--CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKY--SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGH   89 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~--~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlV   89 (184)
                      |..++...|...|...|....  ...+++||++|...|+.++..|...++.+..+||-|+|++|...+.+|+++..++||
T Consensus       230 yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~ili  309 (442)
T KOG0340|consen  230 YILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILI  309 (442)
T ss_pred             eeecchhhhHHHHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEE
Confidence            334444446667777775432  357799999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           90 WTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        90 aT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      ||+      ++++|||+|.+. +|+|+++|.++++|+||..+
T Consensus       310 aTD------VAsRGLDIP~V~-LVvN~diPr~P~~yiHRvGR  344 (442)
T KOG0340|consen  310 ATD------VASRGLDIPTVE-LVVNHDIPRDPKDYIHRVGR  344 (442)
T ss_pred             Eec------hhhcCCCCCcee-EEEecCCCCCHHHHHHhhcc
Confidence            999      999999999999 99999999999999999854

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.77  E-value=1.7e-17  Score=146.11  Aligned_cols=140  Identities=18%  Similarity=0.233  Sum_probs=121.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE-------------------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV-------------------------   87 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v-------------------------   87 (184)
                      ..+.++|.+|++..+++....|...|+++..+||+++..++..++....+|..++                         
T Consensus        52 ~~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~i  131 (591)
T TIGR01389        52 LKGLTVVISPLISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALV  131 (591)
T ss_pred             cCCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEE
Confidence            3467899999999999999999999999999999988777666554444433333                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           88 --------------------------------------------------------------------------------   87 (184)
Q Consensus        88 --------------------------------------------------------------------------------   87 (184)
                                                                                                      
T Consensus       132 ViDEaH~i~~~g~~frp~y~~l~~l~~~~~~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~  211 (591)
T TIGR01389       132 AVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKNNK  211 (591)
T ss_pred             EEeCCcccccccCccHHHHHHHHHHHHhCCCCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecCCCCCCcEEEEEeCCCH
Confidence                                                                                            


Q ss_pred             ----------------EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC
Q psy437           88 ----------------GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ  144 (184)
Q Consensus        88 ----------------lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~  144 (184)
                                      ||+++++++|+.+|..|...|+++..||++|++..|..+++.|++|.+.|+||       +|+|
T Consensus       212 ~~~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p  291 (591)
T TIGR01389       212 QKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKP  291 (591)
T ss_pred             HHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCC
Confidence                            56666667899999999999999999999999999999999999999999999       5999


Q ss_pred             CccEEEecCCCCCccccccccccccCCccc
Q psy437          145 WKRIIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       145 ~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                      +|++|+|+++|.+.++|+|++  +|+||++
T Consensus       292 ~v~~VI~~~~p~s~~~y~Q~~--GRaGR~G  319 (591)
T TIGR01389       292 NVRFVIHYDMPGNLESYYQEA--GRAGRDG  319 (591)
T ss_pred             CCCEEEEcCCCCCHHHHhhhh--ccccCCC
Confidence            999999999999999999999  5888875

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.

>KOG0326|consensus

Probab=99.77  E-value=5.3e-19  Score=141.09  Aligned_cols=117  Identities=13%  Similarity=0.174  Sum_probs=106.9

Q ss_pred             EEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           11 KYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        11 ~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      ||..+....|+..|-.++.+. .-.++||||||...+|.+|..+.+.|++|.++|+.|-++.|..+...|++|.++.|||
T Consensus       300 yYafV~e~qKvhCLntLfskL-qINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVc  378 (459)
T KOG0326|consen  300 YYAFVEERQKVHCLNTLFSKL-QINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVC  378 (459)
T ss_pred             heeeechhhhhhhHHHHHHHh-cccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeee
Confidence            566666667888888887665 6678999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCc
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV  135 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~  135 (184)
                      |+      .+.||+|++.++ +|||+|+|+..++|+||..++|..
T Consensus       379 tD------L~TRGIDiqavN-vVINFDfpk~aEtYLHRIGRsGRF  416 (459)
T KOG0326|consen  379 TD------LFTRGIDIQAVN-VVINFDFPKNAETYLHRIGRSGRF  416 (459)
T ss_pred             hh------hhhcccccceee-EEEecCCCCCHHHHHHHccCCccC
Confidence            99      889999999999 999999999999999999988863

>KOG0335|consensus

Probab=99.75  E-value=4.6e-18  Score=142.77  Aligned_cols=122  Identities=17%  Similarity=0.157  Sum_probs=107.7

Q ss_pred             CCCCeEEEEEEc--cChHHHHHHHHHhhc---CCC-----cEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHH
Q psy437            6 NRANLKYEILPK--KNVLKEVISLIKAKY---SGQ-----SGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNE   75 (184)
Q Consensus         6 ~R~Nl~y~v~~~--~~k~~~L~~~l~~~~---~~~-----~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~   75 (184)
                      .++|+...+...  ..|...|+++|.+..   ...     .++|||.|++.|..++..|...++++..+||..++.+|.+
T Consensus       299 ~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~  378 (482)
T KOG0335|consen  299 TSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQ  378 (482)
T ss_pred             ccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHH
Confidence            456776555543  358899999997543   223     6899999999999999999999999999999999999999


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+..|++|..++||||+      .+|||||+++|+ +||+||||.+..+|+||..+.|.
T Consensus       379 al~~Fr~g~~pvlVaT~------VaaRGlDi~~V~-hVInyDmP~d~d~YvHRIGRTGR  430 (482)
T KOG0335|consen  379 ALNDFRNGKAPVLVATN------VAARGLDIPNVK-HVINYDMPADIDDYVHRIGRTGR  430 (482)
T ss_pred             HHHHhhcCCcceEEEeh------hhhcCCCCCCCc-eeEEeecCcchhhHHHhcccccc
Confidence            99999999999999999      999999999999 99999999999999999977654

>KOG0330|consensus

Probab=99.75  E-value=2.2e-17  Score=134.57  Aligned_cols=138  Identities=16%  Similarity=0.117  Sum_probs=118.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      ....++|.+|||+.|.+|++.+...    |+.+..+-||++...  +..+.+  .+..|||||+.|              
T Consensus       128 ~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~--q~~~L~--kkPhilVaTPGrL~dhl~~Tkgf~le  203 (476)
T KOG0330|consen  128 KLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMML--QANQLS--KKPHILVATPGRLWDHLENTKGFSLE  203 (476)
T ss_pred             CCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHH--HHHHhh--cCCCEEEeCcHHHHHHHHhccCccHH
Confidence            4456999999999999999999864    788999999987432  222222  345677777777              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       204 ~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~  283 (476)
T KOG0330|consen  204 QLKFLVLDEADRLLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVP  283 (476)
T ss_pred             HhHHHhhchHHhhhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEecc
Confidence                                                                                            


Q ss_pred             ---------------------------ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           95 ---------------------------KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        95 ---------------------------~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                                                 ..+..+|--|+..|+.+..+||+|+++.|--..+.|++|...|+|+       
T Consensus       284 ~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRG  363 (476)
T KOG0330|consen  284 GKDKDTYLVYLLNELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRG  363 (476)
T ss_pred             ccccchhHHHHHHhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhccc
Confidence                                       4678888899999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCCCccccccccccc-cCCccc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRED  174 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~~  174 (184)
                      +|+|.|+.|+|||+|....+|+||++++ |+||.+
T Consensus       364 LDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG  398 (476)
T KOG0330|consen  364 LDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSG  398 (476)
T ss_pred             CCCCCceEEEecCCCCcHHHHHHHcccccccCCCc
Confidence            6999999999999999999999999984 888863

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.75  E-value=1.1e-17  Score=143.93  Aligned_cols=113  Identities=13%  Similarity=0.135  Sum_probs=101.5

Q ss_pred             EEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           14 ILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        14 v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      .....+|...|..++... ...++||||++++.++.+++.|...|+.+..+||++++++|.++++.|++|+.++||||+ 
T Consensus       316 ~~~~~~k~~~l~~ll~~~-~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~-  393 (475)
T PRK01297        316 AVAGSDKYKLLYNLVTQN-PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATD-  393 (475)
T ss_pred             EecchhHHHHHHHHHHhc-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEcc-
Confidence            333445777888877653 556899999999999999999999999999999999999999999999999999999999 


Q ss_pred             cccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           94 SKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        94 r~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                           .+++|+|.++++ +|||+|+|.+..+|+||..|.|.
T Consensus       394 -----~l~~GIDi~~v~-~VI~~~~P~s~~~y~Qr~GRaGR  428 (475)
T PRK01297        394 -----VAGRGIHIDGIS-HVINFTLPEDPDDYVHRIGRTGR  428 (475)
T ss_pred             -----ccccCCcccCCC-EEEEeCCCCCHHHHHHhhCccCC
Confidence                 889999999999 99999999999999999976654

>KOG0342|consensus

Probab=99.75  E-value=4.2e-18  Score=142.00  Aligned_cols=120  Identities=12%  Similarity=0.080  Sum_probs=111.2

Q ss_pred             CCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCc
Q psy437            6 NRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV   85 (184)
Q Consensus         6 ~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~   85 (184)
                      +|-+..|.|.+...++..+..+|+++....+.||||+|...+..+++.|....+++..+||+++|..|..+..+|++.+.
T Consensus       302 e~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaes  381 (543)
T KOG0342|consen  302 ERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAES  381 (543)
T ss_pred             hcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhccc
Confidence            45556788988888899999999887555899999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                      -||+||+      +.|||||.|+|+ .|+.+|.|.+.++|+||..+.
T Consensus       382 gIL~cTD------VaARGlD~P~V~-~VvQ~~~P~d~~~YIHRvGRT  421 (543)
T KOG0342|consen  382 GILVCTD------VAARGLDIPDVD-WVVQYDPPSDPEQYIHRVGRT  421 (543)
T ss_pred             ceEEecc------hhhccCCCCCce-EEEEeCCCCCHHHHHHHhccc
Confidence            9999999      999999999999 999999999999999999654

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

Probab=99.75  E-value=1e-17  Score=145.38  Aligned_cols=110  Identities=17%  Similarity=0.208  Sum_probs=98.0

Q ss_pred             cChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHh-CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           18 KNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQ-ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        18 ~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~-~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ..|...|.+++.... ..+++||||+|+..++.+++.|.. .|+++..+||+|++++|..++++|++|+.+|||||+   
T Consensus       350 ~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTd---  426 (518)
T PLN00206        350 KQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATG---  426 (518)
T ss_pred             hhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEec---
Confidence            346677787776431 236899999999999999999975 699999999999999999999999999999999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                         .+++|||.++++ .|||+|+|.+..+|+||.+|.|.
T Consensus       427 ---vl~rGiDip~v~-~VI~~d~P~s~~~yihRiGRaGR  461 (518)
T PLN00206        427 ---VLGRGVDLLRVR-QVIIFDMPNTIKEYIHQIGRASR  461 (518)
T ss_pred             ---HhhccCCcccCC-EEEEeCCCCCHHHHHHhcccccc
Confidence               889999999999 99999999999999999977654

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.74  E-value=5.1e-17  Score=143.41  Aligned_cols=87  Identities=21%  Similarity=0.271  Sum_probs=81.6

Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcc
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKP  159 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e  159 (184)
                      +||+|+++++|+.++..|...|+++..||+++|+..|..+++.|+.|++.|+||       +|+|+|++|||+++|.+.+
T Consensus       239 ~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~  318 (607)
T PRK11057        239 GIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIE  318 (607)
T ss_pred             EEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHH
Confidence            478888889999999999999999999999999999999999999999999999       5999999999999999999


Q ss_pred             ccccccccccCCcccc
Q psy437          160 DYLPPILDLRLGREDI  175 (184)
Q Consensus       160 ~y~~~i~~~~~~r~~~  175 (184)
                      +|+|++  +|+||++.
T Consensus       319 ~y~Qr~--GRaGR~G~  332 (607)
T PRK11057        319 SYYQET--GRAGRDGL  332 (607)
T ss_pred             HHHHHh--hhccCCCC
Confidence            999999  58888754

>KOG0336|consensus

Probab=99.73  E-value=8.1e-18  Score=138.13  Aligned_cols=114  Identities=14%  Similarity=0.120  Sum_probs=102.3

Q ss_pred             EEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           13 EILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        13 ~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .|+...+|++.+..++.+.....+.||||..+..|+.++..|.-.|+.+..+||+-+|.+|+..++.|++|+++|||||+
T Consensus       444 ~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTD  523 (629)
T KOG0336|consen  444 IVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATD  523 (629)
T ss_pred             EecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEec
Confidence            44455568877777776655677899999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           93 VSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        93 tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                            .+++|||.++|. +|||||+|.+.+.|+||..+.|
T Consensus       524 ------laSRGlDv~DiT-HV~NyDFP~nIeeYVHRvGrtG  557 (629)
T KOG0336|consen  524 ------LASRGLDVPDIT-HVYNYDFPRNIEEYVHRVGRTG  557 (629)
T ss_pred             ------hhhcCCCchhcc-eeeccCCCccHHHHHHHhcccc
Confidence                  889999999998 9999999999999999996654

>KOG0353|consensus

Probab=99.72  E-value=3.9e-17  Score=133.32  Aligned_cols=76  Identities=25%  Similarity=0.367  Sum_probs=72.7

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccc
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPD  160 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~  160 (184)
                      ||||-++++||.+|..|...||.+..||+.|.+..++-+|+.|.+|+++|+||       +|+||||||||+++|++.|+
T Consensus       321 iiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksien  400 (695)
T KOG0353|consen  321 IIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIEN  400 (695)
T ss_pred             eEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCCCCeeEEEecccchhHHH
Confidence            66777778999999999999999999999999999999999999999999999       49999999999999999999


Q ss_pred             ccc
Q psy437          161 YLP  163 (184)
Q Consensus       161 y~~  163 (184)
                      |||
T Consensus       401 yyq  403 (695)
T KOG0353|consen  401 YYQ  403 (695)
T ss_pred             HHH
Confidence            999

>KOG0341|consensus

Probab=99.71  E-value=3.9e-17  Score=133.44  Aligned_cols=82  Identities=15%  Similarity=0.138  Sum_probs=76.1

Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcccccccccc
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILD  167 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~  167 (184)
                      .+++.+..+|--.|+.++.||+|-.|+.|+|.-+.|+.|+-.|+||       +|.|+|.||||||+|...|+|+|||++
T Consensus       432 ~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGR  511 (610)
T KOG0341|consen  432 ADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGR  511 (610)
T ss_pred             cChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcc
Confidence            5899999999999999999999999999999999999999999999       699999999999999999999999987


Q ss_pred             -ccCCccccc
Q psy437          168 -LRLGREDIR  176 (184)
Q Consensus       168 -~~~~r~~~~  176 (184)
                       +|-|+.+|-
T Consensus       512 TGRsg~~GiA  521 (610)
T KOG0341|consen  512 TGRSGKTGIA  521 (610)
T ss_pred             cCCCCCccee
Confidence             377776553

>KOG0338|consensus

Probab=99.70  E-value=6.2e-17  Score=135.83  Aligned_cols=104  Identities=17%  Similarity=0.132  Sum_probs=94.8

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      +-..|..++... -...+|||+.|++.|..+.-.|-..|+++.-+||+|+|++|...++.|+++++++||||+      .
T Consensus       413 Rea~l~~l~~rt-f~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTD------v  485 (691)
T KOG0338|consen  413 REAMLASLITRT-FQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATD------V  485 (691)
T ss_pred             cHHHHHHHHHHh-cccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEec------h
Confidence            555666666654 346799999999999999999999999999999999999999999999999999999999      9


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      +|+|||+.||. .||||.||.+.+.|+||..+
T Consensus       486 AsRGLDI~gV~-tVINy~mP~t~e~Y~HRVGR  516 (691)
T KOG0338|consen  486 ASRGLDIEGVQ-TVINYAMPKTIEHYLHRVGR  516 (691)
T ss_pred             hhccCCcccee-EEEeccCchhHHHHHHHhhh
Confidence            99999999999 99999999999999999854

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.70  E-value=4.8e-16  Score=133.14  Aligned_cols=86  Identities=21%  Similarity=0.255  Sum_probs=80.0

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCc
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIK  158 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~  158 (184)
                      ++||+|+++..|+.++..|...|+++..+|+++++..|..+.+.|++|++.|+||       +|+|++++|||+++|.+.
T Consensus       244 ~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~  323 (460)
T PRK11776        244 SCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDP  323 (460)
T ss_pred             ceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEEEecCCCCH
Confidence            3588888889999999999999999999999999999999999999999999999       699999999999999999


Q ss_pred             cccccccccccCCcc
Q psy437          159 PDYLPPILDLRLGRE  173 (184)
Q Consensus       159 e~y~~~i~~~~~~r~  173 (184)
                      +.|+|+++  |+||.
T Consensus       324 ~~yiqR~G--RtGR~  336 (460)
T PRK11776        324 EVHVHRIG--RTGRA  336 (460)
T ss_pred             hHhhhhcc--cccCC
Confidence            99999996  55553

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

Probab=99.69  E-value=6.4e-17  Score=145.33  Aligned_cols=105  Identities=14%  Similarity=0.135  Sum_probs=93.1

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      +...|..++.   .+.++||||+|++.|+.++..|.+.        +.++..|||++++++|.+++++|++|++++||||
T Consensus       260 ~~~~l~~l~~---~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaT  336 (742)
T TIGR03817       260 AADLLADLVA---EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATT  336 (742)
T ss_pred             HHHHHHHHHH---CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEEC
Confidence            4445555553   3579999999999999999998763        5678899999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +      .+++|+|+++++ +|+|+|+|.+..+|+||..|.|.
T Consensus       337 d------~lerGIDI~~vd-~VI~~~~P~s~~~y~qRiGRaGR  372 (742)
T TIGR03817       337 N------ALELGVDISGLD-AVVIAGFPGTRASLWQQAGRAGR  372 (742)
T ss_pred             c------hHhccCCccccc-EEEEeCCCCCHHHHHHhccccCC
Confidence            9      889999999999 99999999999999999977664

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.

>KOG0347|consensus

Probab=99.69  E-value=5.3e-17  Score=137.22  Aligned_cols=92  Identities=16%  Similarity=0.094  Sum_probs=84.4

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEE
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAIS  113 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~v  113 (184)
                      ++.+|||||+...+..++-.|...+++...+|+.|.|++|.+.+++|++....|||||+      ++|||||++||. +|
T Consensus       463 PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTD------VAARGLDIp~V~-HV  535 (731)
T KOG0347|consen  463 PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATD------VAARGLDIPGVQ-HV  535 (731)
T ss_pred             CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeeh------hhhccCCCCCcc-eE
Confidence            56799999999999999999999999999999999999999999999999999999999      999999888888 88


Q ss_pred             eeCCCChHHHHHHHHHhhC
Q psy437          114 YHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus       114 ih~~~p~~~r~~~~~~f~~  132 (184)
                      |||.+|.+.+.|+||+.+.
T Consensus       536 IHYqVPrtseiYVHRSGRT  554 (731)
T KOG0347|consen  536 IHYQVPRTSEIYVHRSGRT  554 (731)
T ss_pred             EEeecCCccceeEeccccc
Confidence            8888888888888877654

>PTZ00424 helicase 45; Provisional

Probab=99.68  E-value=9.4e-17  Score=134.91  Aligned_cols=107  Identities=16%  Similarity=0.221  Sum_probs=95.7

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      +...+..++... ...++||||+|++.++.+++.|...++.+..+||+|++++|..++++|++|+.+|||||+      .
T Consensus       254 ~~~~l~~~~~~~-~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~------~  326 (401)
T PTZ00424        254 KFDTLCDLYETL-TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTD------L  326 (401)
T ss_pred             HHHHHHHHHHhc-CCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcc------c
Confidence            556666666543 557899999999999999999999999999999999999999999999999999999999      7


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +++|+|.++++ +|+|+++|.+...|+|+.+|.|.
T Consensus       327 l~~GiDip~v~-~VI~~~~p~s~~~y~qr~GRagR  360 (401)
T PTZ00424        327 LARGIDVQQVS-LVINYDLPASPENYIHRIGRSGR  360 (401)
T ss_pred             ccCCcCcccCC-EEEEECCCCCHHHEeeccccccc
Confidence            78999999999 99999999999999999877553

>KOG0340|consensus

Probab=99.68  E-value=2.6e-16  Score=127.06  Aligned_cols=89  Identities=18%  Similarity=0.286  Sum_probs=81.2

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCc
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIK  158 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~  158 (184)
                      .++|++++...|+.++..|+.-++++..+|.-|||+.|-..+-.|+++.+++++|       +|||.|..|+||++|.++
T Consensus       256 simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P  335 (442)
T KOG0340|consen  256 SIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDP  335 (442)
T ss_pred             eEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCH
Confidence            3455555557899999999999999999999999999999999999999999999       699999999999999999


Q ss_pred             cccccccccc-cCCccc
Q psy437          159 PDYLPPILDL-RLGRED  174 (184)
Q Consensus       159 e~y~~~i~~~-~~~r~~  174 (184)
                      ++|+||+++. |+||-+
T Consensus       336 ~~yiHRvGRtARAGR~G  352 (442)
T KOG0340|consen  336 KDYIHRVGRTARAGRKG  352 (442)
T ss_pred             HHHHHhhcchhcccCCc
Confidence            9999999996 999964

>KOG0345|consensus

Probab=99.68  E-value=1.4e-16  Score=132.51  Aligned_cols=117  Identities=15%  Similarity=0.139  Sum_probs=107.1

Q ss_pred             CeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHHhccCce
Q psy437            9 NLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVH   86 (184)
Q Consensus         9 Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f~~g~~~   86 (184)
                      -++|.+++...|...|+++|.+. ...++|||.+|+..++.....|...  ..+...+||.|++..|..++++|.+..-.
T Consensus       231 ~~~Y~v~~a~eK~~~lv~~L~~~-~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~  309 (567)
T KOG0345|consen  231 ALEYLVCEADEKLSQLVHLLNNN-KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNG  309 (567)
T ss_pred             cceeeEecHHHHHHHHHHHHhcc-ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCc
Confidence            46899999989999999999874 7789999999999999999988764  67789999999999999999999998888


Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +|.||+      .+|||||++||+ +|+|+|.|++...++||.++.+
T Consensus       310 vl~~TD------VaARGlDip~iD-~VvQ~DpP~~~~~FvHR~GRTa  349 (567)
T KOG0345|consen  310 VLFCTD------VAARGLDIPGID-LVVQFDPPKDPSSFVHRCGRTA  349 (567)
T ss_pred             eEEeeh------hhhccCCCCCce-EEEecCCCCChhHHHhhcchhh
Confidence            999999      999999999999 9999999999999999996543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.68  E-value=9.3e-16  Score=135.59  Aligned_cols=88  Identities=14%  Similarity=0.169  Sum_probs=80.2

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCc
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIK  158 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~  158 (184)
                      ++||+|+++..|+.++..|...|+.+..+|+++++..|..+.+.|++|++.|+||       +|+|+|++||||++|.+.
T Consensus       247 ~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~  326 (629)
T PRK11634        247 AAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDS  326 (629)
T ss_pred             CEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCH
Confidence            3578888888999999999999999999999999999999999999999999999       699999999999999999


Q ss_pred             ccccccccc-ccCCcc
Q psy437          159 PDYLPPILD-LRLGRE  173 (184)
Q Consensus       159 e~y~~~i~~-~~~~r~  173 (184)
                      ++|+|++++ +|+|+.
T Consensus       327 e~yvqRiGRtGRaGr~  342 (629)
T PRK11634        327 ESYVHRIGRTGRAGRA  342 (629)
T ss_pred             HHHHHHhccccCCCCc
Confidence            999999965 355553

>KOG0343|consensus

Probab=99.67  E-value=5.2e-16  Score=131.38  Aligned_cols=115  Identities=18%  Similarity=0.232  Sum_probs=107.3

Q ss_pred             eEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHh--CCCeeEEecCCCCHHHHHHHHHHHhccCceE
Q psy437           10 LKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ--ERINAISYHAGLADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus        10 l~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~--~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v   87 (184)
                      .+|.+++..+|+..|..+|+.+ ...++|||.+|++.+..+.+.+++  .|++...+||+|+|..|..+..+|...+.-|
T Consensus       290 Q~y~~v~l~~Ki~~L~sFI~sh-lk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~v  368 (758)
T KOG0343|consen  290 QSYVIVPLEDKIDMLWSFIKSH-LKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVV  368 (758)
T ss_pred             heEEEEehhhHHHHHHHHHHhc-cccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceE
Confidence            3688888889999999999875 778999999999999999999986  4999999999999999999999999988899


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                      |.||+      .+|||||.+.|+ +|+.+|.|.+..+|+||..++
T Consensus       369 LF~TD------v~aRGLDFpaVd-wViQ~DCPedv~tYIHRvGRt  406 (758)
T KOG0343|consen  369 LFCTD------VAARGLDFPAVD-WVIQVDCPEDVDTYIHRVGRT  406 (758)
T ss_pred             EEeeh------hhhccCCCcccc-eEEEecCchhHHHHHHHhhhh
Confidence            99999      999999999999 999999999999999999654

>KOG0328|consensus

Probab=99.67  E-value=3.3e-15  Score=117.82  Aligned_cols=91  Identities=15%  Similarity=0.203  Sum_probs=85.6

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLI  157 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~  157 (184)
                      .+.+|+|+|+..++=+...|...+..+...|||||++.|+.+...|++|+.+|+++       +|+|.|++|||||+|..
T Consensus       267 tQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~n  346 (400)
T KOG0328|consen  267 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNN  346 (400)
T ss_pred             heEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechhhccCCcceeEEEEecCCCcc
Confidence            47899999999999999999999999899999999999999999999999999998       49999999999999999


Q ss_pred             cccccccccc-ccCCcccc
Q psy437          158 KPDYLPPILD-LRLGREDI  175 (184)
Q Consensus       158 ~e~y~~~i~~-~~~~r~~~  175 (184)
                      .|.|+|||++ +|-||.+.
T Consensus       347 re~YIHRIGRSGRFGRkGv  365 (400)
T KOG0328|consen  347 RELYIHRIGRSGRFGRKGV  365 (400)
T ss_pred             HHHHhhhhccccccCCcce
Confidence            9999999988 68888743

>KOG0327|consensus

Probab=99.66  E-value=3.2e-16  Score=127.49  Aligned_cols=113  Identities=15%  Similarity=0.247  Sum_probs=102.8

Q ss_pred             EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      |.-..++.|+..|+++..   ...+++|||||++.+.++..+|...++.+.++||.|++.+|..++..|++|..++||.|
T Consensus       244 ~i~v~k~~k~~~l~dl~~---~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlItt  320 (397)
T KOG0327|consen  244 YINVEKEEKLDTLCDLYR---RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITT  320 (397)
T ss_pred             eeeccccccccHHHHHHH---hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeec
Confidence            333444558899998886   34789999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +      .+|+|||...++ +|++|++|...++|+||..++|.
T Consensus       321 d------l~argidv~~~s-lvinydlP~~~~~yihR~gr~gr  356 (397)
T KOG0327|consen  321 D------LLARGIDVQQVS-LVVNYDLPARKENYIHRIGRAGR  356 (397)
T ss_pred             c------ccccccchhhcc-eeeeeccccchhhhhhhcccccc
Confidence            9      999999999999 99999999999999999988774

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.66  E-value=6.3e-15  Score=126.22  Aligned_cols=163  Identities=15%  Similarity=0.204  Sum_probs=115.7

Q ss_pred             CCeEEEEEEccCh------HHHHHHHHHhhcCCCcEEEEeccHHH-HHHHHHHHHhCCCeeE-------------EecCC
Q psy437            8 ANLKYEILPKKNV------LKEVISLIKAKYSGQSGIVYCLTRKE-CDSVAAALAQERINAI-------------SYHAG   67 (184)
Q Consensus         8 ~Nl~y~v~~~~~k------~~~L~~~l~~~~~~~~~IIf~~tr~~-~e~la~~L~~~gi~~~-------------~~hg~   67 (184)
                      .++.+.|..+-+.      ...+..++.......+.+.|+.|-.. ...++..+......+.             .++ -
T Consensus       148 ~~v~~lViDEah~ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~-~  226 (456)
T PRK10590        148 DQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVH-F  226 (456)
T ss_pred             ccceEEEeecHHHHhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEE-E
Confidence            4566666665432      23334444332233457788877543 4555554432211110             011 1


Q ss_pred             CCHHHHHHHHHHHhcc--CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----
Q psy437           68 LADKLRNEVQMKWISN--KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----  140 (184)
Q Consensus        68 l~~~~R~~~~~~f~~g--~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----  140 (184)
                      .+...+..++......  ..++||+|+++..|+.++..|...|+.+..+|+++++..|..+++.|++|++.|+||     
T Consensus       227 ~~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~  306 (456)
T PRK10590        227 VDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAA  306 (456)
T ss_pred             cCHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHh
Confidence            2233444555555432  347999999999999999999999999999999999999999999999999999999     


Q ss_pred             --EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 --WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 --~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                        +|+|+|++||||++|.+.++|+|+++  |+||.
T Consensus       307 rGiDip~v~~VI~~~~P~~~~~yvqR~G--RaGR~  339 (456)
T PRK10590        307 RGLDIEELPHVVNYELPNVPEDYVHRIG--RTGRA  339 (456)
T ss_pred             cCCCcccCCEEEEeCCCCCHHHhhhhcc--ccccC
Confidence              69999999999999999999999995  66664

>PTZ00110 helicase; Provisional

Probab=99.66  E-value=3.2e-15  Score=130.50  Aligned_cols=163  Identities=14%  Similarity=0.170  Sum_probs=113.8

Q ss_pred             CeEEEEEEccCh------HHHHHHHHHhhcCCCcEEEEeccH-HHHHHHHHHHHhC-CCeeEE--e--c--CC-------
Q psy437            9 NLKYEILPKKNV------LKEVISLIKAKYSGQSGIVYCLTR-KECDSVAAALAQE-RINAIS--Y--H--AG-------   67 (184)
Q Consensus         9 Nl~y~v~~~~~k------~~~L~~~l~~~~~~~~~IIf~~tr-~~~e~la~~L~~~-gi~~~~--~--h--g~-------   67 (184)
                      ++.|.|..+.+.      ...+..++....+..+.+.|+.|- ...+.++..+... .+.+..  .  .  ..       
T Consensus       277 ~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~  356 (545)
T PTZ00110        277 RVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFV  356 (545)
T ss_pred             hCcEEEeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEE
Confidence            355666655432      122344443322445678888884 4556666665432 111100  0  0  00       


Q ss_pred             CCHHHHHHHHHH----HhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE---
Q psy437           68 LADKLRNEVQMK----WISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV---  140 (184)
Q Consensus        68 l~~~~R~~~~~~----f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va---  140 (184)
                      .+..++...+..    +.....++||+|+++..|+.++..|...|+.+..+|+++++..|..+.+.|++|++.|+||   
T Consensus       357 ~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv  436 (545)
T PTZ00110        357 VEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDV  436 (545)
T ss_pred             EechhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcch
Confidence            111223333333    3324568999999999999999999999999999999999999999999999999999999   


Q ss_pred             ----EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 ----WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ----~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                          +|+|+|++||||++|.+.++|+||++  |+||.
T Consensus       437 ~~rGIDi~~v~~VI~~d~P~s~~~yvqRiG--RtGR~  471 (545)
T PTZ00110        437 ASRGLDVKDVKYVINFDFPNQIEDYVHRIG--RTGRA  471 (545)
T ss_pred             hhcCCCcccCCEEEEeCCCCCHHHHHHHhc--ccccC
Confidence                69999999999999999999999996  55554

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.63  E-value=1.2e-14  Score=123.55  Aligned_cols=138  Identities=14%  Similarity=0.140  Sum_probs=108.4

Q ss_pred             CCcEEEEeccH--HHHHHHHHHHHhCCCee-------------EEecCCCCHHHHHHHHHHHhcc--CceEEEEEeeccc
Q psy437           34 GQSGIVYCLTR--KECDSVAAALAQERINA-------------ISYHAGLADKLRNEVQMKWISN--KVHVGHWTVVSKE   96 (184)
Q Consensus        34 ~~~~IIf~~tr--~~~e~la~~L~~~gi~~-------------~~~hg~l~~~~R~~~~~~f~~g--~~~vlVaT~tr~~   96 (184)
                      ..+.+.|+.|-  .....++..+......+             ..++-.-+...+...+..+...  ..++||+|+++..
T Consensus       178 ~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~  257 (434)
T PRK11192        178 RKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRER  257 (434)
T ss_pred             ccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHH
Confidence            34678888775  34666666664321111             1111111234566777777753  4589999999999


Q ss_pred             HHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcccccccccccc
Q psy437           97 CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLR  169 (184)
Q Consensus        97 ~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~  169 (184)
                      |+.++..|...|+++..+|+++++..|..+.+.|++|.+.|+||       +|+|++++|||+++|.+.+.|+|+++  |
T Consensus       258 ~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~G--R  335 (434)
T PRK11192        258 VHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIG--R  335 (434)
T ss_pred             HHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhccc--c
Confidence            99999999999999999999999999999999999999999999       69999999999999999999999995  5


Q ss_pred             CCcc
Q psy437          170 LGRE  173 (184)
Q Consensus       170 ~~r~  173 (184)
                      +||.
T Consensus       336 ~gR~  339 (434)
T PRK11192        336 TGRA  339 (434)
T ss_pred             cccC
Confidence            5654

>KOG0334|consensus

Probab=99.63  E-value=1.8e-15  Score=135.49  Aligned_cols=118  Identities=14%  Similarity=0.194  Sum_probs=109.5

Q ss_pred             CeEEEEEE-ccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE
Q psy437            9 NLKYEILP-KKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus         9 Nl~y~v~~-~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v   87 (184)
                      ++.+.|+. ...|+..|..+|.......++||||.....|+.+...|.+.|+.|..+|||.++.+|..+++.|+++.+.+
T Consensus       587 ~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~L  666 (997)
T KOG0334|consen  587 TQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNL  666 (997)
T ss_pred             eEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceE
Confidence            45667777 66799999999987767899999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      ||||+      .+|+||+...+. +||||++|.-.++|+||..++|
T Consensus       667 LvaTs------vvarGLdv~~l~-Lvvnyd~pnh~edyvhR~gRTg  705 (997)
T KOG0334|consen  667 LVATS------VVARGLDVKELI-LVVNYDFPNHYEDYVHRVGRTG  705 (997)
T ss_pred             EEehh------hhhcccccccce-EEEEcccchhHHHHHHHhcccc
Confidence            99999      899999999999 9999999999999999996654

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.63  E-value=2.7e-15  Score=127.25  Aligned_cols=104  Identities=13%  Similarity=0.111  Sum_probs=90.5

Q ss_pred             HHHHHHHHHHHhcc--CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           70 DKLRNEVQMKWISN--KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        70 ~~~R~~~~~~f~~g--~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      ..++...+..+...  ..++||+++++..|+.++..|...|+++..+|++++++.|..+.+.|++|++.|+|+       
T Consensus       239 ~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rG  318 (423)
T PRK04837        239 NEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARG  318 (423)
T ss_pred             HHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcC
Confidence            34555566665543  357999999999999999999999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCCCcccccccccc-ccCCcc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      +|+|++++||||++|.+.++|+|++++ +|.|+.
T Consensus       319 iDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~  352 (423)
T PRK04837        319 LHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGAS  352 (423)
T ss_pred             CCccccCEEEEeCCCCchhheEeccccccCCCCC
Confidence            599999999999999999999999964 344443

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.63  E-value=2.1e-15  Score=137.86  Aligned_cols=95  Identities=17%  Similarity=0.167  Sum_probs=88.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC------CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHh
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE------RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQ  106 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~------gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~  106 (184)
                      ...++||||+|++.|+.++..|.+.      +..+.++||+|++++|..+++.|++|+.++||||+      .+++|+|.
T Consensus       283 ~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs------~Le~GIDi  356 (876)
T PRK13767        283 EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSST------SLELGIDI  356 (876)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECC------hHHhcCCC
Confidence            3578999999999999999999862      46789999999999999999999999999999999      88999999


Q ss_pred             cCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          107 ERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       107 ~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++++ +|||++.|.+...|+||..++|.
T Consensus       357 p~Vd-~VI~~~~P~sv~~ylQRiGRaGR  383 (876)
T PRK13767        357 GYID-LVVLLGSPKSVSRLLQRIGRAGH  383 (876)
T ss_pred             CCCc-EEEEeCCCCCHHHHHHhcccCCC
Confidence            9999 99999999999999999988773

>KOG0344|consensus

Probab=99.62  E-value=2.8e-15  Score=127.50  Aligned_cols=125  Identities=13%  Similarity=0.119  Sum_probs=109.9

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHH-HhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAAL-AQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKEC   97 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L-~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~   97 (184)
                      .|+-.+.+++... -.+|.+||+.+.+.|.++...| .-.++.+.++||..++.+|..++++|+.|++.+||||+     
T Consensus       373 ~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTd-----  446 (593)
T KOG0344|consen  373 GKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTD-----  446 (593)
T ss_pred             hHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehh-----
Confidence            4788888888764 5678999999999999999999 77899999999999999999999999999999999999     


Q ss_pred             HHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC----ceEEEEE---ecCCccEEEe
Q psy437           98 DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK----VHLYNVW---KIQWKRIIWI  151 (184)
Q Consensus        98 e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~----~~v~va~---D~~~vr~v~~  151 (184)
                       .++||+|..|++ .|||+|+|++.-.|+||..++|.    ...+..|   |.|.+|.+.+
T Consensus       447 -ll~RGiDf~gvn-~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae  505 (593)
T KOG0344|consen  447 -LLARGIDFKGVN-LVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAE  505 (593)
T ss_pred             -hhhccccccCcc-eEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHH
Confidence             999999999999 99999999999999999977653    3444443   7777776643

>KOG0336|consensus

Probab=99.62  E-value=6.1e-15  Score=121.36  Aligned_cols=166  Identities=14%  Similarity=0.178  Sum_probs=124.6

Q ss_pred             CCCeEEEEEEccChH------HHHHHHHHhhcCCCcEEEEecc-HHHHHHHHHHHHhCCCeeEEecCCCC----------
Q psy437            7 RANLKYEILPKKNVL------KEVISLIKAKYSGQSGIVYCLT-RKECDSVAAALAQERINAISYHAGLA----------   69 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~------~~L~~~l~~~~~~~~~IIf~~t-r~~~e~la~~L~~~gi~~~~~hg~l~----------   69 (184)
                      =.++.|.|....+++      -.+..+|.+.-+..+++.-..| ...+..+++..-+.  +..+|-|.|+          
T Consensus       365 l~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Ke--p~~v~vGsLdL~a~~sVkQ~  442 (629)
T KOG0336|consen  365 LASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKE--PMIVYVGSLDLVAVKSVKQN  442 (629)
T ss_pred             eeeeEEEEecchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhC--ceEEEecccceeeeeeeeee
Confidence            345778887665432      2445555443244444444333 34556666544332  2344444442          


Q ss_pred             -----HHHHHHHHHHHhcc---CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-
Q psy437           70 -----DKLRNEVQMKWISN---KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-  140 (184)
Q Consensus        70 -----~~~R~~~~~~f~~g---~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-  140 (184)
                           ..++..+.+.|...   ..++||++..+..++.++.-+...||++..+|++-.|+.|+...+.|++|.++|+|| 
T Consensus       443 i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaT  522 (629)
T KOG0336|consen  443 IIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVAT  522 (629)
T ss_pred             EEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEe
Confidence                 35566777777653   458999999999999999999999999999999999999999999999999999999 


Q ss_pred             ------EecCCccEEEecCCCCCcccccccccc-ccCCccc
Q psy437          141 ------WKIQWKRIIWIHSLVLIKPDYLPPILD-LRLGRED  174 (184)
Q Consensus       141 ------~D~~~vr~v~~~~~p~~~e~y~~~i~~-~~~~r~~  174 (184)
                            +|++||.||+|||.|...|.|+|++++ +|+||.+
T Consensus       523 DlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G  563 (629)
T KOG0336|consen  523 DLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTG  563 (629)
T ss_pred             chhhcCCCchhcceeeccCCCccHHHHHHHhcccccCCCCc
Confidence                  699999999999999999999999998 4898863

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

Probab=99.58  E-value=5.8e-14  Score=122.00  Aligned_cols=162  Identities=19%  Similarity=0.212  Sum_probs=113.9

Q ss_pred             CCeEEEEEEccCh------HHHHHHHHHhhcCCCcEEEEeccHH-HHHHHHHHHHhCCCee--------------EEecC
Q psy437            8 ANLKYEILPKKNV------LKEVISLIKAKYSGQSGIVYCLTRK-ECDSVAAALAQERINA--------------ISYHA   66 (184)
Q Consensus         8 ~Nl~y~v~~~~~k------~~~L~~~l~~~~~~~~~IIf~~tr~-~~e~la~~L~~~gi~~--------------~~~hg   66 (184)
                      .++.|.|..+-+.      ...+..++.. .+..+.+.|..|-. ..+.++..+...-+.+              ..+. 
T Consensus       269 ~~v~~lViDEad~ml~~gf~~~i~~i~~~-l~~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~-  346 (518)
T PLN00206        269 DNVSVLVLDEVDCMLERGFRDQVMQIFQA-LSQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIW-  346 (518)
T ss_pred             hheeEEEeecHHHHhhcchHHHHHHHHHh-CCCCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEe-
Confidence            4566666655432      2334444433 35567888888764 4556666654321100              0000 


Q ss_pred             CCCHHHH-HHHHHHHhc---cCceEEEEEeecccHHHHHHHHHh-cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-
Q psy437           67 GLADKLR-NEVQMKWIS---NKVHVGHWTVVSKECDSVAAALAQ-ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-  140 (184)
Q Consensus        67 ~l~~~~R-~~~~~~f~~---g~~~vlVaT~tr~~~e~~a~gL~~-~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-  140 (184)
                       .....+ ..+.+.+..   ...++||+++++..|+.++..|.. .|+++..+|+++++..|..+.+.|++|++.|+|| 
T Consensus       347 -~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaT  425 (518)
T PLN00206        347 -VETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVAT  425 (518)
T ss_pred             -ccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEe
Confidence             111222 233333322   234799999999999999999964 7999999999999999999999999999999999 


Q ss_pred             ------EecCCccEEEecCCCCCccccccccccccCCccc
Q psy437          141 ------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       141 ------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                            +|+|++++||||++|.+.++|+|+++  |+||.+
T Consensus       426 dvl~rGiDip~v~~VI~~d~P~s~~~yihRiG--RaGR~g  463 (518)
T PLN00206        426 GVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIG--RASRMG  463 (518)
T ss_pred             cHhhccCCcccCCEEEEeCCCCCHHHHHHhcc--ccccCC
Confidence                  59999999999999999999999995  666653

>KOG0335|consensus

Probab=99.58  E-value=1.6e-14  Score=121.53  Aligned_cols=86  Identities=19%  Similarity=0.142  Sum_probs=82.2

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCc
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIK  158 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~  158 (184)
                      .++|++.+.+.|+.++..|...++++.-||++..+..|....+.|++|+.+++||       +|+|+|+||||||+|.+.
T Consensus       339 ~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~  418 (482)
T KOG0335|consen  339 KTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVLVATNVAARGLDIPNVKHVINYDMPADI  418 (482)
T ss_pred             eEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceEEEehhhhcCCCCCCCceeEEeecCcch
Confidence            6899999999999999999999999999999999999999999999999999999       699999999999999999


Q ss_pred             cccccccccccCCcc
Q psy437          159 PDYLPPILDLRLGRE  173 (184)
Q Consensus       159 e~y~~~i~~~~~~r~  173 (184)
                      ++|+|||+  |.||.
T Consensus       419 d~YvHRIG--RTGR~  431 (482)
T KOG0335|consen  419 DDYVHRIG--RTGRV  431 (482)
T ss_pred             hhHHHhcc--ccccC
Confidence            99999995  66665

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.58  E-value=5.4e-14  Score=120.99  Aligned_cols=100  Identities=16%  Similarity=0.151  Sum_probs=88.4

Q ss_pred             HHHHHHHHHhcc--CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Ee
Q psy437           72 LRNEVQMKWISN--KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WK  142 (184)
Q Consensus        72 ~R~~~~~~f~~g--~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D  142 (184)
                      ++...+..+...  ..++||+|+++..|+.++..|...|+.+..+|+++|+..|..+.+.|++|++.++|+       +|
T Consensus       321 ~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GID  400 (475)
T PRK01297        321 DKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIH  400 (475)
T ss_pred             hHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCc
Confidence            444555555432  348999999999999999999999999999999999999999999999999999999       59


Q ss_pred             cCCccEEEecCCCCCccccccccccccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|++++||++++|.+.++|+|+++  |+||.
T Consensus       401 i~~v~~VI~~~~P~s~~~y~Qr~G--RaGR~  429 (475)
T PRK01297        401 IDGISHVINFTLPEDPDDYVHRIG--RTGRA  429 (475)
T ss_pred             ccCCCEEEEeCCCCCHHHHHHhhC--ccCCC
Confidence            999999999999999999999995  66664

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.57  E-value=5e-14  Score=123.63  Aligned_cols=101  Identities=13%  Similarity=0.154  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           71 KLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        71 ~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      .++...+..+..  ...++||+|+++..|+.++..|...|+.+.++|+++|+..|..+.+.|++|++.|+|+       +
T Consensus       242 ~~k~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGI  321 (572)
T PRK04537        242 EEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGL  321 (572)
T ss_pred             HHHHHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCC
Confidence            344444444443  3457999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|+|++||||++|.+.++|+|+++  |+||.
T Consensus       322 Dip~V~~VInyd~P~s~~~yvqRiG--RaGR~  351 (572)
T PRK04537        322 HIDGVKYVYNYDLPFDAEDYVHRIG--RTARL  351 (572)
T ss_pred             CccCCCEEEEcCCCCCHHHHhhhhc--ccccC
Confidence            9999999999999999999999996  55553

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.57  E-value=1.8e-14  Score=131.56  Aligned_cols=107  Identities=14%  Similarity=0.062  Sum_probs=97.1

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHH-hCCCeeEEecCCCCHHHHHHHHHHHhcc--CceEEEEEeecc
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALA-QERINAISYHAGLADKLRNEVQMKWISN--KVHVGHWTVVSK   95 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~-~~gi~~~~~hg~l~~~~R~~~~~~f~~g--~~~vlVaT~tr~   95 (184)
                      .|+..|.++|+.. ...++||||+++..++.+++.|. ..|+++..+||+|++.+|.++++.|.++  ..+|||||+   
T Consensus       479 ~Ki~~L~~~L~~~-~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTd---  554 (956)
T PRK04914        479 PRVEWLIDFLKSH-RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSE---  554 (956)
T ss_pred             HHHHHHHHHHHhc-CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEech---
Confidence            4888899988764 57899999999999999999994 5699999999999999999999999984  589999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                         ..++|++...++ .|||+|+|-++..|.||..+.+
T Consensus       555 ---vgseGlNlq~a~-~VInfDlP~nP~~~eQRIGR~~  588 (956)
T PRK04914        555 ---IGSEGRNFQFAS-HLVLFDLPFNPDLLEQRIGRLD  588 (956)
T ss_pred             ---hhccCCCccccc-EEEEecCCCCHHHHHHHhcccc
Confidence               788999999999 9999999999999999996543

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.56  E-value=1.9e-14  Score=135.43  Aligned_cols=95  Identities=15%  Similarity=0.111  Sum_probs=86.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCC---------------------------------CeeEEecCCCCHHHHHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQER---------------------------------INAISYHAGLADKLRNEVQMK   79 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~g---------------------------------i~~~~~hg~l~~~~R~~~~~~   79 (184)
                      ...++|||||||+.||.++..|.+..                                 +.+.++||+|++++|..+++.
T Consensus       243 ~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~  322 (1490)
T PRK09751        243 RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQA  322 (1490)
T ss_pred             cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHH
Confidence            45789999999999999999997531                                 125689999999999999999


Q ss_pred             HhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           80 WISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        80 f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |++|+.++||||+      .++.|+|..+++ +|||++.|.+..+|+||..++|.
T Consensus       323 fK~G~LrvLVATs------sLELGIDIg~VD-lVIq~gsP~sVas~LQRiGRAGR  370 (1490)
T PRK09751        323 LKSGELRCVVATS------SLELGIDMGAVD-LVIQVATPLSVASGLQRIGRAGH  370 (1490)
T ss_pred             HHhCCceEEEeCc------HHHccCCcccCC-EEEEeCCCCCHHHHHHHhCCCCC
Confidence            9999999999999      889999999999 99999999999999999998875

>KOG0338|consensus

Probab=99.55  E-value=1.1e-14  Score=122.48  Aligned_cols=160  Identities=14%  Similarity=0.129  Sum_probs=118.0

Q ss_pred             CCCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHH-HHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc
Q psy437            4 SFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRK-ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS   82 (184)
Q Consensus         4 s~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~-~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~   82 (184)
                      +-+|+|+.|+++..+ ++..|..+-.    ..|.=||++..+ .+-.|.+.+-    ++..   + -...|..++-.+..
T Consensus       356 pk~RQTmLFSATMte-eVkdL~slSL----~kPvrifvd~~~~~a~~LtQEFi----RIR~---~-re~dRea~l~~l~~  422 (691)
T KOG0338|consen  356 PKNRQTMLFSATMTE-EVKDLASLSL----NKPVRIFVDPNKDTAPKLTQEFI----RIRP---K-REGDREAMLASLIT  422 (691)
T ss_pred             cccccceeehhhhHH-HHHHHHHhhc----CCCeEEEeCCccccchhhhHHHh----eecc---c-cccccHHHHHHHHH
Confidence            446777777777763 3455554332    245666665433 3444444442    1111   0 01235555555443


Q ss_pred             --cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecC
Q psy437           83 --NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHS  153 (184)
Q Consensus        83 --g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~  153 (184)
                        -+.++||++.+++.|.++---|.--|+++.=+||++.|..|-...+.|+.+.+.+++|       +||+.|..||||.
T Consensus       423 rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLDI~gV~tVINy~  502 (691)
T KOG0338|consen  423 RTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLDIEGVQTVINYA  502 (691)
T ss_pred             HhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCCccceeEEEecc
Confidence              3568999999999988887777888999999999999999999999999999999999       6999999999999


Q ss_pred             CCCCccccccccccc-cCCccccc
Q psy437          154 LVLIKPDYLPPILDL-RLGREDIR  176 (184)
Q Consensus       154 ~p~~~e~y~~~i~~~-~~~r~~~~  176 (184)
                      +|++.+.|+||++++ |+||++.+
T Consensus       503 mP~t~e~Y~HRVGRTARAGRaGrs  526 (691)
T KOG0338|consen  503 MPKTIEHYLHRVGRTARAGRAGRS  526 (691)
T ss_pred             CchhHHHHHHHhhhhhhcccCcce
Confidence            999999999999996 99998543

>PRK14701 reverse gyrase; Provisional

Probab=99.55  E-value=1e-14  Score=138.95  Aligned_cols=117  Identities=12%  Similarity=0.123  Sum_probs=83.9

Q ss_pred             CCCCCCCeEEEEEE----ccChHHHHHHHHHhhcCCCcEEEEeccHHH---HHHHHHHHHhCCCeeEEecCCCCHHHHHH
Q psy437            3 SSFNRANLKYEILP----KKNVLKEVISLIKAKYSGQSGIVYCLTRKE---CDSVAAALAQERINAISYHAGLADKLRNE   75 (184)
Q Consensus         3 ~s~~R~Nl~y~v~~----~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~---~e~la~~L~~~gi~~~~~hg~l~~~~R~~   75 (184)
                      .++.++|+...+..    .......|.++++.  .+.++||||+|++.   |+.+++.|...|+++..+||+     |..
T Consensus       297 v~~~~~~lr~i~~~yi~~~~~~k~~L~~ll~~--~g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~  369 (1638)
T PRK14701        297 VGSGRSALRNIVDVYLNPEKIIKEHVRELLKK--LGKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKK  369 (1638)
T ss_pred             ecCCCCCCCCcEEEEEECCHHHHHHHHHHHHh--CCCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHH
Confidence            35566665443322    22223567777765  35789999999885   589999999999999999996     899


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcC-CcEEEeeCCCCh---HHHHHHHHH
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQER-INAISYHAGLAD---KLRNEVQMK  129 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g-i~~~vih~~~p~---~~r~~~~~~  129 (184)
                      .+++|++|+++|||||+++-+  .+|||||.++ |+ +|+|+|+|+   +.+.|.|..
T Consensus       370 ~l~~F~~G~~~VLVaT~s~~g--vaaRGIDiP~~Vr-yvi~~~~Pk~~~~~e~~~~~~  424 (1638)
T PRK14701        370 GFDLFEEGEIDYLIGVATYYG--TLVRGLDLPERIR-FAVFYGVPKFRFRVDLEDPTI  424 (1638)
T ss_pred             HHHHHHcCCCCEEEEecCCCC--eeEecCccCCccC-EEEEeCCCCCCcchhhcccch
Confidence            999999999999999974422  4566666666 55 666666666   555555544

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.54  E-value=3.9e-14  Score=126.80  Aligned_cols=123  Identities=15%  Similarity=0.100  Sum_probs=102.7

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||++....     .....|...|.+.+.+. ..+.|+||||+|++.++.++..|.+.|+++..+||+++++++..+.
T Consensus       392 Pt~kp~~r~d~~~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~  471 (790)
T PRK09200        392 PTNRPIIRIDYPDKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIA  471 (790)
T ss_pred             CCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHH
Confidence            56777765322     23345888888888653 3577899999999999999999999999999999999998888888


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHh---cCCc----EEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQ---ERIN----AISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~---~gi~----~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ..+..|  +|+|||+      .++||+|+   +++.    -+|||+++|.+.|.|.|+.+++|.
T Consensus       472 ~ag~~g--~VlIATd------mAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR  527 (790)
T PRK09200        472 EAGQKG--AVTVATN------MAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGR  527 (790)
T ss_pred             HcCCCC--eEEEEcc------chhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccC
Confidence            887766  7999999      88999999   5775    399999999999999999977654

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

Probab=99.54  E-value=9.9e-14  Score=124.88  Aligned_cols=100  Identities=13%  Similarity=0.088  Sum_probs=87.2

Q ss_pred             HHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhc--------CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE---
Q psy437           72 LRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQE--------RINAISYHAGLADKLRNEVQMKWISNKVHLYNV---  140 (184)
Q Consensus        72 ~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~--------gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va---  140 (184)
                      ++...+..+.....++||+|++|+.||.+++.|...        +.++.+||+|++++.|..+.+.|++|++.++|+   
T Consensus       259 ~~~~~l~~l~~~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~  338 (742)
T TIGR03817       259 EAADLLADLVAEGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNA  338 (742)
T ss_pred             HHHHHHHHHHHCCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECch
Confidence            455566666666679999999999999999988543        556789999999999999999999999999999   


Q ss_pred             ----EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 ----WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ----~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                          +|++++.+|||+++|.+.++|+|+++  |+||.
T Consensus       339 lerGIDI~~vd~VI~~~~P~s~~~y~qRiG--RaGR~  373 (742)
T TIGR03817       339 LELGVDISGLDAVVIAGFPGTRASLWQQAG--RAGRR  373 (742)
T ss_pred             HhccCCcccccEEEEeCCCCCHHHHHHhcc--ccCCC
Confidence                69999999999999999999999996  55554

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.53  E-value=2e-13  Score=113.20  Aligned_cols=116  Identities=12%  Similarity=0.066  Sum_probs=92.5

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC--eeEEecCCCCHHHHHH----HHHHHhccCceEEEEEe
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI--NAISYHAGLADKLRNE----VQMKWISNKVHVGHWTV   92 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi--~~~~~hg~l~~~~R~~----~~~~f~~g~~~vlVaT~   92 (184)
                      .+...+.+++.....+.++||||+|++.|+.+++.|.+.+.  .+..+||++++.+|.+    +++.|++|+.++||||+
T Consensus       207 ~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~  286 (358)
T TIGR01587       207 GEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ  286 (358)
T ss_pred             cCHHHHHHHHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc
Confidence            35555665554333567999999999999999999988766  5899999999999976    48899999999999999


Q ss_pred             ecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC--------ceEEEEEecC
Q psy437           93 VSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK--------VHLYNVWKIQ  144 (184)
Q Consensus        93 tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~--------~~v~va~D~~  144 (184)
                            .+++|+|.+ ++ .++++..|  ..+|+||.+|.|.        ..+++..+.+
T Consensus       287 ------~~~~GiDi~-~~-~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       287 ------VIEASLDIS-AD-VMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             ------chhceeccC-CC-EEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence                  889999995 66 88888777  5789999966543        2566664444

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.

>KOG4284|consensus

Probab=99.53  E-value=1.9e-14  Score=123.95  Aligned_cols=107  Identities=11%  Similarity=0.112  Sum_probs=99.8

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      |++.|-++++.. +..++||||+....|+.++..|...|+.|.++.|.|+|.+|..++++++.-.++|||+|+      .
T Consensus       259 klq~L~~vf~~i-py~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTD------L  331 (980)
T KOG4284|consen  259 KLQKLTHVFKSI-PYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTD------L  331 (980)
T ss_pred             HHHHHHHHHhhC-chHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecc------h
Confidence            777777777653 778999999999999999999999999999999999999999999999999999999999      9


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .|||+|.+.++ +|+|.|.|++.++|.||..+.|.
T Consensus       332 taRGIDa~~vN-LVVNiD~p~d~eTY~HRIGRAgR  365 (980)
T KOG4284|consen  332 TARGIDADNVN-LVVNIDAPADEETYFHRIGRAGR  365 (980)
T ss_pred             hhccCCccccc-eEEecCCCcchHHHHHHhhhccc
Confidence            99999999999 99999999999999999976653

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.53  E-value=6.9e-14  Score=122.97  Aligned_cols=123  Identities=11%  Similarity=0.033  Sum_probs=96.7

Q ss_pred             CCCCCCe----E-EEEEEccChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANL----K-YEILPKKNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl----~-y~v~~~~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      +.++|++    . |..+....|...|.+.+.... .+.++||||+|++.++.+++.|.+.|+++..+||++++  |+..+
T Consensus       437 Pt~kp~~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~--rE~~i  514 (656)
T PRK12898        437 PTNRPSQRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDA--EEAAI  514 (656)
T ss_pred             CCCCCccceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHH--HHHHH
Confidence            4556665    2 333334468888998886532 35789999999999999999999999999999998654  44555


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc---CCc----EEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE---RIN----AISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~---gi~----~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ..+..+...|+|||+      .++||+|++   +|.    .+|||+++|.+.|.|.|+..++|.
T Consensus       515 i~~ag~~g~VlVATd------mAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGR  572 (656)
T PRK12898        515 VARAGQRGRITVATN------MAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGR  572 (656)
T ss_pred             HHHcCCCCcEEEEcc------chhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccC
Confidence            555555667999999      889999998   553    289999999999999999977654

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.52  E-value=1.6e-13  Score=121.70  Aligned_cols=111  Identities=14%  Similarity=0.118  Sum_probs=98.6

Q ss_pred             EccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           16 PKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        16 ~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      +...++..|.+.|++. ..+.++||||+|++.++.+++.|.+.|+++.++||++++.+|.+++..|+.|++.|+|||+  
T Consensus       423 ~~~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~--  500 (655)
T TIGR00631       423 PTDGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGIN--  500 (655)
T ss_pred             eccchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcC--
Confidence            3445777777777643 2567899999999999999999999999999999999999999999999999999999999  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCC-----CChHHHHHHHHHhhCC
Q psy437           95 KECDSVAAALAQERINAISYHAG-----LADKLRNEVQMKWISN  133 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~-----~p~~~r~~~~~~f~~~  133 (184)
                          .+++|++.++++ +|++.+     +|.+.+.|+|+.+|.|
T Consensus       501 ----~L~rGfDiP~v~-lVvi~DadifG~p~~~~~~iqriGRag  539 (655)
T TIGR00631       501 ----LLREGLDLPEVS-LVAILDADKEGFLRSERSLIQTIGRAA  539 (655)
T ss_pred             ----hhcCCeeeCCCc-EEEEeCcccccCCCCHHHHHHHhcCCC
Confidence                899999999999 887776     8999999999997654

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

>KOG0339|consensus

Probab=99.52  E-value=5e-14  Score=118.58  Aligned_cols=108  Identities=17%  Similarity=0.131  Sum_probs=98.5

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .|+..|+..|-.....++.|||+..+.+++.++..|...|+++..+||+|+|.+|.+++.+|+++..+|+|+|+      
T Consensus       453 ~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatD------  526 (731)
T KOG0339|consen  453 KKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATD------  526 (731)
T ss_pred             HHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEee------
Confidence            37777777775544557899999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      ..|+|||++.++ .|+++|+-.+++.++|+..+.|
T Consensus       527 vaargldI~~ik-TVvnyD~ardIdththrigrtg  560 (731)
T KOG0339|consen  527 VAARGLDIPSIK-TVVNYDFARDIDTHTHRIGRTG  560 (731)
T ss_pred             HhhcCCCccccc-eeecccccchhHHHHHHhhhcc
Confidence            999999999999 9999999999999999996654

>KOG0339|consensus

Probab=99.52  E-value=1.5e-13  Score=115.68  Aligned_cols=134  Identities=16%  Similarity=0.119  Sum_probs=116.7

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec---------------
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS---------------   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr---------------   94 (184)
                      ++-++|.|+|++.|.++...-++    -|+++.+.|||.+..+....|+    ....+||||+.|               
T Consensus       296 gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rv  371 (731)
T KOG0339|consen  296 GPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRV  371 (731)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceee
Confidence            34467889999999998665544    3889999999999877666655    356789999999               


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       372 S~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~  451 (731)
T KOG0339|consen  372 SYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSE  451 (731)
T ss_pred             eEEEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCc
Confidence                                                                                            


Q ss_pred             ---------------------------ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           95 ---------------------------KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        95 ---------------------------~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                                                 .++|.++.-|...|+++..+|+++.|..|+.+...|+.+..+|++|       
T Consensus       452 ~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaarg  531 (731)
T KOG0339|consen  452 EKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARG  531 (731)
T ss_pred             HHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcC
Confidence                                       3789999999999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|+++++.|+|||.-.+.|.|.|+|.  |.||+
T Consensus       532 ldI~~ikTVvnyD~ardIdththrig--rtgRa  562 (731)
T KOG0339|consen  532 LDIPSIKTVVNYDFARDIDTHTHRIG--RTGRA  562 (731)
T ss_pred             CCccccceeecccccchhHHHHHHhh--hcccc
Confidence            59999999999999999999999995  55554

>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=99.50  E-value=4.8e-13  Score=94.76  Aligned_cols=115  Identities=19%  Similarity=0.255  Sum_probs=90.6

Q ss_pred             eEEEEEEcc-ChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE
Q psy437           10 LKYEILPKK-NVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus        10 l~y~v~~~~-~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v   87 (184)
                      |.+.+.+.. .|...+.+.+.+.. .+.++||||++...++.+++.|.+.+.++..+||+++..+|..+++.|.++...+
T Consensus         2 i~~~~~~~~~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~i   81 (131)
T cd00079           2 IKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVV   81 (131)
T ss_pred             cEEEEEECCHHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcE
Confidence            344444443 58888888887642 3678999999999999999999998999999999999999999999999999999


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      |++|.      .++.|++.++.+ .+++.+.|.+...+.|...+
T Consensus        82 li~t~------~~~~G~d~~~~~-~vi~~~~~~~~~~~~Q~~GR  118 (131)
T cd00079          82 LVATD------VIARGIDLPNVS-VVINYDLPWSPSSYLQRIGR  118 (131)
T ss_pred             EEEcC------hhhcCcChhhCC-EEEEeCCCCCHHHheecccc
Confidence            99999      556677766666 56666665555555555433

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.49  E-value=4.7e-13  Score=119.03  Aligned_cols=114  Identities=15%  Similarity=0.152  Sum_probs=98.4

Q ss_pred             EEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           14 ILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        14 v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      +.+...++..|.+.|... ..+.++||||+|++.++.+++.|...|+++.++||++++.+|..++..|+.|++.++|+|+
T Consensus       425 ~~~~~~q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~  504 (652)
T PRK05298        425 VRPTKGQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGIN  504 (652)
T ss_pred             EeeccccHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeC
Confidence            334445677777777543 2467899999999999999999999999999999999999999999999999999999999


Q ss_pred             ecccHHHHHHHHHhcCCcEEEeeCC-----CChHHHHHHHHHhhCCC
Q psy437           93 VSKECDSVAAALAQERINAISYHAG-----LADKLRNEVQMKWISNK  134 (184)
Q Consensus        93 tr~~~e~~a~gL~~~gi~~~vih~~-----~p~~~r~~~~~~f~~~~  134 (184)
                            .+++|++.++++ +|++++     +|.+.+.|+|+.++.|.
T Consensus       505 ------~L~rGfdlp~v~-lVii~d~eifG~~~~~~~yiqr~GR~gR  544 (652)
T PRK05298        505 ------LLREGLDIPEVS-LVAILDADKEGFLRSERSLIQTIGRAAR  544 (652)
T ss_pred             ------HHhCCccccCCc-EEEEeCCcccccCCCHHHHHHHhccccC
Confidence                  999999999999 777766     48899999999977543

>KOG0350|consensus

Probab=99.49  E-value=1.1e-13  Score=116.19  Aligned_cols=106  Identities=11%  Similarity=0.116  Sum_probs=93.7

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHH----hCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALA----QERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~----~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      |--.+..+|... +..++|+|+++.+.+..+++.|.    ..++++..|.|+++.+.|.+.++.|.+|++++|||++   
T Consensus       416 kpl~~~~lI~~~-k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD---  491 (620)
T KOG0350|consen  416 KPLAVYALITSN-KLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSD---  491 (620)
T ss_pred             chHhHHHHHHHh-hcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehh---
Confidence            455566666543 67889999999999999999887    3467788899999999999999999999999999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                         .+|||+|..+++ .||||++|.+.+.|+||.++.+
T Consensus       492 ---~laRGiDv~~v~-~VINYd~P~~~ktyVHR~GRTA  525 (620)
T KOG0350|consen  492 ---ALARGIDVNDVD-NVINYDPPASDKTYVHRAGRTA  525 (620)
T ss_pred             ---hhhcCCcccccc-eEeecCCCchhhHHHHhhcccc
Confidence               999999999999 9999999999999999996643

>KOG0349|consensus

Probab=99.49  E-value=4.6e-14  Score=117.05  Aligned_cols=100  Identities=17%  Similarity=0.213  Sum_probs=91.1

Q ss_pred             HHHhhcCCCcEEEEeccHHHHHHHHHHHHhCC---CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHH
Q psy437           27 LIKAKYSGQSGIVYCLTRKECDSVAAALAQER---INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAA  103 (184)
Q Consensus        27 ~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~g---i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~g  103 (184)
                      .+++ +...++||||.|+.+|+.+.+.|.+.|   +++..+||+..+.+|.+.++.|++++++.||||+      .+|+|
T Consensus       499 ai~~-h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictd------vaarg  571 (725)
T KOG0349|consen  499 AIRR-HAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTD------VAARG  571 (725)
T ss_pred             hhhh-hccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEeh------hhhcc
Confidence            3444 377899999999999999999998864   6899999999999999999999999999999999      99999


Q ss_pred             HHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          104 LAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       104 L~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ||+.|++ ++||.-+|.+..+|+||..+-|.
T Consensus       572 ldi~g~p-~~invtlpd~k~nyvhrigrvgr  601 (725)
T KOG0349|consen  572 LDITGLP-FMINVTLPDDKTNYVHRIGRVGR  601 (725)
T ss_pred             ccccCCc-eEEEEecCcccchhhhhhhccch
Confidence            9999999 99999999999999999976654

>PRK09401 reverse gyrase; Reviewed

Probab=99.47  E-value=1.3e-13  Score=128.64  Aligned_cols=114  Identities=15%  Similarity=0.174  Sum_probs=89.0

Q ss_pred             CCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHH---HHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC
Q psy437            8 ANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKE---CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK   84 (184)
Q Consensus         8 ~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~---~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~   84 (184)
                      .|+........++...|..+++.  .+.++||||+|+..   ++.+++.|...|+++..+||+|     .+.+++|++|+
T Consensus       304 rnI~~~yi~~~~k~~~L~~ll~~--l~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~  376 (1176)
T PRK09401        304 RNIVDSYIVDEDSVEKLVELVKR--LGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGE  376 (1176)
T ss_pred             CCceEEEEEcccHHHHHHHHHHh--cCCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCC
Confidence            45543333333677788888865  34689999999877   9999999999999999999999     23459999999


Q ss_pred             ceEEEEEeecccHHHHHHHHHhcC-CcEEEeeCCCCh------HHHHHHHHHhh
Q psy437           85 VHVGHWTVVSKECDSVAAALAQER-INAISYHAGLAD------KLRNEVQMKWI  131 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~g-i~~~vih~~~p~------~~r~~~~~~f~  131 (184)
                      ++|||||.+.-+  .+|||||.++ |+ +|||+|+|.      ....+.|+.++
T Consensus       377 ~~VLVatas~td--v~aRGIDiP~~Ir-yVI~y~vP~~~~~~~~~~~~~~~~~r  427 (1176)
T PRK09401        377 VDVLVGVASYYG--VLVRGIDLPERIR-YAIFYGVPKFKFSLEEELAPPFLLLR  427 (1176)
T ss_pred             CCEEEEecCCCC--ceeecCCCCccee-EEEEeCCCCEEEeccccccCHHHHHH
Confidence            999999643211  7899999999 88 999999999      55556665543

>KOG0342|consensus

Probab=99.47  E-value=3e-13  Score=113.28  Aligned_cols=76  Identities=11%  Similarity=0.031  Sum_probs=68.4

Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcccccccccc
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILD  167 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~  167 (184)
                      ..+.-.|.-|..-++++.-||+++||+.|+-+-..|+..+.-|+++       .|+|+|.||+.+++|++.++|+||++ 
T Consensus       341 ~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvG-  419 (543)
T KOG0342|consen  341 MSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVG-  419 (543)
T ss_pred             hHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhc-
Confidence            3566777888888999999999999999999999999998888888       59999999999999999999999995 


Q ss_pred             ccCCc
Q psy437          168 LRLGR  172 (184)
Q Consensus       168 ~~~~r  172 (184)
                       |-||
T Consensus       420 -RTaR  423 (543)
T KOG0342|consen  420 -RTAR  423 (543)
T ss_pred             -cccc
Confidence             5555

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.46  E-value=7.5e-13  Score=123.39  Aligned_cols=91  Identities=15%  Similarity=0.112  Sum_probs=82.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                      .+++++|||++++.++.+++.|.+.  ++++..+||+|++++|.+++.+|++|+.+|||||+      .+++|+|.++++
T Consensus       808 r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTd------IierGIDIP~v~  881 (1147)
T PRK10689        808 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPTAN  881 (1147)
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECc------hhhcccccccCC
Confidence            4578999999999999999999986  78899999999999999999999999999999999      999999999999


Q ss_pred             EEEe-----eCCCChHHHHHHHHHhhCCC
Q psy437          111 AISY-----HAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       111 ~~vi-----h~~~p~~~r~~~~~~f~~~~  134 (184)
                       +|+     |+|+|+    |+|+.+|.|.
T Consensus       882 -~VIi~~ad~fglaq----~~Qr~GRvGR  905 (1147)
T PRK10689        882 -TIIIERADHFGLAQ----LHQLRGRVGR  905 (1147)
T ss_pred             -EEEEecCCCCCHHH----HHHHhhccCC
Confidence             665     888875    8999877654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.46  E-value=2.9e-12  Score=114.63  Aligned_cols=140  Identities=13%  Similarity=0.101  Sum_probs=116.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .+.++++.+||+..|.++++.+++    .|+++..+||+++..+|...+..+.+|+..|+|+|+++              
T Consensus       309 ~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvV  388 (681)
T PRK10917        309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI  388 (681)
T ss_pred             cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEE
Confidence            567899999999999999888775    37899999999999999999999999999999998765              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       389 IDE~Hrfg~~qr~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~~~~  468 (681)
T PRK10917        389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEI  468 (681)
T ss_pred             EechhhhhHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCCCCCCCcEEEEeCcccHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ---------------------ccHHHHHHHHHhc--CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC
Q psy437           95 ---------------------KECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ  144 (184)
Q Consensus        95 ---------------------~~~e~~a~gL~~~--gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~  144 (184)
                                           ..++.++..|...  ++++..+|++|++..|..+.+.|++|++.|+|+       +|+|
T Consensus       469 ~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip  548 (681)
T PRK10917        469 AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP  548 (681)
T ss_pred             HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccC
Confidence                                 0123344455432  578899999999999999999999999999999       6999


Q ss_pred             CccEEEecCCCCCcccccc-ccccccCCccc
Q psy437          145 WKRIIWIHSLVLIKPDYLP-PILDLRLGRED  174 (184)
Q Consensus       145 ~vr~v~~~~~p~~~e~y~~-~i~~~~~~r~~  174 (184)
                      +++.|++++.|....+|+| ++  +|+||.+
T Consensus       549 ~v~~VIi~~~~r~gls~lhQ~~--GRvGR~g  577 (681)
T PRK10917        549 NATVMVIENAERFGLAQLHQLR--GRVGRGA  577 (681)
T ss_pred             CCcEEEEeCCCCCCHHHHHHHh--hcccCCC
Confidence            9999999999986555554 66  6888863

>KOG0326|consensus

Probab=99.45  E-value=1.1e-13  Score=110.83  Aligned_cols=109  Identities=17%  Similarity=0.158  Sum_probs=92.9

Q ss_pred             EEecCCCCHHHHHHHHHHHhc-cCc-eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEE
Q psy437           62 ISYHAGLADKLRNEVQMKWIS-NKV-HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYN  139 (184)
Q Consensus        62 ~~~hg~l~~~~R~~~~~~f~~-g~~-~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~v  139 (184)
                      .-|++-....++...+.-+.+ -++ +.||+|++-+.+|.+|..+..-|.+|+-+|+.|.|+.|+.+--.|+.|.++.+|
T Consensus       298 tQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLV  377 (459)
T KOG0326|consen  298 TQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLV  377 (459)
T ss_pred             hhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceee
Confidence            335555555555555655443 233 579999999999999999999999999999999999999999999999999999


Q ss_pred             E-------EecCCccEEEecCCCCCccccccccccccCCc
Q psy437          140 V-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       140 a-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r  172 (184)
                      +       +|++.+..|||||.|+++|.|+|||+  |.||
T Consensus       378 ctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIG--RsGR  415 (459)
T KOG0326|consen  378 CTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIG--RSGR  415 (459)
T ss_pred             ehhhhhcccccceeeEEEecCCCCCHHHHHHHcc--CCcc
Confidence            9       59999999999999999999999995  5555

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.45  E-value=2.6e-12  Score=117.66  Aligned_cols=139  Identities=14%  Similarity=0.084  Sum_probs=120.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .+.+++|.+||+..|.+.++.+.+.    ++++..++|+.+..++..+++.+.+|+.+|||+|+..              
T Consensus       499 ~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llV  578 (926)
T TIGR00580       499 DGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLI  578 (926)
T ss_pred             hCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEE
Confidence            4578999999999999999988753    6788889999999999999999999999998888733              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       579 IDEahrfgv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~R~~V~t~v~~~~~~~i~~~i~~el~  658 (926)
T TIGR00580       579 IDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRRELL  658 (926)
T ss_pred             eecccccchhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCCccceEEEEEecCHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ------------ccHHHHHHHHHh--cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecC
Q psy437           95 ------------KECDSVAAALAQ--ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHS  153 (184)
Q Consensus        95 ------------~~~e~~a~gL~~--~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~  153 (184)
                                  ..++.++..|..  +++++.++|++|++..|..+.+.|++|+..|+|+       +|+|+++.|++++
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                        357788888876  6889999999999999999999999999999999       6999999999999


Q ss_pred             CCC-CccccccccccccCCcc
Q psy437          154 LVL-IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       154 ~p~-~~e~y~~~i~~~~~~r~  173 (184)
                      .|. ...+|+|+++  |+||.
T Consensus       739 a~~~gls~l~Qr~G--RvGR~  757 (926)
T TIGR00580       739 ADKFGLAQLYQLRG--RVGRS  757 (926)
T ss_pred             CCCCCHHHHHHHhc--CCCCC
Confidence            876 4668999984  66664

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.

>PTZ00424 helicase 45; Provisional

Probab=99.44  E-value=4.1e-13  Score=112.84  Aligned_cols=89  Identities=13%  Similarity=0.159  Sum_probs=83.2

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+|+++..|+.++..|...++.+..+|+++|+..|..+.+.|++|++.|+|+       +|+|++++|+++++|.
T Consensus       267 ~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~  346 (401)
T PTZ00424        267 ITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPA  346 (401)
T ss_pred             CCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCC
Confidence            357899999999999999999999999999999999999999999999999999999       6999999999999999


Q ss_pred             CccccccccccccCCccc
Q psy437          157 IKPDYLPPILDLRLGRED  174 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~~  174 (184)
                      +..+|+|+++  |+||.+
T Consensus       347 s~~~y~qr~G--RagR~g  362 (401)
T PTZ00424        347 SPENYIHRIG--RSGRFG  362 (401)
T ss_pred             CHHHEeeccc--ccccCC
Confidence            9999999994  777753

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

Probab=99.43  E-value=8.8e-13  Score=118.07  Aligned_cols=105  Identities=16%  Similarity=0.183  Sum_probs=94.9

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCC-CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER-INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~g-i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      ....+.++++++   .+++||+|||..+|.++..|.+.+ ..+...||+++.+.|..+.++|++|+.+++|||+      
T Consensus       242 ~~~~i~~~v~~~---~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TS------  312 (814)
T COG1201         242 LYERIAELVKKH---RTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATS------  312 (814)
T ss_pred             HHHHHHHHHhhc---CcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEcc------
Confidence            456666666553   589999999999999999999886 8899999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+--|+|.-+|+ .|+|++-|.+.-..+||.+++|.
T Consensus       313 SLELGIDiG~vd-lVIq~~SP~sV~r~lQRiGRsgH  347 (814)
T COG1201         313 SLELGIDIGDID-LVIQLGSPKSVNRFLQRIGRAGH  347 (814)
T ss_pred             chhhccccCCce-EEEEeCCcHHHHHHhHhcccccc
Confidence            556699999999 99999999999999999988874

>KOG0348|consensus

Probab=99.42  E-value=1.2e-12  Score=110.79  Aligned_cols=116  Identities=14%  Similarity=0.126  Sum_probs=99.2

Q ss_pred             eEEEEEEccChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC----------------------CCeeEEe
Q psy437           10 LKYEILPKKNVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE----------------------RINAISY   64 (184)
Q Consensus        10 l~y~v~~~~~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~----------------------gi~~~~~   64 (184)
                      .+|.|+|...++-.|..+|.+.   ....++|||.++++.++.-...|.+.                      +.+..-+
T Consensus       398 qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rL  477 (708)
T KOG0348|consen  398 QRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRL  477 (708)
T ss_pred             hceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEe
Confidence            3688888888888888887654   24567899999999999887777531                      2456678


Q ss_pred             cCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           65 HAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        65 hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                      ||+|+|++|..+++.|....-.||.||+      ++|||||-|.|. +|+.|+.|.+..+|+||..+.
T Consensus       478 HGsm~QeeRts~f~~Fs~~~~~VLLcTD------VAaRGLDlP~V~-~vVQYd~P~s~adylHRvGRT  538 (708)
T KOG0348|consen  478 HGSMEQEERTSVFQEFSHSRRAVLLCTD------VAARGLDLPHVG-LVVQYDPPFSTADYLHRVGRT  538 (708)
T ss_pred             cCchhHHHHHHHHHhhccccceEEEehh------hhhccCCCCCcC-eEEEeCCCCCHHHHHHHhhhh
Confidence            9999999999999999998888999999      999999999999 999999999999999999654

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.42  E-value=9.1e-13  Score=119.40  Aligned_cols=96  Identities=16%  Similarity=0.089  Sum_probs=87.1

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh---CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~---~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      ..+++||||+++.+++.+++.|.+   .++.+..+||+|++++|.++++.|.+|+.+|||||+      .+++||+++||
T Consensus       211 ~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATn------IAErsLtIp~V  284 (812)
T PRK11664        211 ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATN------IAETSLTIEGI  284 (812)
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecc------hHHhcccccCc
Confidence            467899999999999999999987   578899999999999999999999999999999999      99999999999


Q ss_pred             cEEEeeCCCChHHH------------------HHHHHHhhCCCc
Q psy437          110 NAISYHAGLADKLR------------------NEVQMKWISNKV  135 (184)
Q Consensus       110 ~~~vih~~~p~~~r------------------~~~~~~f~~~~~  135 (184)
                      + +||+.|+|...+                  ++.||..+.|..
T Consensus       285 ~-~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~  327 (812)
T PRK11664        285 R-LVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL  327 (812)
T ss_pred             e-EEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC
Confidence            9 999999997543                  688888776653

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.42  E-value=1.4e-12  Score=116.22  Aligned_cols=121  Identities=12%  Similarity=0.045  Sum_probs=100.2

Q ss_pred             CCCCCCeEEE-----EEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYE-----ILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~-----v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-.     ......|...+.+.+.+. ..+.|+||||+|++.++.++..|.+.|+++.++||++++++|..+.
T Consensus       388 Pt~kp~~r~d~~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~  467 (762)
T TIGR03714       388 PTNKPIIRIDYPDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIA  467 (762)
T ss_pred             CCCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHH
Confidence            5677776543     222335888888888653 3678999999999999999999999999999999999999988887


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc---------CCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE---------RINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~---------gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .++..|  .|+|||+      .++||+|++         |+. +|+++++|....+ +|+.+|+|.
T Consensus       468 ~ag~~g--~VlIATd------mAgRGtDI~l~~~v~~~GGL~-vIit~~~ps~rid-~qr~GRtGR  523 (762)
T TIGR03714       468 EAGQKG--AVTVATS------MAGRGTDIKLGKGVAELGGLA-VIGTERMENSRVD-LQLRGRSGR  523 (762)
T ss_pred             HcCCCC--eEEEEcc------ccccccCCCCCccccccCCeE-EEEecCCCCcHHH-HHhhhcccC
Confidence            777666  6899999      889999999         898 9999999987655 999977654

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.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.42  E-value=7.7e-12  Score=111.09  Aligned_cols=140  Identities=16%  Similarity=0.130  Sum_probs=111.9

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .+.++++-+||+..|+++++.+.+    .|+++..++|+++..+|...++...+|+.+|+|+|.++              
T Consensus       283 ~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvV  362 (630)
T TIGR00643       283 AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI  362 (630)
T ss_pred             cCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEE
Confidence            567899999999999999888765    37999999999999888888777777766666666544              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       363 IDEaH~fg~~qr~~l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p~~r~~i~~~~~~~~~~~~~~~~i~  442 (630)
T TIGR00643       363 IDEQHRFGVEQRKKLREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIE  442 (630)
T ss_pred             EechhhccHHHHHHHHHhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeeccCCCCCCceEEEEeCcchHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ------------------------ccHHHHHHHHHh--cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           95 ------------------------KECDSVAAALAQ--ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        95 ------------------------~~~e~~a~gL~~--~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                                              ..++.++..|..  +++++.++|++|++..|..+.+.|++|+..|+|+       +
T Consensus       443 ~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~Gv  522 (630)
T TIGR00643       443 EEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGV  522 (630)
T ss_pred             HHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCc
Confidence                                    012334444532  5778899999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccc-cccccccccCCccc
Q psy437          142 KIQWKRIIWIHSLVLIKPD-YLPPILDLRLGRED  174 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~-y~~~i~~~~~~r~~  174 (184)
                      |+|+++.|++++.|....+ |.|++  +|+||.+
T Consensus       523 DiP~v~~VIi~~~~r~gls~lhQ~~--GRvGR~g  554 (630)
T TIGR00643       523 DVPNATVMVIEDAERFGLSQLHQLR--GRVGRGD  554 (630)
T ss_pred             ccCCCcEEEEeCCCcCCHHHHHHHh--hhcccCC
Confidence            9999999999999985444 45576  6888853

>KOG0346|consensus

Probab=99.41  E-value=7.4e-13  Score=109.85  Aligned_cols=84  Identities=13%  Similarity=0.087  Sum_probs=74.2

Q ss_pred             EEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           11 KYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        11 ~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      ++..+...+|+-.+..+++-..-.++.|||+||...|-.+.-.|...|+++..+.|.|+...|.-++++|-.|-.++|||
T Consensus       245 y~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIA  324 (569)
T KOG0346|consen  245 YQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIA  324 (569)
T ss_pred             EEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEE
Confidence            44455666798888888765456789999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeec
Q psy437           91 TVVS   94 (184)
Q Consensus        91 T~tr   94 (184)
                      |+.-
T Consensus       325 tD~s  328 (569)
T KOG0346|consen  325 TDDS  328 (569)
T ss_pred             ccCc
Confidence            9933

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.41  E-value=2e-12  Score=117.17  Aligned_cols=96  Identities=17%  Similarity=0.086  Sum_probs=86.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh---CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~---~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      ..+++|||++++.+++.+++.|.+   .++.+..+||+|++++|.++++.|.+|+.+|||||+      .+++||+++||
T Consensus       208 ~~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATn------IAErgItIp~V  281 (819)
T TIGR01970       208 ETGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATN------IAETSLTIEGI  281 (819)
T ss_pred             cCCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecc------hHhhcccccCc
Confidence            457899999999999999999987   478999999999999999999999999999999999      99999999999


Q ss_pred             cEEEeeCCCChHH------------------HHHHHHHhhCCCc
Q psy437          110 NAISYHAGLADKL------------------RNEVQMKWISNKV  135 (184)
Q Consensus       110 ~~~vih~~~p~~~------------------r~~~~~~f~~~~~  135 (184)
                      + +||++|+|...                  .++.||..+.|..
T Consensus       282 ~-~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~  324 (819)
T TIGR01970       282 R-VVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL  324 (819)
T ss_pred             e-EEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC
Confidence            9 99999999753                  2478888777653

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.

>TIGR01054 rgy reverse gyrase

Probab=99.40  E-value=1.3e-12  Score=122.01  Aligned_cols=92  Identities=18%  Similarity=0.319  Sum_probs=79.1

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccH---HHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeeccc
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTR---KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKE   96 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr---~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~   96 (184)
                      +...|.++++.  .+.++||||+|+   +.|+.+++.|.+.|+++..+||+|++    .++++|++|+++|||||.+.- 
T Consensus       314 ~~~~L~~ll~~--l~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~t-  386 (1171)
T TIGR01054       314 LKETLLEIVKK--LGTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYY-  386 (1171)
T ss_pred             HHHHHHHHHHH--cCCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHcCCCCEEEEecccc-
Confidence            35667777765  356899999999   99999999999999999999999973    689999999999999973221 


Q ss_pred             HHHHHHHHHhcC-CcEEEeeCCCCh
Q psy437           97 CDSVAAALAQER-INAISYHAGLAD  120 (184)
Q Consensus        97 ~e~~a~gL~~~g-i~~~vih~~~p~  120 (184)
                       +.+|||||.++ |+ +|||+|+|.
T Consensus       387 -dv~aRGIDip~~V~-~vI~~~~P~  409 (1171)
T TIGR01054       387 -GTLVRGLDLPERVR-YAVFLGVPK  409 (1171)
T ss_pred             -CcccccCCCCcccc-EEEEECCCC
Confidence             18899999999 88 999999997

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.39  E-value=3.4e-12  Score=119.08  Aligned_cols=135  Identities=12%  Similarity=0.030  Sum_probs=115.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .+.+++|.|||+..|.++++.+.+.    ++++..++|+.+..++..+++...+|..+|||+|+..              
T Consensus       648 ~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLV  727 (1147)
T PRK10689        648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLI  727 (1147)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEE
Confidence            5678999999999999999988752    5678889999999999999999988999999999743              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       728 IDEahrfG~~~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r~~v~~~~~~~~~~~~k~~il~el~  807 (1147)
T PRK10689        728 VDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREIL  807 (1147)
T ss_pred             EechhhcchhHHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCCCCceEEEEecCcHHHHHHHHHHHh
Confidence                                                                                            


Q ss_pred             ------------ccHHHHHHHHHhc--CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEE---
Q psy437           95 ------------KECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIW---  150 (184)
Q Consensus        95 ------------~~~e~~a~gL~~~--gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~---  150 (184)
                                  ..++.++..|...  ++++.++|++|++..|..+...|++|++.|+||       +|+|++++|+   
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                        2466778888654  788899999999999999999999999999999       6999999999   


Q ss_pred             --ecCCCCCccccccccccccCCcc
Q psy437          151 --IHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       151 --~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                        ||++|    +|+|++  +|+||.
T Consensus       888 ad~fgla----q~~Qr~--GRvGR~  906 (1147)
T PRK10689        888 ADHFGLA----QLHQLR--GRVGRS  906 (1147)
T ss_pred             CCCCCHH----HHHHHh--hccCCC
Confidence              66664    599998  477774

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.39  E-value=7.5e-12  Score=114.71  Aligned_cols=148  Identities=16%  Similarity=0.091  Sum_probs=107.3

Q ss_pred             HHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCC---------------C---C----HHHHHH
Q psy437           24 VISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAG---------------L---A----DKLRNE   75 (184)
Q Consensus        24 L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~---------------l---~----~~~R~~   75 (184)
                      ++..|.... ...+.|.+..|-...+.++++|...     .-++....+.               +   +    ......
T Consensus       196 ~L~rL~~l~~~~~q~IglSATl~~~~~va~~L~~~~~~~~~r~~~iv~~~~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~  275 (876)
T PRK13767        196 SLERLEELAGGEFVRIGLSATIEPLEEVAKFLVGYEDDGEPRDCEIVDARFVKPFDIKVISPVDDLIHTPAEEISEALYE  275 (876)
T ss_pred             HHHHHHHhcCCCCeEEEEecccCCHHHHHHHhcCccccCCCCceEEEccCCCccceEEEeccCccccccccchhHHHHHH
Confidence            334444332 3345677888887778888888532     1111111111               0   0    011122


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHh------cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Ee
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQ------ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WK  142 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~------~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D  142 (184)
                      .+........++||+|+++..|+.++..|..      .+..+.++|+++++..|..+.+.|++|++.++||       +|
T Consensus       276 ~L~~~i~~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GID  355 (876)
T PRK13767        276 TLHELIKEHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGID  355 (876)
T ss_pred             HHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCC
Confidence            3333334445799999999999999999965      2456789999999999999999999999999999       69


Q ss_pred             cCCccEEEecCCCCCccccccccccccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|++++||+++.|.+..+|+|++  +|+||.
T Consensus       356 ip~Vd~VI~~~~P~sv~~ylQRi--GRaGR~  384 (876)
T PRK13767        356 IGYIDLVVLLGSPKSVSRLLQRI--GRAGHR  384 (876)
T ss_pred             CCCCcEEEEeCCCCCHHHHHHhc--ccCCCC
Confidence            99999999999999999999999  588875

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.39  E-value=5.3e-12  Score=115.60  Aligned_cols=95  Identities=12%  Similarity=0.082  Sum_probs=84.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                      .+++++|||++.+.++.+++.|.+.  ++++..+||+|++++|..++++|++|+.+|||||+      .+++|+|.++++
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~------iie~GIDIp~v~  732 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT------IIETGIDIPNAN  732 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC------hhhcccccccCC
Confidence            5678999999999999999999974  78999999999999999999999999999999999      999999999999


Q ss_pred             EEEeeCCCCh-HHHHHHHHHhhCCC
Q psy437          111 AISYHAGLAD-KLRNEVQMKWISNK  134 (184)
Q Consensus       111 ~~vih~~~p~-~~r~~~~~~f~~~~  134 (184)
                       +|++++.|. ..-+++|+.+|.|.
T Consensus       733 -~VIi~~a~~~gls~l~Qr~GRvGR  756 (926)
T TIGR00580       733 -TIIIERADKFGLAQLYQLRGRVGR  756 (926)
T ss_pred             -EEEEecCCCCCHHHHHHHhcCCCC
Confidence             777766654 45578899877554

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.39  E-value=2.6e-12  Score=114.02  Aligned_cols=122  Identities=16%  Similarity=0.088  Sum_probs=101.6

Q ss_pred             CCCCCCeEEEEE-----EccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEIL-----PKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v~-----~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||++.....     ...+|...+.+.+.+. ..+.|+||||+|...++.++..|.+.|+++..+||+  +.+|+..+
T Consensus       369 Ptnkp~~R~d~~d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~i  446 (745)
T TIGR00963       369 PTNRPVIRKDLSDLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEI  446 (745)
T ss_pred             CCCCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHH
Confidence            567777654321     1224777777766432 367899999999999999999999999999999998  88999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcC-------CcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQER-------INAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g-------i~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ..|..+...|+|||+      .++||+|++.       .- +|||+++|.+.|.|.|+.+++|.
T Consensus       447 i~~ag~~g~VtIATn------mAgRGtDI~l~~V~~~GGl-~VI~t~~p~s~ri~~q~~GRtGR  503 (745)
T TIGR00963       447 IAQAGRKGAVTIATN------MAGRGTDIKLEEVKELGGL-YVIGTERHESRRIDNQLRGRSGR  503 (745)
T ss_pred             HHhcCCCceEEEEec------cccCCcCCCccchhhcCCc-EEEecCCCCcHHHHHHHhccccC
Confidence            999999999999999      8899998876       44 99999999999999999977653

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.

>PRK02362 ski2-like helicase; Provisional

Probab=99.38  E-value=3e-12  Score=115.61  Aligned_cols=95  Identities=20%  Similarity=0.165  Sum_probs=83.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCC------------------------------------CeeEEecCCCCHHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQER------------------------------------INAISYHAGLADKLRNEV   76 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~g------------------------------------i~~~~~hg~l~~~~R~~~   76 (184)
                      .+.++||||+|++.|+.++..|....                                    ..++++||||++.+|..+
T Consensus       242 ~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~v  321 (737)
T PRK02362        242 EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELV  321 (737)
T ss_pred             cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHH
Confidence            46799999999999999998886421                                    357889999999999999


Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee----CC-----CChHHHHHHHHHhhCCC
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYH----AG-----LADKLRNEVQMKWISNK  134 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih----~~-----~p~~~r~~~~~~f~~~~  134 (184)
                      ++.|++|.++|||||+      .+|+|++.+..+ +||+    |+     .|-+..+|.|+.++.|.
T Consensus       322 e~~Fr~G~i~VLvaT~------tla~GvnlPa~~-VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR  381 (737)
T PRK02362        322 EDAFRDRLIKVISSTP------TLAAGLNLPARR-VIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGR  381 (737)
T ss_pred             HHHHHcCCCeEEEech------hhhhhcCCCceE-EEEecceeecCCCCceeCCHHHHHHHhhcCCC
Confidence            9999999999999999      889999999998 7776    32     68899999999988875

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.37  E-value=2.8e-12  Score=113.90  Aligned_cols=92  Identities=17%  Similarity=0.224  Sum_probs=79.2

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHH-hccCceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKW-ISNKVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f-~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                      ++++||||+++..++.+++.|.+.  ++.+..+||+|++.  ++.+++| ++|+.+|||||+      .+++||+++||+
T Consensus       395 ~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATd------IAERGIDIp~V~  466 (675)
T PHA02653        395 GSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTP------YLESSVTIRNAT  466 (675)
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccC------hhhccccccCee
Confidence            468999999999999999999986  79999999999974  5677787 689999999999      999999999998


Q ss_pred             EEEeeCC---CCh---------HHHHHHHHHhhCCC
Q psy437          111 AISYHAG---LAD---------KLRNEVQMKWISNK  134 (184)
Q Consensus       111 ~~vih~~---~p~---------~~r~~~~~~f~~~~  134 (184)
                       +||++|   .|.         +..+|+||.+|.|.
T Consensus       467 -~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR  501 (675)
T PHA02653        467 -HVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGR  501 (675)
T ss_pred             -EEEECCCccCCCcccCcccccCHHHHHHhccCcCC
Confidence             999999   565         55667777766554

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

Probab=99.36  E-value=6.4e-12  Score=105.96  Aligned_cols=107  Identities=15%  Similarity=0.161  Sum_probs=93.2

Q ss_pred             hHHHHHHHHHhhc---CCCcEEEEeccHHHHHHHHHHHHhCCCeeE-Ee--------cCCCCHHHHHHHHHHHhccCceE
Q psy437           20 VLKEVISLIKAKY---SGQSGIVYCLTRKECDSVAAALAQERINAI-SY--------HAGLADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus        20 k~~~L~~~l~~~~---~~~~~IIf~~tr~~~e~la~~L~~~gi~~~-~~--------hg~l~~~~R~~~~~~f~~g~~~v   87 (184)
                      |++.+.+++++.+   ...+.|||++.|.+++.++..|.+.|+.+. .+        ..||+|.+..+++++|++|+.+|
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            7777777776543   456799999999999999999999888774 22        24799999999999999999999


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      ||||+      ..-.|||++.++ .|+-|+.-++.-.++||.++.|
T Consensus       429 LVaTS------VgEEGLDIp~vD-lVifYEpvpSeIR~IQR~GRTG  467 (542)
T COG1111         429 LVATS------VGEEGLDIPEVD-LVIFYEPVPSEIRSIQRKGRTG  467 (542)
T ss_pred             EEEcc------cccccCCCCccc-EEEEecCCcHHHHHHHhhCccc
Confidence            99999      667899999999 9999999999999999997654

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.35  E-value=9.8e-12  Score=111.27  Aligned_cols=121  Identities=12%  Similarity=0.168  Sum_probs=91.1

Q ss_pred             CCCCeEEEEEEccChHHHHHHHHHhh-cCCCcEEEEecc--------HHHHHHHHHHHHhC--CCeeEEecCCCCHHHHH
Q psy437            6 NRANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLT--------RKECDSVAAALAQE--RINAISYHAGLADKLRN   74 (184)
Q Consensus         6 ~R~Nl~y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~t--------r~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~   74 (184)
                      .|+.+...+..... ...+.+.+.+. ..+.+++|||++        ...++.+++.|.+.  ++++..+||+|++++|.
T Consensus       443 ~r~~i~~~~~~~~~-~~~~~~~i~~~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~  521 (681)
T PRK10917        443 GRKPITTVVIPDSR-RDEVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKD  521 (681)
T ss_pred             CCCCcEEEEeCccc-HHHHHHHHHHHHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHH
Confidence            35555544444432 33344444322 256789999985        44567778888765  57899999999999999


Q ss_pred             HHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChH-HHHHHHHHhhCCC
Q psy437           75 EVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADK-LRNEVQMKWISNK  134 (184)
Q Consensus        75 ~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~-~r~~~~~~f~~~~  134 (184)
                      .++++|++|+.+|||||+      .+++|+|.++++ +|++++.|.. ...+.|+.+|.|.
T Consensus       522 ~i~~~F~~g~~~ILVaT~------vie~GiDip~v~-~VIi~~~~r~gls~lhQ~~GRvGR  575 (681)
T PRK10917        522 AVMAAFKAGEIDILVATT------VIEVGVDVPNAT-VMVIENAERFGLAQLHQLRGRVGR  575 (681)
T ss_pred             HHHHHHHcCCCCEEEECc------ceeeCcccCCCc-EEEEeCCCCCCHHHHHHHhhcccC
Confidence            999999999999999999      889999999999 8999999874 5666666665443

>PRK13766 Hef nuclease; Provisional

Probab=99.35  E-value=7e-12  Score=113.74  Aligned_cols=109  Identities=16%  Similarity=0.184  Sum_probs=97.3

Q ss_pred             ChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCC--------CCHHHHHHHHHHHhccCceE
Q psy437           19 NVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAG--------LADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus        19 ~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~--------l~~~~R~~~~~~f~~g~~~v   87 (184)
                      .|.+.|.++|.+.   ....++||||+++..|+.+.+.|...|+++..+||.        |++.+|..++++|++|+.++
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            4777888877553   256789999999999999999999999999999886        99999999999999999999


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ||+|+      .+++|+|.++++ +||+|+.|.+...|+||..+.|.
T Consensus       427 LvaT~------~~~eGldi~~~~-~VI~yd~~~s~~r~iQR~GR~gR  466 (773)
T PRK13766        427 LVSTS------VAEEGLDIPSVD-LVIFYEPVPSEIRSIQRKGRTGR  466 (773)
T ss_pred             EEECC------hhhcCCCcccCC-EEEEeCCCCCHHHHHHHhcccCc
Confidence            99999      778899999999 99999999999999999866543

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

Probab=99.34  E-value=9.8e-12  Score=111.91  Aligned_cols=90  Identities=18%  Similarity=0.127  Sum_probs=78.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHH-----HHHHHHhc----cC-------ceEEEEEeeccc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRN-----EVQMKWIS----NK-------VHVGHWTVVSKE   96 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~-----~~~~~f~~----g~-------~~vlVaT~tr~~   96 (184)
                      .+.++||||||++.|+.+++.|.+.++  ..+||+|++.+|.     .++++|++    |.       ..|||||+    
T Consensus       271 ~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATd----  344 (844)
T TIGR02621       271 SGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTS----  344 (844)
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccc----
Confidence            567899999999999999999998887  8899999999999     88999987    44       68999999    


Q ss_pred             HHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           97 CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        97 ~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                        .+++|||++. + .+|+...|  ...|+||..+.|.
T Consensus       345 --VaerGLDId~-d-~VI~d~aP--~esyIQRiGRtgR  376 (844)
T TIGR02621       345 --AGEVGVNISA-D-HLVCDLAP--FESMQQRFGRVNR  376 (844)
T ss_pred             --hhhhcccCCc-c-eEEECCCC--HHHHHHHhcccCC
Confidence              9999999987 6 77787776  5899999966543

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.

>KOG0334|consensus

Probab=99.32  E-value=1.7e-11  Score=110.43  Aligned_cols=137  Identities=15%  Similarity=0.144  Sum_probs=120.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .++-+||.|+|++.+.+|.+++..    .++.+....|+-.   +.+.+...+.| ..|+|||++|              
T Consensus       437 dGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~---~~~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtn  512 (997)
T KOG0334|consen  437 DGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSG---ISQQIAELKRG-AEIVVCTPGRMIDILCANSGRVTN  512 (997)
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCcc---HHHHHHHHhcC-CceEEeccchhhhhHhhcCCcccc
Confidence            445589999999999999888764    4888888888754   44566777777 7899999999              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       513 lrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V  592 (997)
T KOG0334|consen  513 LRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRV  592 (997)
T ss_pred             ccccceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEE
Confidence                                                                                            


Q ss_pred             -------------------------------ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE---
Q psy437           95 -------------------------------KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV---  140 (184)
Q Consensus        95 -------------------------------~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va---  140 (184)
                                                     ..|+.+.+-|...|+.|..+|+|.|+..|+.+-+.|+++.+.+++|   
T Consensus       593 ~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsv  672 (997)
T KOG0334|consen  593 CAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSV  672 (997)
T ss_pred             ecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhh
Confidence                                           5799999999999999988999999999999999999999999999   


Q ss_pred             ----EecCCccEEEecCCCCCcccccccccc-ccCCcc
Q psy437          141 ----WKIQWKRIIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       141 ----~D~~~vr~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                          +|.+++-.|+|||.|.--++|+|+.++ +|+||-
T Consensus       673 varGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrk  710 (997)
T KOG0334|consen  673 VARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRK  710 (997)
T ss_pred             hhcccccccceEEEEcccchhHHHHHHHhcccccCCcc
Confidence                699999999999999999999999988 488885

>KOG0327|consensus

Probab=99.32  E-value=1.4e-11  Score=100.70  Aligned_cols=143  Identities=12%  Similarity=0.150  Sum_probs=114.2

Q ss_pred             CCcEEEEeccH-HHHHHHHHHHHhC--------------CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           34 GQSGIVYCLTR-KECDSVAAALAQE--------------RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        34 ~~~~IIf~~tr-~~~e~la~~L~~~--------------gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      ..+.+.|.+|. ..+..+++.+-..              |++-.+..  ..++++...+-.|-....+.+++++++..+.
T Consensus       200 ~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~--v~k~~k~~~l~dl~~~~~q~~if~nt~r~v~  277 (397)
T KOG0327|consen  200 DVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYIN--VEKEEKLDTLCDLYRRVTQAVIFCNTRRKVD  277 (397)
T ss_pred             chhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeee--ccccccccHHHHHHHhhhcceEEecchhhHH
Confidence            45667777664 4666776665432              33332222  2233466667777666778999999999999


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcccccccccc-ccC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILD-LRL  170 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~-~~~  170 (184)
                      .+-..|...|..+..+|+++.+..|+-+.+.|++|..+|++.       +|+.++..|+||++|...++|+|++++ +|.
T Consensus       278 ~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~  357 (397)
T KOG0327|consen  278 NLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRF  357 (397)
T ss_pred             HHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhccccccc
Confidence            999999999999999999999999999999999999999998       599999999999999999999999988 588


Q ss_pred             Cccccccc
Q psy437          171 GREDIREG  178 (184)
Q Consensus       171 ~r~~~~~~  178 (184)
                      ||+++.-|
T Consensus       358 grkg~~in  365 (397)
T KOG0327|consen  358 GRKGVAIN  365 (397)
T ss_pred             CCCceeee
Confidence            88865443

>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=99.31  E-value=2e-12  Score=84.29  Aligned_cols=75  Identities=15%  Similarity=0.052  Sum_probs=63.7

Q ss_pred             HHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           52 AALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        52 ~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      +.|++.|+++..+||++++++|..+++.|.++...+||+|+      .++.|+|.++++ .|+++++|.+...|.|+..+
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~------~~~~Gid~~~~~-~vi~~~~~~~~~~~~Q~~GR   73 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATD------ILGEGIDLPDAS-HVIFYDPPWSPEEYIQRIGR   73 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESC------GGTTSSTSTTES-EEEESSSESSHHHHHHHHTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeec------cccccccccccc-cccccccCCCHHHHHHHhhc
Confidence            46888999999999999999999999999999999999999      556677777777 77777777777777777766


Q ss_pred             CC
Q psy437          132 SN  133 (184)
Q Consensus       132 ~~  133 (184)
                      -+
T Consensus        74 ~~   75 (78)
T PF00271_consen   74 AG   75 (78)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

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 ....

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.30  E-value=2.6e-11  Score=107.72  Aligned_cols=120  Identities=12%  Similarity=0.126  Sum_probs=90.8

Q ss_pred             CCCeEEEEEEccChHHHHHHHHHhh-cCCCcEEEEeccH--------HHHHHHHHHHHh--CCCeeEEecCCCCHHHHHH
Q psy437            7 RANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTR--------KECDSVAAALAQ--ERINAISYHAGLADKLRNE   75 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr--------~~~e~la~~L~~--~gi~~~~~hg~l~~~~R~~   75 (184)
                      |..+...+.....+ ..+...+.+. ..+.+++|||++.        ..++.+++.|.+  .++++..+||+|++++|..
T Consensus       421 r~~i~~~~~~~~~~-~~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~  499 (630)
T TIGR00643       421 RKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEA  499 (630)
T ss_pred             CCceEEEEeCcchH-HHHHHHHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHH
Confidence            44444444433332 4455555432 2567899999875        456677777775  3788999999999999999


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh-HHHHHHHHHhhCCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD-KLRNEVQMKWISNK  134 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~-~~r~~~~~~f~~~~  134 (184)
                      ++++|++|+.+|||||+      .++.|+|.++++ +|++++.|. ....+.|+..+.|.
T Consensus       500 i~~~F~~g~~~ILVaT~------vie~GvDiP~v~-~VIi~~~~r~gls~lhQ~~GRvGR  552 (630)
T TIGR00643       500 VMEEFREGEVDILVATT------VIEVGVDVPNAT-VMVIEDAERFGLSQLHQLRGRVGR  552 (630)
T ss_pred             HHHHHHcCCCCEEEECc------eeecCcccCCCc-EEEEeCCCcCCHHHHHHHhhhccc
Confidence            99999999999999999      789999999999 888999887 45666777766553

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.29  E-value=2.1e-11  Score=105.71  Aligned_cols=94  Identities=10%  Similarity=-0.069  Sum_probs=86.3

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE-eecccHHHHHHHHHhcCCcE
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT-VVSKECDSVAAALAQERINA  111 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT-~tr~~~e~~a~gL~~~gi~~  111 (184)
                      .+.+.+|||.+.+.++.+++.|.+.|+++..+||++++++|..+++.|.+|+..+|||| +      .+++|+|.++++ 
T Consensus       343 ~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~------~l~eG~Dip~ld-  415 (501)
T PHA02558        343 KGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYG------VFSTGISIKNLH-  415 (501)
T ss_pred             cCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcc------eecccccccccc-
Confidence            45678898888999999999999999999999999999999999999999999999999 7      778999999999 


Q ss_pred             EEeeCCCChHHHHHHHHHhhCC
Q psy437          112 ISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus       112 ~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      .++.+..+.+...|+|+.+|.+
T Consensus       416 ~vIl~~p~~s~~~~~QriGR~~  437 (501)
T PHA02558        416 HVIFAHPSKSKIIVLQSIGRVL  437 (501)
T ss_pred             EEEEecCCcchhhhhhhhhccc
Confidence            8889999999999999997654

>KOG0345|consensus

Probab=99.28  E-value=6.4e-11  Score=99.13  Aligned_cols=135  Identities=12%  Similarity=0.064  Sum_probs=107.5

Q ss_pred             cEEEEeccHHHHHHHHHHHHh-----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec----------------
Q psy437           36 SGIVYCLTRKECDSVAAALAQ-----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS----------------   94 (184)
Q Consensus        36 ~~IIf~~tr~~~e~la~~L~~-----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr----------------   94 (184)
                      -++|.+|||+.|.+|.+.+..     .++++..+-||.+-+   +-+..|++...+|+|+|++|                
T Consensus        81 galIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~---~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rs  157 (567)
T KOG0345|consen   81 GALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVE---EDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRS  157 (567)
T ss_pred             eEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHH---HHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccc
Confidence            479999999999988766542     477899999996543   45677888888999999999                


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       158 Le~LVLDEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~  237 (567)
T KOG0345|consen  158 LEILVLDEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVC  237 (567)
T ss_pred             cceEEecchHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEe
Confidence                                                                                            


Q ss_pred             ----------------------------ccHHHHHHHHH--hcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE----
Q psy437           95 ----------------------------KECDSVAAALA--QERINAISYHAGLADKLRNEVQMKWISNKVHLYNV----  140 (184)
Q Consensus        95 ----------------------------~~~e~~a~gL~--~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va----  140 (184)
                                                  ..+|=.+.-+.  ...+..+.+||.|.++.|+.+.+.|+..+-.++.+    
T Consensus       238 ~a~eK~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TDVa  317 (567)
T KOG0345|consen  238 EADEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTDVA  317 (567)
T ss_pred             cHHHHHHHHHHHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeehhh
Confidence                                        12333333331  24566789999999999999999999855555554    


Q ss_pred             ---EecCCccEEEecCCCCCccccccccccc-cCCcc
Q psy437          141 ---WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       141 ---~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                         +|+|+|.+|+++|+|+.+..++||.+++ |+||+
T Consensus       318 ARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~  354 (567)
T KOG0345|consen  318 ARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGRE  354 (567)
T ss_pred             hccCCCCCceEEEecCCCCChhHHHhhcchhhhccCc
Confidence               6999999999999999999999999985 88887

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.28  E-value=5.5e-11  Score=98.99  Aligned_cols=85  Identities=14%  Similarity=-0.005  Sum_probs=71.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCC--CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQER--INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~g--i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                      .+.++||||+|++.++.++..|++.+  +.+..+||.+++.+|.+.      ++.++||||+      .+++|||.+.+ 
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTd------v~~rGiDi~~~-  337 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTS------TVDVGVDFKRD-  337 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEec------HHhcccCCCCc-
Confidence            45689999999999999999999864  578889999999988755      3678999999      89999999876 


Q ss_pred             EEEeeCCCChHHHHHHHHHhhCC
Q psy437          111 AISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus       111 ~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                       .+++ + |.+..+|+||.+|.|
T Consensus       338 -~vi~-~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       338 -WLIF-S-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             -eEEE-C-CCCHHHHhhhcccCC
Confidence             3443 3 888999999988765

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.27  E-value=3.3e-11  Score=108.58  Aligned_cols=95  Identities=21%  Similarity=0.240  Sum_probs=79.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC---------------------------------CCeeEEecCCCCHHHHHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE---------------------------------RINAISYHAGLADKLRNEVQMK   79 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~---------------------------------gi~~~~~hg~l~~~~R~~~~~~   79 (184)
                      .+.++||||+||+.|+.++..|...                                 ...+.++||||++++|..+.+.
T Consensus       237 ~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~  316 (720)
T PRK00254        237 KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDA  316 (720)
T ss_pred             hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHH
Confidence            4578999999999999888776421                                 2248899999999999999999


Q ss_pred             HhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee-------CCCCh-HHHHHHHHHhhCCC
Q psy437           80 WISNKVHVGHWTVVSKECDSVAAALAQERINAISYH-------AGLAD-KLRNEVQMKWISNK  134 (184)
Q Consensus        80 f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih-------~~~p~-~~r~~~~~~f~~~~  134 (184)
                      |++|..+|||||+      .+|.|++.++++ +||+       ++.|. ..-+|.|+.++.|.
T Consensus       317 F~~G~i~VLvaT~------tLa~Gvnipa~~-vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR  372 (720)
T PRK00254        317 FREGLIKVITATP------TLSAGINLPAFR-VIIRDTKRYSNFGWEDIPVLEIQQMMGRAGR  372 (720)
T ss_pred             HHCCCCeEEEeCc------HHhhhcCCCceE-EEECCceEcCCCCceeCCHHHHHHhhhccCC
Confidence            9999999999999      889999999998 6674       45554 45688999988765

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.26  E-value=1.7e-11  Score=109.63  Aligned_cols=122  Identities=14%  Similarity=0.063  Sum_probs=100.0

Q ss_pred             CCCCCCeEEEEE-----EccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEIL-----PKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v~-----~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.....     ....|...|.+.+.+. ..+.|+||||+|...++.++..|.+.|+++..+||++++.++..+.
T Consensus       404 Ptnkp~~r~d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~  483 (796)
T PRK12906        404 PTNRPVIRKDSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIM  483 (796)
T ss_pred             CCCCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHH
Confidence            566776553322     2234888888888542 3678999999999999999999999999999999999988888888


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc---CCc----EEEeeCCCChHHHHHHHHHhhCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE---RIN----AISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~---gi~----~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +.+..|.  |+|||+      .++||+|++   +|.    -+||++++|.+.|.|.|+.+|+|
T Consensus       484 ~ag~~g~--VtIATn------mAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtG  538 (796)
T PRK12906        484 NAGQRGA--VTIATN------MAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSG  538 (796)
T ss_pred             hcCCCce--EEEEec------cccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhc
Confidence            8888776  899999      888999984   554    28999999999999999997665

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.26  E-value=2.7e-11  Score=107.70  Aligned_cols=96  Identities=13%  Similarity=0.072  Sum_probs=88.2

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccE
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRI  148 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~  148 (184)
                      -+..+.....++||+|++++.++.++..|...|+++..+|+++++..|..+.+.|+.|++.|+|+       ||+|++++
T Consensus       434 eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~l  513 (655)
T TIGR00631       434 EIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSL  513 (655)
T ss_pred             HHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcE
Confidence            34455666778999999999999999999999999999999999999999999999999999987       79999999


Q ss_pred             EEecC-----CCCCccccccccccccCCcc
Q psy437          149 IWIHS-----LVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       149 v~~~~-----~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |++++     .|.+.++|+|++  +|+||.
T Consensus       514 Vvi~DadifG~p~~~~~~iqri--GRagR~  541 (655)
T TIGR00631       514 VAILDADKEGFLRSERSLIQTI--GRAARN  541 (655)
T ss_pred             EEEeCcccccCCCCHHHHHHHh--cCCCCC
Confidence            99999     899999999999  588885

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

>KOG0337|consensus

Probab=99.26  E-value=2.2e-12  Score=106.62  Aligned_cols=109  Identities=13%  Similarity=0.067  Sum_probs=99.2

Q ss_pred             EEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           15 LPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        15 ~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ++..+|...|+.++.+.....+++|||+|+..+|.+...|...|+.+..++|.|++..|..-..+|..++..++|.|+  
T Consensus       242 ~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTd--  319 (529)
T KOG0337|consen  242 VRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTD--  319 (529)
T ss_pred             eccHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEeh--
Confidence            334457788888886654556899999999999999999999999999999999999999999999999999999999  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHh
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMKW  130 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f  130 (184)
                          ..|+|+|++..+ -|+|+++|.+.+-++||..
T Consensus       320 ----vaaRG~diplld-nvinyd~p~~~klFvhRVg  350 (529)
T KOG0337|consen  320 ----VAARGLDIPLLD-NVINYDFPPDDKLFVHRVG  350 (529)
T ss_pred             ----hhhccCCCcccc-ccccccCCCCCceEEEEec
Confidence                899999999999 9999999999999999984

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.25  E-value=2.3e-11  Score=110.18  Aligned_cols=122  Identities=11%  Similarity=0.089  Sum_probs=101.6

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-..     .....|...|.+.+... ..+.|+||||+|++.++.++..|...|+++.++|+  .+.+|+..+
T Consensus       562 PTnrP~~R~D~~d~vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~I  639 (1025)
T PRK12900        562 PTNKPIVRKDMDDLVYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEI  639 (1025)
T ss_pred             CCCCCcceecCCCeEecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHH
Confidence            56677654321     22235888898888543 36789999999999999999999999999999997  588999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc---CCcE----EEeeCCCChHHHHHHHHHhhCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE---RINA----ISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~---gi~~----~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      ..|..+...|+|||+      .++||+|++   +|..    +||+...|.+.|.|.|+.+++|
T Consensus       640 ia~AG~~g~VtIATN------MAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtG  696 (1025)
T PRK12900        640 VAEAGQKGAVTIATN------MAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAG  696 (1025)
T ss_pred             HHhcCCCCeEEEecc------CcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhh
Confidence            999999999999999      889999988   5541    5799999999999999997765

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.25  E-value=1.5e-10  Score=109.72  Aligned_cols=162  Identities=15%  Similarity=0.103  Sum_probs=113.5

Q ss_pred             CeEEEEEEcc-----Ch----HHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhC-C-------------CeeEEe
Q psy437            9 NLKYEILPKK-----NV----LKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQE-R-------------INAISY   64 (184)
Q Consensus         9 Nl~y~v~~~~-----~k----~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~-g-------------i~~~~~   64 (184)
                      |+.|.|..+-     .|    +..+++.|.... .+.+.|-+..|....+.++++|... .             +.....
T Consensus       124 ~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~QrIgLSATI~n~eevA~~L~g~~pv~Iv~~~~~r~~~l~v~vp  203 (1490)
T PRK09751        124 GVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSAQRIGLSATVRSASDVAAFLGGDRPVTVVNPPAMRHPQIRIVVP  203 (1490)
T ss_pred             cCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCCeEEEEEeeCCCHHHHHHHhcCCCCEEEECCCCCcccceEEEEe
Confidence            4567766542     12    334444454332 3456788899999899999999532 1             111111


Q ss_pred             cCCCCH----------------------HHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcC--------------
Q psy437           65 HAGLAD----------------------KLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQER--------------  108 (184)
Q Consensus        65 hg~l~~----------------------~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g--------------  108 (184)
                      ..++..                      .....++....+ ..++||+|++|+.||.++..|....              
T Consensus       204 ~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~il~~i~~-~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~  282 (1490)
T PRK09751        204 VANMDDVSSVASGTGEDSHAGREGSIWPYIETGILDEVLR-HRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDA  282 (1490)
T ss_pred             cCchhhccccccccccccchhhhhhhhHHHHHHHHHHHhc-CCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchh
Confidence            111110                      001123333333 4578999999999999999886421              


Q ss_pred             -------------------CcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccc
Q psy437          109 -------------------INAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYL  162 (184)
Q Consensus       109 -------------------i~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~  162 (184)
                                         ..+.++|++++++.|..+.+.|++|+++++||       +|+++++.||+++.|.+..+|+
T Consensus       283 ~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~L  362 (1490)
T PRK09751        283 AHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGL  362 (1490)
T ss_pred             hhhhhccccchhccccccceeeeeccccCCHHHHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHH
Confidence                               12468999999999999999999999999999       6999999999999999999999


Q ss_pred             cccccccCCcc
Q psy437          163 PPILDLRLGRE  173 (184)
Q Consensus       163 ~~i~~~~~~r~  173 (184)
                      |++  +|+||.
T Consensus       363 QRi--GRAGR~  371 (1490)
T PRK09751        363 QRI--GRAGHQ  371 (1490)
T ss_pred             HHh--CCCCCC
Confidence            999  588885

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.24  E-value=3.6e-11  Score=107.09  Aligned_cols=96  Identities=14%  Similarity=0.067  Sum_probs=87.3

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccE
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRI  148 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~  148 (184)
                      .+..|.....++||+|++++.++.++..|...|+++.++|+++++..|..+.+.|+.|++.|+|+       ||+|++++
T Consensus       438 ~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~l  517 (652)
T PRK05298        438 EIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSL  517 (652)
T ss_pred             HHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcE
Confidence            34556666788999999999999999999999999999999999999999999999999999987       79999999


Q ss_pred             EEecCC-----CCCccccccccccccCCcc
Q psy437          149 IWIHSL-----VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       149 v~~~~~-----p~~~e~y~~~i~~~~~~r~  173 (184)
                      |++++.     |.+.++|+|++  ||+||.
T Consensus       518 Vii~d~eifG~~~~~~~yiqr~--GR~gR~  545 (652)
T PRK05298        518 VAILDADKEGFLRSERSLIQTI--GRAARN  545 (652)
T ss_pred             EEEeCCcccccCCCHHHHHHHh--ccccCC
Confidence            999985     78999999999  588884

>KOG4284|consensus

Probab=99.24  E-value=5.6e-11  Score=102.91  Aligned_cols=75  Identities=13%  Similarity=0.104  Sum_probs=71.1

Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccc
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDL  168 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~  168 (184)
                      .|+-+|..|...|++|..|.+.|.|+.|--+....+.-.++|+|+       +|-+++.+|+|.|.|.+-+.|+|||+  
T Consensus       284 ra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIG--  361 (980)
T KOG4284|consen  284 RAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIG--  361 (980)
T ss_pred             hhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhccCCccccceEEecCCCcchHHHHHHhh--
Confidence            689999999999999999999999999999999999999999999       59999999999999999999999995  


Q ss_pred             cCCc
Q psy437          169 RLGR  172 (184)
Q Consensus       169 ~~~r  172 (184)
                      |+||
T Consensus       362 RAgR  365 (980)
T KOG4284|consen  362 RAGR  365 (980)
T ss_pred             hccc
Confidence            7776

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.23  E-value=4.6e-11  Score=109.46  Aligned_cols=101  Identities=17%  Similarity=0.195  Sum_probs=86.8

Q ss_pred             HHHHHHHHhcc--CceEEEEEeecccHHHHHHHH-HhcCCcEEEeeCCCChHHHHHHHHHhhCC--CceEEEE-------
Q psy437           73 RNEVQMKWISN--KVHVGHWTVVSKECDSVAAAL-AQERINAISYHAGLADKLRNEVQMKWISN--KVHLYNV-------  140 (184)
Q Consensus        73 R~~~~~~f~~g--~~~vlVaT~tr~~~e~~a~gL-~~~gi~~~vih~~~p~~~r~~~~~~f~~~--~~~v~va-------  140 (184)
                      |...+..+.+.  .-++||+|.++..++.++..| ...|+++.+||+++|+..|..+.+.|+++  ...|+++       
T Consensus       480 Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTdvgseG  559 (956)
T PRK04914        480 RVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSEIGSEG  559 (956)
T ss_pred             HHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEechhhccC
Confidence            44444455442  458999999999999999999 67899999999999999999999999974  5889988       


Q ss_pred             EecCCccEEEecCCCCCccccccccccc-cCCcc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                      .|.+.+++|||||+|.+++.|.|+|+++ |.|+.
T Consensus       560 lNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~  593 (956)
T PRK04914        560 RNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQK  593 (956)
T ss_pred             CCcccccEEEEecCCCCHHHHHHHhcccccCCCC
Confidence            5999999999999999999999999764 66664

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.20  E-value=4.3e-10  Score=100.15  Aligned_cols=85  Identities=13%  Similarity=0.063  Sum_probs=73.4

Q ss_pred             ceEEEEEeecccHHHHHHHHHhc--CCcEEEeeCCCChHHHHHHHHHh-hCCCceEEEE-------EecCCccEEEecC-
Q psy437           85 VHVGHWTVVSKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKW-ISNKVHLYNV-------WKIQWKRIIWIHS-  153 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~--gi~~~vih~~~p~~~r~~~~~~f-~~~~~~v~va-------~D~~~vr~v~~~~-  153 (184)
                      .++||++++.++|+.+++.|...  ++.+..+|+++|+.  +...+.| ++|+.+|++|       +|+|+|++||+++ 
T Consensus       396 g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~  473 (675)
T PHA02653        396 SSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGR  473 (675)
T ss_pred             CcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEECCC
Confidence            47999999999999999999876  79999999999985  3444555 7899999999       6999999999998 


Q ss_pred             --CCC---------CccccccccccccCCcc
Q psy437          154 --LVL---------IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       154 --~p~---------~~e~y~~~i~~~~~~r~  173 (184)
                        .|.         +..+|.||.  +|+||.
T Consensus       474 ~k~p~~~~g~~~~iSkasa~QRa--GRAGR~  502 (675)
T PHA02653        474 VYVPEPFGGKEMFISKSMRTQRK--GRVGRV  502 (675)
T ss_pred             ccCCCcccCcccccCHHHHHHhc--cCcCCC
Confidence              665         777999998  588886

>KOG0344|consensus

Probab=99.20  E-value=3e-10  Score=97.17  Aligned_cols=97  Identities=16%  Similarity=0.126  Sum_probs=86.3

Q ss_pred             HHHHhcc-CceEEEEEeecccHHHHHHHH-HhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCcc
Q psy437           77 QMKWISN-KVHVGHWTVVSKECDSVAAAL-AQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKR  147 (184)
Q Consensus        77 ~~~f~~g-~~~vlVaT~tr~~~e~~a~gL-~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr  147 (184)
                      .+-+.+| .-++||+.-+...|..+..-| ..++|++.|||++.++..|+...+.|+.|++-++++       +|..+++
T Consensus       379 rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn  458 (593)
T KOG0344|consen  379 RQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVN  458 (593)
T ss_pred             HHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcc
Confidence            3334444 347999999999999999999 899999999999999999999999999999999999       5999999


Q ss_pred             EEEecCCCCCcccccccccc-ccCCcc
Q psy437          148 IIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      .|||||.|.+.-+|+|+|++ +|+||.
T Consensus       459 ~VInyD~p~s~~syihrIGRtgRag~~  485 (593)
T KOG0344|consen  459 LVINYDFPQSDLSYIHRIGRTGRAGRS  485 (593)
T ss_pred             eEEecCCCchhHHHHHHhhccCCCCCC
Confidence            99999999999999999976 366664

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

Probab=99.18  E-value=6.6e-10  Score=96.69  Aligned_cols=107  Identities=20%  Similarity=0.260  Sum_probs=101.9

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE--------------------------
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV--------------------------   87 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v--------------------------   87 (184)
                      .+.+||..|-....++-...|...|+.++++++.++.++|..++.++..|+.++                          
T Consensus        57 ~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~v  136 (590)
T COG0514          57 EGLTLVVSPLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVA  136 (590)
T ss_pred             CCCEEEECchHHHHHHHHHHHHHcCceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEE
Confidence            468999999999999999999999999999999999999999999999998877                          


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           88 --------------------------------------------------------------------------------   87 (184)
Q Consensus        88 --------------------------------------------------------------------------------   87 (184)
                                                                                                      
T Consensus       137 IDEAHCiSqWGhdFRP~Y~~lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfdRpNi~~~v~~~~~~~  216 (590)
T COG0514         137 IDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPS  216 (590)
T ss_pred             echHHHHhhcCCccCHhHHHHHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCCCchhhhhhhhcccHH
Confidence                                                                                            


Q ss_pred             -----------------EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE
Q psy437           88 -----------------GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        88 -----------------lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va  140 (184)
                                       ||||.||++||.+|++|...|+++..||+||+...|..+|+.|..++++|+||
T Consensus       217 ~q~~fi~~~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVA  286 (590)
T COG0514         217 DQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVA  286 (590)
T ss_pred             HHHHHHHhhccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEE
Confidence                             78888889999999999999999999999999999999999999999999998

>KOG0354|consensus

Probab=99.17  E-value=1.9e-10  Score=101.59  Aligned_cols=106  Identities=18%  Similarity=0.189  Sum_probs=91.2

Q ss_pred             ChHHHHHHHHHhhc---CCCcEEEEeccHHHHHHHHHHHHh---CCCeeEEec--------CCCCHHHHHHHHHHHhccC
Q psy437           19 NVLKEVISLIKAKY---SGQSGIVYCLTRKECDSVAAALAQ---ERINAISYH--------AGLADKLRNEVQMKWISNK   84 (184)
Q Consensus        19 ~k~~~L~~~l~~~~---~~~~~IIf~~tr~~~e~la~~L~~---~gi~~~~~h--------g~l~~~~R~~~~~~f~~g~   84 (184)
                      .|++.|.+.|.+.+   +...+||||.||+.|+.|..+|..   .|+++..+-        .||++++..+++++|++|+
T Consensus       395 pkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~  474 (746)
T KOG0354|consen  395 PKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGE  474 (746)
T ss_pred             hhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCC
Confidence            48888888886543   556799999999999999999983   244443333        4899999999999999999


Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      .++||||+      ..-+|||+..++ .||-||...++-..+||.+|
T Consensus       475 ~NvLVATS------V~EEGLDI~ec~-lVIcYd~~snpIrmIQrrGR  514 (746)
T KOG0354|consen  475 INVLVATS------VAEEGLDIGECN-LVICYDYSSNPIRMVQRRGR  514 (746)
T ss_pred             ccEEEEec------chhccCCccccc-EEEEecCCccHHHHHHHhcc
Confidence            99999999      777899999999 99999999999999999966

>PRK01172 ski2-like helicase; Provisional

Probab=99.16  E-value=2.7e-10  Score=102.03  Aligned_cols=95  Identities=19%  Similarity=0.117  Sum_probs=78.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC-----C--------------------CeeEEecCCCCHHHHHHHHHHHhccCceE
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE-----R--------------------INAISYHAGLADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~-----g--------------------i~~~~~hg~l~~~~R~~~~~~f~~g~~~v   87 (184)
                      .++++||||+|++.|+.++..|...     .                    ..+.++||+|++++|..+.+.|++|..+|
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            4678999999999999999988653     1                    24778999999999999999999999999


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEee--------CCCChHHHHHHHHHhhCCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYH--------AGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih--------~~~p~~~r~~~~~~f~~~~  134 (184)
                      ||||+      .+|.|++.++.. +|+.        +..|-+..++.|+.++.|.
T Consensus       315 LvaT~------~la~Gvnipa~~-VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR  362 (674)
T PRK01172        315 IVATP------TLAAGVNLPARL-VIVRDITRYGNGGIRYLSNMEIKQMIGRAGR  362 (674)
T ss_pred             EEecc------hhhccCCCcceE-EEEcCceEeCCCCceeCCHHHHHHHhhcCCC
Confidence            99999      889999999965 3332        1124577889999988765

>PRK02362 ski2-like helicase; Provisional

Probab=99.16  E-value=3.7e-10  Score=102.08  Aligned_cols=152  Identities=13%  Similarity=0.113  Sum_probs=106.7

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC---------eeEEecC------C----CCH---HHHHHHHHH
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI---------NAISYHA------G----LAD---KLRNEVQMK   79 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi---------~~~~~hg------~----l~~---~~R~~~~~~   79 (184)
                      +.++..++...+..+.|.++.|-..++.++++|...-+         ....+.+      +    +..   ......+..
T Consensus       159 e~il~rl~~~~~~~qii~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (737)
T PRK02362        159 EVTLAKLRRLNPDLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLD  238 (737)
T ss_pred             HHHHHHHHhcCCCCcEEEEcccCCCHHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHH
Confidence            44444454332445677788888888899999863211         1111111      0    110   112222333


Q ss_pred             HhccCceEEEEEeecccHHHHHHHHHhcC------------------------------------CcEEEeeCCCChHHH
Q psy437           80 WISNKVHVGHWTVVSKECDSVAAALAQER------------------------------------INAISYHAGLADKLR  123 (184)
Q Consensus        80 f~~g~~~vlVaT~tr~~~e~~a~gL~~~g------------------------------------i~~~vih~~~p~~~r  123 (184)
                      ......++||++++|++|+.+|..|....                                    ..+.++|+|+|+..|
T Consensus       239 ~~~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR  318 (737)
T PRK02362        239 TLEEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHR  318 (737)
T ss_pred             HHHcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHH
Confidence            33345689999999999999998885321                                    235789999999999


Q ss_pred             HHHHHHhhCCCceEEEE-------EecCCccEEEe----cC-----CCCCccccccccccccCCcccc
Q psy437          124 NEVQMKWISNKVHLYNV-------WKIQWKRIIWI----HS-----LVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       124 ~~~~~~f~~~~~~v~va-------~D~~~vr~v~~----~~-----~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      ..+.+.|++|.+.|+||       +|.|.++.||+    |+     .|.+..+|+|++  +|+||.+.
T Consensus       319 ~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~--GRAGR~g~  384 (737)
T PRK02362        319 ELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMA--GRAGRPGL  384 (737)
T ss_pred             HHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHh--hcCCCCCC
Confidence            99999999999999999       59999999997    65     688999999999  58888654

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.15  E-value=8.5e-10  Score=100.29  Aligned_cols=138  Identities=12%  Similarity=0.032  Sum_probs=102.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHHHHHH-----HHHHH-hccCceEEEEEeecccHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADKLRNE-----VQMKW-ISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~~R~~-----~~~~f-~~g~~~vlVaT~tr~~~e   98 (184)
                      +..+.|+|+.|-.. +.++..+...        .+++..++-.++...+..     .+... .....++||+++++++++
T Consensus       148 ~~lqlilmSATl~~-~~l~~~~~~~~~I~~~gr~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~~ei~  226 (812)
T PRK11664        148 DDLKLLIMSATLDN-DRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQ  226 (812)
T ss_pred             ccceEEEEecCCCH-HHHHHhcCCCCEEEecCccccceEEeccCchhhhHHHHHHHHHHHHHHhCCCCEEEEcCCHHHHH
Confidence            34567888888754 4566665321        123333333333322221     23333 334568999999999999


Q ss_pred             HHHHHHHh---cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCc----------
Q psy437           99 SVAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIK----------  158 (184)
Q Consensus        99 ~~a~gL~~---~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~----------  158 (184)
                      .++..|..   .++.+..+|+++|++.+..+.+.|++|+.+|++|       +|+|+|++||++++|+..          
T Consensus       227 ~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~  306 (812)
T PRK11664        227 RVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTR  306 (812)
T ss_pred             HHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcce
Confidence            99999976   6888889999999999999999999999999999       699999999999998754          


Q ss_pred             --------cccccccccccCCcc
Q psy437          159 --------PDYLPPILDLRLGRE  173 (184)
Q Consensus       159 --------e~y~~~i~~~~~~r~  173 (184)
                              .+|.||.  +|+||-
T Consensus       307 L~~~~iSkasa~QR~--GRaGR~  327 (812)
T PRK11664        307 LVTQRISQASMTQRA--GRAGRL  327 (812)
T ss_pred             eEEEeechhhhhhhc--cccCCC
Confidence                    4799998  588885

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.13  E-value=1.1e-09  Score=99.44  Aligned_cols=138  Identities=12%  Similarity=0.016  Sum_probs=100.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHHHH-----HHHHHH-HhccCceEEEEEeecccHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADKLR-----NEVQMK-WISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~~R-----~~~~~~-f~~g~~~vlVaT~tr~~~e   98 (184)
                      +..+.|++..|-.. +.+.+.|...        .+++..++-.....++     ...+.. +.....++||++++.++++
T Consensus       145 ~dlqlIlmSATl~~-~~l~~~l~~~~vI~~~gr~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~~eI~  223 (819)
T TIGR01970       145 EDLKILAMSATLDG-ERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIR  223 (819)
T ss_pred             CCceEEEEeCCCCH-HHHHHHcCCCcEEEecCcceeeeeEEeecchhhhHHHHHHHHHHHHHHhcCCcEEEEECCHHHHH
Confidence            34567888888664 3456665321        1233333333322222     122222 2333467999999999999


Q ss_pred             HHHHHHHh---cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCc----------
Q psy437           99 SVAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIK----------  158 (184)
Q Consensus        99 ~~a~gL~~---~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~----------  158 (184)
                      .++..|..   .++.+..+|+++|++.+..+.+.|++|+.+|+++       +|+|+|++||++++|+..          
T Consensus       224 ~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~  303 (819)
T TIGR01970       224 RVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITR  303 (819)
T ss_pred             HHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCce
Confidence            99999976   5888889999999999999999999999999999       699999999999999754          


Q ss_pred             --------cccccccccccCCcc
Q psy437          159 --------PDYLPPILDLRLGRE  173 (184)
Q Consensus       159 --------e~y~~~i~~~~~~r~  173 (184)
                              .+|.||.  +|+||.
T Consensus       304 L~~~~iSkasa~QR~--GRAGR~  324 (819)
T TIGR01970       304 LETVRISQASATQRA--GRAGRL  324 (819)
T ss_pred             eeEEEECHHHHHhhh--hhcCCC
Confidence                    2478998  588885

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.

>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=99.13  E-value=9.3e-11  Score=76.35  Aligned_cols=69  Identities=19%  Similarity=0.227  Sum_probs=64.7

Q ss_pred             HHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          103 ALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       103 gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      .|...|+++..+|+++|+..|..+.+.|.++...++++       +|.|++++|+++++|.+...|.|.+  +|+||.
T Consensus         2 ~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~--GR~~R~   77 (78)
T PF00271_consen    2 FLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRI--GRAGRI   77 (78)
T ss_dssp             HHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHH--TTSSTT
T ss_pred             ChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHh--hcCCCC
Confidence            57889999999999999999999999999999999999       5999999999999999999999999  477774

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 ....

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.09  E-value=5.9e-10  Score=99.48  Aligned_cols=102  Identities=16%  Similarity=0.066  Sum_probs=85.8

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc-CceEEEEEeeccc
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN-KVHVGHWTVVSKE   96 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g-~~~vlVaT~tr~~   96 (184)
                      .|+..+..+++.+ ..+.++||||.+...++.++..|.     +.++||++++.+|.+++++|++| .+++||+|.    
T Consensus       480 ~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~Sk----  550 (732)
T TIGR00603       480 NKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSK----  550 (732)
T ss_pred             HHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEec----
Confidence            4666666666432 256789999999999999998873     46689999999999999999975 789999998    


Q ss_pred             HHHHHHHHHhcCCcEEEeeCCCC-hHHHHHHHHHhhC
Q psy437           97 CDSVAAALAQERINAISYHAGLA-DKLRNEVQMKWIS  132 (184)
Q Consensus        97 ~e~~a~gL~~~gi~~~vih~~~p-~~~r~~~~~~f~~  132 (184)
                        ...+|+|.++++ ++|+++.| .+.+.|+||.+|-
T Consensus       551 --VgdeGIDlP~a~-vvI~~s~~~gS~~q~iQRlGRi  584 (732)
T TIGR00603       551 --VGDTSIDLPEAN-VLIQISSHYGSRRQEAQRLGRI  584 (732)
T ss_pred             --ccccccCCCCCC-EEEEeCCCCCCHHHHHHHhccc
Confidence              778999999999 99999887 6999999999653

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).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.09  E-value=4.5e-10  Score=104.99  Aligned_cols=94  Identities=16%  Similarity=0.108  Sum_probs=80.9

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe---eEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN---AISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~---~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      ..+.+||||++..+++.+++.|.+.+++   +..+||+|++++|..+++.  .|..+|||||+      .+++||+++||
T Consensus       285 ~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATN------IAEtSITIpgI  356 (1294)
T PRK11131        285 GPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATN------VAETSLTVPGI  356 (1294)
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEecc------HHhhccccCcc
Confidence            4577999999999999999999987765   6689999999999999886  57889999999      99999999999


Q ss_pred             cEEEeeCCC---------------C---hHHHHHHHHHhhCCCc
Q psy437          110 NAISYHAGL---------------A---DKLRNEVQMKWISNKV  135 (184)
Q Consensus       110 ~~~vih~~~---------------p---~~~r~~~~~~f~~~~~  135 (184)
                      + +||++|+               |   -+..+|.||.++.|..
T Consensus       357 ~-yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~  399 (1294)
T PRK11131        357 K-YVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV  399 (1294)
T ss_pred             e-EEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCC
Confidence            9 9999984               3   3456788888777654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.08  E-value=6.3e-10  Score=98.23  Aligned_cols=86  Identities=12%  Similarity=-0.119  Sum_probs=72.4

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC---Ccc-----E
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ---WKR-----I  148 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~---~vr-----~  148 (184)
                      .-++||+|.+..+++.++..|...|+++.++|++.++..+..+...+..  ..|+||       .|++   +|+     +
T Consensus       473 ~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~~~~rE~~ii~~ag~~--g~VlVATdmAgRGtDI~l~~~V~~~GGLh  550 (656)
T PRK12898        473 GRPVLVGTRSVAASERLSALLREAGLPHQVLNAKQDAEEAAIVARAGQR--GRITVATNMAGRGTDIKLEPGVAARGGLH  550 (656)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCCcHHHHHHHHHHcCCC--CcEEEEccchhcccCcCCccchhhcCCCE
Confidence            3579999999999999999999999999999999877776666655544  458887       5998   777     9


Q ss_pred             EEecCCCCCccccccccccccCCcc
Q psy437          149 IWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       149 v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ||++++|.+.+.|.|+++  |.||.
T Consensus       551 VI~~d~P~s~r~y~hr~G--RTGRq  573 (656)
T PRK12898        551 VILTERHDSARIDRQLAG--RCGRQ  573 (656)
T ss_pred             EEEcCCCCCHHHHHHhcc--cccCC
Confidence            999999999999999996  55553

>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=99.08  E-value=1.5e-09  Score=76.65  Aligned_cols=89  Identities=19%  Similarity=0.178  Sum_probs=81.7

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+|++...++.++..|...+..+..+|++++...+..+...|..+...++++       +|.|....|+++++|.
T Consensus        28 ~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~  107 (131)
T cd00079          28 GGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPW  107 (131)
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCCC
Confidence            457999999999999999999989999899999999999999999999999888887       5999999999999999


Q ss_pred             CccccccccccccCCccc
Q psy437          157 IKPDYLPPILDLRLGRED  174 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~~  174 (184)
                      +...+.|.++  |+||.+
T Consensus       108 ~~~~~~Q~~G--R~~R~~  123 (131)
T cd00079         108 SPSSYLQRIG--RAGRAG  123 (131)
T ss_pred             CHHHheeccc--ccccCC
Confidence            9999999995  666654

>KOG0352|consensus

Probab=99.07  E-value=5.8e-10  Score=92.82  Aligned_cols=108  Identities=26%  Similarity=0.346  Sum_probs=98.1

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE-------------------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV-------------------------   87 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v-------------------------   87 (184)
                      ..+-+|||.+-......-...|....+++..+.+.|+..+|.+++-.+...+.++                         
T Consensus        60 ~~gITIV~SPLiALIkDQiDHL~~LKVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r  139 (641)
T KOG0352|consen   60 HGGITIVISPLIALIKDQIDHLKRLKVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANR  139 (641)
T ss_pred             hCCeEEEehHHHHHHHHHHHHHHhcCCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhh
Confidence            3457899999999888888888888999999999999999999988887655433                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           88 --------------------------------------------------------------------------------   87 (184)
Q Consensus        88 --------------------------------------------------------------------------------   87 (184)
                                                                                                      
T Consensus       140 ~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFYD  219 (641)
T KOG0352|consen  140 DVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYD  219 (641)
T ss_pred             ceeeeEEechhhhHhhhccccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchhhhhhHH
Confidence                                                                                            


Q ss_pred             ---------------------------------------EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHH
Q psy437           88 ---------------------------------------GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQM  128 (184)
Q Consensus        88 ---------------------------------------lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~  128 (184)
                                                             ||||.||..||.+|-+|.+.||.+.+||+|+..+.|+.+|+
T Consensus       220 ~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe  299 (641)
T KOG0352|consen  220 NHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQE  299 (641)
T ss_pred             HHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHH
Confidence                                                   89999999999999999999999999999999999999999


Q ss_pred             HhhCCCceEEEE
Q psy437          129 KWISNKVHLYNV  140 (184)
Q Consensus       129 ~f~~~~~~v~va  140 (184)
                      .|++++++|++|
T Consensus       300 ~WM~~~~PvI~A  311 (641)
T KOG0352|consen  300 KWMNNEIPVIAA  311 (641)
T ss_pred             HHhcCCCCEEEE
Confidence            999999999998

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.06  E-value=1e-08  Score=85.15  Aligned_cols=86  Identities=10%  Similarity=0.069  Sum_probs=72.9

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCC--cEEEeeCCCChHHHHHH----HHHhhCCCceEEEE-------EecCCccEE
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERI--NAISYHAGLADKLRNEV----QMKWISNKVHLYNV-------WKIQWKRII  149 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi--~~~vih~~~p~~~r~~~----~~~f~~~~~~v~va-------~D~~~vr~v  149 (184)
                      ...++||++++++.|+.++..|...+.  .+..+|+++++..|...    .+.|++++..++|+       +|++ +..|
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            345899999999999999999977665  47999999999999774    67899999999999       6996 7888


Q ss_pred             EecCCCCCccccccccccccCCcc
Q psy437          150 WIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       150 ~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +++..|  .++|+|+++  |+||.
T Consensus       300 i~~~~~--~~~~iqr~G--R~gR~  319 (358)
T TIGR01587       300 ITELAP--IDSLIQRLG--RLHRY  319 (358)
T ss_pred             EEcCCC--HHHHHHHhc--cccCC
Confidence            888776  789999996  55554

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.

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

Probab=99.02  E-value=9.5e-10  Score=94.42  Aligned_cols=85  Identities=25%  Similarity=0.389  Sum_probs=72.6

Q ss_pred             cChHHHHHHHHHhhc-------CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           18 KNVLKEVISLIKAKY-------SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        18 ~~k~~~L~~~l~~~~-------~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      .+|.+.+..+.+..+       -.+++|||++||+.|..+|..|...|+++..||+||+..+|..+...|.+++..++|.
T Consensus       417 ~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVT  496 (830)
T COG1202         417 SEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVT  496 (830)
T ss_pred             hHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEee
Confidence            357777777665432       3568999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcC
Q psy437           91 TVVSKECDSVAAALAQER  108 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~g  108 (184)
                      |-      .+|.|.|.|.
T Consensus       497 TA------AL~AGVDFPA  508 (830)
T COG1202         497 TA------ALAAGVDFPA  508 (830)
T ss_pred             hh------hhhcCCCCch
Confidence            99      5666666554

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.01  E-value=1.6e-09  Score=70.21  Aligned_cols=78  Identities=19%  Similarity=0.144  Sum_probs=64.8

Q ss_pred             HHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHH
Q psy437           49 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQM  128 (184)
Q Consensus        49 ~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~  128 (184)
                      .+++.|...++++..+||++++++|..+++.|.++...+||+|+      .++.|++.+.++ .|+.++.|.+...+.|+
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~------~~~~Gi~~~~~~-~vi~~~~~~~~~~~~Q~   74 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATD------VAERGLDLPGVD-LVIIYDLPWSPASYIQR   74 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECC------hhhCCcChhcCC-EEEEeCCCCCHHHHHHh
Confidence            56778888899999999999999999999999999999999999      667787777777 67777777777777776


Q ss_pred             HhhCC
Q psy437          129 KWISN  133 (184)
Q Consensus       129 ~f~~~  133 (184)
                      ..+.+
T Consensus        75 ~gR~~   79 (82)
T smart00490       75 IGRAG   79 (82)
T ss_pred             hcccc
Confidence            65543

>KOG0346|consensus

Probab=99.01  E-value=1.3e-09  Score=90.90  Aligned_cols=73  Identities=10%  Similarity=0.067  Sum_probs=62.6

Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----------------------------------
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----------------------------------  140 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----------------------------------  140 (184)
                      .|=++---|..-||..+|+|+.||...|-.+.++|-.|--++++|                                   
T Consensus       280 r~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~~~~~eee~kgk~~e~~~kndkkskkK~D~  359 (569)
T KOG0346|consen  280 RCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSADGDKLEEEVKGKSDEKNPKNDKKSKKKLDK  359 (569)
T ss_pred             hhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccchhhhhccccccccccCCCCccccccccCc
Confidence            344444456788999999999999999999999999999999988                                   


Q ss_pred             -------EecCCccEEEecCCCCCccccccccccc
Q psy437          141 -------WKIQWKRIIWIHSLVLIKPDYLPPILDL  168 (184)
Q Consensus       141 -------~D~~~vr~v~~~~~p~~~e~y~~~i~~~  168 (184)
                             +|..+|..|+|||+|.+.++|+||++++
T Consensus       360 E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRT  394 (569)
T KOG0346|consen  360 ESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRT  394 (569)
T ss_pred             hhchhccccchheeeeeecCCCCchHHHHHhcccc
Confidence                   2566788999999999999999999753

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.00  E-value=2.1e-09  Score=96.81  Aligned_cols=89  Identities=12%  Similarity=-0.113  Sum_probs=78.2

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Eec---CCcc-----
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKI---QWKR-----  147 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~---~~vr-----  147 (184)
                      ...++||+|.+...++.++..|...|+++.++|+++++..+..+.+.+..|  .|+||       .|+   |+|+     
T Consensus       427 ~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL  504 (790)
T PRK09200        427 TGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGL  504 (790)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCc
Confidence            456899999999999999999999999999999999999998888888776  57777       599   7999     


Q ss_pred             EEEecCCCCCcccccccccc-ccCCcc
Q psy437          148 IIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      +||++++|.+.+.|.|++++ +|.|..
T Consensus       505 ~VI~~d~p~s~r~y~qr~GRtGR~G~~  531 (790)
T PRK09200        505 AVIGTERMESRRVDLQLRGRSGRQGDP  531 (790)
T ss_pred             EEEeccCCCCHHHHHHhhccccCCCCC
Confidence            99999999999999999965 355544

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.97  E-value=4.5e-09  Score=91.25  Aligned_cols=87  Identities=13%  Similarity=-0.076  Sum_probs=77.0

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE--------EecCCccEEEecCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV--------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va--------~D~~~vr~v~~~~~p~  156 (184)
                      .+++|.+.....++.++..|...|+++.++|+++|++.|..+.+.|+.|+..++++        ||+|++..|++..+|+
T Consensus       345 ~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~~p~~  424 (501)
T PHA02558        345 ENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSK  424 (501)
T ss_pred             CCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEecCCc
Confidence            35666666677999999999999999999999999999999999999998888876        6999999999999999


Q ss_pred             CccccccccccccCCcc
Q psy437          157 IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~  173 (184)
                      +...|+|+++  |.+|.
T Consensus       425 s~~~~~QriG--R~~R~  439 (501)
T PHA02558        425 SKIIVLQSIG--RVLRK  439 (501)
T ss_pred             chhhhhhhhh--ccccC
Confidence            9999999996  55553

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.97  E-value=3.7e-09  Score=99.17  Aligned_cols=94  Identities=16%  Similarity=0.113  Sum_probs=79.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCC---CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQER---INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~g---i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      .++.+|||+++..+++.+++.|.+.+   +.+..+||+|++++|.++++.+  +..+|||||+      .++++|+++||
T Consensus       278 ~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATN------IAEtSLTIpgV  349 (1283)
T TIGR01967       278 GPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATN------VAETSLTVPGI  349 (1283)
T ss_pred             CCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEecc------HHHhccccCCe
Confidence            45789999999999999999998764   4578899999999999886543  3468999999      88999999999


Q ss_pred             cEEEeeCCCCh------------------HHHHHHHHHhhCCCc
Q psy437          110 NAISYHAGLAD------------------KLRNEVQMKWISNKV  135 (184)
Q Consensus       110 ~~~vih~~~p~------------------~~r~~~~~~f~~~~~  135 (184)
                      + +||+.|++.                  +..+|.||.++.|.+
T Consensus       350 ~-yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~  392 (1283)
T TIGR01967       350 H-YVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV  392 (1283)
T ss_pred             e-EEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCC
Confidence            9 999999765                  456889998877653

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.

>KOG0343|consensus

Probab=98.94  E-value=2.9e-08  Score=85.00  Aligned_cols=163  Identities=13%  Similarity=0.162  Sum_probs=119.0

Q ss_pred             CCCCCCeEEEEEEccChH------HHHHHHHHhhcCCCcEEEEeccHH-HHHHHHHHHHhCCCeeEEecCC---------
Q psy437            4 SFNRANLKYEILPKKNVL------KEVISLIKAKYSGQSGIVYCLTRK-ECDSVAAALAQERINAISYHAG---------   67 (184)
Q Consensus         4 s~~R~Nl~y~v~~~~~k~------~~L~~~l~~~~~~~~~IIf~~tr~-~~e~la~~L~~~gi~~~~~hg~---------   67 (184)
                      +|+-+||...|....+++      ..|-.+|....+..+++.|..|.. .+..++.. .........+|..         
T Consensus       210 ~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRL-sL~dP~~vsvhe~a~~atP~~L  288 (758)
T KOG0343|consen  210 NFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARL-SLKDPVYVSVHENAVAATPSNL  288 (758)
T ss_pred             CCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHh-hcCCCcEEEEeccccccChhhh
Confidence            456677777766554321      223333433334568999977654 34444432 2223334445521         


Q ss_pred             ------CCHHHHHHHHHHHhcc--CceEEEEEeecccHHHHHHHHH--hcCCcEEEeeCCCChHHHHHHHHHhhCCCceE
Q psy437           68 ------LADKLRNEVQMKWISN--KVHVGHWTVVSKECDSVAAALA--QERINAISYHAGLADKLRNEVQMKWISNKVHL  137 (184)
Q Consensus        68 ------l~~~~R~~~~~~f~~g--~~~vlVaT~tr~~~e~~a~gL~--~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v  137 (184)
                            +.-+++..++-.|...  +.++||+.++.+.+.-+.....  .+|++...+||.|.|..|..+-..|.+.+--|
T Consensus       289 ~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~v  368 (758)
T KOG0343|consen  289 QQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVV  368 (758)
T ss_pred             hheEEEEehhhHHHHHHHHHHhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceE
Confidence                  2236778889999875  4578999999999888887775  58999999999999999999999999888777


Q ss_pred             EEE-------EecCCccEEEecCCCCCcccccccccc
Q psy437          138 YNV-------WKIQWKRIIWIHSLVLIKPDYLPPILD  167 (184)
Q Consensus       138 ~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~  167 (184)
                      +.|       +|.|-|.||+.+|-|.+.+.|+||+++
T Consensus       369 LF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGR  405 (758)
T KOG0343|consen  369 LFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGR  405 (758)
T ss_pred             EEeehhhhccCCCcccceEEEecCchhHHHHHHHhhh
Confidence            777       699999999999999999999999964

>KOG0349|consensus

Probab=98.92  E-value=4.3e-09  Score=87.91  Aligned_cols=87  Identities=16%  Similarity=0.180  Sum_probs=78.8

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcC---CcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQER---INAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSL  154 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~g---i~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~  154 (184)
                      -+.|++|.|+.+|+.+-+.|...|   .+++.+|+|..++.|..-.+.|+.++++.+++       +|+..+.++||..+
T Consensus       506 dkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtl  585 (725)
T KOG0349|consen  506 DKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTL  585 (725)
T ss_pred             CceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEec
Confidence            367999999999999999997665   57888999999999999999999999999988       69999999999999


Q ss_pred             CCCccccccccccccCCcc
Q psy437          155 VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       155 p~~~e~y~~~i~~~~~~r~  173 (184)
                      |....+|+|||+  |+||.
T Consensus       586 pd~k~nyvhrig--rvgra  602 (725)
T KOG0349|consen  586 PDDKTNYVHRIG--RVGRA  602 (725)
T ss_pred             Ccccchhhhhhh--ccchh
Confidence            999999999995  66664

>PRK00254 ski2-like helicase; Provisional

Probab=98.92  E-value=3.2e-08  Score=89.44  Aligned_cols=141  Identities=14%  Similarity=0.096  Sum_probs=97.1

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCC-------ee---EEecC------CCC---HHHHHHHHHHHhccCceEEEEEee
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERI-------NA---ISYHA------GLA---DKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi-------~~---~~~hg------~l~---~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      ...+.|.+..|-..++.++++|....+       +.   ..+++      +..   ...-...+.+......++||+|++
T Consensus       168 ~~~qiI~lSATl~n~~~la~wl~~~~~~~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~vLVF~~s  247 (720)
T PRK00254        168 GRAQILGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVKKGKGALVFVNT  247 (720)
T ss_pred             cCCcEEEEEccCCCHHHHHHHhCCccccCCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHHhCCCEEEEEcC
Confidence            345667788888778899999864211       11   11111      100   011112233334445689999999


Q ss_pred             cccHHHHHHHHHhc---------------------------------CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE
Q psy437           94 SKECDSVAAALAQE---------------------------------RINAISYHAGLADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        94 r~~~e~~a~gL~~~---------------------------------gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va  140 (184)
                      |+.|+.+|..|...                                 ...+..+|+|+++..|..+.+.|++|.++|+||
T Consensus       248 r~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~~G~i~VLva  327 (720)
T PRK00254        248 RRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITA  327 (720)
T ss_pred             hHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHHCCCCeEEEe
Confidence            99999988777321                                 112588999999999999999999999999999


Q ss_pred             -------EecCCccEEEe-------cCCCC-CccccccccccccCCcccc
Q psy437          141 -------WKIQWKRIIWI-------HSLVL-IKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       141 -------~D~~~vr~v~~-------~~~p~-~~e~y~~~i~~~~~~r~~~  175 (184)
                             +|+|.++.||.       ++.|. ...+|+|++  +|+||.+.
T Consensus       328 T~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~--GRAGR~~~  375 (720)
T PRK00254        328 TPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMM--GRAGRPKY  375 (720)
T ss_pred             CcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhh--hccCCCCc
Confidence                   59999999994       55554 344789998  58888643

>PRK01172 ski2-like helicase; Provisional

Probab=98.90  E-value=2.7e-08  Score=89.30  Aligned_cols=151  Identities=15%  Similarity=0.117  Sum_probs=100.1

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC---------eeEEecCC------C--CHHHHHHHHHHHhccC
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI---------NAISYHAG------L--ADKLRNEVQMKWISNK   84 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi---------~~~~~hg~------l--~~~~R~~~~~~f~~g~   84 (184)
                      +.+...++...+..+.|.+..|-..++.++++|...-+         ....++.+      .  ....-...+.......
T Consensus       157 e~ll~~~~~~~~~~riI~lSATl~n~~~la~wl~~~~~~~~~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~  236 (674)
T PRK01172        157 ETVLSSARYVNPDARILALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDG  236 (674)
T ss_pred             HHHHHHHHhcCcCCcEEEEeCccCCHHHHHHHhCCCccCCCCCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCC
Confidence            34444443222345677788998888999998853211         11112111      0  0111122333333445


Q ss_pred             ceEEEEEeecccHHHHHHHHHhc-----C--------------------CcEEEeeCCCChHHHHHHHHHhhCCCceEEE
Q psy437           85 VHVGHWTVVSKECDSVAAALAQE-----R--------------------INAISYHAGLADKLRNEVQMKWISNKVHLYN  139 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~-----g--------------------i~~~vih~~~p~~~r~~~~~~f~~~~~~v~v  139 (184)
                      .++||++++++.|+.+|..|...     .                    ..+..+|+++|+..|..+.+.|++|.+.|+|
T Consensus       237 ~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLv  316 (674)
T PRK01172        237 GQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIV  316 (674)
T ss_pred             CcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEE
Confidence            68999999999999999988542     1                    1246789999999999999999999999999


Q ss_pred             E-------EecCCccEEEecCC---------CCCccccccccccccCCcccc
Q psy437          140 V-------WKIQWKRIIWIHSL---------VLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       140 a-------~D~~~vr~v~~~~~---------p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      |       +|+|.. .|+..+.         |-+..+|.|++  +|+||.+.
T Consensus       317 aT~~la~Gvnipa~-~VII~~~~~~~~~~~~~~s~~~~~Qm~--GRAGR~g~  365 (674)
T PRK01172        317 ATPTLAAGVNLPAR-LVIVRDITRYGNGGIRYLSNMEIKQMI--GRAGRPGY  365 (674)
T ss_pred             ecchhhccCCCcce-EEEEcCceEeCCCCceeCCHHHHHHHh--hcCCCCCC
Confidence            9       599985 4555554         34566778998  58888753

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

Probab=98.88  E-value=1.3e-08  Score=86.79  Aligned_cols=122  Identities=16%  Similarity=0.112  Sum_probs=94.9

Q ss_pred             EEEEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      ..|.+....++.|++.|++. ..+..++|-+-|++.||.+.++|.+.|+++.++|++.+.-+|.+++..++.|...|||.
T Consensus       423 ievRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVG  502 (663)
T COG0556         423 IEVRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVG  502 (663)
T ss_pred             eeeecCCCcHHHHHHHHHHHHhcCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEe
Confidence            44556666778888777652 36688999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcE-EEeeCCCC---hHHHHHHHHHh---hCCCceEEE
Q psy437           91 TVVSKECDSVAAALAQERINA-ISYHAGLA---DKLRNEVQMKW---ISNKVHLYN  139 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~-~vih~~~p---~~~r~~~~~~f---~~~~~~v~v  139 (184)
                      .+      .+=.|||.|-++- .++-+|.+   .+.++-+|=.+   ++-...|+.
T Consensus       503 IN------LLREGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~~GkvIl  552 (663)
T COG0556         503 IN------LLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIL  552 (663)
T ss_pred             eh------hhhccCCCcceeEEEEeecCccccccccchHHHHHHHHhhccCCeEEE
Confidence            99      7788999998882 23444433   35555566543   333444444

>KOG0350|consensus

Probab=98.88  E-value=3e-09  Score=89.85  Aligned_cols=89  Identities=10%  Similarity=0.094  Sum_probs=79.5

Q ss_pred             ceEEEEEeecccHHHHHHHHH----hcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecC
Q psy437           85 VHVGHWTVVSKECDSVAAALA----QERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHS  153 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~----~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~  153 (184)
                      .++||+|++-..+-++++-|.    ..+..+--+-+++.++.|.-..+.|..|++.++++       +|+.+|..|||||
T Consensus       430 ~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd  509 (620)
T KOG0350|consen  430 NRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYD  509 (620)
T ss_pred             ceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecC
Confidence            478999999988888888885    34444455889999999999999999999999999       5999999999999


Q ss_pred             CCCCccccccccccc-cCCcc
Q psy437          154 LVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       154 ~p~~~e~y~~~i~~~-~~~r~  173 (184)
                      +|.+...|+||++++ |+||+
T Consensus       510 ~P~~~ktyVHR~GRTARAgq~  530 (620)
T KOG0350|consen  510 PPASDKTYVHRAGRTARAGQD  530 (620)
T ss_pred             CCchhhHHHHhhcccccccCC
Confidence            999999999999995 99998

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

Probab=98.87  E-value=1.1e-07  Score=83.52  Aligned_cols=146  Identities=13%  Similarity=0.119  Sum_probs=121.3

Q ss_pred             HHHhhcCCCcEEEEeccHHHHHHH----HHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------
Q psy437           27 LIKAKYSGQSGIVYCLTRKECDSV----AAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------   94 (184)
Q Consensus        27 ~l~~~~~~~~~IIf~~tr~~~e~l----a~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------   94 (184)
                      .+.....+.++..-+||-=.|++-    .++|...|+++..+-|.+..+.|.+++++..+|+++++|.|-+-        
T Consensus       304 ml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~  383 (677)
T COG1200         304 MLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFH  383 (677)
T ss_pred             HHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeec
Confidence            333333677889999997666554    45555669999999999999999999999999999999998776        


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       384 ~LgLVIiDEQHRFGV~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~  463 (677)
T COG1200         384 NLGLVIIDEQHRFGVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVY  463 (677)
T ss_pred             ceeEEEEeccccccHHHHHHHHHhCCCCCcEEEEeCCCchHHHHHHHhccccchhhccCCCCCCceEEEEeccccHHHHH
Confidence                                                                                            


Q ss_pred             ----------------------------ccHHHHHHHHH--hcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE----
Q psy437           95 ----------------------------KECDSVAAALA--QERINAISYHAGLADKLRNEVQMKWISNKVHLYNV----  140 (184)
Q Consensus        95 ----------------------------~~~e~~a~gL~--~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va----  140 (184)
                                                  +.++.++..|.  .++..+..+||-|+.+.++.+++.|++|++.|+||    
T Consensus       464 e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVI  543 (677)
T COG1200         464 ERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVI  543 (677)
T ss_pred             HHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEE
Confidence                                        35667777775  35677899999999999999999999999999999    


Q ss_pred             ---EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 ---WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ---~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                         .|.||-...+..+.-.-=-+-+|.. ++|+||=
T Consensus       544 EVGVdVPnATvMVIe~AERFGLaQLHQL-RGRVGRG  578 (677)
T COG1200         544 EVGVDVPNATVMVIENAERFGLAQLHQL-RGRVGRG  578 (677)
T ss_pred             EecccCCCCeEEEEechhhhhHHHHHHh-ccccCCC
Confidence               4999999999888766666778874 8999995

>PRK09401 reverse gyrase; Reviewed

Probab=98.85  E-value=1.9e-08  Score=94.63  Aligned_cols=79  Identities=15%  Similarity=0.007  Sum_probs=71.6

Q ss_pred             ceEEEEEeeccc---HHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----------EecCC-ccEE
Q psy437           85 VHVGHWTVVSKE---CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----------WKIQW-KRII  149 (184)
Q Consensus        85 ~~vlVaT~tr~~---~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----------~D~~~-vr~v  149 (184)
                      .++||+++++..   |+.++..|...|+++..+|+++    +..+ +.|++|++.|+|+           +|+|+ ||+|
T Consensus       329 ~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l----~~~l-~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryV  403 (1176)
T PRK09401        329 DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF----ERKF-EKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYA  403 (1176)
T ss_pred             CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH----HHHH-HHHHCCCCCEEEEecCCCCceeecCCCCcceeEE
Confidence            479999999988   9999999999999999999999    2233 9999999999998           49999 8999


Q ss_pred             EecCCCC------Cccccccccccc
Q psy437          150 WIHSLVL------IKPDYLPPILDL  168 (184)
Q Consensus       150 ~~~~~p~------~~e~y~~~i~~~  168 (184)
                      |||++|+      ..+.|.|+++++
T Consensus       404 I~y~vP~~~~~~~~~~~~~~~~~r~  428 (1176)
T PRK09401        404 IFYGVPKFKFSLEEELAPPFLLLRL  428 (1176)
T ss_pred             EEeCCCCEEEeccccccCHHHHHHH
Confidence            9999999      889999999875

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.85  E-value=2.4e-08  Score=90.18  Aligned_cols=96  Identities=16%  Similarity=0.118  Sum_probs=79.5

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+....     .....|...|.+.+.+. ..+.|+||||+|...++.++..|.+.|+++..+||.  +.+|+..+
T Consensus       394 Ptnkp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~I  471 (830)
T PRK12904        394 PTNRPMIRIDHPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEI  471 (830)
T ss_pred             CCCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHH
Confidence            66778776442     12235888888888652 367899999999999999999999999999999995  78999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE  107 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~  107 (184)
                      .+|..+...|+|||+      .++||+|++
T Consensus       472 ia~Ag~~g~VtIATN------mAGRGtDI~  495 (830)
T PRK12904        472 IAQAGRPGAVTIATN------MAGRGTDIK  495 (830)
T ss_pred             HHhcCCCceEEEecc------cccCCcCcc
Confidence            999999999999999      667776643

>PRK13766 Hef nuclease; Provisional

Probab=98.82  E-value=2.1e-08  Score=91.20  Aligned_cols=89  Identities=15%  Similarity=0.166  Sum_probs=82.0

Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCC--------CChHHHHHHHHHhhCCCceEEEE-------EecCCc
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAG--------LADKLRNEVQMKWISNKVHLYNV-------WKIQWK  146 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~--------~p~~~r~~~~~~f~~~~~~v~va-------~D~~~v  146 (184)
                      .+..++||+|..+..|+.++..|...|+++..+|+.        +++..|..+.+.|++|...++++       +|+|++
T Consensus       363 ~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~  442 (773)
T PRK13766        363 NPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSV  442 (773)
T ss_pred             CCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccC
Confidence            456789999999999999999999999998889886        99999999999999999999999       699999


Q ss_pred             cEEEecCCCCCccccccccccccCCc
Q psy437          147 RIIWIHSLVLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       147 r~v~~~~~p~~~e~y~~~i~~~~~~r  172 (184)
                      ++||+|++|.+...|+|++  +|.||
T Consensus       443 ~~VI~yd~~~s~~r~iQR~--GR~gR  466 (773)
T PRK13766        443 DLVIFYEPVPSEIRSIQRK--GRTGR  466 (773)
T ss_pred             CEEEEeCCCCCHHHHHHHh--cccCc
Confidence            9999999999999999988  47777

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=98.82  E-value=1.9e-08  Score=65.08  Aligned_cols=73  Identities=23%  Similarity=0.336  Sum_probs=65.8

Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccccCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLG  171 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~  171 (184)
                      .++..|...++.+.++|++++...+..+.+.|.++...++++       +|.|+++.|+.+++|.+...|.|.++  |++
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~g--R~~   79 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIG--RAG   79 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhc--ccc
Confidence            466778888999999999999999999999999999988887       59999999999999999999999994  666


Q ss_pred             cc
Q psy437          172 RE  173 (184)
Q Consensus       172 r~  173 (184)
                      |.
T Consensus        80 R~   81 (82)
T smart00490       80 RA   81 (82)
T ss_pred             cC
Confidence            64

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

Probab=98.81  E-value=2.3e-07  Score=84.12  Aligned_cols=85  Identities=13%  Similarity=0.071  Sum_probs=71.4

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHH-----HHHHHhhC----CC-------ceEEEE------
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRN-----EVQMKWIS----NK-------VHLYNV------  140 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~-----~~~~~f~~----~~-------~~v~va------  140 (184)
                      ...++||+|+++..|+.++..|...++  ..+|++|++..|.     .+++.|++    ++       ..|+||      
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            345799999999999999999998887  8999999999999     77888987    43       678888      


Q ss_pred             -EecCCccEEEecCCCCCccccccccccc-cCCc
Q psy437          141 -WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       141 -~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r  172 (184)
                       +|++. ..||++..|  .++|+||++++ |.|+
T Consensus       349 GLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~  379 (844)
T TIGR02621       349 GVNISA-DHLVCDLAP--FESMQQRFGRVNRFGE  379 (844)
T ss_pred             cccCCc-ceEEECCCC--HHHHHHHhcccCCCCC
Confidence             69987 788887766  59999999752 5555

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.

>PRK09694 helicase Cas3; Provisional

Probab=98.80  E-value=6e-08  Score=88.69  Aligned_cols=90  Identities=13%  Similarity=0.037  Sum_probs=75.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCC---CeeEEecCCCCHHHHH----HHHHHH-hccC---ceEEEEEeecccHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQER---INAISYHAGLADKLRN----EVQMKW-ISNK---VHVGHWTVVSKECDSVA  101 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~g---i~~~~~hg~l~~~~R~----~~~~~f-~~g~---~~vlVaT~tr~~~e~~a  101 (184)
                      .+.+++|||||.+.|+.+++.|++.+   .++..+||.+.+.+|.    ++++.| ++|+   ..|||+|.      .+.
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQ------ViE  632 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQ------VVE  632 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECc------chh
Confidence            56789999999999999999999764   6799999999999984    567778 5565   47999999      899


Q ss_pred             HHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437          102 AALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus       102 ~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                      +|||. +.+ .+|....|  ...++||..|-
T Consensus       633 ~GLDI-d~D-vlItdlaP--idsLiQRaGR~  659 (878)
T PRK09694        633 QSLDL-DFD-WLITQLCP--VDLLFQRLGRL  659 (878)
T ss_pred             heeec-CCC-eEEECCCC--HHHHHHHHhcc
Confidence            99999 578 78887777  56999999653

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.80  E-value=1.1e-08  Score=92.68  Aligned_cols=95  Identities=14%  Similarity=0.109  Sum_probs=76.9

Q ss_pred             CCCCCCeEEE-----EEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYE-----ILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~-----v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-.     ......|...+++.+.+. ..+.|+||||+|.+.++.++..|.+.|+++..+||++++.+|..+.
T Consensus       408 Ptnkp~~R~d~~d~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia  487 (896)
T PRK13104        408 PTNRSMIRKDEADLVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIA  487 (896)
T ss_pred             CCCCCcceecCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHH
Confidence            5677776532     122335888888777543 3678999999999999999999999999999999999999999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHh
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQ  106 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~  106 (184)
                      +.|+.|.  |+|||+      .++||+|+
T Consensus       488 ~Ag~~G~--VtIATN------mAGRGtDI  508 (896)
T PRK13104        488 EAGRPGA--VTIATN------MAGRGTDI  508 (896)
T ss_pred             hCCCCCc--EEEecc------CccCCcce
Confidence            9999994  999999      55555554

>KOG0332|consensus

Probab=98.77  E-value=3.1e-08  Score=81.29  Aligned_cols=108  Identities=10%  Similarity=0.043  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHHhcc-C-ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           70 DKLRNEVQMKWISN-K-VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        70 ~~~R~~~~~~f~~g-~-~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      .+++..++-.+-.. . .+-||+|-|+..+..++..|...|..+.++||+|.-..|..+...|+.|+.+|+++       
T Consensus       314 ~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~ARG  393 (477)
T KOG0332|consen  314 RDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCARG  393 (477)
T ss_pred             hhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhhcc
Confidence            34555555553322 1 25699999999999999999999999999999999999999999999999999998       


Q ss_pred             EecCCccEEEecCCCCC------cccccccccc-ccCCcccccc
Q psy437          141 WKIQWKRIIWIHSLVLI------KPDYLPPILD-LRLGREDIRE  177 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~------~e~y~~~i~~-~~~~r~~~~~  177 (184)
                      +|.+.|..|+|||+|..      .|.|+|||++ +|-||.++.=
T Consensus       394 iDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~  437 (477)
T KOG0332|consen  394 IDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAI  437 (477)
T ss_pred             cccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEE
Confidence            69999999999999975      5789999988 5888875543

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.77  E-value=7.1e-08  Score=90.63  Aligned_cols=87  Identities=14%  Similarity=0.068  Sum_probs=73.4

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCc---EEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEec
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERIN---AISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIH  152 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~---~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~  152 (184)
                      +..+|||++++..+++.++..|...+++   +..+|+++|++.+..+.+.  .|+.+|++|       +|+|+|++||++
T Consensus       285 ~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~  362 (1294)
T PRK11131        285 GPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDP  362 (1294)
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEEC
Confidence            4567999999999999999999887765   5679999999999887765  467899999       699999999998


Q ss_pred             C---------------CC---CCccccccccccccCCcc
Q psy437          153 S---------------LV---LIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       153 ~---------------~p---~~~e~y~~~i~~~~~~r~  173 (184)
                      +               +|   .|..+|.||.  +|+||.
T Consensus       363 Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRa--GRAGR~  399 (1294)
T PRK11131        363 GTARISRYSYRTKVQRLPIEPISQASANQRK--GRCGRV  399 (1294)
T ss_pred             CCccccccccccCcccCCeeecCHhhHhhhc--cccCCC
Confidence            5               44   4557899999  588885

>KOG0351|consensus

Probab=98.77  E-value=6.4e-08  Score=88.72  Aligned_cols=107  Identities=24%  Similarity=0.302  Sum_probs=98.1

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc--CceE------------------------
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN--KVHV------------------------   87 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g--~~~v------------------------   87 (184)
                      ++-+||..|-....+.....|...+|++.+++|+++..+|..+++.+.+|  .+++                        
T Consensus       304 ~gitvVISPL~SLm~DQv~~L~~~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~  383 (941)
T KOG0351|consen  304 GGVTVVISPLISLMQDQVTHLSKKGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYAR  383 (941)
T ss_pred             CCceEEeccHHHHHHHHHHhhhhcCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCC
Confidence            34578888889999999999988899999999999999999999999999  5555                        


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           88 --------------------------------------------------------------------------------   87 (184)
Q Consensus        88 --------------------------------------------------------------------------------   87 (184)
                                                                                                      
T Consensus       384 ~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sfnR~NL~yeV  463 (941)
T KOG0351|consen  384 GLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKSSFNRPNLKYEV  463 (941)
T ss_pred             CeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecccCCCCCceEEE
Confidence                                                                                            


Q ss_pred             -------------------------EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE
Q psy437           88 -------------------------GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        88 -------------------------lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va  140 (184)
                                               ||||.+|.+||.++..|...|+++..||+||+.+.|..+|++|.+++++|+||
T Consensus       464 ~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivA  541 (941)
T KOG0351|consen  464 SPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVA  541 (941)
T ss_pred             EeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEE
Confidence                                     77777779999999999999999999999999999999999999999999998

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

Probab=98.75  E-value=1e-07  Score=81.59  Aligned_cols=104  Identities=9%  Similarity=0.050  Sum_probs=88.2

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      +...+...+..+....+++|||.+...++.++..|...|+ +..+.|..++.+|..++++|++|+.++||.+.      .
T Consensus       269 ~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~------v  341 (442)
T COG1061         269 KIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVK------V  341 (442)
T ss_pred             HHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEee------e
Confidence            4444555554322357899999999999999999998888 88999999999999999999999999999999      7


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      +-.|.|.|++++.++=.+ ..+.+.|+|+.++
T Consensus       342 l~EGvDiP~~~~~i~~~~-t~S~~~~~Q~lGR  372 (442)
T COG1061         342 LDEGVDIPDADVLIILRP-TGSRRLFIQRLGR  372 (442)
T ss_pred             ccceecCCCCcEEEEeCC-CCcHHHHHHHhhh
Confidence            788999999995555555 9999999999854

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

Probab=98.73  E-value=3.5e-07  Score=82.59  Aligned_cols=163  Identities=16%  Similarity=0.051  Sum_probs=121.9

Q ss_pred             CeEEEEEEcc-----C----hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC---------------eeEEe
Q psy437            9 NLKYEILPKK-----N----VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI---------------NAISY   64 (184)
Q Consensus         9 Nl~y~v~~~~-----~----k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi---------------~~~~~   64 (184)
                      |+.|.+...-     +    -+...++.|.+.....+-|-...|....+.++++|...+-               .+..-
T Consensus       149 ~vr~VIVDEiHel~~sKRG~~Lsl~LeRL~~l~~~~qRIGLSATV~~~~~varfL~g~~~~~~Iv~~~~~k~~~i~v~~p  228 (814)
T COG1201         149 DVRYVIVDEIHALAESKRGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGFGDPCEIVDVSAAKKLEIKVISP  228 (814)
T ss_pred             CCcEEEeehhhhhhccccchhhhhhHHHHHhhCcccEEEeehhccCCHHHHHHHhcCCCCceEEEEcccCCcceEEEEec
Confidence            5667766432     1    2233334444433356778899999999999999975531               11111


Q ss_pred             cCCC-----CHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcC-CcEEEeeCCCChHHHHHHHHHhhCCCceEE
Q psy437           65 HAGL-----ADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQER-INAISYHAGLADKLRNEVQMKWISNKVHLY  138 (184)
Q Consensus        65 hg~l-----~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g-i~~~vih~~~p~~~r~~~~~~f~~~~~~v~  138 (184)
                      ...+     .-..+...+....+.....||+|+||..+|.++..|...+ ..+.+=|+.++...|..+-+.|++|.++.+
T Consensus       229 ~~~~~~~~~~~~~~~~~i~~~v~~~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lrav  308 (814)
T COG1201         229 VEDLIYDEELWAALYERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAV  308 (814)
T ss_pred             CCccccccchhHHHHHHHHHHHhhcCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEE
Confidence            1111     1123445556666666689999999999999999998776 777888899999999999999999999999


Q ss_pred             EE-------EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          139 NV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       139 va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ||       +|+-+|..|+++.-|++.-..+||++  |+|..
T Consensus       309 V~TSSLELGIDiG~vdlVIq~~SP~sV~r~lQRiG--RsgHr  348 (814)
T COG1201         309 VATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIG--RAGHR  348 (814)
T ss_pred             EEccchhhccccCCceEEEEeCCcHHHHHHhHhcc--ccccc
Confidence            99       69999999999999999999999994  66654

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

Probab=98.72  E-value=1.8e-08  Score=86.77  Aligned_cols=152  Identities=18%  Similarity=0.287  Sum_probs=107.1

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCC---------C--CHHHHHHHH-----HHHhc-
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAG---------L--ADKLRNEVQ-----MKWIS-   82 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~---------l--~~~~R~~~~-----~~f~~-   82 (184)
                      +++-|+..|+..+++.+-|-...|....+.+|..|...   ...|...         .  ...++..++     ..|.+ 
T Consensus       358 RLdGLI~RLr~l~~~AQ~i~LSATVgNp~elA~~l~a~---lV~y~~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~  434 (830)
T COG1202         358 RLDGLIGRLRYLFPGAQFIYLSATVGNPEELAKKLGAK---LVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTE  434 (830)
T ss_pred             chhhHHHHHHHhCCCCeEEEEEeecCChHHHHHHhCCe---eEeecCCCCChhHeeeeecCchHHHHHHHHHHHHHHhhh
Confidence            66777777877666666666788999999999999542   2222110         0  112222222     23332 


Q ss_pred             ---c-CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEE-
Q psy437           83 ---N-KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIW-  150 (184)
Q Consensus        83 ---g-~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~-  150 (184)
                         | ..+.||+|.+|+.|..+|..|+..|+++..||+|+|...|.-+-+.|.++.+.++|.       .|.|--.-|+ 
T Consensus       435 sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFE  514 (830)
T COG1202         435 SSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFE  514 (830)
T ss_pred             hccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHH
Confidence               1 347899999999999999999999999999999999999999999999999999997       3888643332 


Q ss_pred             --ecCCCCCccccccccccccCCcccc
Q psy437          151 --IHSLVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       151 --~~~~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                        -+..-.-...-+|..+ +|+||.+.
T Consensus       515 sLaMG~~WLs~~EF~QM~-GRAGRp~y  540 (830)
T COG1202         515 SLAMGIEWLSVREFQQML-GRAGRPDY  540 (830)
T ss_pred             HHHcccccCCHHHHHHHh-cccCCCCc
Confidence              2223333445556655 79999744

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.66  E-value=1.7e-06  Score=77.83  Aligned_cols=76  Identities=14%  Similarity=0.039  Sum_probs=60.8

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHh-CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQ-ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~-~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .|.......+... ..+.++||.+||++.+.++.+.|.+ .|..+..+||+++..+|.+...+..+|+.+|+|+|.+.
T Consensus       174 GKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsa  251 (679)
T PRK05580        174 GKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSA  251 (679)
T ss_pred             hHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHH
Confidence            4555444433221 1456899999999999999999986 47889999999999999999888999999999998865

>TIGR00595 priA primosomal protein N'

Probab=98.65  E-value=1e-06  Score=76.58  Aligned_cols=76  Identities=14%  Similarity=0.053  Sum_probs=59.4

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhC-CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .|.......+... ..+.++|+.+|+...+.++++.|++. |.++..+||+++..+|.+...+..+|+.+|+|+|.+.
T Consensus         9 GKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsa   86 (505)
T TIGR00595         9 GKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSA   86 (505)
T ss_pred             CHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHH
Confidence            3554444333221 14568999999999999999999864 7788999999999999998888888988888888765

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).

>KOG4150|consensus

Probab=98.62  E-value=2.1e-07  Score=80.31  Aligned_cols=105  Identities=17%  Similarity=0.227  Sum_probs=87.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----C----CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----R----INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAAL  104 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----g----i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL  104 (184)
                      .+-.+|-||++|+.||-+....++.    +    -.+..|.||-+.++|.++......|....||+|+      .+.-|+
T Consensus       524 ~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTN------ALELGI  597 (1034)
T KOG4150|consen  524 HGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATN------ALELGI  597 (1034)
T ss_pred             cCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecc------hhhhcc
Confidence            5678999999999999876655431    1    1356799999999999999999999999999999      556688


Q ss_pred             HhcCCcEEEeeCCCChHHHHHHHHHhhCC-----CceEEEEEecC
Q psy437          105 AQERINAISYHAGLADKLRNEVQMKWISN-----KVHLYNVWKIQ  144 (184)
Q Consensus       105 ~~~gi~~~vih~~~p~~~r~~~~~~f~~~-----~~~v~va~D~~  144 (184)
                      |+-+++ .|+|.|+|.+.-+..|+..+.|     ++.++||++-|
T Consensus       598 DIG~LD-AVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~P  641 (1034)
T KOG4150|consen  598 DIGHLD-AVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGP  641 (1034)
T ss_pred             ccccce-eEEEccCchhHHHHHHHhccccccCCCceEEEEEeccc
Confidence            999999 9999999999999999986655     46888885444

>KOG0348|consensus

Probab=98.62  E-value=1.4e-07  Score=80.71  Aligned_cols=104  Identities=13%  Similarity=0.131  Sum_probs=79.4

Q ss_pred             HHHHHHHHHHHhccC------ceEEEEEeecccHHHHHHHHH----h------------------cCCcEEEeeCCCChH
Q psy437           70 DKLRNEVQMKWISNK------VHVGHWTVVSKECDSVAAALA----Q------------------ERINAISYHAGLADK  121 (184)
Q Consensus        70 ~~~R~~~~~~f~~g~------~~vlVaT~tr~~~e~~a~gL~----~------------------~gi~~~vih~~~p~~  121 (184)
                      ++-|.-.+-.|+...      .++||+-++...||-=...+.    .                  .+.+.+-+||+|.|.
T Consensus       405 pKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~Qe  484 (708)
T KOG0348|consen  405 PKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQE  484 (708)
T ss_pred             CchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHH
Confidence            455666666665432      367888888866554333221    1                  123357899999999


Q ss_pred             HHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccc-cCCcc
Q psy437          122 LRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       122 ~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                      .|+-+.+.|....--|+.+       +|.|+|++|+.||.|.+..+|+|||+++ |+|+.
T Consensus       485 eRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~k  544 (708)
T KOG0348|consen  485 ERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEK  544 (708)
T ss_pred             HHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCC
Confidence            9999999999877777777       6999999999999999999999999986 88875

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.62  E-value=1e-07  Score=85.83  Aligned_cols=87  Identities=13%  Similarity=-0.095  Sum_probs=77.7

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Eec---CCcc-----
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKI---QWKR-----  147 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~---~~vr-----  147 (184)
                      ..-+|||.|.+...++.++..|...|+++.++|++.++..+..+.+.++.|.  |+||       .|+   ++|.     
T Consensus       439 ~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGL  516 (796)
T PRK12906        439 KGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGL  516 (796)
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCc
Confidence            4568999999999999999999999999999999999999999999998887  5555       499   4899     


Q ss_pred             EEEecCCCCCccccccccccccCCcc
Q psy437          148 IIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +||++++|.+.+.|.|.++  |.||-
T Consensus       517 hVI~te~pes~ri~~Ql~G--RtGRq  540 (796)
T PRK12906        517 AVIGTERHESRRIDNQLRG--RSGRQ  540 (796)
T ss_pred             EEEeeecCCcHHHHHHHhh--hhccC
Confidence            9999999999999999996  55553

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

Probab=98.62  E-value=2.4e-07  Score=78.73  Aligned_cols=110  Identities=16%  Similarity=0.165  Sum_probs=91.6

Q ss_pred             eEEecCCCCHHHHHHHHHHH-hccCceEEEEEeecccHHHHHHHHHhcCCcEE-Ee--------eCCCChHHHHHHHHHh
Q psy437           61 AISYHAGLADKLRNEVQMKW-ISNKVHVGHWTVVSKECDSVAAALAQERINAI-SY--------HAGLADKLRNEVQMKW  130 (184)
Q Consensus        61 ~~~~hg~l~~~~R~~~~~~f-~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~-vi--------h~~~p~~~r~~~~~~f  130 (184)
                      ..+-|..|. ..+..+.+.| +++..+|||+|.-|..+|.++..|...|+.+. .+        .-||.|.....+...|
T Consensus       343 ~~v~HPKl~-~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~F  421 (542)
T COG1111         343 SGVEHPKLE-KLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQF  421 (542)
T ss_pred             ccCCCccHH-HHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHH
Confidence            444566664 3456666677 35678999999999999999999999988853 22        2469999999999999


Q ss_pred             hCCCceEEEE-------EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          131 ISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       131 ~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +.|...|+||       +|+|++..|+-|+...|+--++||.+  |-||.
T Consensus       422 r~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~G--RTGR~  469 (542)
T COG1111         422 RKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKG--RTGRK  469 (542)
T ss_pred             hcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhC--ccccC
Confidence            9999999999       69999999999999999999999984  66665

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.60  E-value=2e-07  Score=84.59  Aligned_cols=95  Identities=17%  Similarity=0.140  Sum_probs=75.9

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-..     .....|...+++.+.+. ..+.|+||||.|...++.++..|...|+++.++||++++.++..+.
T Consensus       413 PTnkp~~R~d~~d~iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~  492 (908)
T PRK13107        413 PTNRPMVRKDMADLVYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVA  492 (908)
T ss_pred             CCCCCccceeCCCcEEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHH
Confidence            56667654221     12235788887777543 3678899999999999999999999999999999999999999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHh
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQ  106 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~  106 (184)
                      +.|+.|.  |+|||+      .++||.|+
T Consensus       493 ~Ag~~G~--VtIATn------mAGRGTDI  513 (908)
T PRK13107        493 QAGRTGA--VTIATN------MAGRGTDI  513 (908)
T ss_pred             hCCCCCc--EEEecC------CcCCCcce
Confidence            9999988  899999      44555543

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.60  E-value=2e-07  Score=83.69  Aligned_cols=87  Identities=16%  Similarity=-0.063  Sum_probs=75.4

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC---------Ccc
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ---------WKR  147 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~---------~vr  147 (184)
                      .-++||+|.+...++.++..|...|+++.++|+++.+..+..+.+.|..|  .|++|       .|++         ++.
T Consensus       424 ~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~  501 (762)
T TIGR03714       424 GQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLA  501 (762)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeE
Confidence            45899999999999999999999999999999999999998888877777  56676       5999         999


Q ss_pred             EEEecCCCCCcccccccccc-ccCCcc
Q psy437          148 IIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      .|+++++|....+ .|++++ +|.|..
T Consensus       502 vIit~~~ps~rid-~qr~GRtGRqG~~  527 (762)
T TIGR03714       502 VIGTERMENSRVD-LQLRGRSGRQGDP  527 (762)
T ss_pred             EEEecCCCCcHHH-HHhhhcccCCCCc
Confidence            9999999998877 999965 355544

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.60  E-value=4.4e-07  Score=85.56  Aligned_cols=136  Identities=10%  Similarity=-0.007  Sum_probs=94.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHH------HHH----HHHHH-HhccCceEEEEEee
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADK------LRN----EVQMK-WISNKVHVGHWTVV   93 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~------~R~----~~~~~-f~~g~~~vlVaT~t   93 (184)
                      +.-+.|++..|-. ++.+++.+...        .+++..++..+...      +..    ..+.. ...+..+|||++++
T Consensus       210 pdLKlIlmSATld-~~~fa~~F~~apvI~V~Gr~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg  288 (1283)
T TIGR01967       210 PDLKIIITSATID-PERFSRHFNNAPIIEVSGRTYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPG  288 (1283)
T ss_pred             CCCeEEEEeCCcC-HHHHHHHhcCCCEEEECCCcccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCC
Confidence            4456788888875 57788877532        23344444322210      111    11222 22355689999999


Q ss_pred             cccHHHHHHHHHhcC---CcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC-------
Q psy437           94 SKECDSVAAALAQER---INAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL-------  156 (184)
Q Consensus        94 r~~~e~~a~gL~~~g---i~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~-------  156 (184)
                      +++++.++..|...+   +.+..+|+++|+..+..+.+.+  +..+|++|       +|+|+|++||++++++       
T Consensus       289 ~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~  366 (1283)
T TIGR01967       289 EREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYR  366 (1283)
T ss_pred             HHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccccc
Confidence            999999999997654   4567899999999998774443  23588888       6999999999998654       


Q ss_pred             -----------CccccccccccccCCcc
Q psy437          157 -----------IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 -----------~~e~y~~~i~~~~~~r~  173 (184)
                                 |..+|.||.  +|+||.
T Consensus       367 ~~~~~L~~~~ISkasa~QRa--GRAGR~  392 (1283)
T TIGR01967       367 TKVQRLPIEPISQASANQRK--GRCGRV  392 (1283)
T ss_pred             cCccccCCccCCHHHHHHHh--hhhCCC
Confidence                       456899998  588885

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.

>KOG0329|consensus

Probab=98.59  E-value=5.8e-07  Score=70.75  Aligned_cols=130  Identities=21%  Similarity=0.299  Sum_probs=91.9

Q ss_pred             cEEEEeccHHHHHHHHHHHHh-----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec----------------
Q psy437           36 SGIVYCLTRKECDSVAAALAQ-----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS----------------   94 (184)
Q Consensus        36 ~~IIf~~tr~~~e~la~~L~~-----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr----------------   94 (184)
                      +.+|.|.||+.|=++.+....     .+.+++++.||++-+.-++++..    --.|+|+|++|                
T Consensus       112 svlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~----~PhivVgTPGrilALvr~k~l~lk~vk  187 (387)
T KOG0329|consen  112 SVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN----CPHIVVGTPGRILALVRNRSLNLKNVK  187 (387)
T ss_pred             EEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC----CCeEEEcCcHHHHHHHHhccCchhhcc
Confidence            468899999999998876653     47899999999987665555544    55799999998                


Q ss_pred             ----ccHHHHHHHHHh------------cCCcEEEeeCCCChHHHHHHHHHhhCC-------------------------
Q psy437           95 ----KECDSVAAALAQ------------ERINAISYHAGLADKLRNEVQMKWISN-------------------------  133 (184)
Q Consensus        95 ----~~~e~~a~gL~~------------~gi~~~vih~~~p~~~r~~~~~~f~~~-------------------------  133 (184)
                          .+|+.+-..||-            ++-.+..+.+-++++.|.--+ .|+.+                         
T Consensus       188 hFvlDEcdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~-kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLk  266 (387)
T KOG0329|consen  188 HFVLDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCH-KFMQDPMEIFVDDEAKLTLHGLQQYYVKLK  266 (387)
T ss_pred             eeehhhHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHH-hhhcCchhhhccchhhhhhhhHHHHHHhhh
Confidence                467777666642            122245667777777664222 22211                         


Q ss_pred             ------------------CceE-------------EEE-------EecCCccEEEecCCCCCccccccccccccCCc
Q psy437          134 ------------------KVHL-------------YNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       134 ------------------~~~v-------------~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r  172 (184)
                                        .+-|             +||       .|+..+..|+|||+|.+++.|+|++.  |+||
T Consensus       267 e~eKNrkl~dLLd~LeFNQVvIFvKsv~Rl~f~kr~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~--rAgr  341 (387)
T KOG0329|consen  267 ENEKNRKLNDLLDVLEFNQVVIFVKSVQRLSFQKRLVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVA--RAGR  341 (387)
T ss_pred             hhhhhhhhhhhhhhhhhcceeEeeehhhhhhhhhhhHHhhhhccccCcccceeeeccCCCCCchHHHHHhh--hhhc
Confidence                              1111             233       49999999999999999999999995  6666

>TIGR01054 rgy reverse gyrase

Probab=98.59  E-value=2.7e-07  Score=87.04  Aligned_cols=69  Identities=13%  Similarity=0.158  Sum_probs=63.7

Q ss_pred             ceEEEEEeec---ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----------EecCC-ccEE
Q psy437           85 VHVGHWTVVS---KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----------WKIQW-KRII  149 (184)
Q Consensus        85 ~~vlVaT~tr---~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----------~D~~~-vr~v  149 (184)
                      .++||+++++   ..|+.++..|...|+++..+|+++++    ...+.|++|++.|+|+           +|+|+ |++|
T Consensus       327 ~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~v  402 (1171)
T TIGR01054       327 TGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYA  402 (1171)
T ss_pred             CCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHcCCCCEEEEeccccCcccccCCCCccccEE
Confidence            5789999999   99999999999999999999999984    5789999999999998           49999 8999


Q ss_pred             EecCCCCC
Q psy437          150 WIHSLVLI  157 (184)
Q Consensus       150 ~~~~~p~~  157 (184)
                      |++++|+.
T Consensus       403 I~~~~P~~  410 (1171)
T TIGR01054       403 VFLGVPKF  410 (1171)
T ss_pred             EEECCCCE
Confidence            99999985

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.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.59  E-value=2.7e-07  Score=82.53  Aligned_cols=90  Identities=11%  Similarity=-0.103  Sum_probs=79.0

Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCC--c-----c
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQW--K-----R  147 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~--v-----r  147 (184)
                      ...-+|||.|.+...+|.++..|...|+++.++|++  +..|+...-.|.++...|+||       .|++.  |     -
T Consensus       403 ~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl  480 (745)
T TIGR00963       403 AKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGL  480 (745)
T ss_pred             hcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCc
Confidence            345579999999999999999999999999999999  888888899999999999999       49988  4     4


Q ss_pred             EEEecCCCCCcccccccccc-ccCCcc
Q psy437          148 IIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      +||++++|.+...|.|++++ +|.|..
T Consensus       481 ~VI~t~~p~s~ri~~q~~GRtGRqG~~  507 (745)
T TIGR00963       481 YVIGTERHESRRIDNQLRGRSGRQGDP  507 (745)
T ss_pred             EEEecCCCCcHHHHHHHhccccCCCCC
Confidence            99999999999999999964 244443

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=98.57  E-value=2.2e-06  Score=71.45  Aligned_cols=77  Identities=12%  Similarity=-0.006  Sum_probs=63.5

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcC--CcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQER--INAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSL  154 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~g--i~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~  154 (184)
                      ..++||++++++.|+.++..|...+  +.+..+|++++++.|...      ++..++||       +|++.+ +|+ ++ 
T Consensus       272 ~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-  342 (357)
T TIGR03158       272 GERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-  342 (357)
T ss_pred             CCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-
Confidence            3579999999999999999998764  567789999999988643      36788888       699987 666 45 


Q ss_pred             CCCccccccccccccCC
Q psy437          155 VLIKPDYLPPILDLRLG  171 (184)
Q Consensus       155 p~~~e~y~~~i~~~~~~  171 (184)
                      |.+.++|+||++  |+|
T Consensus       343 p~~~~~yiqR~G--R~g  357 (357)
T TIGR03158       343 ARDAAAFWQRLG--RLG  357 (357)
T ss_pred             CCCHHHHhhhcc--cCC
Confidence            999999999994  554

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.

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

Probab=98.54  E-value=4e-06  Score=77.57  Aligned_cols=141  Identities=15%  Similarity=0.076  Sum_probs=117.0

Q ss_pred             cCCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec-------------
Q psy437           32 YSGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS-------------   94 (184)
Q Consensus        32 ~~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr-------------   94 (184)
                      ..+.++.|.+||.=.|++-.+.|.++    .+++..+..=.+.++...+++...+|++.|||.|-.-             
T Consensus       641 ~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLl  720 (1139)
T COG1197         641 MDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLL  720 (1139)
T ss_pred             cCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeE
Confidence            36788999999999999988888764    4556667766778999999999999999999998644             


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       721 IIDEEqRFGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl  800 (1139)
T COG1197         721 IIDEEQRFGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILREL  800 (1139)
T ss_pred             EEechhhcCccHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             -------------ccHHHHHHHHH--hcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEec
Q psy437           95 -------------KECDSVAAALA--QERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIH  152 (184)
Q Consensus        95 -------------~~~e~~a~gL~--~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~  152 (184)
                                   ...+.++..|.  .|..+..|.||.|+...-+.++..|-.|+..|+|+       +|+|+...+|..
T Consensus       801 ~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe  880 (1139)
T COG1197         801 LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIE  880 (1139)
T ss_pred             hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEe
Confidence                         46777788884  57888899999999999999999999999999999       599999999866


Q ss_pred             CCCCCccccccccccccCCcc
Q psy437          153 SLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       153 ~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +-=+-=-+.++. |++|+||-
T Consensus       881 ~AD~fGLsQLyQ-LRGRVGRS  900 (1139)
T COG1197         881 RADKFGLAQLYQ-LRGRVGRS  900 (1139)
T ss_pred             ccccccHHHHHH-hccccCCc
Confidence            544444445554 47999995

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.50  E-value=4.7e-07  Score=81.20  Aligned_cols=84  Identities=11%  Similarity=-0.041  Sum_probs=71.8

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC-CceEEEE-------EecCCccEEEecCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN-KVHLYNV-------WKIQWKRIIWIHSL  154 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~-~~~v~va-------~D~~~vr~v~~~~~  154 (184)
                      ..-++||+|+....++.++..|.     +.++||++|+..|..+.+.|++| .+.++++       +|+|+++.||+++.
T Consensus       495 ~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~  569 (732)
T TIGR00603       495 RGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVGDTSIDLPEANVLIQISS  569 (732)
T ss_pred             cCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHhCCCccEEEEecccccccCCCCCCEEEEeCC
Confidence            44589999999889999999883     35689999999999999999865 7788877       69999999999999


Q ss_pred             C-CCcccccccccc-ccCC
Q psy437          155 V-LIKPDYLPPILD-LRLG  171 (184)
Q Consensus       155 p-~~~e~y~~~i~~-~~~~  171 (184)
                      | .+...|+||++| +|.+
T Consensus       570 ~~gS~~q~iQRlGRilR~~  588 (732)
T TIGR00603       570 HYGSRRQEAQRLGRILRAK  588 (732)
T ss_pred             CCCCHHHHHHHhcccccCC
Confidence            8 599999999965 2444

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).

>KOG0337|consensus

Probab=98.47  E-value=2.4e-06  Score=71.32  Aligned_cols=104  Identities=10%  Similarity=0.071  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHhccCce---EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE------
Q psy437           70 DKLRNEVQMKWISNKVH---VGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV------  140 (184)
Q Consensus        70 ~~~R~~~~~~f~~g~~~---vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va------  140 (184)
                      +++|...+...+.+.+.   -+|+..+++.+|-+..+|...|+.+..+-+.+.+..|..--+.|+.++..++|.      
T Consensus       244 ~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaR  323 (529)
T KOG0337|consen  244 KAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAAR  323 (529)
T ss_pred             cHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhc
Confidence            46777888887776654   899999999999999999999999888999999999999999999999888887      


Q ss_pred             -EecCCccEEEecCCCCCccccccccccc-cCCcc
Q psy437          141 -WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       141 -~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                       .|+|....|+|||.|.+..-++||+++. |+||.
T Consensus       324 G~diplldnvinyd~p~~~klFvhRVgr~aragrt  358 (529)
T KOG0337|consen  324 GLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRT  358 (529)
T ss_pred             cCCCccccccccccCCCCCceEEEEecchhhcccc
Confidence             5999999999999999999999999885 77774

>TIGR00595 priA primosomal protein N'

Probab=98.47  E-value=9.3e-07  Score=76.90  Aligned_cols=88  Identities=10%  Similarity=0.023  Sum_probs=70.8

Q ss_pred             HHHHHHHHHhC--CCeeEEecCCCCHHHH--HHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc-EEEeeCCC---
Q psy437           47 CDSVAAALAQE--RINAISYHAGLADKLR--NEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN-AISYHAGL---  118 (184)
Q Consensus        47 ~e~la~~L~~~--gi~~~~~hg~l~~~~R--~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~-~~vih~~~---  118 (184)
                      ++.+.+.|.+.  +.++..+|+++++.++  ..++++|.+|+.+|||+|.      .+++|+|.+++. +.|+++|.   
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~------~i~kG~d~~~v~lV~vl~aD~~l~  344 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ------MIAKGHHFPNVTLVGVLDADSGLH  344 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCc------ccccCCCCCcccEEEEEcCccccc
Confidence            58888888876  7889999999987665  8999999999999999999      899999999999 34588886   


Q ss_pred             -Ch------HHHHHHHHHhhCCC----ceEEEE
Q psy437          119 -AD------KLRNEVQMKWISNK----VHLYNV  140 (184)
Q Consensus       119 -p~------~~r~~~~~~f~~~~----~~v~va  140 (184)
                       |.      ....++|..++.|.    ..+++-
T Consensus       345 ~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiq  377 (505)
T TIGR00595       345 SPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQ  377 (505)
T ss_pred             CcccchHHHHHHHHHHHHhccCCCCCCCEEEEE
Confidence             42      34667888877654    455543

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.47  E-value=1.2e-06  Score=79.37  Aligned_cols=72  Identities=25%  Similarity=0.241  Sum_probs=62.3

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC---------------------C----------------CeeEEecCCCCHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE---------------------R----------------INAISYHAGLADKLRNE   75 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~---------------------g----------------i~~~~~hg~l~~~~R~~   75 (184)
                      .+++++|||+||+.+...|..|...                     +                ..+++.|+||+.++|..
T Consensus       252 ~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~  331 (766)
T COG1204         252 EGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQL  331 (766)
T ss_pred             cCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHH
Confidence            6789999999999999999998720                     0                14678999999999999


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                      +.+.|+.|.++|||||+      .+|.|.+-|.-.
T Consensus       332 vE~~Fr~g~ikVlv~Tp------TLA~GVNLPA~~  360 (766)
T COG1204         332 VEDAFRKGKIKVLVSTP------TLAAGVNLPART  360 (766)
T ss_pred             HHHHHhcCCceEEEech------HHhhhcCCcceE
Confidence            99999999999999999      779997777654

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

Probab=98.44  E-value=6.6e-07  Score=81.99  Aligned_cols=95  Identities=15%  Similarity=0.174  Sum_probs=82.6

Q ss_pred             CCCcEEEEeccHHHHHHHH----HHHHhCC----CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVA----AALAQER----INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAAL  104 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la----~~L~~~g----i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL  104 (184)
                      .+.++|+|+.+++.++.+.    ..+...+    ..+..|+|++..++|.++...|+.|+..++++|+      .+--|+
T Consensus       305 ~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~------Alelgi  378 (851)
T COG1205         305 NGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATN------ALELGI  378 (851)
T ss_pred             cCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecch------hhhhce
Confidence            6789999999999999997    4444445    5688899999999999999999999999999999      445578


Q ss_pred             HhcCCcEEEeeCCCCh-HHHHHHHHHhhCCC
Q psy437          105 AQERINAISYHAGLAD-KLRNEVQMKWISNK  134 (184)
Q Consensus       105 ~~~gi~~~vih~~~p~-~~r~~~~~~f~~~~  134 (184)
                      |+-+++ .|++.+.|. +.-++.|+.++.|.
T Consensus       379 diG~ld-avi~~g~P~~s~~~~~Q~~GRaGR  408 (851)
T COG1205         379 DIGSLD-AVIAYGYPGVSVLSFRQRAGRAGR  408 (851)
T ss_pred             eehhhh-hHhhcCCCCchHHHHHHhhhhccC
Confidence            999999 999999999 89999999876654

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

Probab=98.36  E-value=2.9e-06  Score=79.84  Aligned_cols=92  Identities=9%  Similarity=0.057  Sum_probs=77.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC------CC---eeEEecCCCCHHHHHHHHHHHhccCc-eEEEEEeecccHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE------RI---NAISYHAGLADKLRNEVQMKWISNKV-HVGHWTVVSKECDSVAA  102 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~------gi---~~~~~hg~l~~~~R~~~~~~f~~g~~-~vlVaT~tr~~~e~~a~  102 (184)
                      .+.++||||.++..|+.+++.|.+.      ++   .+..++|+.+  ++..++++|+++.. .|+|+++      .+..
T Consensus       697 ~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvd------mL~T  768 (1123)
T PRK11448        697 GEGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVD------LLTT  768 (1123)
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEec------cccc
Confidence            3478999999999999999888653      22   4566888875  57789999999887 5788888      8899


Q ss_pred             HHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437          103 ALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus       103 gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      |+|.|.+. .++.+..+.+...|+|...|..
T Consensus       769 G~DvP~v~-~vVf~rpvkS~~lf~QmIGRgt  798 (1123)
T PRK11448        769 GIDVPSIC-NLVFLRRVRSRILYEQMLGRAT  798 (1123)
T ss_pred             CCCccccc-EEEEecCCCCHHHHHHHHhhhc
Confidence            99999999 9999999999999999997643

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.23  E-value=3.5e-06  Score=77.20  Aligned_cols=89  Identities=15%  Similarity=-0.084  Sum_probs=76.9

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC---CccE----
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ---WKRI----  148 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~---~vr~----  148 (184)
                      ..-+|||+|.+...+|.+++.|...||++.++|+  .+..|+...-.|.++...|+||       .||+   .|..    
T Consensus       597 ~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL  674 (1025)
T PRK12900        597 KGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGL  674 (1025)
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCc
Confidence            3458999999999999999999999999999997  6888888899999999999999       4998   5544    


Q ss_pred             -EEecCCCCCcccccccccc-ccCCcc
Q psy437          149 -IWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       149 -v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                       ||+.+.|.+...|.|++++ +|.|..
T Consensus       675 ~VIgterhes~Rid~Ql~GRtGRqGdp  701 (1025)
T PRK12900        675 FILGSERHESRRIDRQLRGRAGRQGDP  701 (1025)
T ss_pred             eeeCCCCCchHHHHHHHhhhhhcCCCC
Confidence             4999999999999999965 355544

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

Probab=98.23  E-value=2.1e-05  Score=72.29  Aligned_cols=98  Identities=13%  Similarity=0.091  Sum_probs=84.4

Q ss_pred             HHHHHHhccCceEEEEEeecccHHHHH----HHHHhcC----CcEEEeeCCCChHHHHHHHHHhhCCCceEEEE------
Q psy437           75 EVQMKWISNKVHVGHWTVVSKECDSVA----AALAQER----INAISYHAGLADKLRNEVQMKWISNKVHLYNV------  140 (184)
Q Consensus        75 ~~~~~f~~g~~~vlVaT~tr~~~e~~a----~gL~~~g----i~~~vih~~~p~~~r~~~~~~f~~~~~~v~va------  140 (184)
                      .+...+..+..+.||++.+|+.+|.+.    +.+...+    ..+.+++++++...|..+.+.|++|++.++++      
T Consensus       297 ~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~Alel  376 (851)
T COG1205         297 TLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALEL  376 (851)
T ss_pred             HHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhh
Confidence            445555668889999999999999997    4454555    44689999999999999999999999999998      


Q ss_pred             -EecCCccEEEecCCCC-CccccccccccccCCccc
Q psy437          141 -WKIQWKRIIWIHSLVL-IKPDYLPPILDLRLGRED  174 (184)
Q Consensus       141 -~D~~~vr~v~~~~~p~-~~e~y~~~i~~~~~~r~~  174 (184)
                       .|+-++..|++...|. +.-++.|+.  +|+||..
T Consensus       377 gidiG~ldavi~~g~P~~s~~~~~Q~~--GRaGR~~  410 (851)
T COG1205         377 GIDIGSLDAVIAYGYPGVSVLSFRQRA--GRAGRRG  410 (851)
T ss_pred             ceeehhhhhHhhcCCCCchHHHHHHhh--hhccCCC
Confidence             5999999999999999 889999998  5888864

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

Probab=98.15  E-value=0.00011  Score=67.49  Aligned_cols=84  Identities=19%  Similarity=0.195  Sum_probs=64.7

Q ss_pred             eEEEEEEcc--C--hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC----C-CeeEE-ecCCCCHHHHHHHHHH
Q psy437           10 LKYEILPKK--N--VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE----R-INAIS-YHAGLADKLRNEVQMK   79 (184)
Q Consensus        10 l~y~v~~~~--~--k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~----g-i~~~~-~hg~l~~~~R~~~~~~   79 (184)
                      -.|++.-..  .  -+-.+..+.... ++.++.+.+||...+.++++.|.+.    | ..+.. |||.|+.++++..+++
T Consensus        98 ~SFaiiAPTGvGKTTfg~~~sl~~a~-kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~  176 (1187)
T COG1110          98 KSFAIIAPTGVGKTTFGLLMSLYLAK-KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALER  176 (1187)
T ss_pred             CceEEEcCCCCchhHHHHHHHHHHHh-cCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHH
Confidence            345555332  2  345555555443 6678899999999999999988753    2 44333 9999999999999999


Q ss_pred             HhccCceEEEEEeec
Q psy437           80 WISNKVHVGHWTVVS   94 (184)
Q Consensus        80 f~~g~~~vlVaT~tr   94 (184)
                      +.+|..+|+|.|+.+
T Consensus       177 i~~gdfdIlitTs~F  191 (1187)
T COG1110         177 IESGDFDILITTSQF  191 (1187)
T ss_pred             HhcCCccEEEEeHHH
Confidence            999999999999988

>KOG0354|consensus

Probab=98.13  E-value=1.4e-05  Score=71.36  Aligned_cols=100  Identities=15%  Similarity=0.102  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHhcc-CceEEEEEeecccHHHHHHHHH---hcCCcE--------EEeeCCCChHHHHHHHHHhhCCCceEE
Q psy437           71 KLRNEVQMKWISN-KVHVGHWTVVSKECDSVAAALA---QERINA--------ISYHAGLADKLRNEVQMKWISNKVHLY  138 (184)
Q Consensus        71 ~~R~~~~~~f~~g-~~~vlVaT~tr~~~e~~a~gL~---~~gi~~--------~vih~~~p~~~r~~~~~~f~~~~~~v~  138 (184)
                      ..+..+++.|..+ ..++||+|.+|..|+.+-.+|.   ..||++        .....||.+..-..+...|+.|.+.|+
T Consensus       399 ~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvL  478 (746)
T KOG0354|consen  399 KLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVL  478 (746)
T ss_pred             HHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEE
Confidence            4566677777754 5689999999999999999997   334553        334469999999999999999999999


Q ss_pred             EE-------EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          139 NV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       139 va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ||       +|++.+..||.||...++-.-+|+.+  | ||.
T Consensus       479 VATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrG--R-gRa  517 (746)
T KOG0354|consen  479 VATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRG--R-GRA  517 (746)
T ss_pred             EEecchhccCCcccccEEEEecCCccHHHHHHHhc--c-ccc
Confidence            99       69999999999999999999999985  5 665

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.07  E-value=7.5e-06  Score=73.68  Aligned_cols=85  Identities=8%  Similarity=0.001  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHhC--CCeeEEecCCCCH--HHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc-EEEeeCCC
Q psy437           44 RKECDSVAAALAQE--RINAISYHAGLAD--KLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN-AISYHAGL  118 (184)
Q Consensus        44 r~~~e~la~~L~~~--gi~~~~~hg~l~~--~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~-~~vih~~~  118 (184)
                      ...++.+++.|.+.  +.++..+|+++.+  +++++++++|.+|+.+|||+|.      .+|+|+|.+++. +.++++|.
T Consensus       436 g~G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~------~iakG~d~p~v~lV~il~aD~  509 (679)
T PRK05580        436 GPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQ------MLAKGHDFPNVTLVGVLDADL  509 (679)
T ss_pred             eccHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEECh------hhccCCCCCCcCEEEEEcCch
Confidence            35788999999885  8889999999874  6799999999999999999999      899999999999 23488886


Q ss_pred             ChH----------HHHHHHHHhhCCC
Q psy437          119 ADK----------LRNEVQMKWISNK  134 (184)
Q Consensus       119 p~~----------~r~~~~~~f~~~~  134 (184)
                      +-.          .+.++|..++.|.
T Consensus       510 ~l~~pdfra~Er~~~~l~q~~GRagR  535 (679)
T PRK05580        510 GLFSPDFRASERTFQLLTQVAGRAGR  535 (679)
T ss_pred             hccCCccchHHHHHHHHHHHHhhccC
Confidence            643          3678888877653

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.06  E-value=4.1e-05  Score=71.36  Aligned_cols=104  Identities=7%  Similarity=-0.057  Sum_probs=83.4

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC---ceEEEEEeec
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK---VHVGHWTVVS   94 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~---~~vlVaT~tr   94 (184)
                      .|+..|..+|.+. ..+.++||||......+.|...|...|++...++|+++..+|..++++|.+..   .-+|++|.  
T Consensus       471 gKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTr--  548 (1033)
T PLN03142        471 GKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTR--  548 (1033)
T ss_pred             hHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEecc--
Confidence            4666666655432 15678999999999999999999999999999999999999999999997532   34577777  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHH
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMK  129 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~  129 (184)
                          ..+.||+-...+ .||++|+|=++....|+.
T Consensus       549 ----AGGlGINLt~Ad-~VIiyD~dWNP~~d~QAi  578 (1033)
T PLN03142        549 ----AGGLGINLATAD-IVILYDSDWNPQVDLQAQ  578 (1033)
T ss_pred             ----ccccCCchhhCC-EEEEeCCCCChHHHHHHH
Confidence                335577888888 999999988877777765

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

Probab=98.06  E-value=6.1e-05  Score=61.79  Aligned_cols=131  Identities=13%  Similarity=0.089  Sum_probs=92.5

Q ss_pred             HHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           23 EVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        23 ~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      .|..+|.++. .+.|.+||+++.+..++++..|++.  ....++.|+.  .+.|.+-.++|++|+..+||.|.      .
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTT------I  364 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTT------I  364 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEee------h
Confidence            5667776542 4578999999999999999999653  3345677764  56799999999999999999999      8


Q ss_pred             HHHHHHhcCCcEEEeeCCCCh-HHHHHHHHHhhCCCceEEEEEecCCcc-EEEecCCCCCccccccccc
Q psy437          100 VAAALAQERINAISYHAGLAD-KLRNEVQMKWISNKVHLYNVWKIQWKR-IIWIHSLVLIKPDYLPPIL  166 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~-~~r~~~~~~f~~~~~~v~va~D~~~vr-~v~~~~~p~~~e~y~~~i~  166 (184)
                      +-||...+++++.|+.+.-+- +...-+|=+.+-|.-     .|.|+=. .-+|+...+++..-.++|.
T Consensus       365 LERGVTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs-----~~~PtGdv~FFH~G~skaM~~A~keIk  428 (441)
T COG4098         365 LERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRS-----LERPTGDVLFFHYGKSKAMKQARKEIK  428 (441)
T ss_pred             hhcccccccceEEEecCCcccccHHHHHHHhhhccCC-----CcCCCCcEEEEeccchHHHHHHHHHHH
Confidence            999999999998888777543 334445545554431     1333222 1246666666655555553

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

Probab=98.06  E-value=1.8e-05  Score=72.41  Aligned_cols=92  Identities=21%  Similarity=0.263  Sum_probs=77.7

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEecc---HHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLT---RKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~t---r~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ...+.+.+++++  -+.-+|||+++   ++.++.+++.|+.+|+++..+|++     +.+.++.|..|++++||.+.+.-
T Consensus       322 ~~~e~~~elvk~--lG~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyY  394 (1187)
T COG1110         322 ESLEKVVELVKK--LGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYY  394 (1187)
T ss_pred             ccHHHHHHHHHH--hCCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccc
Confidence            445666777766  34579999999   999999999999999999999985     47889999999999999998775


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLA  119 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p  119 (184)
                      .  .+.||||-|..--.++-+|.|
T Consensus       395 G--~lVRGlDLP~rirYaIF~GvP  416 (1187)
T COG1110         395 G--VLVRGLDLPHRIRYAVFYGVP  416 (1187)
T ss_pred             c--ceeecCCchhheeEEEEecCC
Confidence            5  778999988644488999999

>KOG0347|consensus

Probab=98.06  E-value=2.5e-05  Score=67.40  Aligned_cols=136  Identities=16%  Similarity=0.107  Sum_probs=121.8

Q ss_pred             EEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec------------------
Q psy437           37 GIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS------------------   94 (184)
Q Consensus        37 ~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr------------------   94 (184)
                      ++|+++||+.|.++.+.|..    .++.++.+.|||+.+...+++.+    .-.|+|||++|                  
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATPGRlweli~e~n~~l~~~k~v  341 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATPGRLWELIEEDNTHLGNFKKV  341 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecchHHHHHHHhhhhhhhhhhhc
Confidence            99999999999999999975    48999999999998877777766    56799999999                  


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       342 kcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~  421 (731)
T KOG0347|consen  342 KCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFR  421 (731)
T ss_pred             eEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCcc
Confidence                                                                                            


Q ss_pred             ----------------------------------------------------ccHHHHHHHHHhcCCcEEEeeCCCChHH
Q psy437           95 ----------------------------------------------------KECDSVAAALAQERINAISYHAGLADKL  122 (184)
Q Consensus        95 ----------------------------------------------------~~~e~~a~gL~~~gi~~~vih~~~p~~~  122 (184)
                                                                          ..+.+++..|..-+|+.+.+|+.|-|..
T Consensus       422 ~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKq  501 (731)
T KOG0347|consen  422 GKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQ  501 (731)
T ss_pred             CCCeeEecCcchhHHHHHHHHhhcCCccccceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHH
Confidence                                                                3578888899999999999999999999


Q ss_pred             HHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccc-cCCccccc
Q psy437          123 RNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGREDIR  176 (184)
Q Consensus       123 r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~~~~  176 (184)
                      |-.-++.|+...-.|++|       +|||+|.|||||.+|.+.|-|+||-+++ |++-++++
T Consensus       502 RLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvs  563 (731)
T KOG0347|consen  502 RLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVS  563 (731)
T ss_pred             HHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccccCCCeE
Confidence            999999999998899998       6999999999999999999999999775 77766553

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

Probab=98.05  E-value=3e-05  Score=66.49  Aligned_cols=85  Identities=7%  Similarity=0.004  Sum_probs=79.9

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..+++|+|.....++.++..|..+|+ +.++.++.|+..|..+.+.|+.|...++|.       +|+|++..+|......
T Consensus       283 ~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~  361 (442)
T COG1061         283 GDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTG  361 (442)
T ss_pred             CCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeeccceecCCCCcEEEEeCCCC
Confidence            56899999999999999999999999 799999999999999999999988999888       6999999999999999


Q ss_pred             Cccccccccccc-c
Q psy437          157 IKPDYLPPILDL-R  169 (184)
Q Consensus       157 ~~e~y~~~i~~~-~  169 (184)
                      |.-.|+|+++++ |
T Consensus       362 S~~~~~Q~lGR~LR  375 (442)
T COG1061         362 SRRLFIQRLGRGLR  375 (442)
T ss_pred             cHHHHHHHhhhhcc
Confidence            999999999874 5

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

Probab=97.98  E-value=4e-05  Score=67.67  Aligned_cols=98  Identities=12%  Similarity=0.182  Sum_probs=69.5

Q ss_pred             CCCeEEEEEEccChHHHHHHHHHhh-cCCCcEEEEeccHH--------HHHHHHHHHHhC--CCeeEEecCCCCHHHHHH
Q psy437            7 RANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRK--------ECDSVAAALAQE--RINAISYHAGLADKLRNE   75 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~--------~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~   75 (184)
                      |.-|.=.+.+. ++...+.+.+++. .++.++.+.|+-.+        .++.+++.|...  ++++..+||.|+..++++
T Consensus       446 RkpI~T~~i~~-~~~~~v~e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~  524 (677)
T COG1200         446 RKPITTVVIPH-ERRPEVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDA  524 (677)
T ss_pred             CCceEEEEecc-ccHHHHHHHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHH
Confidence            44444333333 2445555555432 35678888887544        456667777642  677999999999999999


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcE
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINA  111 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~  111 (184)
                      ++++|++|+++|||||.      ++--|.|.|+-.+
T Consensus       525 vM~~Fk~~e~~ILVaTT------VIEVGVdVPnATv  554 (677)
T COG1200         525 VMEAFKEGEIDILVATT------VIEVGVDVPNATV  554 (677)
T ss_pred             HHHHHHcCCCcEEEEee------EEEecccCCCCeE
Confidence            99999999999999999      5555677776654

>PRK09694 helicase Cas3; Provisional

Probab=97.96  E-value=7.9e-05  Score=68.65  Aligned_cols=86  Identities=12%  Similarity=0.049  Sum_probs=68.0

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcC---CcEEEeeCCCChHHH----HHHHHHh-hCCC---ceEEEE-------EecC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQER---INAISYHAGLADKLR----NEVQMKW-ISNK---VHLYNV-------WKIQ  144 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~g---i~~~vih~~~p~~~r----~~~~~~f-~~~~---~~v~va-------~D~~  144 (184)
                      ...+++|.++|.+.+..+++.|...+   .++..+|+.+++..|    ..+.+.| ++|+   ..|+|+       +|+ 
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDI-  637 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDL-  637 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeec-
Confidence            34579999999999999999997654   678999999999988    4566667 5555   468888       599 


Q ss_pred             CccEEEecCCCCCccccccccccccCCcc
Q psy437          145 WKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       145 ~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ++..+|....|  .+.++|+++  |+||-
T Consensus       638 d~DvlItdlaP--idsLiQRaG--R~~R~  662 (878)
T PRK09694        638 DFDWLITQLCP--VDLLFQRLG--RLHRH  662 (878)
T ss_pred             CCCeEEECCCC--HHHHHHHHh--ccCCC
Confidence            47888887777  689999996  55553

>KOG0950|consensus

Probab=97.94  E-value=1.7e-05  Score=71.94  Aligned_cols=117  Identities=20%  Similarity=0.218  Sum_probs=86.2

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC--------------------------------------CCeeEEecCCCCHHHHHH
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE--------------------------------------RINAISYHAGLADKLRNE   75 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~--------------------------------------gi~~~~~hg~l~~~~R~~   75 (184)
                      +.++||||++|+.|+.+|..+...                                      -..+++.|+|++.++|+.
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            345999999999999998665420                                      125788999999999999


Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcE---EEeeCCCChHHHHHHHHHhhCCCc-------eEEEE--Eec
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINA---ISYHAGLADKLRNEVQMKWISNKV-------HLYNV--WKI  143 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~---~vih~~~p~~~r~~~~~~f~~~~~-------~v~va--~D~  143 (184)
                      +...|++|-+.|++||+      .+|.|..-|--++   .-+-+.-..+.-+|-|...+.|..       .++++  +++
T Consensus       540 iE~afr~g~i~vl~aTS------TlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~  613 (1008)
T KOG0950|consen  540 IEAAFREGNIFVLVATS------TLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEK  613 (1008)
T ss_pred             HHHHHHhcCeEEEEecc------hhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccch
Confidence            99999999999999999      7788888877662   224444455666788887666543       44444  677


Q ss_pred             CCccEEEecCCCC
Q psy437          144 QWKRIIWIHSLVL  156 (184)
Q Consensus       144 ~~vr~v~~~~~p~  156 (184)
                      ..++-++...+|.
T Consensus       614 ~~~~~lv~~~~~~  626 (1008)
T KOG0950|consen  614 KRVRELVNSPLKP  626 (1008)
T ss_pred             hHHHHHHhccccc
Confidence            6666665555543

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

Probab=97.92  E-value=8.8e-05  Score=69.01  Aligned_cols=103  Identities=12%  Similarity=0.110  Sum_probs=79.5

Q ss_pred             CCCCCeEEEEEEccC--hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHH
Q psy437            5 FNRANLKYEILPKKN--VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKW   80 (184)
Q Consensus         5 ~~R~Nl~y~v~~~~~--k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f   80 (184)
                      .+|--+.=.|.+.+.  ..+.|...|   ..+++.--.+|..+..+.++..|++.  ..++++.||.|+..+-+.++..|
T Consensus       775 ~~R~pV~T~V~~~d~~~ireAI~REl---~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F  851 (1139)
T COG1197         775 EDRLPVKTFVSEYDDLLIREAILREL---LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDF  851 (1139)
T ss_pred             CCCcceEEEEecCChHHHHHHHHHHH---hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHH
Confidence            345445544444443  223333333   24566655678889999999999975  66789999999999999999999


Q ss_pred             hccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeC
Q psy437           81 ISNKVHVGHWTVVSKECDSVAAALAQERINAISYHA  116 (184)
Q Consensus        81 ~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~  116 (184)
                      .+|+.+|||||.      .+-.|+|+|+.++.+||-
T Consensus       852 ~~g~~dVLv~TT------IIEtGIDIPnANTiIIe~  881 (1139)
T COG1197         852 YNGEYDVLVCTT------IIETGIDIPNANTIIIER  881 (1139)
T ss_pred             HcCCCCEEEEee------eeecCcCCCCCceEEEec
Confidence            999999999999      889999999999877763

>KOG0948|consensus

Probab=97.80  E-value=6.6e-05  Score=66.93  Aligned_cols=115  Identities=19%  Similarity=0.275  Sum_probs=85.5

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC---------------------------------------eeEE
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI---------------------------------------NAIS   63 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi---------------------------------------~~~~   63 (184)
                      .++..+... ...|+|||+-++++||..|-.+.+..+                                       ....
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            444444443 667899999999999999977753211                                       3466


Q ss_pred             ecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE---
Q psy437           64 YHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV---  140 (184)
Q Consensus        64 ~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va---  140 (184)
                      .||||-+--++-+.--|..|-+++|.||.|+      +-||+-|.-.                         -|..+   
T Consensus       452 HHsGLLPIlKE~IEILFqEGLvKvLFATETF------siGLNMPAkT-------------------------VvFT~~rK  500 (1041)
T KOG0948|consen  452 HHSGLLPILKEVIEILFQEGLVKVLFATETF------SIGLNMPAKT-------------------------VVFTAVRK  500 (1041)
T ss_pred             ccccchHHHHHHHHHHHhccHHHHHHhhhhh------hhccCCccee-------------------------EEEeeccc
Confidence            8999999989889889999999999999966      4466554432                         12222   


Q ss_pred             EecCCccEEEecCCCCCccccccccccccCCccccccc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGREDIREG  178 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~~~~~  178 (184)
                      ||=.+.|||       +.=+|+|=-  +|+||+++-+-
T Consensus       501 fDG~~fRwi-------ssGEYIQMS--GRAGRRG~Ddr  529 (1041)
T KOG0948|consen  501 FDGKKFRWI-------SSGEYIQMS--GRAGRRGIDDR  529 (1041)
T ss_pred             cCCcceeee-------cccceEEec--ccccccCCCCC
Confidence            788888888       677899976  79999977654

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.57  E-value=0.00025  Score=66.28  Aligned_cols=98  Identities=9%  Similarity=-0.013  Sum_probs=80.9

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC---ceEEEE-------EecCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK---VHLYNV-------WKIQW  145 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~---~~v~va-------~D~~~  145 (184)
                      ++..+.....+|||+|.-....+.+...|...|+..+.|+|++|...|..+.+.|....   ..+++.       ++...
T Consensus       479 LL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrAGGlGINLt~  558 (1033)
T PLN03142        479 LLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLAT  558 (1033)
T ss_pred             HHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccccccCCchhh
Confidence            34445556678999999888999999999999999999999999999999999997532   223333       58899


Q ss_pred             ccEEEecCCCCCccccccccccc-cCCcc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                      ...||+||+|.++..+.|.+.+. |.|-.
T Consensus       559 Ad~VIiyD~dWNP~~d~QAidRaHRIGQk  587 (1033)
T PLN03142        559 ADIVILYDSDWNPQVDLQAQDRAHRIGQK  587 (1033)
T ss_pred             CCEEEEeCCCCChHHHHHHHHHhhhcCCC
Confidence            99999999999999999999775 66653

>KOG0329|consensus

Probab=97.57  E-value=1.5e-05  Score=62.98  Aligned_cols=40  Identities=13%  Similarity=0.090  Sum_probs=35.5

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +|||+      ...+|||+..++ .|+|||||.+..+|+|+..+.|.
T Consensus       302 ~vat~------lfgrgmdiervN-i~~NYdmp~~~DtYlHrv~rAgr  341 (387)
T KOG0329|consen  302 LVATD------LFGRGMDIERVN-IVFNYDMPEDSDTYLHRVARAGR  341 (387)
T ss_pred             hHHhh------hhccccCcccce-eeeccCCCCCchHHHHHhhhhhc
Confidence            88999      557899999999 99999999999999999966553

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

Probab=97.53  E-value=0.00062  Score=58.92  Aligned_cols=86  Identities=14%  Similarity=0.070  Sum_probs=76.6

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCC---
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSL---  154 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~---  154 (184)
                      -++||.|-|++++|.+..+|...||++.-+|.++..-.|..+.++.+.|...|+|.       +|+|.|++|...|-   
T Consensus       447 eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKe  526 (663)
T COG0556         447 ERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKE  526 (663)
T ss_pred             CeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCcc
Confidence            68999999999999999999999999999999999999999999999999999999       49999999998874   


Q ss_pred             --CCCccccccccccccCCc
Q psy437          155 --VLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       155 --p~~~e~y~~~i~~~~~~r  172 (184)
                        ..|.-+.+|-|  +|++|
T Consensus       527 GFLRse~SLIQtI--GRAAR  544 (663)
T COG0556         527 GFLRSERSLIQTI--GRAAR  544 (663)
T ss_pred             ccccccchHHHHH--HHHhh
Confidence              44555666777  46665

>KOG0947|consensus

Probab=97.52  E-value=0.00036  Score=63.82  Aligned_cols=81  Identities=20%  Similarity=0.257  Sum_probs=62.6

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC---------------------------------------eeE
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI---------------------------------------NAI   62 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi---------------------------------------~~~   62 (184)
                      -.|+..|.+. .--|+||||-+++.|+..|++|...++                                       ..+
T Consensus       556 l~lin~L~k~-~lLP~VvFvFSkkrCde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGia  634 (1248)
T KOG0947|consen  556 LDLINHLRKK-NLLPVVVFVFSKKRCDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIA  634 (1248)
T ss_pred             HHHHHHHhhc-ccCceEEEEEccccHHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcch
Confidence            3445555443 556899999999999999999863211                                       367


Q ss_pred             EecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           63 SYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        63 ~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      +.|||+=+--++-+..-|..|-++||.||.|+      |-|++-|.-
T Consensus       635 VHH~GlLPivKE~VE~LFqrGlVKVLFATETF------AMGVNMPAR  675 (1248)
T KOG0947|consen  635 VHHGGLLPIVKEVVELLFQRGLVKVLFATETF------AMGVNMPAR  675 (1248)
T ss_pred             hhcccchHHHHHHHHHHHhcCceEEEeehhhh------hhhcCCCce
Confidence            79999999999999999999999999999966      556665543

>KOG0951|consensus

Probab=97.52  E-value=0.00087  Score=62.97  Aligned_cols=99  Identities=18%  Similarity=0.124  Sum_probs=75.1

Q ss_pred             HHhhcCCCcEEEEeccHHHHHHHHHHHHhC-------------------------------------CCeeEEecCCCCH
Q psy437           28 IKAKYSGQSGIVYCLTRKECDSVAAALAQE-------------------------------------RINAISYHAGLAD   70 (184)
Q Consensus        28 l~~~~~~~~~IIf~~tr~~~e~la~~L~~~-------------------------------------gi~~~~~hg~l~~   70 (184)
                      +.++....+.|||+.+|+.+...|.+++..                                     .+..+..|+||+.
T Consensus       540 Vm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R  619 (1674)
T KOG0951|consen  540 VLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNR  619 (1674)
T ss_pred             HHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCc
Confidence            334456789999999999999998887610                                     1356789999999


Q ss_pred             HHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeC------C----CChHHHHHHHHHhhCC
Q psy437           71 KLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHA------G----LADKLRNEVQMKWISN  133 (184)
Q Consensus        71 ~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~------~----~p~~~r~~~~~~f~~~  133 (184)
                      .+|..+.+.|..|.++++|+|-      .+|.|+.-++.. ++|-+      +    .+-+..+-.|...+.|
T Consensus       620 ~dR~~~EdLf~~g~iqvlvsta------tlawgvnlpaht-Viikgtqvy~pekg~w~elsp~dv~qmlgrag  685 (1674)
T KOG0951|consen  620 KDRELVEDLFADGHIQVLVSTA------TLAWGVNLPAHT-VIIKGTQVYDPEKGRWTELSPLDVMQMLGRAG  685 (1674)
T ss_pred             chHHHHHHHHhcCceeEEEeeh------hhhhhcCCCcce-EEecCccccCcccCccccCCHHHHHHHHhhcC
Confidence            9999999999999999999999      779999988875 44433      2    2334555555555444

>PRK14701 reverse gyrase; Provisional

Probab=97.41  E-value=0.0029  Score=61.99  Aligned_cols=101  Identities=8%  Similarity=-0.094  Sum_probs=82.7

Q ss_pred             HHHHHHHHhccCceEEEEEeecccH---HHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE---------
Q psy437           73 RNEVQMKWISNKVHVGHWTVVSKEC---DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV---------  140 (184)
Q Consensus        73 R~~~~~~f~~g~~~vlVaT~tr~~~---e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va---------  140 (184)
                      +..+++-.......+||+|++++.+   +.+|..|...|+++.++|++     |...++.|++|++.|+||         
T Consensus       319 k~~L~~ll~~~g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~G~~~VLVaT~s~~gvaa  393 (1638)
T PRK14701        319 KEHVRELLKKLGKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEEGEIDYLIGVATYYGTLV  393 (1638)
T ss_pred             HHHHHHHHHhCCCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHcCCCCEEEEecCCCCeeE
Confidence            3344333333335789999999865   89999999999999999996     889999999999999998         


Q ss_pred             --EecCC-ccEEEecCCCC---Ccccccccc-----------ccccCCccccccc
Q psy437          141 --WKIQW-KRIIWIHSLVL---IKPDYLPPI-----------LDLRLGREDIREG  178 (184)
Q Consensus       141 --~D~~~-vr~v~~~~~p~---~~e~y~~~i-----------~~~~~~r~~~~~~  178 (184)
                        +|+|+ ||+|+|+++|+   +.+.|+|++           +..++||++++..
T Consensus       394 RGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~  448 (1638)
T PRK14701        394 RGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIE  448 (1638)
T ss_pred             ecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcch
Confidence              39999 99999999999   999999997           2247788776543

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

Probab=97.25  E-value=0.0015  Score=60.55  Aligned_cols=79  Identities=11%  Similarity=0.017  Sum_probs=61.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQER  108 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g  108 (184)
                      .+++++||++|.+..+.++..|..    .++++  +..+.+ ..|.+++++|++++..||++|+      ..++|+|.+|
T Consensus       673 ~~g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~--l~q~~~-~~r~~ll~~F~~~~~~iLlgt~------sf~EGVD~~g  743 (850)
T TIGR01407       673 TSPKILVLFTSYEMLHMVYDMLNELPEFEGYEV--LAQGIN-GSRAKIKKRFNNGEKAILLGTS------SFWEGVDFPG  743 (850)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHhhhccccCceE--EecCCC-ccHHHHHHHHHhCCCeEEEEcc------eeecccccCC
Confidence            567899999999999999999975    24443  333433 5789999999999999999998      5589999998


Q ss_pred             CcE-EEeeCCCCh
Q psy437          109 INA-ISYHAGLAD  120 (184)
Q Consensus       109 i~~-~vih~~~p~  120 (184)
                      ... .|+=.++|-
T Consensus       744 ~~l~~viI~~LPf  756 (850)
T TIGR01407       744 NGLVCLVIPRLPF  756 (850)
T ss_pred             CceEEEEEeCCCC
Confidence            662 444477773

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.

>KOG0952|consensus

Probab=97.17  E-value=0.00088  Score=61.85  Aligned_cols=80  Identities=19%  Similarity=0.238  Sum_probs=63.9

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC----C-------------------CeeEEecCCCCHHHHHHHH
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE----R-------------------INAISYHAGLADKLRNEVQ   77 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~----g-------------------i~~~~~hg~l~~~~R~~~~   77 (184)
                      .+.+.+++.   .+.+.+|||.||..+-..|+.|.+.    |                   ......|+||..++|..+.
T Consensus       339 ~~kv~e~~~---~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E  415 (1230)
T KOG0952|consen  339 YDKVVEFLQ---EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVE  415 (1230)
T ss_pred             HHHHHHHHH---cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHH
Confidence            444555553   5789999999999999999988742    1                   1346689999999999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      ..|..|.++|+|||+      .+|=|..-|..
T Consensus       416 ~~F~~G~i~vL~cTa------TLAwGVNLPA~  441 (1230)
T KOG0952|consen  416 KEFKEGHIKVLCCTA------TLAWGVNLPAY  441 (1230)
T ss_pred             HHHhcCCceEEEecc------eeeeccCCcce
Confidence            999999999999999      55667666654

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.15  E-value=0.0059  Score=56.01  Aligned_cols=129  Identities=12%  Similarity=0.079  Sum_probs=87.0

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-..     .....|...+++.+.+. ..+.|+||.|.|.+..+.++..|.+.|++..++++.-.  +++..+
T Consensus       390 PTnkP~~R~D~~d~iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~--e~EA~I  467 (925)
T PRK12903        390 PTNKPVIRKDEPDSIFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQN--AREAEI  467 (925)
T ss_pred             CCCCCeeeeeCCCcEEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccch--hhHHHH
Confidence            56777765332     12235788888777643 36789999999999999999999999999999988633  333332


Q ss_pred             HHHhccC-ceEEEEEeecccHHHHHHHHHhc-C--Cc----EEEeeCCCChHHHHHHHHHhhCC------CceEEEEE
Q psy437           78 MKWISNK-VHVGHWTVVSKECDSVAAALAQE-R--IN----AISYHAGLADKLRNEVQMKWISN------KVHLYNVW  141 (184)
Q Consensus        78 ~~f~~g~-~~vlVaT~tr~~~e~~a~gL~~~-g--i~----~~vih~~~p~~~r~~~~~~f~~~------~~~v~va~  141 (184)
                      -. ..|+ ..|.|||+      .+.||=|+. |  +.    -+||....|.+.|---|-.+++|      ..+.++.+
T Consensus       468 Ia-~AG~~GaVTIATN------MAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSL  538 (925)
T PRK12903        468 IA-KAGQKGAITIATN------MAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISL  538 (925)
T ss_pred             HH-hCCCCCeEEEecc------cccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEec
Confidence            22 3453 46889999      444554332 1  00    17888889988887777665543      34555554

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=97.04  E-value=0.0054  Score=56.22  Aligned_cols=87  Identities=14%  Similarity=-0.026  Sum_probs=71.9

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCc---------
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWK---------  146 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~v---------  146 (184)
                      ..-+|||+|.+..++|.++..|...|+++.++|+.  +..|+.....|.+++..|+||       .|++-=         
T Consensus       429 ~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~  506 (830)
T PRK12904        429 KGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAA  506 (830)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhh
Confidence            34589999999999999999999999999999995  888888899999999999999       366542         


Q ss_pred             -----------------------------cEEEecCCCCCccccccccccccCCcc
Q psy437          147 -----------------------------RIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       147 -----------------------------r~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                                                   =+||-...|.|  .-+.+.|++|+||-
T Consensus       507 ~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhes--rRid~QlrGRagRQ  560 (830)
T PRK12904        507 LLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHES--RRIDNQLRGRSGRQ  560 (830)
T ss_pred             hhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCch--HHHHHHhhcccccC
Confidence                                         36676666665  34667778899995

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=96.98  E-value=0.0094  Score=53.85  Aligned_cols=86  Identities=16%  Similarity=0.110  Sum_probs=60.5

Q ss_pred             CCCCCCeEEEE----E-EccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI----L-PKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v----~-~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||++....    . ....|...+++.+.+. ..+.|+||.|.|.+..|.++..|.+.|++..++.+.-..++-..+-
T Consensus       391 Ptnkp~~R~d~~d~iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa  470 (764)
T PRK12326        391 PPNKPNIREDEADRVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIA  470 (764)
T ss_pred             CCCCCceeecCCCceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHH
Confidence            56677765431    1 2234788888777543 3678999999999999999999999999999999874433322222


Q ss_pred             HHHhccC-ceEEEEEe
Q psy437           78 MKWISNK-VHVGHWTV   92 (184)
Q Consensus        78 ~~f~~g~-~~vlVaT~   92 (184)
                      +   .|+ ..|.|||+
T Consensus       471 ~---AG~~gaVTIATN  483 (764)
T PRK12326        471 E---AGKYGAVTVSTQ  483 (764)
T ss_pred             h---cCCCCcEEEEec
Confidence            2   233 36889999

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

Probab=96.97  E-value=0.0024  Score=60.59  Aligned_cols=83  Identities=7%  Similarity=0.047  Sum_probs=67.7

Q ss_pred             CceEEEEEeecccHHHHHHHHHh------cCC---cEEEeeCCCChHHHHHHHHHhhCCCce-EEEE-------EecCCc
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQ------ERI---NAISYHAGLADKLRNEVQMKWISNKVH-LYNV-------WKIQWK  146 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~------~gi---~~~vih~~~p~~~r~~~~~~f~~~~~~-v~va-------~D~~~v  146 (184)
                      ..+.||+|.+...|+.++..|..      +++   .+.+++++.+.  +..+.+.|++++.+ |+|+       +|+|.|
T Consensus       698 ~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~~--~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v  775 (1123)
T PRK11448        698 EGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSIDK--PDQLIRRFKNERLPNIVVTVDLLTTGIDVPSI  775 (1123)
T ss_pred             CCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCccc--hHHHHHHHhCCCCCeEEEEecccccCCCcccc
Confidence            35789999999999999888754      233   34679999875  56688999998764 5555       699999


Q ss_pred             cEEEecCCCCCccccccccccc
Q psy437          147 RIIWIHSLVLIKPDYLPPILDL  168 (184)
Q Consensus       147 r~v~~~~~p~~~e~y~~~i~~~  168 (184)
                      ..|+.+..++|.-.|+|.|+|+
T Consensus       776 ~~vVf~rpvkS~~lf~QmIGRg  797 (1123)
T PRK11448        776 CNLVFLRRVRSRILYEQMLGRA  797 (1123)
T ss_pred             cEEEEecCCCCHHHHHHHHhhh
Confidence            9999999999999999999763

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=96.87  E-value=0.0026  Score=58.00  Aligned_cols=87  Identities=14%  Similarity=0.100  Sum_probs=64.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHh----ccCceEEEEEeecccHHHHHHHHHhcC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI----SNKVHVGHWTVVSKECDSVAAALAQER  108 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~----~g~~~vlVaT~tr~~~e~~a~gL~~~g  108 (184)
                      .+.+++|-|||...|..+...|+..+.++..+||.+...+|.+.++.+.    .+...|+|+|.      ++-.|+|.. 
T Consensus       439 ~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQ------VIEagvDid-  511 (733)
T COG1203         439 EGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ------VIEAGVDID-  511 (733)
T ss_pred             cCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEee------EEEEEeccc-
Confidence            5678999999999999999999998878999999999999988877655    46778999999      333344443 


Q ss_pred             CcEEEeeCCCChHHHHHHHHH
Q psy437          109 INAISYHAGLADKLRNEVQMK  129 (184)
Q Consensus       109 i~~~vih~~~p~~~r~~~~~~  129 (184)
                      .+ .+|  -=+....+-+||.
T Consensus       512 fd-~mI--Te~aPidSLIQR~  529 (733)
T COG1203         512 FD-VLI--TELAPIDSLIQRA  529 (733)
T ss_pred             cC-eee--ecCCCHHHHHHHH
Confidence            22 111  2244555666665

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=96.80  E-value=0.0061  Score=56.13  Aligned_cols=56  Identities=14%  Similarity=0.038  Sum_probs=51.9

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va  140 (184)
                      ..-+|||.|.+...+|.++..|...|+++.++|++.+++.+.-+.+.|+.|.  |+||
T Consensus       448 ~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIA  503 (908)
T PRK13107        448 RGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIA  503 (908)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEe
Confidence            3457999999999999999999999999999999999999999999999998  6666

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.75  E-value=0.011  Score=53.32  Aligned_cols=77  Identities=17%  Similarity=0.167  Sum_probs=63.8

Q ss_pred             cChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhC-C-CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           18 KNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQE-R-INAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        18 ~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~-g-i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ..|.+..++++.+.. .+.++||.++....+.++.+.|++. | ..++.+|+++++.+|.+...+..+|+.+|+|.|.+-
T Consensus       171 SGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSA  250 (665)
T PRK14873        171 EDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSA  250 (665)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEccee
Confidence            346666666654332 4678999999999999999999864 4 678999999999999999999999999999999876

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

Probab=96.72  E-value=0.0066  Score=55.02  Aligned_cols=87  Identities=14%  Similarity=0.025  Sum_probs=69.5

Q ss_pred             CCCeEEEEEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhC-CCeeEEecCCCCHHHHHHHHHHHhccC
Q psy437            7 RANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISNK   84 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~hg~l~~~~R~~~~~~f~~g~   84 (184)
                      .+.|.+-|+-. .|.+..++.+.+. ..+.++||.+|....+.++.+.|+.. |.+++.+|+++++.+|...-.+.++|+
T Consensus       218 ~~~Ll~GvTGS-GKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~  296 (730)
T COG1198         218 APFLLDGVTGS-GKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGE  296 (730)
T ss_pred             cceeEeCCCCC-cHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCC
Confidence            44455555443 4666666666433 25678999999999999999999764 888999999999999999999999999


Q ss_pred             ceEEEEEeec
Q psy437           85 VHVGHWTVVS   94 (184)
Q Consensus        85 ~~vlVaT~tr   94 (184)
                      .+|+|.|.+-
T Consensus       297 ~~vVIGtRSA  306 (730)
T COG1198         297 ARVVIGTRSA  306 (730)
T ss_pred             ceEEEEechh
Confidence            9999998865

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=96.66  E-value=0.033  Score=47.78  Aligned_cols=89  Identities=7%  Similarity=0.041  Sum_probs=77.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHH--HHHHhcCCc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVA--AALAQERIN  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a--~gL~~~gi~  110 (184)
                      ..+.++||++|--+=-.+.+.|.+.++....+|--.++.+-.++-..|.+|+.++|++|.      +.-  +...+.|++
T Consensus       299 ~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TE------R~HFfrRy~irGi~  372 (442)
T PF06862_consen  299 KMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTE------RFHFFRRYRIRGIR  372 (442)
T ss_pred             CCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEh------HHhhhhhceecCCc
Confidence            456799999999999999999999999999999999999999999999999999999999      433  344788999


Q ss_pred             EEEeeCCCChHHHHHHHH
Q psy437          111 AISYHAGLADKLRNEVQM  128 (184)
Q Consensus       111 ~~vih~~~p~~~r~~~~~  128 (184)
                       .++=|++|....-|..=
T Consensus       373 -~viFY~~P~~p~fY~El  389 (442)
T PF06862_consen  373 -HVIFYGPPENPQFYSEL  389 (442)
T ss_pred             -EEEEECCCCChhHHHHH
Confidence             99999999988766543

; GO: 0005634 nucleus

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

Probab=96.62  E-value=0.0056  Score=56.30  Aligned_cols=83  Identities=18%  Similarity=0.140  Sum_probs=70.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQER  108 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g  108 (184)
                      ..+..+||.+=..+.+.+++.|.+    ..+.+..+||.|+.++..++.+--..|.-+|++||+      .+-..|.++|
T Consensus       258 ~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATN------IAETSLTI~g  331 (845)
T COG1643         258 GSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATN------IAETSLTIPG  331 (845)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEcc------ccccceeeCC
Confidence            567889999999999999999997    357788899999999988887777777677999999      6678999999


Q ss_pred             CcEEEeeCCCChHH
Q psy437          109 INAISYHAGLADKL  122 (184)
Q Consensus       109 i~~~vih~~~p~~~  122 (184)
                      |+ .|+-.|+.+..
T Consensus       332 Ir-~VIDsG~ak~~  344 (845)
T COG1643         332 IR-YVIDSGLAKEK  344 (845)
T ss_pred             eE-EEecCCccccc
Confidence            99 88887766543

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.44  E-value=0.0093  Score=54.99  Aligned_cols=56  Identities=16%  Similarity=0.036  Sum_probs=52.1

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va  140 (184)
                      ..-+|||+|.+...+|.++..|...|+++.++|+..++..+.-+.+.|+.|.  |+||
T Consensus       443 ~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIA  498 (896)
T PRK13104        443 RKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIA  498 (896)
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEe
Confidence            4457999999999999999999999999999999999999999999999996  6666

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=96.34  E-value=0.028  Score=51.96  Aligned_cols=93  Identities=16%  Similarity=0.118  Sum_probs=64.2

Q ss_pred             CCCCCCeEEE-----EEEccChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYE-----ILPKKNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~-----v~~~~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-.     ......|...+++.+...+ .+.|++|-|.|.+..|.++..|.+.|++..++.+.-...+-.-+-
T Consensus       413 PTnkP~~R~D~~d~vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa  492 (913)
T PRK13103        413 PPNKPLARKDFNDLVYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIA  492 (913)
T ss_pred             CCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhHHHHHH
Confidence            5667765421     1223358888887776443 678999999999999999999999999988777764433222222


Q ss_pred             HHHhcc-CceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           78 MKWISN-KVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        78 ~~f~~g-~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                         ..| ...|.|||+           |..+|-+
T Consensus       493 ---~AG~~GaVTIATN-----------MAGRGTD  512 (913)
T PRK13103        493 ---QAGRPGALTIATN-----------MAGRGTD  512 (913)
T ss_pred             ---cCCCCCcEEEecc-----------CCCCCCC
Confidence               234 346889999           7666665

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

Probab=96.26  E-value=0.0053  Score=45.71  Aligned_cols=85  Identities=13%  Similarity=0.074  Sum_probs=57.8

Q ss_pred             HHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC--eeEEecCCCCHHHHHHHHHHHhccCceEEEEEe--ecccHHHH
Q psy437           25 ISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI--NAISYHAGLADKLRNEVQMKWISNKVHVGHWTV--VSKECDSV  100 (184)
Q Consensus        25 ~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi--~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~--tr~~~e~~  100 (184)
                      .++++.  .++.++||++|.+..+.+.+.+...+.  ....+.-  +..++..+++.|+.++..||+++.  ++      
T Consensus         2 ~~l~~~--~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~------   71 (167)
T PF13307_consen    2 LELISA--VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSF------   71 (167)
T ss_dssp             HHHHHC--CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCC------
T ss_pred             hHHHhc--CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccE------
Confidence            445544  568899999999999999999986532  1122222  356789999999999999999987  55      


Q ss_pred             HHHHHhcCCcE-EEeeCCCC
Q psy437          101 AAALAQERINA-ISYHAGLA  119 (184)
Q Consensus       101 a~gL~~~gi~~-~vih~~~p  119 (184)
                      +.|+|.+|-.+ .|+=.++|
T Consensus        72 ~EGiD~~~~~~r~vii~glP   91 (167)
T PF13307_consen   72 SEGIDFPGDLLRAVIIVGLP   91 (167)
T ss_dssp             GSSS--ECESEEEEEEES--
T ss_pred             EEeecCCCchhheeeecCCC
Confidence            56888886332 77777777

>KOG0922|consensus

Probab=96.23  E-value=0.017  Score=51.19  Aligned_cols=79  Identities=14%  Similarity=0.093  Sum_probs=64.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC------CC--eeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE------RI--NAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAAL  104 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~------gi--~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL  104 (184)
                      +++-.+||-.-.++.+...+.|.+.      +.  -...+||.|+.++..++.+.--.|.-+||++|+      ....-+
T Consensus       257 ~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTN------IAETSl  330 (674)
T KOG0922|consen  257 PPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTN------IAETSL  330 (674)
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcc------eeeeeE
Confidence            5566799999999999999998864      11  135689999999999998888889999999999      555678


Q ss_pred             HhcCCcEEEeeCCC
Q psy437          105 AQERINAISYHAGL  118 (184)
Q Consensus       105 ~~~gi~~~vih~~~  118 (184)
                      .++||. .|+--|+
T Consensus       331 TI~GI~-YVVDsG~  343 (674)
T KOG0922|consen  331 TIDGIR-YVVDSGF  343 (674)
T ss_pred             EecceE-EEEcCCc
Confidence            999998 8875553

>KOG0953|consensus

Probab=95.97  E-value=0.017  Score=50.43  Aligned_cols=68  Identities=10%  Similarity=0.064  Sum_probs=54.3

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCCHHHHHHHHHHHhc--cCceEEEEEe
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLADKLRNEVQMKWIS--NKVHVGHWTV   92 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~~~~R~~~~~~f~~--g~~~vlVaT~   92 (184)
                      .+..-+++. +++-+|| |-|+++.=.+...+.+.|.. +++++|+++++.|.+.-..|-+  ++.+|||||+
T Consensus       347 ~~~~sl~nl-k~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsD  417 (700)
T KOG0953|consen  347 TALGSLSNL-KPGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASD  417 (700)
T ss_pred             hhhhhhccC-CCCCeEE-EeehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeec
Confidence            444455443 4444444 66888888889999988877 9999999999999999999986  8999999999

>COG1204 Superfamily II helicase [General function prediction only]

Probab=95.86  E-value=0.2  Score=46.06  Aligned_cols=140  Identities=19%  Similarity=0.133  Sum_probs=89.8

Q ss_pred             cEEEEeccHHHHHHHHHHHHhCCC-----------------eeEEecCCCC------HHHHHHHHHHHhccCceEEEEEe
Q psy437           36 SGIVYCLTRKECDSVAAALAQERI-----------------NAISYHAGLA------DKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        36 ~~IIf~~tr~~~e~la~~L~~~gi-----------------~~~~~hg~l~------~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      +.+=...|-..++.+|.+|....+                 .....+|+..      ..........-.+...++||+++
T Consensus       182 rivgLSATlpN~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLvFv~  261 (766)
T COG1204         182 RIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVH  261 (766)
T ss_pred             EEEEEeeecCCHHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEEEEe
Confidence            333367888899999999975311                 2233444432      12222223333344557999999


Q ss_pred             ecccHHHHHHHHHh-----------c----C---Cc-------------------EEEeeCCCChHHHHHHHHHhhCCCc
Q psy437           93 VSKECDSVAAALAQ-----------E----R---IN-------------------AISYHAGLADKLRNEVQMKWISNKV  135 (184)
Q Consensus        93 tr~~~e~~a~gL~~-----------~----g---i~-------------------~~vih~~~p~~~r~~~~~~f~~~~~  135 (184)
                      +|+.++..|+.|.+           .    +   +.                   +..=|+|+|.+.|.++-+.|+.|++
T Consensus       262 sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~~Fr~g~i  341 (766)
T COG1204         262 SRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKI  341 (766)
T ss_pred             cCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHHHHhcCCc
Confidence            99999999988862           0    0   00                   1445899999999999999999999


Q ss_pred             eEEEE-------EecCCccEEE----ecC-----CCCCccccccccccccCCcccccc
Q psy437          136 HLYNV-------WKIQWKRIIW----IHS-----LVLIKPDYLPPILDLRLGREDIRE  177 (184)
Q Consensus       136 ~v~va-------~D~~~vr~v~----~~~-----~p~~~e~y~~~i~~~~~~r~~~~~  177 (184)
                      +|+|+       -+.|--+-||    -|+     .+-+.-+|+|=.  +|+||.++-+
T Consensus       342 kVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~--GRAGRPg~d~  397 (766)
T COG1204         342 KVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMA--GRAGRPGYDD  397 (766)
T ss_pred             eEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhcc--CcCCCCCcCC
Confidence            99999       2555433332    334     222334455544  6999975543

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

Probab=95.82  E-value=0.037  Score=51.88  Aligned_cols=71  Identities=21%  Similarity=0.311  Sum_probs=54.9

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC----------------------------CCe-------------e
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE----------------------------RIN-------------A   61 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~----------------------------gi~-------------~   61 (184)
                      .++..+... ..-|.|+|+-|++.|+..+..+...                            +++             .
T Consensus       369 ~iv~~l~~~-~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGi  447 (1041)
T COG4581         369 EIVNKLDKD-NLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDLAEEDRELPLQILEISALLLRGI  447 (1041)
T ss_pred             HHHhhhhhh-cCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhh
Confidence            345555443 6678999999999999988777511                            121             3


Q ss_pred             EEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           62 ISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        62 ~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ++.|+||=+..|..+...|..|-++|+.||.|+
T Consensus       448 avHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~  480 (1041)
T COG4581         448 AVHHAGLLPAIKELVEELFQEGLVKVVFATETF  480 (1041)
T ss_pred             hhhccccchHHHHHHHHHHhccceeEEeehhhh
Confidence            578999999999999999999999999999944

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=95.80  E-value=0.075  Score=49.02  Aligned_cols=100  Identities=11%  Similarity=0.098  Sum_probs=68.6

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHH-H
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNE-V   76 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~-~   76 (184)
                      |.+||++.-..     .....|...+++.+.+. ..+.|++|-|.|.+..|.++..|.+.|++..++++.-.+.+++. +
T Consensus       388 Ptnkp~~R~d~~d~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~I  467 (870)
T CHL00122        388 PTHRPMLRKDLPDLIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAKPENVRRESEI  467 (870)
T ss_pred             CCCCCccceeCCCeEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCCCccchhHHHH
Confidence            66777765332     12224777777766443 36789999999999999999999999999999998632222222 2


Q ss_pred             HHHHhccC-ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCC
Q psy437           77 QMKWISNK-VHVGHWTVVSKECDSVAAALAQERINAISYHAG  117 (184)
Q Consensus        77 ~~~f~~g~-~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~  117 (184)
                      +.+  .|+ ..|.|||+           |..+|.+ ..+-++
T Consensus       468 IA~--AG~~G~VTIATN-----------MAGRGTD-I~Lgg~  495 (870)
T CHL00122        468 VAQ--AGRKGSITIATN-----------MAGRGTD-IILGGN  495 (870)
T ss_pred             HHh--cCCCCcEEEecc-----------ccCCCcC-eecCCc
Confidence            222  343 46889999           7777776 555554

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=95.76  E-value=0.099  Score=48.68  Aligned_cols=127  Identities=10%  Similarity=0.074  Sum_probs=84.9

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-..     .....|...+++.+.+. ..+.|++|-|.|.+..|.++..|.+.|++..++++.-...+-.-+-
T Consensus       532 Pt~kp~~r~d~~d~iy~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~se~ls~~L~~~gi~h~vLNak~~~~Ea~iia  611 (970)
T PRK12899        532 PTFKPCLRIDHNDEFYMTEREKYHAIVAEIASIHRKGNPILIGTESVEVSEKLSRILRQNRIEHTVLNAKNHAQEAEIIA  611 (970)
T ss_pred             CCCCCceeeeCCCcEecCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCcceecccchhhhHHHHHH
Confidence            56677655221     12234777777766543 3677899999999999999999999999998888863322222222


Q ss_pred             HHHhccC-ceEEEEEeecccHHHHHHHHHhc---------CCcEEEeeCCCChHHHHHHHHHhhCC------CceEEEEE
Q psy437           78 MKWISNK-VHVGHWTVVSKECDSVAAALAQE---------RINAISYHAGLADKLRNEVQMKWISN------KVHLYNVW  141 (184)
Q Consensus        78 ~~f~~g~-~~vlVaT~tr~~~e~~a~gL~~~---------gi~~~vih~~~p~~~r~~~~~~f~~~------~~~v~va~  141 (184)
                         ..|+ ..|.|||+      .+.||-|+.         |+  +||--..|.+.|-.-|=.+++|      ....++.+
T Consensus       612 ---~AG~~g~VTIATN------mAGRGTDIkl~~~v~~~GGL--hVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSl  680 (970)
T PRK12899        612 ---GAGKLGAVTVATN------MAGRGTDIKLDEEAVAVGGL--YVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSF  680 (970)
T ss_pred             ---hcCCCCcEEEeec------cccCCcccccCchHHhcCCc--EEEeeccCchHHHHHHHhcccccCCCCCceeEEEEc
Confidence               2343 46899999      445554432         22  7888889999988888765543      45566654

>KOG1000|consensus

Probab=95.73  E-value=0.1  Score=45.25  Aligned_cols=152  Identities=11%  Similarity=0.100  Sum_probs=95.8

Q ss_pred             hHHHHHHHHHhh-----cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc-CceEEEEEee
Q psy437           20 VLKEVISLIKAK-----YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN-KVHVGHWTVV   93 (184)
Q Consensus        20 k~~~L~~~l~~~-----~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g-~~~vlVaT~t   93 (184)
                      |.....++|..+     .++.+.+|||......+.|...+.+.++...-+.|..++.+|....+.|... ++.|-|-..+
T Consensus       473 K~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsIt  552 (689)
T KOG1000|consen  473 KAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSIT  552 (689)
T ss_pred             ccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEe
Confidence            555566666441     2566789999999999999999999999999999999999999999999864 3443222221


Q ss_pred             cccHHHHHHHHHhcCCcEEEeeCCCCh------HHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCcccccccccc
Q psy437           94 SKECDSVAAALAQERINAISYHAGLAD------KLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILD  167 (184)
Q Consensus        94 r~~~e~~a~gL~~~gi~~~vih~~~p~------~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~e~y~~~i~~  167 (184)
                      -     ..-||+...-+ .|+-+.++-      ..++.+||......+.|....-+.-..   .+..| ...+-++.+..
T Consensus       553 A-----~gvGLt~tAa~-~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~D---dy~Wp-~l~~KL~vl~s  622 (689)
T KOG1000|consen  553 A-----AGVGLTLTAAS-VVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTAD---DYMWP-MLQQKLDVLGS  622 (689)
T ss_pred             e-----cccceeeeccc-eEEEEEecCCCceEEechhhhhhccccceeeEEEEEecCchH---HHHHH-HHHHHHHHHhh
Confidence            1     12366665555 444444443      568999999888776554432111000   00111 12234555555


Q ss_pred             ccCCcccccccccc
Q psy437          168 LRLGREDIREGETM  181 (184)
Q Consensus       168 ~~~~r~~~~~~~~~  181 (184)
                      +-+|.++++.-+.|
T Consensus       623 ~gl~s~~~~~~e~~  636 (689)
T KOG1000|consen  623 VGLSSDTFRTAEKM  636 (689)
T ss_pred             cccCcccceeeccc
Confidence            56666666544444

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

Probab=95.68  E-value=0.085  Score=47.80  Aligned_cols=93  Identities=14%  Similarity=0.110  Sum_probs=66.5

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHH---------------------HHHHHHHHHhc-cCce
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADK---------------------LRNEVQMKWIS-NKVH   86 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~---------------------~R~~~~~~f~~-g~~~   86 (184)
                      +.+++|||.++..|..+.+.|.+.     +..+.+++++.+.+                     ....++++|+. +..+
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            478999999999999999988654     34566666654332                     22468888876 6789


Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +||.++      .+-.|.|.|.+.++.+  +-|-..-..+|...|.+.
T Consensus       594 ilIVvd------mllTGFDaP~l~tLyl--dKplk~h~LlQai~R~nR  633 (667)
T TIGR00348       594 LLIVVD------MLLTGFDAPILNTLYL--DKPLKYHGLLQAIARTNR  633 (667)
T ss_pred             EEEEEc------ccccccCCCccceEEE--eccccccHHHHHHHHhcc
Confidence            999999      8888999999985444  344444456776655554

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

>cd00268 DEADc DEAD-box helicases

Probab=95.57  E-value=0.16  Score=38.40  Aligned_cols=56  Identities=13%  Similarity=0.085  Sum_probs=42.9

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .+.++||.|+|+..+.++++.+...    ++.+..++|+.+..++....+    +..+|+|+|+
T Consensus        68 ~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~  127 (203)
T cd00268          68 DGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATP  127 (203)
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEECh
Confidence            3457899999999999988777643    778888999988765543332    5678999998

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=95.52  E-value=0.11  Score=48.15  Aligned_cols=100  Identities=14%  Similarity=0.089  Sum_probs=68.8

Q ss_pred             CCCCCCeEEEEE-----EccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHH-H
Q psy437            4 SFNRANLKYEIL-----PKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNE-V   76 (184)
Q Consensus         4 s~~R~Nl~y~v~-----~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~-~   76 (184)
                      |.+||.+.-...     ....|...+++.+.+. ..+.|++|-|.|.+..|.++..|.+.|++..++++.-.+.+++. +
T Consensus       403 PTnkP~~R~d~~d~vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~I  482 (939)
T PRK12902        403 PTNRPRRRQDWPDQVYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAKPENVEREAEI  482 (939)
T ss_pred             CCCCCeeeecCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCCCcchHhHHHH
Confidence            567777653321     2235788888777644 36789999999999999999999999999999998622223332 2


Q ss_pred             HHHHhccC-ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCC
Q psy437           77 QMKWISNK-VHVGHWTVVSKECDSVAAALAQERINAISYHAG  117 (184)
Q Consensus        77 ~~~f~~g~-~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~  117 (184)
                      +.+  .|+ ..|-|||+           |..+|-+ ..+-++
T Consensus       483 Ia~--AG~~GaVTIATN-----------MAGRGTD-IkLgGn  510 (939)
T PRK12902        483 VAQ--AGRKGAVTIATN-----------MAGRGTD-IILGGN  510 (939)
T ss_pred             HHh--cCCCCcEEEecc-----------CCCCCcC-EeeCCc
Confidence            222  343 36789999           7777766 555444

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

Probab=95.48  E-value=0.18  Score=46.40  Aligned_cols=95  Identities=12%  Similarity=0.018  Sum_probs=71.0

Q ss_pred             ChHHHHHHHH-Hhh-cCCC--cEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc-CceEE-EEEe
Q psy437           19 NVLKEVISLI-KAK-YSGQ--SGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN-KVHVG-HWTV   92 (184)
Q Consensus        19 ~k~~~L~~~l-~~~-~~~~--~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g-~~~vl-VaT~   92 (184)
                      .|...+.+++ ... ..+.  +.++|++.....+-+...|...++....++|+++.+.|...++.|.++ ...++ +.+.
T Consensus       692 ~k~~~l~~ll~~~~~~~~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~k  771 (866)
T COG0553         692 GKLQALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLK  771 (866)
T ss_pred             hHHHHHHHHHHHHHHhhcccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEec
Confidence            4666666666 222 1344  799999999999999999999998899999999999999999999996 34444 4444


Q ss_pred             ecccHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           93 VSKECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        93 tr~~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                      +      ...||+--+-+ .|+++|..-
T Consensus       772 a------gg~glnLt~a~-~vi~~d~~w  792 (866)
T COG0553         772 A------GGLGLNLTGAD-TVILFDPWW  792 (866)
T ss_pred             c------cccceeecccc-eEEEecccc
Confidence            1      12355555666 999999843

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

Probab=95.31  E-value=0.097  Score=49.19  Aligned_cols=80  Identities=9%  Similarity=-0.063  Sum_probs=58.3

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe--eEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC-
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN--AISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI-  109 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~--~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi-  109 (184)
                      .+++++|+++|.+..+.+++.|......  ...+-=|++...|.+++++|++++-.||++|.++      ++|+|.+|= 
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sF------wEGVD~pg~~  824 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSF------WEGIDIPGDE  824 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcc------cCccccCCCc
Confidence            5678999999999999999999754221  1122224444578999999999888899999955      778888874 


Q ss_pred             -cEEEeeCCCC
Q psy437          110 -NAISYHAGLA  119 (184)
Q Consensus       110 -~~~vih~~~p  119 (184)
                       + .|+=.++|
T Consensus       825 l~-~viI~kLP  834 (928)
T PRK08074        825 LS-CLVIVRLP  834 (928)
T ss_pred             eE-EEEEecCC
Confidence             4 44445544

>KOG0391|consensus

Probab=95.26  E-value=0.26  Score=46.99  Aligned_cols=116  Identities=10%  Similarity=0.154  Sum_probs=83.0

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCc--eEEEEEeecc
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV--HVGHWTVVSK   95 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~--~vlVaT~tr~   95 (184)
                      .|++.|.-+|.+. ..+..++||+.-.+..+-+-..|..+|+--.-+.|..+-++|...+++|-.+.-  ..|..|.+.+
T Consensus      1260 GKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSgg 1339 (1958)
T KOG0391|consen 1260 GKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGG 1339 (1958)
T ss_pred             chHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCc
Confidence            4666666555432 256789999999999999999999999988889999999999999999987542  3455566442


Q ss_pred             cHHHHHHHHHhcCCcEEE-eeCC----CChHHHHHHHHHhhCCCceEEEE
Q psy437           96 ECDSVAAALAQERINAIS-YHAG----LADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~v-ih~~----~p~~~r~~~~~~f~~~~~~v~va  140 (184)
                      -      |++--|-+++| |--|    |.....++-||.++..++.|+=.
T Consensus      1340 v------GiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRL 1383 (1958)
T KOG0391|consen 1340 V------GINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRL 1383 (1958)
T ss_pred             c------ccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEe
Confidence            2      45555777322 3333    45566677777777777777654

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=95.20  E-value=0.12  Score=48.51  Aligned_cols=130  Identities=15%  Similarity=0.059  Sum_probs=85.4

Q ss_pred             CCCCCCeEEE-----EEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYE-----ILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~-----v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||.+.-.     ......|...+++.+.+. ..+.|++|-|.|.+..|.++..|...|++..++.+....++-.-+-
T Consensus       592 PTnrP~~R~D~~D~vy~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA  671 (1112)
T PRK12901        592 PTNRPIARKDKEDLVYKTKREKYNAVIEEITELSEAGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVA  671 (1112)
T ss_pred             CCCCCcceecCCCeEecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHH
Confidence            5667765532     112235788888777653 3678999999999999999999999999988888875544433333


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc---CCc----EEEeeCCCChHHHHHHHHHhhCC------CceEEEEE
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE---RIN----AISYHAGLADKLRNEVQMKWISN------KVHLYNVW  141 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~---gi~----~~vih~~~p~~~r~~~~~~f~~~------~~~v~va~  141 (184)
                      +.=.  ...|-|||+      .+.||=|+.   ++.    -+||--..+.+.|---|=.+++|      ..+.++.+
T Consensus       672 ~AG~--~GaVTIATN------MAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSL  740 (1112)
T PRK12901        672 EAGQ--PGTVTIATN------MAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSL  740 (1112)
T ss_pred             hcCC--CCcEEEecc------CcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEc
Confidence            3322  235789999      444453332   111    17777888888887777665543      34555553

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

Probab=95.04  E-value=0.094  Score=47.22  Aligned_cols=86  Identities=17%  Similarity=0.072  Sum_probs=61.2

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCCHHHHHHHHHHHhccCc-eEEEEEeecccHHHH
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLADKLRNEVQMKWISNKV-HVGHWTVVSKECDSV  100 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~~~~R~~~~~~f~~g~~-~vlVaT~tr~~~e~~  100 (184)
                      .|..++..  .++.++||++|.+..+.+++.|...... ....+|.   ..+...+++|..+.- .++|+|.      ..
T Consensus       470 ~i~~~~~~--~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~---~~~~~~l~~f~~~~~~~~lv~~g------sf  538 (654)
T COG1199         470 YLREILKA--SPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGE---DEREELLEKFKASGEGLILVGGG------SF  538 (654)
T ss_pred             HHHHHHhh--cCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCC---CcHHHHHHHHHHhcCCeEEEeec------cc
Confidence            34444433  4568999999999999999999876542 3344444   456689999998665 8999999      66


Q ss_pred             HHHHHhcCCcE-EEeeCCCC
Q psy437          101 AAALAQERINA-ISYHAGLA  119 (184)
Q Consensus       101 a~gL~~~gi~~-~vih~~~p  119 (184)
                      ++|+|.+|=.. .|+=.++|
T Consensus       539 ~EGVD~~g~~l~~vvI~~lP  558 (654)
T COG1199         539 WEGVDFPGDALRLVVIVGLP  558 (654)
T ss_pred             cCcccCCCCCeeEEEEEecC
Confidence            88999887431 45555554

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

Probab=95.02  E-value=0.28  Score=45.51  Aligned_cols=121  Identities=12%  Similarity=0.029  Sum_probs=86.2

Q ss_pred             CcEEEEeccHHHHHHHHHHHHh--------CCCeeEEecCCC-------CHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           35 QSGIVYCLTRKECDSVAAALAQ--------ERINAISYHAGL-------ADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        35 ~~~IIf~~tr~~~e~la~~L~~--------~gi~~~~~hg~l-------~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      -+.||-..| -+++.+++.|..        ..+++..++..-       ...-+..+......+...|||+-++.++.+.
T Consensus       196 LKiIimSAT-ld~~rfs~~f~~apvi~i~GR~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~  274 (845)
T COG1643         196 LKLIIMSAT-LDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIER  274 (845)
T ss_pred             ceEEEEecc-cCHHHHHHHcCCCCEEEecCCccceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHH
Confidence            344554444 457888888874        245666655322       2223444555555678899999999999999


Q ss_pred             HHHHHHh----cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437          100 VAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus       100 ~a~gL~~----~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      .++.|..    +.+.++-+|+.+|.+.-..+-+--..|+-+|++|       +-||+||+|+.-.+.+
T Consensus       275 ~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak  342 (845)
T COG1643         275 TAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAK  342 (845)
T ss_pred             HHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCccc
Confidence            9999987    5566788999999998877666555565558888       5999999998765544

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

Probab=94.65  E-value=0.35  Score=43.54  Aligned_cols=74  Identities=5%  Similarity=-0.007  Sum_probs=54.7

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCCHHHHHHHHHHHhcc----CceEEEEEeeccc
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLADKLRNEVQMKWISN----KVHVGHWTVVSKE   96 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~~~~R~~~~~~f~~g----~~~vlVaT~tr~~   96 (184)
                      +.+..++..  ..+.++|.+.|.+..+.+++.|... ++ ...+.|..+  .|..++++|+..    +..||++|.++  
T Consensus       460 ~~~~~~~~~--~~G~~lvLfTS~~~~~~~~~~l~~~-l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sf--  532 (636)
T TIGR03117       460 LSTAAILRK--AQGGTLVLTTAFSHISAIGQLVELG-IPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGA--  532 (636)
T ss_pred             HHHHHHHHH--cCCCEEEEechHHHHHHHHHHHHhh-cCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCcc--
Confidence            445555543  5678999999999999999999753 32 334455432  467789999974    67899999955  


Q ss_pred             HHHHHHHHHh
Q psy437           97 CDSVAAALAQ  106 (184)
Q Consensus        97 ~e~~a~gL~~  106 (184)
                          +.|+|.
T Consensus       533 ----weGvDv  538 (636)
T TIGR03117       533 ----WTGIDL  538 (636)
T ss_pred             ----cccccc
Confidence                789999

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.

>KOG0385|consensus

Probab=94.40  E-value=0.42  Score=43.64  Aligned_cols=108  Identities=9%  Similarity=0.060  Sum_probs=75.4

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCc---eEEEEEeecccH
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV---HVGHWTVVSKEC   97 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~---~vlVaT~tr~~~   97 (184)
                      ++.|+..|.+  .+.+++||..-....+.+-.+....++...-+.|.++.++|...++.|-....   -.|+.|.     
T Consensus       476 LDkLL~~Lk~--~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTR-----  548 (971)
T KOG0385|consen  476 LDKLLPKLKE--QGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTR-----  548 (971)
T ss_pred             HHHHHHHHHh--CCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecc-----
Confidence            3444444544  67889999998888999999999999999999999999999999999987543   2355565     


Q ss_pred             HHHHHHHHhc--CCcEEEeeCCC---Ch---HHHHHHHHHhhCCCceEEE
Q psy437           98 DSVAAALAQE--RINAISYHAGL---AD---KLRNEVQMKWISNKVHLYN  139 (184)
Q Consensus        98 e~~a~gL~~~--gi~~~vih~~~---p~---~~r~~~~~~f~~~~~~v~v  139 (184)
                         |.||.+.  .-+ .||=||-   ||   ..-+..||.+....|.|+=
T Consensus       549 ---AGGLGINL~aAD-tVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~R  594 (971)
T KOG0385|consen  549 ---AGGLGINLTAAD-TVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYR  594 (971)
T ss_pred             ---cccccccccccc-EEEEecCCCCchhhhHHHHHHHhhCCcCceEEEE
Confidence               7777554  444 5554443   33   3345555556555554443

>KOG1002|consensus

Probab=93.72  E-value=0.21  Score=43.46  Aligned_cols=65  Identities=8%  Similarity=0.149  Sum_probs=55.2

Q ss_pred             ChHHHHHHHHH---hhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437           19 NVLKEVISLIK---AKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus        19 ~k~~~L~~~l~---~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      .|++.|.+.|.   +.....++|||..-....+-+.-.|.+.|+++.-+-|+|++..|..+++.|+++
T Consensus       620 TKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd  687 (791)
T KOG1002|consen  620 TKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKND  687 (791)
T ss_pred             hHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccC
Confidence            47888877653   223456789999888888889999999999999999999999999999999985

>KOG0952|consensus

Probab=93.69  E-value=0.45  Score=44.82  Aligned_cols=136  Identities=15%  Similarity=0.144  Sum_probs=86.2

Q ss_pred             EeccHHHHHHHHHHHHhC---CC--------------eeEEecCC--CCH-----HHHHHHHHHHhccCceEEEEEeecc
Q psy437           40 YCLTRKECDSVAAALAQE---RI--------------NAISYHAG--LAD-----KLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        40 f~~tr~~~e~la~~L~~~---gi--------------~~~~~hg~--l~~-----~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ...|-..-+++|.+|+-.   |+              ...-+-+.  +.+     +....-..+|.....+|+|++.+|+
T Consensus       281 LSATlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~~~g~qVlvFvhsR~  360 (1230)
T KOG0952|consen  281 LSATLPNYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFLQEGHQVLVFVHSRN  360 (1230)
T ss_pred             eeccCCCHHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHHHHHHHHHHHHcCCeEEEEEecCh
Confidence            567888889999999752   32              11111222  111     1122334456667789999999999


Q ss_pred             cHHHHHHHHHhcCC----c-------------------EEEeeCCCChHHHHHHHHHhhCCCceEEEE-----E--ecCC
Q psy437           96 ECDSVAAALAQERI----N-------------------AISYHAGLADKLRNEVQMKWISNKVHLYNV-----W--KIQW  145 (184)
Q Consensus        96 ~~e~~a~gL~~~gi----~-------------------~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----~--D~~~  145 (184)
                      .+-+.|+-|...+.    .                   ..+=|+||+-+.|.++-+.|..|.+.|+++     +  +.|.
T Consensus       361 ~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i~vL~cTaTLAwGVNLPA  440 (1230)
T KOG0952|consen  361 ETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHIKVLCCTATLAWGVNLPA  440 (1230)
T ss_pred             HHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCceEEEecceeeeccCCcc
Confidence            98888888743211    1                   156799999999999999999999999998     2  5554


Q ss_pred             ccEEE-ecCCCCCccccc--------cccccccCCccccc
Q psy437          146 KRIIW-IHSLVLIKPDYL--------PPILDLRLGREDIR  176 (184)
Q Consensus       146 vr~v~-~~~~p~~~e~y~--------~~i~~~~~~r~~~~  176 (184)
                      ---+| ..+...+.+.-+        ..|. +|+||..+.
T Consensus       441 ~aViIKGT~~ydsskg~f~dlgilDVlQif-GRAGRPqFd  479 (1230)
T KOG0952|consen  441 YAVIIKGTQVYDSSKGSFVDLGILDVLQIF-GRAGRPQFD  479 (1230)
T ss_pred             eEEEecCCcccccccCceeeehHHHHHHHH-hccCCCCCC
Confidence            33332 223333333222        2222 699998554

>KOG0923|consensus

Probab=93.66  E-value=0.23  Score=44.65  Aligned_cols=124  Identities=15%  Similarity=0.144  Sum_probs=86.9

Q ss_pred             eEEEEEEccChHHHHHHHHHhhc---CCCcEEEEeccHHHHHHHHHHHHhC---------CCeeEEecCCCCHHHHHHHH
Q psy437           10 LKYEILPKKNVLKEVISLIKAKY---SGQSGIVYCLTRKECDSVAAALAQE---------RINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus        10 l~y~v~~~~~k~~~L~~~l~~~~---~~~~~IIf~~tr~~~e~la~~L~~~---------gi~~~~~hg~l~~~~R~~~~   77 (184)
                      ++|.-.|..+-++..+.-+.+.+   +.+-.|||-.-.+..+...+.|+..         .+-+..+|++|+++...++.
T Consensus       446 i~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIF  525 (902)
T KOG0923|consen  446 IFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIF  525 (902)
T ss_pred             eecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhc
Confidence            55655566555554444443322   4445688876666666666666532         34577899999999999998


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh------------------HHHHHHHHHhhCC------
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD------------------KLRNEVQMKWISN------  133 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~------------------~~r~~~~~~f~~~------  133 (184)
                      +---.|--+|+.||+      .+-..|.++||. +||--|+.+                  +.-+..||..+.|      
T Consensus       526 ePtP~gaRKVVLATN------IAETSlTIdgI~-yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtgPGK  598 (902)
T KOG0923|consen  526 EPTPPGARKVVLATN------IAETSLTIDGIK-YVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTGPGK  598 (902)
T ss_pred             CCCCCCceeEEEeec------chhhceeecCeE-EEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCCCCc
Confidence            888889999999999      666788999998 998887766                  4456777776655      


Q ss_pred             CceEEEE
Q psy437          134 KVHLYNV  140 (184)
Q Consensus       134 ~~~v~va  140 (184)
                      |.+++.+
T Consensus       599 CfRLYt~  605 (902)
T KOG0923|consen  599 CFRLYTA  605 (902)
T ss_pred             eEEeech
Confidence            3466665

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

Probab=93.17  E-value=0.85  Score=33.00  Aligned_cols=58  Identities=16%  Similarity=0.082  Sum_probs=43.0

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ...+|+.+|++..++++...+...    ++++..+|++.+...   -...+..++..|+|+|+.+
T Consensus        44 ~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ilv~T~~~  105 (169)
T PF00270_consen   44 DARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISE---DQREVLSNQADILVTTPEQ  105 (169)
T ss_dssp             SSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHH---HHHHHHHTTSSEEEEEHHH
T ss_pred             CceEEEEeecccccccccccccccccccccccccccccccccc---cccccccccccccccCcch
Confidence            358899999999999999888764    457888899887431   1222226788999999943

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

>KOG0384|consensus

Probab=93.06  E-value=0.47  Score=45.26  Aligned_cols=108  Identities=11%  Similarity=0.121  Sum_probs=80.0

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc---cCceEEEEEeecccHH
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS---NKVHVGHWTVVSKECD   98 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~---g~~~vlVaT~tr~~~e   98 (184)
                      +.|+..|++  .+.+++||..-....+.|+++|...+++.--+.|++..+.|...++.|-.   ...-.|.+|.      
T Consensus       689 DKLL~rLk~--~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTR------  760 (1373)
T KOG0384|consen  689 DKLLPRLKE--GGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTR------  760 (1373)
T ss_pred             HHHHHHHhc--CCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecc------
Confidence            344444543  67889999999999999999999999999999999999999999999986   3445688888      


Q ss_pred             HHHHHHHhc--CCcEEEeeCCC---ChH---HHHHHHHHhhCCCceEEEE
Q psy437           99 SVAAALAQE--RINAISYHAGL---ADK---LRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        99 ~~a~gL~~~--gi~~~vih~~~---p~~---~r~~~~~~f~~~~~~v~va  140 (184)
                        |.||.+.  --+ .||=+|-   ||.   .-...||.+..+.|.|+=.
T Consensus       761 --AGGLGINLatAD-TVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRL  807 (1373)
T KOG0384|consen  761 --AGGLGINLATAD-TVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRL  807 (1373)
T ss_pred             --cCcccccccccc-eEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEE
Confidence              8888654  344 4444443   332   2345666677776666544

>KOG0390|consensus

Probab=93.05  E-value=1.6  Score=40.17  Aligned_cols=115  Identities=8%  Similarity=-0.040  Sum_probs=70.6

Q ss_pred             hHHHHHHHHHhhc-CCCcEEEEecc-HHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCc--eEEEEEeecc
Q psy437           20 VLKEVISLIKAKY-SGQSGIVYCLT-RKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV--HVGHWTVVSK   95 (184)
Q Consensus        20 k~~~L~~~l~~~~-~~~~~IIf~~t-r~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~--~vlVaT~tr~   95 (184)
                      |+..|..++.... ...--.+++.. +...+.+.+..+..|..+..+||.|+..+|..+++.|-+-..  .|..++..-+
T Consensus       579 kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAg  658 (776)
T KOG0390|consen  579 KLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAG  658 (776)
T ss_pred             HHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccc
Confidence            5555555542210 11112344444 444444455555679999999999999999999999986433  4555544211


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCC---ChHHHHHHHHHhhCCCceEEEE
Q psy437           96 ECDSVAAALAQERINAISYHAGL---ADKLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~---p~~~r~~~~~~f~~~~~~v~va  140 (184)
                           +.||.-=|-+ .+|=+|.   |...++.+-|+||.|+-+.+-+
T Consensus       659 -----g~GinLiGAs-Rlil~D~dWNPa~d~QAmaR~~RdGQKk~v~i  700 (776)
T KOG0390|consen  659 -----GEGLNLIGAS-RLILFDPDWNPAVDQQAMARAWRDGQKKPVYI  700 (776)
T ss_pred             -----cCceeecccc-eEEEeCCCCCchhHHHHHHHhccCCCcceEEE
Confidence                 2466555655 4554554   6677778888899887654443

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=93.00  E-value=0.55  Score=43.96  Aligned_cols=67  Identities=12%  Similarity=0.043  Sum_probs=49.8

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ..++-.+.....+.+++|.++|+..|.+.++++..    .|+++..+.||++.+++...+      ..+|+|+|+++
T Consensus       123 Af~LP~l~~aL~g~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y------~~DIVygTPgR  193 (970)
T PRK12899        123 TAVMPLYLNALTGKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY------QCDVVYGTASE  193 (970)
T ss_pred             HHHHHHHHHHhhcCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc------CCCEEEECCCh
Confidence            33444443322344688889999999999998875    478999999999988776443      37899999976

>KOG0924|consensus

Probab=92.93  E-value=0.16  Score=45.78  Aligned_cols=102  Identities=13%  Similarity=0.158  Sum_probs=69.4

Q ss_pred             eEEEEEEccChHHHHHHHHHhhc---CCCcEEEEeccHHH----HHHHHHHHHhC------CCeeEEecCCCCHHHHHHH
Q psy437           10 LKYEILPKKNVLKEVISLIKAKY---SGQSGIVYCLTRKE----CDSVAAALAQE------RINAISYHAGLADKLRNEV   76 (184)
Q Consensus        10 l~y~v~~~~~k~~~L~~~l~~~~---~~~~~IIf~~tr~~----~e~la~~L~~~------gi~~~~~hg~l~~~~R~~~   76 (184)
                      +.|.-.+.++-.+..+......+   .++-.+||..-.++    |+.+.+.|.+.      ++.+..+++.|++....++
T Consensus       536 ~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~ki  615 (1042)
T KOG0924|consen  536 IMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKI  615 (1042)
T ss_pred             EEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhh
Confidence            44554555444443333221111   33557889866554    44555555432      6788899999999998888


Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCC
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGL  118 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~  118 (184)
                      .+.--.|.-++||||+      .+-..|.++||. +||--|.
T Consensus       616 Fq~a~~~vRK~IvATN------IAETSLTi~gI~-yVID~Gy  650 (1042)
T KOG0924|consen  616 FQKAEGGVRKCIVATN------IAETSLTIPGIR-YVIDTGY  650 (1042)
T ss_pred             cccCCCCceeEEEecc------chhhceeecceE-EEEecCc
Confidence            8888888889999999      666789999999 8876653

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=92.76  E-value=0.69  Score=42.23  Aligned_cols=75  Identities=15%  Similarity=0.143  Sum_probs=54.8

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC-CCeeEEecCCCCHHHHHHHHHHHhc----cCceEEEEEeecccHHHHHHHHHhcC
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWIS----NKVHVGHWTVVSKECDSVAAALAQER  108 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~hg~l~~~~R~~~~~~f~~----g~~~vlVaT~tr~~~e~~a~gL~~~g  108 (184)
                      ++.++||++|.+..+.++..|... +.+ ...+|.   ..|..+++.|++    ++..||++|.+      .++|+|.+|
T Consensus       534 ~gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~---~~~~~ll~~f~~~~~~~~~~VL~g~~s------f~EGVD~pG  603 (697)
T PRK11747        534 HKGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGD---QPRQRLLEKHKKRVDEGEGSVLFGLQS------FAEGLDLPG  603 (697)
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCC---chHHHHHHHHHHHhccCCCeEEEEecc------ccccccCCC
Confidence            345899999999999999998743 333 334553   357788888874    56789999984      488999987


Q ss_pred             --CcEEEeeCCCC
Q psy437          109 --INAISYHAGLA  119 (184)
Q Consensus       109 --i~~~vih~~~p  119 (184)
                        .+ .|+=.++|
T Consensus       604 d~l~-~vII~kLP  615 (697)
T PRK11747        604 DYLT-QVIITKIP  615 (697)
T ss_pred             CceE-EEEEEcCC
Confidence              45 56666655

>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=92.30  E-value=1.8  Score=37.40  Aligned_cols=91  Identities=9%  Similarity=0.024  Sum_probs=75.7

Q ss_pred             HHHHHh--ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE---------EecC
Q psy437           76 VQMKWI--SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV---------WKIQ  144 (184)
Q Consensus        76 ~~~~f~--~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va---------~D~~  144 (184)
                      ++-.+.  .....+||+.++-=+--++-..|...+++.+.+|=-.+++.-..+-..|..|+..+++.         +.+.
T Consensus       290 iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~ir  369 (442)
T PF06862_consen  290 ILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYRIR  369 (442)
T ss_pred             HHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhceec
Confidence            444444  24567999999988877888889999999888999999999999999999999999998         3999


Q ss_pred             CccEEEecCCCCCcccccccccc
Q psy437          145 WKRIIWIHSLVLIKPDYLPPILD  167 (184)
Q Consensus       145 ~vr~v~~~~~p~~~e~y~~~i~~  167 (184)
                      .+++|+=|.+|..++-| .+++.
T Consensus       370 Gi~~viFY~~P~~p~fY-~El~n  391 (442)
T PF06862_consen  370 GIRHVIFYGPPENPQFY-SELLN  391 (442)
T ss_pred             CCcEEEEECCCCChhHH-HHHHh
Confidence            99999999999887654 55543

; GO: 0005634 nucleus

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=92.00  E-value=0.58  Score=30.61  Aligned_cols=37  Identities=22%  Similarity=0.269  Sum_probs=31.2

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      +..+.++||.+-..+...+..|+..|+++..+.||++
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            4567888999877788889999999998888999975

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.

>KOG0950|consensus

Probab=92.00  E-value=0.42  Score=44.43  Aligned_cols=90  Identities=21%  Similarity=0.344  Sum_probs=67.3

Q ss_pred             ceEEEEEeecccHHHHHHHHHhc-----------C-----------------Cc----------EEEeeCCCChHHHHHH
Q psy437           85 VHVGHWTVVSKECDSVAAALAQE-----------R-----------------IN----------AISYHAGLADKLRNEV  126 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~-----------g-----------------i~----------~~vih~~~p~~~r~~~  126 (184)
                      .++||++++|+.||.+|..+.+.           +                 ++          +...|+|+..+.|+++
T Consensus       461 ~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER~~i  540 (1008)
T KOG0950|consen  461 SSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEEREII  540 (1008)
T ss_pred             CeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchHHHH
Confidence            35899999999999988655210           1                 11          2567899999999999


Q ss_pred             HHHhhCCCceEEEE-------EecCCccEEEecCC----CCCccccccccccccCCccccc
Q psy437          127 QMKWISNKVHLYNV-------WKIQWKRIIWIHSL----VLIKPDYLPPILDLRLGREDIR  176 (184)
Q Consensus       127 ~~~f~~~~~~v~va-------~D~~~vr~v~~~~~----p~~~e~y~~~i~~~~~~r~~~~  176 (184)
                      -..|+.|.+.|++|       .+-|-.|.++-..+    +.+.-.|.|-+  +|+||.++.
T Consensus       541 E~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~--GRAGR~gid  599 (1008)
T KOG0950|consen  541 EAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMV--GRAGRTGID  599 (1008)
T ss_pred             HHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhh--hhhhhcccc
Confidence            99999999999999       27777677665533    34556788888  588887543

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

Probab=91.98  E-value=0.39  Score=43.85  Aligned_cols=109  Identities=6%  Similarity=-0.025  Sum_probs=70.3

Q ss_pred             EEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHH--HHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc-E
Q psy437           37 GIVYCLTRKECDSVAAALAQE--RINAISYHAGLADK--LRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN-A  111 (184)
Q Consensus        37 ~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~--~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~-~  111 (184)
                      .|+++-  .-+|.+++.|...  +.++..+.++....  .-...+..|.+|+.+|||.|.      .+|.|++.+++. +
T Consensus       485 ~L~~~G--~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQ------miaKG~~fp~vtLV  556 (730)
T COG1198         485 HLRAVG--PGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQ------MIAKGHDFPNVTLV  556 (730)
T ss_pred             eeEEec--ccHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecch------hhhcCCCcccceEE
Confidence            355443  3467777777763  67777777776543  345779999999999999999      999999999988 3


Q ss_pred             EEeeCC-------CChHHHHH---HHHHhhCCC----ceEEEE-E--ecCCccEEEecC
Q psy437          112 ISYHAG-------LADKLRNE---VQMKWISNK----VHLYNV-W--KIQWKRIIWIHS  153 (184)
Q Consensus       112 ~vih~~-------~p~~~r~~---~~~~f~~~~----~~v~va-~--D~~~vr~v~~~~  153 (184)
                      .|+++|       +=.++|.+   .|=..+.|.    ..|++- +  |.|.++.+.+.|
T Consensus       557 gvl~aD~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i~~~~~~d  615 (730)
T COG1198         557 GVLDADTGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAIQALKRGD  615 (730)
T ss_pred             EEEechhhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHHHHHHhcC
Confidence            445554       33344432   222333332    344443 2  666666666554

>KOG4150|consensus

Probab=91.84  E-value=0.41  Score=42.52  Aligned_cols=97  Identities=12%  Similarity=0.127  Sum_probs=76.1

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHH------hcCC-c-EEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALA------QERI-N-AISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~------~~gi-~-~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      ++-+.....++.|-+|.+|+-||.+-....      .+++ . +..|.||-..+.|..+-+..-.|++--++|       
T Consensus       517 ~~~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELG  596 (1034)
T KOG4150|consen  517 LFAEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELG  596 (1034)
T ss_pred             HHHHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhc
Confidence            455566678899999999999887643321      1111 1 255899999999999999877777766666       


Q ss_pred             EecCCccEEEecCCCCCccccccccccccCCccc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                      +|+-.+..|++...|-+.-+..|..  +|+||++
T Consensus       597 IDIG~LDAVl~~GFP~S~aNl~QQ~--GRAGRRN  628 (1034)
T KOG4150|consen  597 IDIGHLDAVLHLGFPGSIANLWQQA--GRAGRRN  628 (1034)
T ss_pred             cccccceeEEEccCchhHHHHHHHh--ccccccC
Confidence            5999999999999999999999987  6999974

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=91.78  E-value=0.63  Score=42.51  Aligned_cols=82  Identities=7%  Similarity=0.002  Sum_probs=56.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCC-------eeEEecCCCCHHHHHHHHHHHhc----cCceEEEEEeecccHHHHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERI-------NAISYHAGLADKLRNEVQMKWIS----NKVHVGHWTVVSKECDSVA  101 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi-------~~~~~hg~l~~~~R~~~~~~f~~----g~~~vlVaT~tr~~~e~~a  101 (184)
                      .++.++||++|.+..+.+.+.+.+.|+       +..+.-+ -+..++..++++|..    ++..||.|+-.-    .++
T Consensus       521 ~pgg~lvfFpSy~~l~~v~~~~~~~~~~~~i~~~k~i~~E~-~~~~~~~~~l~~f~~~~~~~~gavL~av~gG----k~s  595 (705)
T TIGR00604       521 IPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVET-KDAQETSDALERYKQAVSEGRGAVLLSVAGG----KVS  595 (705)
T ss_pred             CCCcEEEEccCHHHHHHHHHHHHhcCHHHHHhcCCCEEEeC-CCcchHHHHHHHHHHHHhcCCceEEEEecCC----ccc
Confidence            456789999999999999988876543       1122211 222578899999975    355688888211    568


Q ss_pred             HHHHhcC--CcEEEeeCCCCh
Q psy437          102 AALAQER--INAISYHAGLAD  120 (184)
Q Consensus       102 ~gL~~~g--i~~~vih~~~p~  120 (184)
                      +|+|.+|  .+ .|+=.|+|-
T Consensus       596 EGIDf~~~~~r-~ViivGlPf  615 (705)
T TIGR00604       596 EGIDFCDDLGR-AVIMVGIPY  615 (705)
T ss_pred             CccccCCCCCc-EEEEEccCC
Confidence            8999887  55 555588886

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).

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=91.69  E-value=0.75  Score=42.76  Aligned_cols=89  Identities=10%  Similarity=0.034  Sum_probs=67.5

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----EecCCcc--------EE
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----WKIQWKR--------II  149 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----~D~~~vr--------~v  149 (184)
                      ..-+|||.|.+-...|.++..|...||+..|+|+---...-.-+-+..+.|.+.|-.-     -||.--.        +|
T Consensus       425 ~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk~~e~EA~IIa~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhV  504 (925)
T PRK12903        425 KGQPILIGTAQVEDSETLHELLLEANIPHTVLNAKQNAREAEIIAKAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYV  504 (925)
T ss_pred             cCCCEEEEeCcHHHHHHHHHHHHHCCCCceeecccchhhHHHHHHhCCCCCeEEEecccccCCcCccCchhHHHcCCcEE
Confidence            3458999999999999999999999999999999755555556655666665554433     3776433        89


Q ss_pred             EecCCCCCccccccccccccCCcc
Q psy437          150 WIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       150 ~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |....|.+.  -+.+.|++|+||-
T Consensus       505 IgTerheSr--RIDnQLrGRaGRQ  526 (925)
T PRK12903        505 LGTDKAESR--RIDNQLRGRSGRQ  526 (925)
T ss_pred             EecccCchH--HHHHHHhcccccC
Confidence            988887764  4566788999996

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

Probab=91.60  E-value=1.5  Score=40.82  Aligned_cols=77  Identities=12%  Similarity=-0.019  Sum_probs=56.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcC--Cc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQER--IN  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g--i~  110 (184)
                      .+++++|+++|.+..+.+++.|....++. ...|.-.  .|.+++++|++++..||++|.      ..++|+|.+|  ..
T Consensus       646 ~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~------sFwEGVD~p~~~~~  716 (820)
T PRK07246        646 LQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLG------SFWEGVDFVQADRM  716 (820)
T ss_pred             cCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecc------hhhCCCCCCCCCeE
Confidence            56789999999999999999997655444 3444211  356789999998889999998      4588999864  33


Q ss_pred             EEEeeCCCC
Q psy437          111 AISYHAGLA  119 (184)
Q Consensus       111 ~~vih~~~p  119 (184)
                       .++=.++|
T Consensus       717 -~viI~kLP  724 (820)
T PRK07246        717 -IEVITRLP  724 (820)
T ss_pred             -EEEEecCC
Confidence             33446666

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=91.37  E-value=2.9  Score=28.39  Aligned_cols=70  Identities=21%  Similarity=0.112  Sum_probs=47.4

Q ss_pred             ChHHHHHHHHHhhc---CCCcEEEEeccHHHHHHHHHHHHhCC---CeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           19 NVLKEVISLIKAKY---SGQSGIVYCLTRKECDSVAAALAQER---INAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        19 ~k~~~L~~~l~~~~---~~~~~IIf~~tr~~~e~la~~L~~~g---i~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .|...+...+....   ...+.++.|++...+++..+.+....   ..+..++++.......    ........++++|.
T Consensus        12 GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~i~i~t~   87 (144)
T cd00046          12 GKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQE----KLLSGKTDIVVGTP   87 (144)
T ss_pred             chhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHHH----HHhcCCCCEEEECc
Confidence            45544444443321   45788999999999999888877543   7788888876554443    33345678899888

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

>KOG0920|consensus

Probab=90.55  E-value=0.49  Score=44.17  Aligned_cols=92  Identities=11%  Similarity=0.127  Sum_probs=71.0

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC-------CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE-------RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~-------gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ..|+..|-+....+..|||-+.-.....+.+.|...       .+-+..+|+.|+..+...+...--.|..+||++|+  
T Consensus       401 ~~li~~I~~~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTN--  478 (924)
T KOG0920|consen  401 EDLIEYIDEREFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATN--  478 (924)
T ss_pred             HHHHHhcccCCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhh--
Confidence            334444433223567899999999999999999742       24567799999999999998888899999999999  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           95 KECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                          .+...+.++++- +||-.|.-+
T Consensus       479 ----IAETSITIdDVv-yVIDsG~~K  499 (924)
T KOG0920|consen  479 ----IAETSITIDDVV-YVIDSGLVK  499 (924)
T ss_pred             ----hHhhcccccCeE-EEEecCeee
Confidence                777788888885 777666543

>KOG0953|consensus

Probab=90.05  E-value=1.4  Score=39.05  Aligned_cols=91  Identities=16%  Similarity=0.053  Sum_probs=61.5

Q ss_pred             EEEEeecccHHHHHHHHHhcCCc-EEEeeCCCChHHHHHHHHHhhC--CCceEEEEEe------cCCccEEEecCCCCCc
Q psy437           88 GHWTVVSKECDSVAAALAQERIN-AISYHAGLADKLRNEVQMKWIS--NKVHLYNVWK------IQWKRIIWIHSLVLIK  158 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~-~~vih~~~p~~~r~~~~~~f~~--~~~~v~va~D------~~~vr~v~~~~~p~~~  158 (184)
                      +||- +|++.=.+.+.+++.|.. +.||-|++|+.-|..=-..|-+  +.+.|+||-|      .-+||-||=+++-+-.
T Consensus       361 vV~F-Skk~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL~IrRiiF~sl~Kys  439 (700)
T KOG0953|consen  361 VVAF-SKKDIFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNLNIRRIIFYSLIKYS  439 (700)
T ss_pred             EEEe-ehhhHHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeecccccccccceeEEEEeecccCC
Confidence            5544 467777777888888876 8999999999888655455765  8999999932      1345666655554222


Q ss_pred             c--------ccccccccccCCcc--ccccccc
Q psy437          159 P--------DYLPPILDLRLGRE--DIREGET  180 (184)
Q Consensus       159 e--------~y~~~i~~~~~~r~--~~~~~~~  180 (184)
                      .        +.+..|. +|+||-  ..++|++
T Consensus       440 g~e~~~it~sqikQIA-GRAGRf~s~~~~G~v  470 (700)
T KOG0953|consen  440 GRETEDITVSQIKQIA-GRAGRFGSKYPQGEV  470 (700)
T ss_pred             cccceeccHHHHHHHh-hcccccccCCcCceE
Confidence            2        2233442 799995  7788764

>KOG0949|consensus

Probab=89.42  E-value=2.2  Score=40.37  Aligned_cols=139  Identities=17%  Similarity=0.244  Sum_probs=83.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCe--eEEecCCCC-----HHHHHHHHHHHhcc------------CceEEE
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERIN--AISYHAGLA-----DKLRNEVQMKWISN------------KVHVGH   89 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~--~~~~hg~l~-----~~~R~~~~~~f~~g------------~~~vlV   89 (184)
                      ..-|+|.|.--|..|+.+|..+..    ....  -.-+|..+.     ..+|.+..+.|.+.            .-.+++
T Consensus       849 ~~lpaicfn~dr~fcekla~kv~~~Le~~e~Ee~k~k~m~k~kk~~~~a~~r~Kt~e~~~k~~~~~ek~~~~k~d~~~~~  928 (1330)
T KOG0949|consen  849 NMLPAICFNTDRDFCEKLALKVHRQLESMEMEEKKDKLMEKMKKEAKRARDREKTKESWIKESIAAEKSFQMKNDKKNIK  928 (1330)
T ss_pred             cccchhcccchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccce
Confidence            556899998888888887765532    1100  001121111     24566666666631            123344


Q ss_pred             EEeec-----------------ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCC
Q psy437           90 WTVVS-----------------KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQW  145 (184)
Q Consensus        90 aT~tr-----------------~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~  145 (184)
                      +|--.                 ++++..---|-.+||  .+=|+||....|.-+-=-|+.|.++|+.|       ++.|=
T Consensus       929 ~~f~dp~~~~~~~~f~~~~~~~g~~~~~~id~lyRGi--G~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPC 1006 (1330)
T KOG0949|consen  929 YTFLDPLTKLTDYEFEEETKFIGNTDFEFIDMLYRGI--GVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPC 1006 (1330)
T ss_pred             EEecCcccccchhhhhhhccccCCCcHHHHHHHHhcc--cccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCc
Confidence            43211                 333333333344565  67799999999999988899999999999       47775


Q ss_pred             ccEEEec-CCCCCccccccccccccCCcccc
Q psy437          146 KRIIWIH-SLVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       146 vr~v~~~-~~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      -.-|+-- ++--++-.|-|-.  +|+||+++
T Consensus      1007 rTVvF~gDsLQL~plny~Qma--GRAGRRGF 1035 (1330)
T KOG0949|consen 1007 RTVVFAGDSLQLDPLNYKQMA--GRAGRRGF 1035 (1330)
T ss_pred             eeEEEeccccccCchhHHhhh--cccccccc
Confidence            4444433 3444555666654  79999844

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=89.01  E-value=0.64  Score=30.98  Aligned_cols=38  Identities=21%  Similarity=0.237  Sum_probs=31.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLAD   70 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~   70 (184)
                      +..+.++||.+-..+...+..|...|+.+..+.||+..
T Consensus        60 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~~   97 (100)
T cd01523          60 DDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMKA   97 (100)
T ss_pred             CCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHHh
Confidence            44678889998778889999999999998788998753

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>KOG0924|consensus

Probab=88.40  E-value=5.4  Score=36.48  Aligned_cols=119  Identities=4%  Similarity=-0.032  Sum_probs=81.5

Q ss_pred             EEEEeccHHHHHHHHHHHHh--------CCCeeEEecCCCCHHHHH-HHHHHHh-----ccCceEEEEEeecccHHHHHH
Q psy437           37 GIVYCLTRKECDSVAAALAQ--------ERINAISYHAGLADKLRN-EVQMKWI-----SNKVHVGHWTVVSKECDSVAA  102 (184)
Q Consensus        37 ~IIf~~tr~~~e~la~~L~~--------~gi~~~~~hg~l~~~~R~-~~~~~f~-----~g~~~vlVaT~tr~~~e~~a~  102 (184)
                      -||.++-.-+++..+.++..        .-+++..+|...+.++=- .++.+-.     .+...|||+-.+..++|-...
T Consensus       502 KliVtSATm~a~kf~nfFgn~p~f~IpGRTyPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~  581 (1042)
T KOG0924|consen  502 KLIVTSATMDAQKFSNFFGNCPQFTIPGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCD  581 (1042)
T ss_pred             eEEEeeccccHHHHHHHhCCCceeeecCCccceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHH
Confidence            34444444568888888862        236788888877655422 2222222     344678999998876555444


Q ss_pred             HH--------Hhc--CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCC
Q psy437          103 AL--------AQE--RINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLV  155 (184)
Q Consensus       103 gL--------~~~--gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p  155 (184)
                      .+        ..+  ++.++-|-..||++....+-+.--.|--.++||       +-+|+|++||.-...
T Consensus       582 ~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy~  651 (1042)
T KOG0924|consen  582 IIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGYC  651 (1042)
T ss_pred             HHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCce
Confidence            33        233  677788999999999888877777777789998       589999999876543

>KOG0392|consensus

Probab=88.18  E-value=4.4  Score=39.27  Aligned_cols=89  Identities=12%  Similarity=0.155  Sum_probs=66.2

Q ss_pred             hHHHHHHHHHhhc---------------CCCcEEEEeccHHHHHHHHHHHHhCCCe-eE--EecCCCCHHHHHHHHHHHh
Q psy437           20 VLKEVISLIKAKY---------------SGQSGIVYCLTRKECDSVAAALAQERIN-AI--SYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus        20 k~~~L~~~l~~~~---------------~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~--~~hg~l~~~~R~~~~~~f~   81 (184)
                      |+..|.++|.+-.               ...+++|||.-+...+-+.+.|.+.-.+ +.  .+.|..++.+|.++.++|-
T Consensus      1311 Kl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN 1390 (1549)
T KOG0392|consen 1311 KLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFN 1390 (1549)
T ss_pred             hHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhc
Confidence            7888888876421               1235799999999999999988775443 33  5789999999999999999


Q ss_pred             cc-CceEEEEEeecccHHHHHHHHHhcCCcEEE
Q psy437           82 SN-KVHVGHWTVVSKECDSVAAALAQERINAIS  113 (184)
Q Consensus        82 ~g-~~~vlVaT~tr~~~e~~a~gL~~~gi~~~v  113 (184)
                      ++ .++||.-|.--|     .=||+--|-+++|
T Consensus      1391 ~DptIDvLlLTThVG-----GLGLNLTGADTVV 1418 (1549)
T KOG0392|consen 1391 EDPTIDVLLLTTHVG-----GLGLNLTGADTVV 1418 (1549)
T ss_pred             CCCceeEEEEeeecc-----ccccccCCCceEE
Confidence            98 778887776221     2356667777433

>KOG1123|consensus

Probab=87.64  E-value=5.2  Score=35.31  Aligned_cols=46  Identities=15%  Similarity=0.099  Sum_probs=36.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      .+.+.|||.-..-.....|-.|.+     -+++|..++.+|.++++.|..+
T Consensus       542 RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq~n  587 (776)
T KOG1123|consen  542 RGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQTN  587 (776)
T ss_pred             cCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhcccC
Confidence            677899998776666666665543     4688999999999999999864

>KOG0387|consensus

Probab=87.58  E-value=8.9  Score=35.53  Aligned_cols=107  Identities=13%  Similarity=0.126  Sum_probs=76.0

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHH-hCCCeeEEecCCCCHHHHHHHHHHHhccCc-eE-EEEEeec
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALA-QERINAISYHAGLADKLRNEVQMKWISNKV-HV-GHWTVVS   94 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~-~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~-~v-lVaT~tr   94 (184)
                      .|+..+..+|..- ..+.++++|..|+...+.+...|. ..|+...-+.|..+...|..+.++|-.++. .| |..|.  
T Consensus       530 GKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTr--  607 (923)
T KOG0387|consen  530 GKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTR--  607 (923)
T ss_pred             chHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEec--
Confidence            3777777666432 146689999999999999999998 689999999999999999999999998765 33 34444  


Q ss_pred             ccHHHHHHHH--HhcCCcEEEeeCCC---ChHHHHHHHHHhhCCC
Q psy437           95 KECDSVAAAL--AQERINAISYHAGL---ADKLRNEVQMKWISNK  134 (184)
Q Consensus        95 ~~~e~~a~gL--~~~gi~~~vih~~~---p~~~r~~~~~~f~~~~  134 (184)
                            +.||  +--|.+ -||=+|.   |+..-...-|+|+=|.
T Consensus       608 ------vGGLGlNLTgAn-RVIIfDPdWNPStD~QAreRawRiGQ  645 (923)
T KOG0387|consen  608 ------VGGLGLNLTGAN-RVIIFDPDWNPSTDNQARERAWRIGQ  645 (923)
T ss_pred             ------ccccccccccCc-eEEEECCCCCCccchHHHHHHHhhcC
Confidence                  4444  445655 5555554   3444444445576543

>KOG0388|consensus

Probab=87.34  E-value=4.4  Score=37.21  Aligned_cols=111  Identities=18%  Similarity=0.242  Sum_probs=76.6

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCce-EEEEEeecccHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH-VGHWTVVSKECD   98 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~-vlVaT~tr~~~e   98 (184)
                      +++.|+..|+.  .+...++|..-.+..+-+..+|...++.-.-+.|.....+|..+...|...++= .|..|.      
T Consensus      1032 ~LDeLL~kLka--egHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTR------ 1103 (1185)
T KOG0388|consen 1032 VLDELLPKLKA--EGHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTR------ 1103 (1185)
T ss_pred             eHHHHHHHhhc--CCceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecc------
Confidence            34444444543  567899999999999999999999999999999999999999999999984442 244455      


Q ss_pred             HHHHHHHhc--CCc-EEEeeCCCCh----HHHHHHHHHhhCCCceEEEE
Q psy437           99 SVAAALAQE--RIN-AISYHAGLAD----KLRNEVQMKWISNKVHLYNV  140 (184)
Q Consensus        99 ~~a~gL~~~--gi~-~~vih~~~p~----~~r~~~~~~f~~~~~~v~va  140 (184)
                        |.||.+.  ..+ +.+|-.|-.+    ..-+..||-.....+.|+-.
T Consensus      1104 --AGGLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl 1150 (1185)
T KOG0388|consen 1104 --AGGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRL 1150 (1185)
T ss_pred             --cCcccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeee
Confidence              6677543  233 2344444444    44455666666666666543

>smart00450 RHOD Rhodanese Homology Domain

Probab=87.21  E-value=0.94  Score=29.32  Aligned_cols=38  Identities=16%  Similarity=0.281  Sum_probs=32.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCCH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLAD   70 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~~   70 (184)
                      +..+.|+||.+-..+..++..|...|+. +..+.||+..
T Consensus        55 ~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~~   93 (100)
T smart00450       55 KDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYKE   93 (100)
T ss_pred             CCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHHH
Confidence            4566888999988899999999999998 7888999753

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.

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

Probab=86.89  E-value=1.4  Score=40.75  Aligned_cols=87  Identities=15%  Similarity=0.120  Sum_probs=59.0

Q ss_pred             CCCCCCCeEEEEEE-----ccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHH
Q psy437            3 SSFNRANLKYEILP-----KKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEV   76 (184)
Q Consensus         3 ~s~~R~Nl~y~v~~-----~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~   76 (184)
                      -+.+||++...-..     ...|+..+++.+... ..+.|.||-+.+.+..|.+++.|.+.|++..++.+.-..++-..+
T Consensus       392 iPTnrp~~R~D~~D~vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk~h~~EA~Ii  471 (822)
T COG0653         392 IPTNRPIIRLDEPDLVYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAKNHAREAEII  471 (822)
T ss_pred             ccCCCcccCCCCccccccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhHHHHHHhcCCCceeeccccHHHHHHHH
Confidence            35677776432221     123788887777643 367889999999999999999999999998887776553333333


Q ss_pred             HHHHhccCc-eEEEEEe
Q psy437           77 QMKWISNKV-HVGHWTV   92 (184)
Q Consensus        77 ~~~f~~g~~-~vlVaT~   92 (184)
                      -+.   |+. .|=|||+
T Consensus       472 a~A---G~~gaVTiATN  485 (822)
T COG0653         472 AQA---GQPGAVTIATN  485 (822)
T ss_pred             hhc---CCCCccccccc
Confidence            322   333 3458888

>KOG0389|consensus

Probab=86.87  E-value=12  Score=34.83  Aligned_cols=114  Identities=10%  Similarity=0.069  Sum_probs=84.8

Q ss_pred             ChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCce--EEEEEeecc
Q psy437           19 NVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH--VGHWTVVSK   95 (184)
Q Consensus        19 ~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~--vlVaT~tr~   95 (184)
                      .|+..|..+|.+.. .+.+++||..-....+.+-..|.-.++.-.-+.|...-.+|..++++|-..+.-  .|..|.   
T Consensus       761 gK~r~L~~LLp~~k~~G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTK---  837 (941)
T KOG0389|consen  761 GKCRKLKELLPKIKKKGDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTK---  837 (941)
T ss_pred             hhHhHHHHHHHHHhhcCCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeec---
Confidence            47777777775432 457899999888888888999999999999999998889999999999886642  345555   


Q ss_pred             cHHHHHHHH--HhcCCcEEEeeCCCC------hHHHHHHHHHhhCCCceEEEEE
Q psy437           96 ECDSVAAAL--AQERINAISYHAGLA------DKLRNEVQMKWISNKVHLYNVW  141 (184)
Q Consensus        96 ~~e~~a~gL--~~~gi~~~vih~~~p------~~~r~~~~~~f~~~~~~v~va~  141 (184)
                           |.|+  +--+-+ .||=+|+.      ...++..||.+....+.|+=.+
T Consensus       838 -----AGG~GINLt~An-~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLI  885 (941)
T KOG0389|consen  838 -----AGGFGINLTCAN-TVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLI  885 (941)
T ss_pred             -----cCcceecccccc-eEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEE
Confidence                 5455  444555 44444442      4668889999998888777654

>KOG2340|consensus

Probab=86.74  E-value=1.9  Score=38.06  Aligned_cols=85  Identities=7%  Similarity=-0.006  Sum_probs=67.0

Q ss_pred             cEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHH--HHHHhcCCcEEE
Q psy437           36 SGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVA--AALAQERINAIS  113 (184)
Q Consensus        36 ~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a--~gL~~~gi~~~v  113 (184)
                      -++||.|+--+--.+-.++.+.++....+|---++..-.+.-+-|..|..++|++|.      ++.  +.-.+.||+ .|
T Consensus       554 ~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTE------R~hffrR~~ikGVk-~v  626 (698)
T KOG2340|consen  554 GILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTE------RAHFFRRYHIKGVK-NV  626 (698)
T ss_pred             ceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEeh------hhhhhhhheeccee-eE
Confidence            369999999999999999999888776666555555556667789999999999999      433  445788998 88


Q ss_pred             eeCCCChHHHHHHH
Q psy437          114 YHAGLADKLRNEVQ  127 (184)
Q Consensus       114 ih~~~p~~~r~~~~  127 (184)
                      +-|++|..+.-|.-
T Consensus       627 VfYqpP~~P~FYsE  640 (698)
T KOG2340|consen  627 VFYQPPNNPHFYSE  640 (698)
T ss_pred             EEecCCCCcHHHHH
Confidence            88999987765543

>KOG0949|consensus

Probab=86.51  E-value=1  Score=42.33  Aligned_cols=65  Identities=18%  Similarity=0.130  Sum_probs=49.1

Q ss_pred             EEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh-HHHHHHHHHhhCC
Q psy437           62 ISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD-KLRNEVQMKWISN  133 (184)
Q Consensus        62 ~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~-~~r~~~~~~f~~~  133 (184)
                      .+.|+||....|..+.--|+.|+.+|++||.      .++-|++-|--. +|+-+|-=| +.-+|-|-+.+.|
T Consensus       966 G~HHaglNr~yR~~VEvLFR~g~L~VlfaT~------TLsLGiNMPCrT-VvF~gDsLQL~plny~QmaGRAG 1031 (1330)
T KOG0949|consen  966 GVHHAGLNRKYRSLVEVLFRQGHLQVLFATE------TLSLGINMPCRT-VVFAGDSLQLDPLNYKQMAGRAG 1031 (1330)
T ss_pred             cccccccchHHHHHHHHHhhcCceEEEEEee------ehhcccCCCcee-EEEeccccccCchhHHhhhcccc
Confidence            4589999999999999999999999999999      556666666543 666555333 5566777665554

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=86.35  E-value=1.8  Score=28.56  Aligned_cols=37  Identities=11%  Similarity=-0.015  Sum_probs=30.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCC-eeEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERI-NAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi-~~~~~hg~l~   69 (184)
                      +..+.|+||.+-..+...+..|...|+ ++..+.||+.
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            456788999998888888999998998 4777888874

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.

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=86.33  E-value=2.4  Score=27.65  Aligned_cols=46  Identities=17%  Similarity=0.281  Sum_probs=34.0

Q ss_pred             HHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           24 VISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        24 L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +.+.+....+..+.++||.+-..+...+..|...|+. +..+.||+.
T Consensus        46 ~~~~~~~~~~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~~   92 (96)
T cd01444          46 LDDWLGDLDRDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGFE   92 (96)
T ss_pred             HHHHHhhcCCCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCHH
Confidence            3334433225567888999988999999999999985 667888864

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>KOG0384|consensus

Probab=86.05  E-value=2.3  Score=40.85  Aligned_cols=97  Identities=10%  Similarity=0.058  Sum_probs=79.2

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE----------EecCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV----------WKIQW  145 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va----------~D~~~  145 (184)
                      ++-+++.+.-+|||++-=-++.+.+|.+|...+++---+-|.+|...|.....-|-.-...-+|+          ++..-
T Consensus       691 LL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRAGGLGINLat  770 (1373)
T KOG0384|consen  691 LLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRAGGLGINLAT  770 (1373)
T ss_pred             HHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEecccCcccccccc
Confidence            45555667778999998888999999999999999888999999999999999997655555554          47777


Q ss_pred             ccEEEecCCCCCccccccccccc-cCCc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~-~~~r  172 (184)
                      -..||.||-=..+.+-+|-..+- |.|-
T Consensus       771 ADTVIIFDSDWNPQNDLQAqARaHRIGQ  798 (1373)
T KOG0384|consen  771 ADTVIIFDSDWNPQNDLQAQARAHRIGQ  798 (1373)
T ss_pred             cceEEEeCCCCCcchHHHHHHHHHhhcc
Confidence            78999999999999988887653 5553

>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors

Probab=85.97  E-value=11  Score=29.19  Aligned_cols=62  Identities=13%  Similarity=0.045  Sum_probs=29.7

Q ss_pred             HHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE------------EeecccHHHHHHHHHhcCCcEE
Q psy437           49 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW------------TVVSKECDSVAAALAQERINAI  112 (184)
Q Consensus        49 ~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa------------T~tr~~~e~~a~gL~~~gi~~~  112 (184)
                      .+.+.|...++....+.+.....  ...++.+.+..+++++.            ++-......+++.|-..|.+-.
T Consensus        46 ~~i~~l~~~~vdgii~~~~~~~~--~~~~~~~~~~~ipvV~i~~~~~~~~~~V~~d~~~~g~~a~~~l~~~G~~~i  119 (269)
T cd06281          46 EILRSFEQRRMDGIIIAPGDERD--PELVDALASLDLPIVLLDRDMGGGADAVLFDHAAGMRQAVEYLISLGHRRI  119 (269)
T ss_pred             HHHHHHHHcCCCEEEEecCCCCc--HHHHHHHHhCCCCEEEEecccCCCCCEEEECcHHHHHHHHHHHHHCCCcEE
Confidence            44445555566555544432211  23344444444444333            3333455667777766676633

This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.

>KOG0922|consensus

Probab=85.85  E-value=16  Score=33.15  Aligned_cols=163  Identities=10%  Similarity=0.031  Sum_probs=101.6

Q ss_pred             CCeE-EEEEEccC------hHHHHHHHHHhhcC--CC-cEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCC
Q psy437            8 ANLK-YEILPKKN------VLKEVISLIKAKYS--GQ-SGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLA   69 (184)
Q Consensus         8 ~Nl~-y~v~~~~~------k~~~L~~~l~~~~~--~~-~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~   69 (184)
                      |+|. |+|.--++      ..+.|+.+|++...  +. +.||-..| -+++..++++...        .+++..+|-.-+
T Consensus       159 p~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R~~LklIimSAT-lda~kfS~yF~~a~i~~i~GR~fPVei~y~~~p  237 (674)
T KOG0922|consen  159 PLLSKYSVIILDEAHERSLHTDILLGLLKKILKKRPDLKLIIMSAT-LDAEKFSEYFNNAPILTIPGRTFPVEILYLKEP  237 (674)
T ss_pred             CccccccEEEEechhhhhhHHHHHHHHHHHHHhcCCCceEEEEeee-ecHHHHHHHhcCCceEeecCCCCceeEEeccCC
Confidence            4453 66654331      34555555554322  22 34444444 4588999999763        356666555433


Q ss_pred             HHH----HHHHHHH--HhccCceEEEEEeecccHHHHHHHHHhc------CCc--EEEeeCCCChHHHHHHHHHhhCCCc
Q psy437           70 DKL----RNEVQMK--WISNKVHVGHWTVVSKECDSVAAALAQE------RIN--AISYHAGLADKLRNEVQMKWISNKV  135 (184)
Q Consensus        70 ~~~----R~~~~~~--f~~g~~~vlVaT~tr~~~e~~a~gL~~~------gi~--~~vih~~~p~~~r~~~~~~f~~~~~  135 (184)
                      ..+    -..+.-+  .......|||+-.+..++|.++..|...      +++  .+.+|+.||......+-+.-..|.-
T Consensus       238 ~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~R  317 (674)
T KOG0922|consen  238 TADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKR  317 (674)
T ss_pred             chhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcc
Confidence            211    1111111  1134558999999999999988888433      221  2669999999998887777777888


Q ss_pred             eEEEE-------EecCCccEEEecCC------------------CCCccccccccccccCCcc
Q psy437          136 HLYNV-------WKIQWKRIIWIHSL------------------VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       136 ~v~va-------~D~~~vr~v~~~~~------------------p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|+++       .-||.|++|+.-..                  |-|..+-.||-  +|+||+
T Consensus       318 KvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRa--GRAGRt  378 (674)
T KOG0922|consen  318 KVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRA--GRAGRT  378 (674)
T ss_pred             eEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhc--ccCCCC
Confidence            88888       58899999976543                  33455556665  588886

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

Probab=85.71  E-value=6.1  Score=35.98  Aligned_cols=84  Identities=14%  Similarity=0.136  Sum_probs=60.2

Q ss_pred             CceEEEEEeecccHHHHHHHHHhc-----CCcEEEeeCCCChHH---------------------HHHHHHHhhC-CCce
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQE-----RINAISYHAGLADKL---------------------RNEVQMKWIS-NKVH  136 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~-----gi~~~vih~~~p~~~---------------------r~~~~~~f~~-~~~~  136 (184)
                      ..+.+|+|.++..|..+...|+..     +..+.|++++-+.+.                     ...+.+.|+. +.+.
T Consensus       514 ~~kamvv~~sr~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~  593 (667)
T TIGR00348       514 KFKAMVVAISRYACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPK  593 (667)
T ss_pred             cCceeEEEecHHHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCce
Confidence            367899999999999888887543     345678887755431                     1245566765 5666


Q ss_pred             EEEE-------EecCCccEEEecCCCCCccccccccccc
Q psy437          137 LYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDL  168 (184)
Q Consensus       137 v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~  168 (184)
                      |++.       ||.|.+..++..-+.++. ..+|-|.|+
T Consensus       594 ilIVvdmllTGFDaP~l~tLyldKplk~h-~LlQai~R~  631 (667)
T TIGR00348       594 LLIVVDMLLTGFDAPILNTLYLDKPLKYH-GLLQAIART  631 (667)
T ss_pred             EEEEEcccccccCCCccceEEEecccccc-HHHHHHHHh
Confidence            6665       799999999887776654 589999763

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

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=85.62  E-value=1  Score=31.39  Aligned_cols=38  Identities=13%  Similarity=0.161  Sum_probs=31.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCC--eeEEecCCCCH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERI--NAISYHAGLAD   70 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi--~~~~~hg~l~~   70 (184)
                      +..+.++||.+-..+...+..|...|+  ++..+.||+..
T Consensus        71 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~~  110 (122)
T cd01526          71 KDSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLKA  110 (122)
T ss_pred             CCCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHHH
Confidence            456788899998888889999999999  58889999753

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=84.50  E-value=7.5  Score=36.09  Aligned_cols=102  Identities=17%  Similarity=0.112  Sum_probs=65.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCC--c
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERI--N  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi--~  110 (184)
                      .+...-||++|...++.+++.....+.++..+.|.-+..+   + +.|  ++.+|+|||+      .+.-|++....  +
T Consensus       281 ~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d---v-~~W--~~~~VviYT~------~itvG~Sf~~~HF~  348 (824)
T PF02399_consen  281 AGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED---V-ESW--KKYDVVIYTP------VITVGLSFEEKHFD  348 (824)
T ss_pred             CCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc---c-ccc--cceeEEEEec------eEEEEeccchhhce
Confidence            4556678999999999999988888888888887655442   2 333  5689999999      66677765433  2


Q ss_pred             -EEEe--eCCCChHHHHHHHHHhhC---CCceEEEEEecCCc
Q psy437          111 -AISY--HAGLADKLRNEVQMKWIS---NKVHLYNVWKIQWK  146 (184)
Q Consensus       111 -~~vi--h~~~p~~~r~~~~~~f~~---~~~~v~va~D~~~v  146 (184)
                       .++|  ......+..+-+|-.++-   ..-.+++.+|-..+
T Consensus       349 ~~f~yvk~~~~gpd~~s~~Q~lgRvR~l~~~ei~v~~d~~~~  390 (824)
T PF02399_consen  349 SMFAYVKPMSYGPDMVSVYQMLGRVRSLLDNEIYVYIDASGA  390 (824)
T ss_pred             EEEEEecCCCCCCcHHHHHHHHHHHHhhccCeEEEEEecccc
Confidence             2223  122235566667766542   23366666555433

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

>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1

Probab=83.87  E-value=2.1  Score=28.09  Aligned_cols=36  Identities=17%  Similarity=0.138  Sum_probs=28.5

Q ss_pred             CCcEEEEecc--HHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           34 GQSGIVYCLT--RKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        34 ~~~~IIf~~t--r~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      ..+.++||.+  +..+...+..|.+.|+. +..+.||+.
T Consensus        50 ~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~   88 (92)
T cd01532          50 DTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ   88 (92)
T ss_pred             CCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence            5578889998  56677888999999984 777888874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.

>KOG0389|consensus

Probab=83.54  E-value=9.2  Score=35.45  Aligned_cols=63  Identities=14%  Similarity=0.097  Sum_probs=45.2

Q ss_pred             HHHhhcCCCcEEEEeccHHHHHHHHHHHHh--CCCeeEEecCCCCHHHHHHHHHHHhcc--CceEEEEEe
Q psy437           27 LIKAKYSGQSGIVYCLTRKECDSVAAALAQ--ERINAISYHAGLADKLRNEVQMKWISN--KVHVGHWTV   92 (184)
Q Consensus        27 ~l~~~~~~~~~IIf~~tr~~~e~la~~L~~--~gi~~~~~hg~l~~~~R~~~~~~f~~g--~~~vlVaT~   92 (184)
                      +|++...++|-+|.||+-. .+.+-..|.+  ..+.+..|||.  +++|..+-..+.++  ...||+.|=
T Consensus       441 yLkq~g~~gpHLVVvPsST-leNWlrEf~kwCPsl~Ve~YyGS--q~ER~~lR~~i~~~~~~ydVllTTY  507 (941)
T KOG0389|consen  441 YLKQIGNPGPHLVVVPSST-LENWLREFAKWCPSLKVEPYYGS--QDERRELRERIKKNKDDYDVLLTTY  507 (941)
T ss_pred             HHHHcCCCCCcEEEecchh-HHHHHHHHHHhCCceEEEeccCc--HHHHHHHHHHHhccCCCccEEEEEe
Confidence            3444445788899999744 3444444443  36889999996  68999998888876  678888775

>cd01535 4RHOD_Repeat_4 Member of the Rhodanese Homology Domain superfamily, repeat 4

Probab=83.39  E-value=4.1  Score=29.45  Aligned_cols=48  Identities=15%  Similarity=0.151  Sum_probs=35.5

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC-eeEEecCCCC
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI-NAISYHAGLA   69 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi-~~~~~hg~l~   69 (184)
                      ..|...+.......+.||+|.+-..+...+..|...|+ ++..+.||+.
T Consensus        37 ~~l~~~l~~l~~~~~vVv~c~~g~~a~~aa~~L~~~G~~~v~~L~GG~~   85 (145)
T cd01535          37 AQLAQALEKLPAAERYVLTCGSSLLARFAAADLAALTVKPVFVLEGGTA   85 (145)
T ss_pred             HHHHHHHHhcCCCCCEEEEeCCChHHHHHHHHHHHcCCcCeEEecCcHH
Confidence            34444454332346788999998888888999998888 6888999964

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative catalytic Cys residue.

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=83.24  E-value=5  Score=28.94  Aligned_cols=47  Identities=13%  Similarity=0.021  Sum_probs=33.1

Q ss_pred             CCCHHHHHHHHHHHhccCc-eEEEEEeecccHHHHHHHHHhcCCcE-EEeeCCCC
Q psy437           67 GLADKLRNEVQMKWISNKV-HVGHWTVVSKECDSVAAALAQERINA-ISYHAGLA  119 (184)
Q Consensus        67 ~l~~~~R~~~~~~f~~g~~-~vlVaT~tr~~~e~~a~gL~~~gi~~-~vih~~~p  119 (184)
                      +.+..+...++++|+...- .||++|.      .+++|+|.+|-.+ .|+=.++|
T Consensus        30 ~~~~~~~~~~l~~f~~~~~~~iL~~~~------~~~EGiD~~g~~~r~vii~glP   78 (141)
T smart00492       30 GEDGKETGKLLEKYVEACENAILLATA------RFSEGVDFPGDYLRAVIIDGLP   78 (141)
T ss_pred             CCChhHHHHHHHHHHHcCCCEEEEEcc------ceecceecCCCCeeEEEEEecC
Confidence            4455567888999987543 6899888      4688999887431 55556676

>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily

Probab=83.19  E-value=2.1  Score=29.05  Aligned_cols=38  Identities=21%  Similarity=0.183  Sum_probs=30.3

Q ss_pred             CCCcEEEEeccH--HHHHHHHHHHHhCCCeeEEecCCCCH
Q psy437           33 SGQSGIVYCLTR--KECDSVAAALAQERINAISYHAGLAD   70 (184)
Q Consensus        33 ~~~~~IIf~~tr--~~~e~la~~L~~~gi~~~~~hg~l~~   70 (184)
                      +..+.++||.+-  ..+..++..|...|+++..+.||+..
T Consensus        63 ~~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~~~  102 (110)
T cd01521          63 KEKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGLDW  102 (110)
T ss_pred             CCCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCHHH
Confidence            456788899865  36788889999999998889999743

This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.

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

Probab=83.08  E-value=4.7  Score=37.39  Aligned_cols=89  Identities=11%  Similarity=0.038  Sum_probs=54.6

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHHHhc-cCceEE-EEEeecccHHHHHHHHHh
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMKWIS-NKVHVG-HWTVVSKECDSVAAALAQ  106 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~f~~-g~~~vl-VaT~tr~~~e~~a~gL~~  106 (184)
                      .+++||||.+...|+.++..|.+.     |--+..+.|+-+  +-...++.|.. ...+-| |..+      .+..|.|.
T Consensus       426 ~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~--~~q~~Id~f~~ke~~P~Iaitvd------lL~TGiDv  497 (875)
T COG4096         426 IGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAE--QAQALIDNFIDKEKYPRIAITVD------LLTTGVDV  497 (875)
T ss_pred             cCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccch--hhHHHHHHHHhcCCCCceEEehh------hhhcCCCc
Confidence            468999999999999999999864     233555555533  33455666665 444444 4444      77777777


Q ss_pred             cCCcEEEeeCCCChHHHHHHHHHhh
Q psy437          107 ERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus       107 ~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      +-+-.+|+ .-.=.|.-.|.|-.++
T Consensus       498 pev~nlVF-~r~VrSktkF~QMvGR  521 (875)
T COG4096         498 PEVVNLVF-DRKVRSKTKFKQMVGR  521 (875)
T ss_pred             hheeeeee-hhhhhhHHHHHHHhcC
Confidence            77653333 3333344445555544

>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2

Probab=83.06  E-value=1.8  Score=28.81  Aligned_cols=37  Identities=16%  Similarity=0.260  Sum_probs=31.0

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCCH
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLAD   70 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~~   70 (184)
                      ..+.++||.+-..+...+..|.+.|+. +..+.||+..
T Consensus        58 ~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~~   95 (101)
T cd01528          58 DKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGIDA   95 (101)
T ss_pred             CCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHHH
Confidence            567889999988888899999999995 7788998754

Subgroup 2 includes uncharacterized putative rhodanese-related domains.

>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily

Probab=83.05  E-value=18  Score=27.44  Aligned_cols=15  Identities=7%  Similarity=-0.144  Sum_probs=7.6

Q ss_pred             cHHHHHHHHHhcCCc
Q psy437           96 ECDSVAAALAQERIN  110 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~  110 (184)
                      ....++..|...|..
T Consensus       103 ~g~~~~~~l~~~g~~  117 (264)
T cd06267         103 GAYLAVEHLIELGHR  117 (264)
T ss_pred             HHHHHHHHHHHCCCc
Confidence            344555566554543

Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=83.02  E-value=2  Score=28.24  Aligned_cols=36  Identities=25%  Similarity=0.151  Sum_probs=29.1

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      ..+.++||.+-..+...+..|...|+.+..+.||+.
T Consensus        56 ~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~~   91 (95)
T cd01534          56 GARIVLADDDGVRADMTASWLAQMGWEVYVLEGGLA   91 (95)
T ss_pred             CCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcHH
Confidence            456888999876677888899999999777888874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators

Probab=82.91  E-value=19  Score=27.60  Aligned_cols=60  Identities=15%  Similarity=0.042  Sum_probs=28.0

Q ss_pred             HHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE------------EeecccHHHHHHHHHhcCCc
Q psy437           49 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW------------TVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        49 ~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa------------T~tr~~~e~~a~gL~~~gi~  110 (184)
                      .+.+.|...++....+.......  ...++.+....+++++.            ++.......++..|...|.+
T Consensus        46 ~~~~~l~~~~vdgiii~~~~~~~--~~~~~~~~~~~ipvV~~~~~~~~~~~~v~~d~~~~g~~~~~~l~~~g~~  117 (266)
T cd06282          46 DAVETLLRQRVDGLILTVADAAT--SPALDLLDAERVPYVLAYNDPQPGRPSVSVDNRAAARDVAQALAALGHR  117 (266)
T ss_pred             HHHHHHHhcCCCEEEEecCCCCc--hHHHHHHhhCCCCEEEEeccCCCCCCEEeeCcHHHHHHHHHHHHHcCcc
Confidence            44455555566655554332211  12344444444444322            22223456666677666655

This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding

>PRK09189 uroporphyrinogen-III synthase; Validated

Probab=82.90  E-value=5.4  Score=31.10  Aligned_cols=84  Identities=10%  Similarity=-0.050  Sum_probs=51.6

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCee---EEecCCCCHHHHHHHHHHHhccCceEEEEEeeccc
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINA---ISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKE   96 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~---~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~   96 (184)
                      .-+.|.+.+.........|+|......-+.+.+.|.+.|+.+   .+|.-...........+.|..++..++++|++. .
T Consensus       103 ~~e~L~~~~~~~~~~~~~vL~~rg~~~r~~l~~~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~i~f~S~~-~  181 (240)
T PRK09189        103 DGVRLAETVAAALAPTARLLYLAGRPRAPVFEDRLAAAGIPFRVAECYDMLPVMYSPATLSAILGGAPFDAVLLYSRV-A  181 (240)
T ss_pred             CHHHHHHHHHHhcCCCCcEEEeccCcccchhHHHHHhCCCeeEEEEEEEeecCCCChHHHHHHHhcCCCCEEEEeCHH-H
Confidence            345666666543223344555545555688999999998764   446443333334466777888889999999865 3


Q ss_pred             HHHHHHHH
Q psy437           97 CDSVAAAL  104 (184)
Q Consensus        97 ~e~~a~gL  104 (184)
                      ++.....+
T Consensus       182 ~~~f~~~~  189 (240)
T PRK09189        182 ARRFFALM  189 (240)
T ss_pred             HHHHHHHH
Confidence            44444433

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=82.20  E-value=4.3  Score=27.65  Aligned_cols=37  Identities=19%  Similarity=0.200  Sum_probs=30.2

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +..+.|+||.+-..+...+..|...|++ +..|-||+.
T Consensus        77 ~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~~  114 (118)
T cd01449          77 PDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSWS  114 (118)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChHH
Confidence            4567888999977888899999999985 777888863

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=81.98  E-value=1.8  Score=28.79  Aligned_cols=37  Identities=19%  Similarity=0.494  Sum_probs=29.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +..+.||||.+-..+...+..|...|+. +..+.||+.
T Consensus        60 ~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          60 KGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             CCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence            4567888999877777888899999995 777888864

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=81.95  E-value=3.5  Score=39.28  Aligned_cols=89  Identities=17%  Similarity=-0.016  Sum_probs=68.9

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----EecCC--------ccEE
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----WKIQW--------KRII  149 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----~D~~~--------vr~v  149 (184)
                      ..-+|||.|.+-...|.+++.|...||+.-|+|+-.-...-.-+-+..+.|.++|-.-     -||.-        ==+|
T Consensus       627 ~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~AG~~GaVTIATNMAGRGTDIkLg~~V~e~GGL~V  706 (1112)
T PRK12901        627 AGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAEAGQPGTVTIATNMAGRGTDIKLSPEVKAAGGLAI  706 (1112)
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHhcCCCCcEEEeccCcCCCcCcccchhhHHcCCCEE
Confidence            3457999999999999999999999999889999877777777777788887666553     26642        2467


Q ss_pred             EecCCCCCccccccccccccCCcc
Q psy437          150 WIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       150 ~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |-...+.|  .-+-+.|++|+||-
T Consensus       707 IgTerheS--rRID~QLrGRaGRQ  728 (1112)
T PRK12901        707 IGTERHES--RRVDRQLRGRAGRQ  728 (1112)
T ss_pred             EEccCCCc--HHHHHHHhcccccC
Confidence            77777665  35667788999996

>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase

Probab=81.49  E-value=6.1  Score=26.41  Aligned_cols=67  Identities=16%  Similarity=0.129  Sum_probs=45.3

Q ss_pred             EEEeccHHHHHHHHHHHHhCCCeeEEecCCCCH------------HHHHHHHHHHhccCceEEEEEeecccHHHHHHHH
Q psy437           38 IVYCLTRKECDSVAAALAQERINAISYHAGLAD------------KLRNEVQMKWISNKVHVGHWTVVSKECDSVAAAL  104 (184)
Q Consensus        38 IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~------------~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL  104 (184)
                      |+.+-....+..+++.|...+..+....|-+-.            ....+.+.+...+--.|++|||.-.+=|.+|..+
T Consensus         2 liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i   80 (100)
T PF01751_consen    2 LIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEI   80 (100)
T ss_dssp             EEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHH
T ss_pred             EEEEeCHHHHHHHHHHcCCCCEEEEEeCCcccccccccccccccccccchhhHHHhhhccEeeecCCCChHHHHHHHHH
Confidence            677888888888888887444566666664432            1235556666566678999999887777777655

This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=81.40  E-value=2.7  Score=27.73  Aligned_cols=37  Identities=22%  Similarity=0.222  Sum_probs=29.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCC-eeEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERI-NAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi-~~~~~hg~l~   69 (184)
                      +..+.++||++-..+...+..|.+.|+ ++..+.||++
T Consensus        53 ~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~~   90 (99)
T cd01527          53 GANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGLD   90 (99)
T ss_pred             CCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCHH
Confidence            345788899998778888999998888 4767899864

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]

Probab=81.30  E-value=5.7  Score=31.28  Aligned_cols=65  Identities=11%  Similarity=0.052  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHhCCCeeEEecCCCCHH-----HH-HHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCc
Q psy437           45 KECDSVAAALAQERINAISYHAGLADK-----LR-NEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERIN  110 (184)
Q Consensus        45 ~~~e~la~~L~~~gi~~~~~hg~l~~~-----~R-~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~  110 (184)
                      +....-...|.+.|+.-..+.|||++.     .| ...+..++....-.+.|--.+.+ |..++.|...+++
T Consensus        42 ~~l~k~~~el~kkGy~g~llSGGm~srg~VPl~kf~d~lK~lke~~~l~inaHvGfvd-E~~~eklk~~~vd  112 (275)
T COG1856          42 KSLLKRCMELEKKGYEGCLLSGGMDSRGKVPLWKFKDELKALKERTGLLINAHVGFVD-ESDLEKLKEELVD  112 (275)
T ss_pred             HHHHHHHHHHHhcCceeEEEeCCcCCCCCccHHHHHHHHHHHHHhhCeEEEEEeeecc-HHHHHHHHHhcCc
Confidence            333344456777899999999999852     22 23344444333334555555555 6777777777776

>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily

Probab=80.97  E-value=2.2  Score=28.45  Aligned_cols=36  Identities=14%  Similarity=0.159  Sum_probs=29.7

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      ..+.|+||.+-..+...+..|...|+. +..+.||+.
T Consensus        66 ~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~~  102 (106)
T cd01519          66 DKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSWL  102 (106)
T ss_pred             CCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcHH
Confidence            457888999988888899999999985 677888864

This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=80.83  E-value=2.3  Score=28.76  Aligned_cols=37  Identities=16%  Similarity=0.179  Sum_probs=29.7

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCe--eEEecCCCCH
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERIN--AISYHAGLAD   70 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~--~~~~hg~l~~   70 (184)
                      ..+.++||.+-..+...+..|...|+.  +..+.||++.
T Consensus        66 ~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~~  104 (109)
T cd01533          66 RTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQG  104 (109)
T ss_pred             CCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHHH
Confidence            457888998877777788999999994  7778999753

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

>KOG0923|consensus

Probab=80.61  E-value=5.1  Score=36.43  Aligned_cols=145  Identities=9%  Similarity=0.075  Sum_probs=87.2

Q ss_pred             EEEEEEccC------hHHHHHHHHHhhc--CCCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHHH-H
Q psy437           11 KYEILPKKN------VLKEVISLIKAKY--SGQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADKL-R   73 (184)
Q Consensus        11 ~y~v~~~~~------k~~~L~~~l~~~~--~~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~~-R   73 (184)
                      .|+|.-.+.      ..+.|..++++..  .+.--++..+-.-+|+.....|...        .+++..++-.-+..+ -
T Consensus       378 sYSViiiDEAHERTL~TDILfgLvKDIar~RpdLKllIsSAT~DAekFS~fFDdapIF~iPGRRyPVdi~Yt~~PEAdYl  457 (902)
T KOG0923|consen  378 SYSVIIVDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAEKFSAFFDDAPIFRIPGRRYPVDIFYTKAPEADYL  457 (902)
T ss_pred             ceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcceEEeeccccCHHHHHHhccCCcEEeccCcccceeeecccCCchhHH
Confidence            377765432      4455666665432  2222334444445688888888653        345655554433221 1


Q ss_pred             HHHHHHHh-----ccCceEEEEEeecccHHHHHHHH-------Hh--cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEE
Q psy437           74 NEVQMKWI-----SNKVHVGHWTVVSKECDSVAAAL-------AQ--ERINAISYHAGLADKLRNEVQMKWISNKVHLYN  139 (184)
Q Consensus        74 ~~~~~~f~-----~g~~~vlVaT~tr~~~e~~a~gL-------~~--~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~v  139 (184)
                      ..++....     +--..|||+-....+.|.+..-|       ..  +.+-++-||+++|++...-+-+--..|.-.|++
T Consensus       458 dAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVL  537 (902)
T KOG0923|consen  458 DAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVL  537 (902)
T ss_pred             HHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEE
Confidence            11222211     11246888888777665555444       22  234358899999999988888777888889999


Q ss_pred             E-------EecCCccEEEecCCC
Q psy437          140 V-------WKIQWKRIIWIHSLV  155 (184)
Q Consensus       140 a-------~D~~~vr~v~~~~~p  155 (184)
                      |       +-|++|.+||.-...
T Consensus       538 ATNIAETSlTIdgI~yViDpGf~  560 (902)
T KOG0923|consen  538 ATNIAETSLTIDGIKYVIDPGFV  560 (902)
T ss_pred             eecchhhceeecCeEEEecCccc
Confidence            9       589999999865443

>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems

Probab=80.29  E-value=25  Score=27.30  Aligned_cols=74  Identities=18%  Similarity=0.115  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeeccc-HHHHHHHHHhcCCcEEEeeCCCC
Q psy437           46 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKE-CDSVAAALAQERINAISYHAGLA  119 (184)
Q Consensus        46 ~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~-~e~~a~gL~~~gi~~~vih~~~p  119 (184)
                      ..+.+.+.+++.|+.+..+.+.-+.+...+.++.+....+..||..+...+ ++.....+...++++..++.+++
T Consensus        17 ~~~~~~~~a~~~g~~~~~~~~~~~~~~~~~~i~~l~~~~vdgiIi~~~~~~~~~~~i~~~~~~~iPvV~~~~~~~   91 (273)
T cd06309          17 ETKSIKDAAEKRGFDLKFADAQQKQENQISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRGVD   91 (273)
T ss_pred             HHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEcCCccccchHHHHHHHHCCCCEEEEecCcC
Confidence            344555666677888877765545555556777777777777766654433 23444556777888666765543

Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=80.24  E-value=5.8  Score=36.47  Aligned_cols=89  Identities=16%  Similarity=-0.020  Sum_probs=70.4

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----EecCC----------c-
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----WKIQW----------K-  146 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----~D~~~----------v-  146 (184)
                      ..-+|||.|.+-.+.|.++..|...||+..|+|+.-....-.-+.+..+.|.+.|-.-     -||.-          | 
T Consensus       426 ~GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk~~~~EA~IIa~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~  505 (764)
T PRK12326        426 TGQPVLVGTHDVAESEELAERLRAAGVPAVVLNAKNDAEEARIIAEAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVA  505 (764)
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccCchHhHHHHHHhcCCCCcEEEEecCCCCccCeecCCCcccchHHHH
Confidence            4457999999999999999999999999999999877777777778888887666554     25542          2 


Q ss_pred             ----cEEEecCCCCCccccccccccccCCcc
Q psy437          147 ----RIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       147 ----r~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                          =+||-...|.|.  -+.+.|++|+||-
T Consensus       506 ~~GGLhVIgTerheSr--RID~QLrGRaGRQ  534 (764)
T PRK12326        506 ELGGLHVIGTGRHRSE--RLDNQLRGRAGRQ  534 (764)
T ss_pred             HcCCcEEEeccCCchH--HHHHHHhcccccC
Confidence                377877777765  6777888999996

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	184
2v1x_A	591	Crystal Structure Of Human Recq-Like Dna Helicase L		5e-14
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		4e-11
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		2e-10

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 59/96 (61%), Gaps = 4/96 (4%)
Query: 1   FISSFNRANLKYEILPK----KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ 56
           F +SFNR NL YE+  K    ++ +++++ LI  +Y GQSGI+YC ++K+ + V  +L  
Sbjct: 230 FTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQN 289
Query: 57  ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV 92
             I+A +YHA L  + +  V  KW +N++ V   TV
Sbjct: 290 LGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV 325

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 58/91 (63%), Gaps = 1/91 (1%)
Query: 2   ISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINA 61
           ISSF+R N++Y ++ K   L +++  ++ +  G+SGI+YC +R + +  AA L  + I+A
Sbjct: 205 ISSFDRPNIRYMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISA 263
Query: 62  ISYHAGLADKLRNEVQMKWISNKVHVGHWTV 92
            +YHAGL + +R +VQ K+  + + +   TV
Sbjct: 264 AAYHAGLENNVRADVQEKFQRDDLQIVVATV 294

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 56/91 (61%), Gaps = 1/91 (1%)
Query: 2   ISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINA 61
           ISSF+R N++Y +  K   L ++   ++ +  G+SGI+YC +R + +  AA L  + I+A
Sbjct: 205 ISSFDRPNIRYXLXEKFKPLDQLXRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISA 263
Query: 62  ISYHAGLADKLRNEVQMKWISNKVHVGHWTV 92
            +YHAGL + +R +VQ K+  + + +   TV
Sbjct: 264 AAYHAGLENNVRADVQEKFQRDDLQIVVATV 294

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	184
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	7e-37
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	5e-29

>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 =  133 bits (336), Expect = 7e-37
 Identities = 34/91 (37%), Positives = 57/91 (62%), Gaps = 4/91 (4%)

Query: 1   FISSFNRANLKYEILPK----KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ 56
           F +SFNR NL YE+  K    ++ +++++ LI  +Y GQSGI+YC ++K+ + V  +L  
Sbjct: 230 FTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQN 289

Query: 57  ERINAISYHAGLADKLRNEVQMKWISNKVHV 87
             I+A +YHA L  + +  V  KW +N++ V
Sbjct: 290 LGIHAGAYHANLEPEDKTTVHRKWSANEIQV 320

>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 =  110 bits (278), Expect = 5e-29
 Identities = 30/87 (34%), Positives = 56/87 (64%), Gaps = 1/87 (1%)

Query: 1   FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN 60
            ISSF+R N++Y ++ K   L +++  ++ +  G+SGI+YC +R + +  AA L  + I+
Sbjct: 204 QISSFDRPNIRYMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGIS 262

Query: 61  AISYHAGLADKLRNEVQMKWISNKVHV 87
           A +YHAGL + +R +VQ K+  + + +
Sbjct: 263 AAAYHAGLENNVRADVQEKFQRDDLQI 289

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	184
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.87
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.87
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.86
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.84
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.84
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.84
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.84
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.83
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.82
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.81
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.68
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.77
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.75
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.74
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.73
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.69
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.68
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.68
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.67
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.67
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.66
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.66
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.65
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.64
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.63
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.63
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.62
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.62
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.61
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.61
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.61
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.6
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.6
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.6
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.59
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.58
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.58
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.58
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.57
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.56
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.55
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.55
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.55
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.55
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.54
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.53
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.53
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.52
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.52
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.52
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.51
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.51
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.5
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.5
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.49
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.21
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.47
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.46
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.45
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.45
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.45
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.44
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.44
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.43
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.42
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.41
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.4
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.39
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.39
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.38
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.38
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.37
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.37
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.37
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.36
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.36
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.35
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.35
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.34
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.33
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.33
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.32
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.32
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.32
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.32
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.3
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.29
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.28
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.27
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.27
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.26
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.25
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.24
3h1t_A	590	Type I site-specific restriction-modification syst	99.24
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.23
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.23
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.2
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.17
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.16
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.16
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.15
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.14
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.13
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.12
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.12
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.12
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.12
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.1
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.09
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.09
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.08
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.08
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.07
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.05
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.05
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.04
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.02
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	98.99
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	98.98
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.93
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.93
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.84
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.83
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.81
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.71
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.7
3h1t_A	590	Type I site-specific restriction-modification syst	98.7
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.5
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.48
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	98.33
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.11
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	97.99
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	97.94
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	97.93
2l82_A	162	Designed protein OR32; structural genomics, northe	97.92
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	97.67
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	97.35
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	97.24
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	96.59
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	96.03
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	95.55
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	95.48
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	95.37
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	95.05
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	94.92
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	94.7
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	94.57
3bor_A	237	Human initiation factor 4A-II; translation initiat	94.32
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	94.16
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	93.88
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	93.55
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	93.53
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	93.16
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	92.85
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	92.61
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	91.86
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	91.69
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	91.62
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	90.27
2jtq_A	85	Phage shock protein E; solution structure rhodanes	90.06
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	89.67
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	88.92
3ipz_A	109	Monothiol glutaredoxin-S14, chloroplastic; electro	88.85
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	88.68
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	88.16
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	87.85
3zyw_A	111	Glutaredoxin-3; metal binding protein; 1.84A {Homo	87.76
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	87.54
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	87.47
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	87.34
3b6e_A	216	Interferon-induced helicase C domain-containing P;	87.19
3jy6_A	276	Transcriptional regulator, LACI family; NYSGXRC, P	87.16
3ipz_A	109	Monothiol glutaredoxin-S14, chloroplastic; electro	86.89
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	85.49
3h75_A	350	Periplasmic sugar-binding domain protein; protein	85.14
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	84.91
2yan_A	105	Glutaredoxin-3; oxidoreductase; HET: GSH; 1.90A {H	84.84
3l49_A	291	ABC sugar (ribose) transporter, periplasmic substr	84.59
3o74_A	272	Fructose transport system repressor FRUR; dual tra	84.56
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	84.31
3tb6_A	298	Arabinose metabolism transcriptional repressor; tr	84.27
3m9w_A	313	D-xylose-binding periplasmic protein; xylose bindi	83.3
3gx8_A	121	Monothiol glutaredoxin-5, mitochondrial; TRX fold,	82.72
3uug_A	330	Multiple sugar-binding periplasmic receptor CHVE;	82.53
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	82.08
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	81.75
2xw6_A	134	MGS, methylglyoxal synthase; lyase; 1.08A {Thermus	81.08
1tq1_A	129	AT5G66040, senescence-associated family protein; C	80.99
3l6u_A	293	ABC-type sugar transport system periplasmic compo;	80.65

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

Probab=99.87  E-value=1.4e-21  Score=144.15  Aligned_cols=125  Identities=14%  Similarity=0.190  Sum_probs=109.0

Q ss_pred             CCCCCCCCeEEEEE--EccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHH
Q psy437            2 ISSFNRANLKYEIL--PKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMK   79 (184)
Q Consensus         2 ~~s~~R~Nl~y~v~--~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~   79 (184)
                      .++..++||...+.  +...|...|.+++... .+.++||||+|+..++.+++.|...|+++..+||+|++.+|..+++.
T Consensus         2 ~~~~~~~~i~~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~   80 (163)
T 2hjv_A            2 AAGLTTRNIEHAVIQVREENKFSLLKDVLMTE-NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNE   80 (163)
T ss_dssp             ----CCCCEEEEEEECCGGGHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH
T ss_pred             CcccCcccceEEEEECChHHHHHHHHHHHHhc-CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHH
Confidence            35678899864444  4457999999999765 67899999999999999999999999999999999999999999999


Q ss_pred             HhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           80 WISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        80 f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |++|+.+|||+|+      .+++|+|.++++ .|+|+++|.+...|+|+..+.|.
T Consensus        81 f~~g~~~vlv~T~------~~~~Gld~~~~~-~Vi~~~~p~~~~~~~qr~GR~~R  128 (163)
T 2hjv_A           81 FKRGEYRYLVATD------VAARGIDIENIS-LVINYDLPLEKESYVHRTGRTGR  128 (163)
T ss_dssp             HHTTSCSEEEECG------GGTTTCCCSCCS-EEEESSCCSSHHHHHHHTTTSSC
T ss_pred             HHcCCCeEEEECC------hhhcCCchhcCC-EEEEeCCCCCHHHHHHhccccCc
Confidence            9999999999999      778899999999 99999999999999999976543

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.87  E-value=9.7e-22  Score=169.40  Aligned_cols=125  Identities=27%  Similarity=0.501  Sum_probs=115.5

Q ss_pred             CCCCCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHh
Q psy437            2 ISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus         2 ~~s~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~   81 (184)
                      ..+++|||+.|.+.+...+...|.+++.+. .+.++||||+|++.++.+++.|.+.|+.+..|||+|++++|..+++.|.
T Consensus       205 ~~~~~r~~l~~~v~~~~~~~~~l~~~l~~~-~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~  283 (523)
T 1oyw_A          205 ISSFDRPNIRYMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQ  283 (523)
T ss_dssp             ECCCCCTTEEEEEEECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             eCCCCCCceEEEEEeCCCHHHHHHHHHHhc-CCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHH
Confidence            468899999999999988999999999764 6779999999999999999999999999999999999999999999999


Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +|+.+|||||++.      +.|+|.++++ .|+|+++|.+.+.|+|+..|.|.
T Consensus       284 ~g~~~vlVaT~a~------~~GiD~p~v~-~VI~~~~p~s~~~y~Qr~GRaGR  329 (523)
T 1oyw_A          284 RDDLQIVVATVAF------GMGINKPNVR-FVVHFDIPRNIESYYQETGRAGR  329 (523)
T ss_dssp             TTSCSEEEECTTS------CTTTCCTTCC-EEEESSCCSSHHHHHHHHTTSCT
T ss_pred             cCCCeEEEEechh------hCCCCccCcc-EEEEECCCCCHHHHHHHhccccC
Confidence            9999999999944      6699999999 99999999999999999977653

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.86  E-value=1.2e-21  Score=170.97  Aligned_cols=126  Identities=30%  Similarity=0.546  Sum_probs=111.7

Q ss_pred             CCCCCCCCeEEEEEEccC----hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            2 ISSFNRANLKYEILPKKN----VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         2 ~~s~~R~Nl~y~v~~~~~----k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      ..+++|||++|.+.....    +...|.+++.+...+.++||||+|++.++.+++.|...|+.+..|||+|++++|..++
T Consensus       231 ~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~  310 (591)
T 2v1x_A          231 TASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVH  310 (591)
T ss_dssp             ECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             ecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHH
Confidence            468999999999997653    5567777775544678999999999999999999999999999999999999999999


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++|++|+.+|||||++.      +.|+|+++++ +|||+++|.+.+.|+|+..|.|.
T Consensus       311 ~~F~~g~~~VlVAT~a~------~~GID~p~V~-~VI~~~~p~s~~~y~Qr~GRaGR  360 (591)
T 2v1x_A          311 RKWSANEIQVVVATVAF------GMGIDKPDVR-FVIHHSMSKSMENYYQESGRAGR  360 (591)
T ss_dssp             HHHHTTSSSEEEECTTS------CTTCCCSCEE-EEEESSCCSSHHHHHHHHTTSCT
T ss_pred             HHHHcCCCeEEEEechh------hcCCCccccc-EEEEeCCCCCHHHHHHHhccCCc
Confidence            99999999999999944      6699999999 99999999999999999977653

>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=99.84  E-value=4.3e-21  Score=142.88  Aligned_cols=114  Identities=14%  Similarity=0.214  Sum_probs=104.0

Q ss_pred             EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      |..++...|...|.+++... ...++||||+|+..++.++..|...|+++..+||+|++.+|..+++.|++|+.++||||
T Consensus        10 ~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT   88 (172)
T 1t5i_A           10 YVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVAT   88 (172)
T ss_dssp             EEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEES
T ss_pred             EEECChHHHHHHHHHHHHhC-CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEEC
Confidence            44455667999999999764 67899999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +      .+++|+|.++++ .|+|+++|.+...|+|+..+.|
T Consensus        89 ~------~~~~Gldi~~~~-~Vi~~d~p~~~~~~~qr~GR~~  123 (172)
T 1t5i_A           89 N------LFGRGMDIERVN-IAFNYDMPEDSDTYLHRVARAG  123 (172)
T ss_dssp             S------CCSTTCCGGGCS-EEEESSCCSSHHHHHHHHHHHT
T ss_pred             C------chhcCcchhhCC-EEEEECCCCCHHHHHHHhcccc
Confidence            9      668899999999 9999999999999999996543

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

Probab=99.84  E-value=7.1e-20  Score=135.15  Aligned_cols=115  Identities=12%  Similarity=0.200  Sum_probs=95.3

Q ss_pred             EEEEEEccC-hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEE
Q psy437           11 KYEILPKKN-VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGH   89 (184)
Q Consensus        11 ~y~v~~~~~-k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlV   89 (184)
                      +|..++... |...|.+++... ...++||||+|++.++.++..|...|+.+..+||+|++.+|..+++.|++|+.++||
T Consensus         7 ~~~~~~~~~~K~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv   85 (165)
T 1fuk_A            7 FYVNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILI   85 (165)
T ss_dssp             EEEEEESGGGHHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEE
T ss_pred             EEEECCcchhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEE
Confidence            355556556 999999998764 778999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           90 WTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        90 aT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +|+      .+++|+|.++++ .|+|+++|.+..+|+|+..+.|
T Consensus        86 ~T~------~~~~G~d~~~~~-~Vi~~~~p~~~~~~~qr~GR~g  122 (165)
T 1fuk_A           86 STD------LLARGIDVQQVS-LVINYDLPANKENYIHRIGRGG  122 (165)
T ss_dssp             EEG------GGTTTCCCCSCS-EEEESSCCSSGGGGGGSSCSCC
T ss_pred             EcC------hhhcCCCcccCC-EEEEeCCCCCHHHHHHHhcccc
Confidence            999      556677666666 6666666666666666665443

>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=99.84  E-value=2.2e-20  Score=140.64  Aligned_cols=122  Identities=17%  Similarity=0.182  Sum_probs=95.0

Q ss_pred             CCCCeEEEE--EEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437            6 NRANLKYEI--LPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus         6 ~R~Nl~y~v--~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      ..+||...+  ++...|...|.++|....+..++||||+|+..++.++..|...|+++..+||+|++.+|..+++.|++|
T Consensus        16 ~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g   95 (185)
T 2jgn_A           16 TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG   95 (185)
T ss_dssp             CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHT
T ss_pred             CCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcC
Confidence            467886444  445579999999997643567899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +.+|||+|+      .+++|+|.++++ .|+++++|.+...|+|+..+.|.
T Consensus        96 ~~~vLvaT~------~~~~Gldi~~~~-~VI~~d~p~s~~~~~Qr~GR~~R  139 (185)
T 2jgn_A           96 KSPILVATA------VAARGLDISNVK-HVINFDLPSDIEEYVHRIGRTGR  139 (185)
T ss_dssp             SSSEEEEEC------------CCCSBS-EEEESSCCSSHHHHHHHHTTBCC
T ss_pred             CCeEEEEcC------hhhcCCCcccCC-EEEEeCCCCCHHHHHHHccccCC
Confidence            999999999      889999999999 99999999999999999976543

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

Probab=99.84  E-value=1.8e-20  Score=141.89  Aligned_cols=119  Identities=12%  Similarity=0.154  Sum_probs=106.4

Q ss_pred             CCCeEEEE--EEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC
Q psy437            7 RANLKYEI--LPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK   84 (184)
Q Consensus         7 R~Nl~y~v--~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~   84 (184)
                      .+|+...+  ++...|...|.++|.+  .+.++||||+|+..++.+++.|...|+++..+||+|++.+|..+++.|++|+
T Consensus        27 ~~~i~q~~~~~~~~~K~~~L~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~  104 (191)
T 2p6n_A           27 SLDVIQEVEYVKEEAKMVYLLECLQK--TPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGK  104 (191)
T ss_dssp             -CCSEEEEEECCGGGHHHHHHHHHTT--SCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             CcCceEEEEEcChHHHHHHHHHHHHh--CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCC
Confidence            46665443  3455799999998865  4568999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+|||+|+      .+++|+|.++++ .|+|+++|.+...|+|+..+.|.
T Consensus       105 ~~vLvaT~------~~~~Gldi~~v~-~VI~~d~p~~~~~~~qr~GR~gR  147 (191)
T 2p6n_A          105 KDVLVATD------VASKGLDFPAIQ-HVINYDMPEEIENYVHRIGRTGC  147 (191)
T ss_dssp             CSEEEECH------HHHTTCCCCCCS-EEEESSCCSSHHHHHHHHTTSCC
T ss_pred             CEEEEEcC------chhcCCCcccCC-EEEEeCCCCCHHHHHHHhCcccc
Confidence            99999999      889999999999 99999999999999999987664

>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=99.83  E-value=2.1e-20  Score=143.62  Aligned_cols=113  Identities=19%  Similarity=0.199  Sum_probs=104.0

Q ss_pred             EEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           14 ILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        14 v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      ..+...|+..|.+++... .+.++||||+|+..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+ 
T Consensus        12 ~~~~~~k~~~l~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-   89 (212)
T 3eaq_A           12 PAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-   89 (212)
T ss_dssp             ECCTTSHHHHHHHHHHHH-CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-
T ss_pred             eCCHHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-
Confidence            344567999999999764 778999999999999999999999999999999999999999999999999999999999 


Q ss_pred             cccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           94 SKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        94 r~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                           .+++|+|.++++ +|+|+|+|.+...|+|+.++.|.
T Consensus        90 -----~~~~Gidi~~v~-~Vi~~~~p~~~~~~~qr~GR~gR  124 (212)
T 3eaq_A           90 -----VAARGLDIPQVD-LVVHYRLPDRAEAYQHRSGRTGR  124 (212)
T ss_dssp             -----TTTCSSSCCCBS-EEEESSCCSSHHHHHHHHTTBCC
T ss_pred             -----hhhcCCCCccCc-EEEECCCCcCHHHHHHHhcccCC
Confidence                 778999999999 99999999999999999977653

>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=99.82  E-value=4.6e-20  Score=137.40  Aligned_cols=119  Identities=12%  Similarity=0.161  Sum_probs=103.6

Q ss_pred             CCeEEEEE--EccC-hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC
Q psy437            8 ANLKYEIL--PKKN-VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK   84 (184)
Q Consensus         8 ~Nl~y~v~--~~~~-k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~   84 (184)
                      +||...+.  +... |...|.+++... ...++||||+|+..++.++..|...|+.+..+||+|++.+|..+++.|++|+
T Consensus         6 ~~i~q~~~~~~~~~~K~~~L~~ll~~~-~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~   84 (175)
T 2rb4_A            6 NNIRQYYVLCEHRKDKYQALCNIYGSI-TIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGK   84 (175)
T ss_dssp             CCEEEEEEECSSHHHHHHHHHHHHTTS-CCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTS
T ss_pred             CCceEEEEEcCChHhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCC
Confidence            46653333  3333 889999888653 6778999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCC------hHHHHHHHHHhhCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLA------DKLRNEVQMKWISNK  134 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p------~~~r~~~~~~f~~~~  134 (184)
                      .++||||+      .+++|+|.++++ .|+|+++|      .+..+|+|+.++.|.
T Consensus        85 ~~vLvaT~------~~~~Gid~~~~~-~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR  133 (175)
T 2rb4_A           85 EKVLITTN------VCARGIDVKQVT-IVVNFDLPVKQGEEPDYETYLHRIGRTGR  133 (175)
T ss_dssp             CSEEEECC------SCCTTTCCTTEE-EEEESSCCC--CCSCCHHHHHHHHCBC--
T ss_pred             CeEEEEec------chhcCCCcccCC-EEEEeCCCCCccccCCHHHHHHHhccccc
Confidence            99999999      668899999999 99999999      999999999977654

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

Probab=99.81  E-value=9.8e-20  Score=146.86  Aligned_cols=115  Identities=17%  Similarity=0.179  Sum_probs=105.0

Q ss_pred             EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      |..++...|+..|.+++... .+.++||||+|+..++.++..|...|+.+..+||+|++.+|..+++.|++|+.+|||||
T Consensus         7 ~i~~~~~~K~~~L~~ll~~~-~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT   85 (300)
T 3i32_A            7 AVPAPVRGRLEVLSDLLYVA-SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVAT   85 (300)
T ss_dssp             EEECCSSSHHHHHHHHHHHH-CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEEC
T ss_pred             EEECCHHHHHHHHHHHHHhc-CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEe
Confidence            44445567999999999765 68899999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +      .+++|+|.++++ +|||+|+|.+...|+|+.++.|.
T Consensus        86 ~------va~~Gidi~~v~-~VI~~d~p~s~~~y~Qr~GRagR  121 (300)
T 3i32_A           86 D------VAARGLDIPQVD-LVVHYRMPDRAEAYQHRSGRTGR  121 (300)
T ss_dssp             S------TTTCSTTCCCCS-EEEESSCCSSTTHHHHHHTCCC-
T ss_pred             c------hhhcCcccccee-EEEEcCCCCCHHHHHHHccCcCc
Confidence            9      778999999999 99999999999999999977653

>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=99.68  E-value=4e-21  Score=142.61  Aligned_cols=119  Identities=14%  Similarity=0.125  Sum_probs=105.8

Q ss_pred             CCCeEEE--EEEc-cChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437            7 RANLKYE--ILPK-KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus         7 R~Nl~y~--v~~~-~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      |+||.+.  .++. ..|...|.+++... .+.++||||+|+..++.+++.|...|+.+..+||+|++.+|..+++.|++|
T Consensus         1 R~~i~~~~~~~~~~~~k~~~l~~ll~~~-~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g   79 (170)
T 2yjt_D            1 RKKIHQWYYRADDLEHKTALLVHLLKQP-EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEG   79 (170)
Confidence            6677533  3344 56889998888653 667899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +.++||||+      .+++|+|.++++ .|+|+++|.+...|+|+..+.|
T Consensus        80 ~~~vLvaT~------~~~~Gid~~~~~-~Vi~~~~p~~~~~~~qr~GR~~  122 (170)
T 2yjt_D           80 RVNVLVATD------VAARGIDIPDVS-HVFNFDMPRSGDTYLHRIGRTA  122 (170)
Confidence            999999999      889999999999 9999999999999999996643

>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=99.77  E-value=1.5e-18  Score=146.06  Aligned_cols=110  Identities=15%  Similarity=0.185  Sum_probs=100.8

Q ss_pred             EccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           16 PKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        16 ~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ....|...|.+++.+  ...++||||+|++.|+.+++.|.+.|+++..+||++++.+|..++++|++|+.+|||||+   
T Consensus       284 ~~~~k~~~l~~~l~~--~~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~---  358 (434)
T 2db3_A          284 NKYAKRSKLIEILSE--QADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS---  358 (434)
T ss_dssp             CGGGHHHHHHHHHHH--CCTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG---
T ss_pred             CcHHHHHHHHHHHHh--CCCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch---
Confidence            344688899998876  345599999999999999999999999999999999999999999999999999999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                         .+++|||.++++ +|+|+|+|.+..+|+||..|.|.
T Consensus       359 ---v~~rGlDi~~v~-~VI~~d~p~~~~~y~qriGR~gR  393 (434)
T 2db3_A          359 ---VASRGLDIKNIK-HVINYDMPSKIDDYVHRIGRTGR  393 (434)
T ss_dssp             ---GGTSSCCCTTCC-EEEESSCCSSHHHHHHHHTTSSC
T ss_pred             ---hhhCCCCcccCC-EEEEECCCCCHHHHHHHhccccc
Confidence               789999999999 99999999999999999987654

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.75  E-value=2e-17  Score=144.44  Aligned_cols=86  Identities=24%  Similarity=0.347  Sum_probs=78.7

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccc
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPD  160 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~  160 (184)
                      ||++++++.|+.++..|...|+.+..||+++++..|..+++.|++|++.|+||       +|+|+|++|||+++|++.++
T Consensus       271 IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~  350 (591)
T 2v1x_A          271 IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMEN  350 (591)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHH
T ss_pred             EEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHH
Confidence            55555557899999999999999999999999999999999999999999999       69999999999999999999


Q ss_pred             cccccccccCCcccc
Q psy437          161 YLPPILDLRLGREDI  175 (184)
Q Consensus       161 y~~~i~~~~~~r~~~  175 (184)
                      |+|++  +|+||++.
T Consensus       351 y~Qr~--GRaGR~G~  363 (591)
T 2v1x_A          351 YYQES--GRAGRDDM  363 (591)
T ss_dssp             HHHHH--TTSCTTSS
T ss_pred             HHHHh--ccCCcCCC
Confidence            99999  58888653

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.74  E-value=4.7e-17  Score=140.18  Aligned_cols=140  Identities=17%  Similarity=0.194  Sum_probs=121.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE-------------------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV-------------------------   87 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v-------------------------   87 (184)
                      ..+.+||.+|++..+.+....|...|+++..++|+.+..++......+..|..++                         
T Consensus        64 ~~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~v  143 (523)
T 1oyw_A           64 LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLL  143 (523)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEE
T ss_pred             hCCCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEE
Confidence            3468999999999999999999999999999999888766655555444444444                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           88 --------------------------------------------------------------------------------   87 (184)
Q Consensus        88 --------------------------------------------------------------------------------   87 (184)
                                                                                                      
T Consensus       144 ViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~~~r~~l~~~v~~~~~~  223 (523)
T 1oyw_A          144 AVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKP  223 (523)
T ss_dssp             EESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECCCCCTTEEEEEEECSSH
T ss_pred             EEeCccccCcCCCccHHHHHHHHHHHHhCCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCCCCCCceEEEEEeCCCH
Confidence                                                                                            


Q ss_pred             ----------------EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC
Q psy437           88 ----------------GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ  144 (184)
Q Consensus        88 ----------------lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~  144 (184)
                                      ||+|++++.|+.++..|...|+++..||+++++..|..+++.|++|++.|+||       +|+|
T Consensus       224 ~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p  303 (523)
T 1oyw_A          224 LDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKP  303 (523)
T ss_dssp             HHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCT
T ss_pred             HHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCcc
Confidence                            55555557899999999999999999999999999999999999999999999       5999


Q ss_pred             CccEEEecCCCCCccccccccccccCCccc
Q psy437          145 WKRIIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       145 ~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                      ++++|||+++|++.++|+|++  +|+||++
T Consensus       304 ~v~~VI~~~~p~s~~~y~Qr~--GRaGR~g  331 (523)
T 1oyw_A          304 NVRFVVHFDIPRNIESYYQET--GRAGRDG  331 (523)
T ss_dssp             TCCEEEESSCCSSHHHHHHHH--TTSCTTS
T ss_pred             CccEEEEECCCCCHHHHHHHh--ccccCCC
Confidence            999999999999999999999  5888864

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

Probab=99.73  E-value=3.3e-17  Score=135.92  Aligned_cols=122  Identities=17%  Similarity=0.169  Sum_probs=107.6

Q ss_pred             CCCCeEEEEEE--ccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437            6 NRANLKYEILP--KKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus         6 ~R~Nl~y~v~~--~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      ..+|+.+.+..  ...+...|.+++.......++||||+|++.++.+++.|.+.|+.+..+||++++++|..++++|++|
T Consensus       246 ~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g  325 (417)
T 2i4i_A          246 TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSG  325 (417)
T ss_dssp             CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             CccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcC
Confidence            35566544443  3458888888887643567899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +.+|||||+      .+++|+|.++++ +|+|+++|.+...|+|+..|.|.
T Consensus       326 ~~~vlvaT~------~~~~Gidip~v~-~Vi~~~~p~s~~~~~Qr~GR~gR  369 (417)
T 2i4i_A          326 KSPILVATA------VAARGLDISNVK-HVINFDLPSDIEEYVHRIGRTGR  369 (417)
T ss_dssp             SSCEEEECH------HHHTTSCCCCEE-EEEESSCCSSHHHHHHHHTTBCC
T ss_pred             CCCEEEECC------hhhcCCCcccCC-EEEEEcCCCCHHHHHHhcCcccc
Confidence            999999999      889999999999 99999999999999999987654

>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=99.69  E-value=9.1e-17  Score=133.23  Aligned_cols=106  Identities=14%  Similarity=0.181  Sum_probs=98.6

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      |...|.+++... ...++||||+|++.++.+++.|.+.|+.+..+||++++++|..+++.|++|+.+|||+|+      .
T Consensus       263 k~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~------~  335 (410)
T 2j0s_A          263 KFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD------V  335 (410)
T ss_dssp             HHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG------G
T ss_pred             HHHHHHHHHHhc-CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC------h
Confidence            788888888664 667999999999999999999999999999999999999999999999999999999999      7


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +++|+|.++++ +|+|+++|.+...|+|+..|.|
T Consensus       336 ~~~Gidi~~v~-~Vi~~~~p~s~~~~~Qr~GR~g  368 (410)
T 2j0s_A          336 WARGLDVPQVS-LIINYDLPNNRELYIHRIGRSG  368 (410)
T ss_dssp             GSSSCCCTTEE-EEEESSCCSSHHHHHHHHTTSS
T ss_pred             hhCcCCcccCC-EEEEECCCCCHHHHHHhccccc
Confidence            78899999999 9999999999999999997654

>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=99.68  E-value=7e-17  Score=139.47  Aligned_cols=104  Identities=14%  Similarity=0.186  Sum_probs=92.6

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC---CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE---RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~---gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      .+...+.......++||||+|+..|+.++..|.+.   ++++..+||+|++.+|..+++.|++|+.+|||||+      .
T Consensus       328 ~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~------~  401 (563)
T 3i5x_A          328 HIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD------V  401 (563)
T ss_dssp             HHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG------G
T ss_pred             HHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc------h
Confidence            33344433235778999999999999999999876   99999999999999999999999999999999999      7


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +++|+|.++++ +|||+++|.+...|+|+..|.|
T Consensus       402 ~~~GiDip~v~-~VI~~~~p~s~~~y~Qr~GRag  434 (563)
T 3i5x_A          402 GARGMDFPNVH-EVLQIGVPSELANYIHRIGRTA  434 (563)
T ss_dssp             GTSSCCCTTCC-EEEEESCCSSTTHHHHHHTTSS
T ss_pred             hhcCCCcccCC-EEEEECCCCchhhhhhhcCccc
Confidence            78999999999 9999999999999999997754

>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=99.68  E-value=2.8e-16  Score=129.87  Aligned_cols=108  Identities=17%  Similarity=0.172  Sum_probs=98.4

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .+...+..++... ...++||||+|++.++.++..|.+.++.+..+||+|++++|..+++.|++|+.+|||||+      
T Consensus       252 ~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~------  324 (412)
T 3fht_A          252 EKFQALCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN------  324 (412)
T ss_dssp             HHHHHHHHHHHHH-SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG------
T ss_pred             HHHHHHHHHHhhc-CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC------
Confidence            4777788877654 678999999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCC------hHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLA------DKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p------~~~r~~~~~~f~~~~  134 (184)
                      .+++|+|.++++ +|+|+++|      .+...|+|+.+|.|.
T Consensus       325 ~~~~Gidip~~~-~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR  365 (412)
T 3fht_A          325 VCARGIDVEQVS-VVINFDLPVDKDGNPDNETYLHRIGRTGR  365 (412)
T ss_dssp             GGTSSCCCTTEE-EEEESSCCBCSSSSBCHHHHHHHHTTSSC
T ss_pred             ccccCCCccCCC-EEEEECCCCCCCCCcchheeecccCcccC
Confidence            778899999999 99999999      678999999977654

>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=99.67  E-value=3.9e-16  Score=126.87  Aligned_cols=110  Identities=15%  Similarity=0.224  Sum_probs=100.8

Q ss_pred             EccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           16 PKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        16 ~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ....+...|.+++..  .+.++||||+|++.++.+++.|.+.|+.+..+||++++++|..+++.|.+|+.+|||+|+   
T Consensus       222 ~~~~~~~~l~~~l~~--~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~---  296 (367)
T 1hv8_A          222 NENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD---  296 (367)
T ss_dssp             CGGGHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT---
T ss_pred             ChHHHHHHHHHHHhc--CCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC---
Confidence            344688888888854  677899999999999999999999999999999999999999999999999999999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                         .+++|+|.++++ .|+|+++|.+..+|+|+..|.|.
T Consensus       297 ---~~~~Gid~~~~~-~Vi~~~~~~s~~~~~Q~~GR~~R  331 (367)
T 1hv8_A          297 ---VMSRGIDVNDLN-CVINYHLPQNPESYMHRIGRTGR  331 (367)
T ss_dssp             ---THHHHCCCSCCS-EEEESSCCSCHHHHHHHSTTTCC
T ss_pred             ---hhhcCCCcccCC-EEEEecCCCCHHHhhhccccccc
Confidence               889999999999 99999999999999999976543

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

Probab=99.67  E-value=9.3e-17  Score=139.58  Aligned_cols=104  Identities=14%  Similarity=0.186  Sum_probs=92.5

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC---CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE---RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~---gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      .+...+.......++||||+|+..|+.+++.|.+.   ++.+..+||+|++++|..++++|++|+.+|||||+      .
T Consensus       277 ~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~------~  350 (579)
T 3sqw_A          277 HIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD------V  350 (579)
T ss_dssp             HHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG------G
T ss_pred             HHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc------h
Confidence            33444443235678999999999999999999876   99999999999999999999999999999999999      7


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      +++|+|.++++ +|||+++|.+...|+|+..|.|
T Consensus       351 ~~~GiDip~v~-~VI~~~~p~s~~~y~Qr~GRag  383 (579)
T 3sqw_A          351 GARGMDFPNVH-EVLQIGVPSELANYIHRIGRTA  383 (579)
T ss_dssp             GTSSCCCTTCC-EEEEESCCSSTTHHHHHHTTSS
T ss_pred             hhcCCCcccCC-EEEEcCCCCCHHHhhhhccccc
Confidence            78899999999 9999999999999999997654

>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=99.66  E-value=1.5e-16  Score=130.79  Aligned_cols=111  Identities=13%  Similarity=0.204  Sum_probs=100.7

Q ss_pred             EccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc
Q psy437           16 PKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        16 ~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ....+...|.+++... ...++||||+|++.++.+++.|.+.|+++..+||++++++|..++++|++|+.+|||+|+   
T Consensus       233 ~~~~~~~~l~~~l~~~-~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~---  308 (391)
T 1xti_A          233 KDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN---  308 (391)
T ss_dssp             CGGGHHHHHHHHHHHS-CCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC---
T ss_pred             CchhHHHHHHHHHHhc-CCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC---
Confidence            4446888888888664 778999999999999999999999999999999999999999999999999999999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                         .+++|+|.++++ .|+|+++|.+...|+|+..|.|.
T Consensus       309 ---~~~~Gidi~~~~-~Vi~~~~p~s~~~~~Qr~GR~~R  343 (391)
T 1xti_A          309 ---LFGRGMDIERVN-IAFNYDMPEDSDTYLHRVARAGR  343 (391)
T ss_dssp             ---CCSSCBCCTTEE-EEEESSCCSSHHHHHHHHCBCSS
T ss_pred             ---hhhcCCCcccCC-EEEEeCCCCCHHHHHHhcccccC
Confidence               557799999999 99999999999999999976543

>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=99.66  E-value=3.6e-16  Score=128.25  Aligned_cols=121  Identities=14%  Similarity=0.126  Sum_probs=102.6

Q ss_pred             CCCCeEEEEEEcc---ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc
Q psy437            6 NRANLKYEILPKK---NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS   82 (184)
Q Consensus         6 ~R~Nl~y~v~~~~---~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~   82 (184)
                      ..+++........   .+...+..++.. ....++||||++++.++.+++.|...|+.+..+||+|++++|..+++.|++
T Consensus       213 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~  291 (395)
T 3pey_A          213 NVDAIKQLYMDCKNEADKFDVLTELYGL-MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFRE  291 (395)
T ss_dssp             SCTTEEEEEEECSSHHHHHHHHHHHHTT-TTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHT
T ss_pred             ccccccEEEEEcCchHHHHHHHHHHHHh-ccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHC
Confidence            3455544444332   366666666644 366899999999999999999999999999999999999999999999999


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh------HHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD------KLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~------~~r~~~~~~f~~~~  134 (184)
                      |+.+|||||+      .+++|+|.++++ +|+|+++|.      +...|+|+.+|.|.
T Consensus       292 g~~~vlv~T~------~~~~Gidip~~~-~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR  342 (395)
T 3pey_A          292 GRSKVLITTN------VLARGIDIPTVS-MVVNYDLPTLANGQADPATYIHRIGRTGR  342 (395)
T ss_dssp             TSCCEEEECG------GGSSSCCCTTEE-EEEESSCCBCTTSSBCHHHHHHHHTTSSC
T ss_pred             CCCCEEEECC------hhhcCCCcccCC-EEEEcCCCCCCcCCCCHHHhhHhcccccc
Confidence            9999999999      678899999999 999999999      99999999977653

>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=99.65  E-value=2e-16  Score=130.61  Aligned_cols=122  Identities=12%  Similarity=0.191  Sum_probs=105.0

Q ss_pred             CCCCCeE--EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc
Q psy437            5 FNRANLK--YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS   82 (184)
Q Consensus         5 ~~R~Nl~--y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~   82 (184)
                      ...+++.  |.......|...+..++... ...++||||+|++.++.+++.|...|+.+..+||+|++++|..+++.|++
T Consensus       228 ~~~~~~~~~~~~~~~~~k~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~  306 (400)
T 1s2m_A          228 LTLKGITQYYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQ  306 (400)
T ss_dssp             CBCTTEEEEEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHT
T ss_pred             cccCCceeEEEEechhhHHHHHHHHHhhc-CCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhc
Confidence            3455664  33334446788888888653 66799999999999999999999999999999999999999999999999


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+.+|||+|+      .+++|+|.++++ .|+|+++|.+...|+|+..|.|.
T Consensus       307 g~~~vLv~T~------~~~~Gidip~~~-~Vi~~~~p~s~~~~~Qr~GR~gR  351 (400)
T 1s2m_A          307 GKVRTLVCSD------LLTRGIDIQAVN-VVINFDFPKTAETYLHRIGRSGR  351 (400)
T ss_dssp             TSSSEEEESS------CSSSSCCCTTEE-EEEESSCCSSHHHHHHHHCBSSC
T ss_pred             CCCcEEEEcC------ccccCCCccCCC-EEEEeCCCCCHHHHHHhcchhcC
Confidence            9999999999      667899999999 99999999999999999976543

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

Probab=99.64  E-value=1e-15  Score=112.57  Aligned_cols=101  Identities=14%  Similarity=0.112  Sum_probs=87.9

Q ss_pred             HHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           71 KLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        71 ~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      .+|...+..+..  ...++||+|+++..++.++..|...|+++..+|+++|+..|..+.+.|++|++.|+++       +
T Consensus        20 ~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gl   99 (163)
T 2hjv_A           20 ENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGI   99 (163)
T ss_dssp             GGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTC
T ss_pred             HHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCC
Confidence            344444444432  2347999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|+++++|.+.+.|+|+++  |+||.
T Consensus       100 d~~~~~~Vi~~~~p~~~~~~~qr~G--R~~R~  129 (163)
T 2hjv_A          100 DIENISLVINYDLPLEKESYVHRTG--RTGRA  129 (163)
T ss_dssp             CCSCCSEEEESSCCSSHHHHHHHTT--TSSCT
T ss_pred             chhcCCEEEEeCCCCCHHHHHHhcc--ccCcC
Confidence            9999999999999999999999995  55554

>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=99.63  E-value=3.2e-16  Score=134.28  Aligned_cols=108  Identities=8%  Similarity=0.105  Sum_probs=58.2

Q ss_pred             ChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC------------CCeeEEecCCCCHHHHHHHHHHHhc-
Q psy437           19 NVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE------------RINAISYHAGLADKLRNEVQMKWIS-   82 (184)
Q Consensus        19 ~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~------------gi~~~~~hg~l~~~~R~~~~~~f~~-   82 (184)
                      .|...|.++|.+.   ..+.++||||+++..++.+++.|...            |.....+||+|++++|..++++|++ 
T Consensus       372 ~K~~~L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~  451 (556)
T 4a2p_A          372 PKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTS  451 (556)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC----------------------------
T ss_pred             hHHHHHHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhccc
Confidence            4788888888643   36789999999999999999999875            5566667889999999999999999 


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+.+|||||+      .+++|||.++++ .|||+|+|.+...|+|+.+| |.
T Consensus       452 g~~~vLvaT~------~~~~GiDip~v~-~VI~~d~p~s~~~~~Qr~GR-gR  495 (556)
T 4a2p_A          452 KDNRLLIATS------VADEGIDIVQCN-LVVLYEYSGNVTKMIQVRGR-GR  495 (556)
T ss_dssp             --CCEEEEEC-----------------C-EEEEETCCSCHHHHHHC------
T ss_pred             CceEEEEEcC------chhcCCCchhCC-EEEEeCCCCCHHHHHHhcCC-CC
Confidence            9999999999      889999999999 99999999999999999988 54

>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=99.63  E-value=1.5e-16  Score=131.68  Aligned_cols=108  Identities=13%  Similarity=0.160  Sum_probs=90.3

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .+...+..++... ...++||||+|++.++.+++.|...++.+..+||+|++++|..+++.|++|+.+|||||+      
T Consensus       266 ~~~~~l~~~~~~~-~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~------  338 (414)
T 3eiq_A          266 WKLDTLCDLYETL-TITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTD------  338 (414)
T ss_dssp             THHHHHHHHHHSS-CCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECS------
T ss_pred             hHHHHHHHHHHhC-CCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECC------
Confidence            4888888888654 667999999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .+++|+|.++++ +|||+++|.+...|+|+..|.|.
T Consensus       339 ~~~~Gidip~v~-~Vi~~~~p~s~~~~~Qr~GR~gR  373 (414)
T 3eiq_A          339 LLARGIDVQQVS-LVINYDLPTNRENYIHRIGRGGR  373 (414)
T ss_dssp             SCC--CCGGGCS-CEEESSCCSSTHHHHHHSCCC--
T ss_pred             ccccCCCccCCC-EEEEeCCCCCHHHhhhhcCcccC
Confidence            668899999999 89999999999999999976543

>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=99.62  E-value=2.5e-16  Score=140.44  Aligned_cols=122  Identities=12%  Similarity=0.028  Sum_probs=101.2

Q ss_pred             CCCCCCeEE-----EEEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKY-----EILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y-----~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      +.+||++..     .......|...|.+.+.+. ..+.++||||+|++.++.++..|.+.|+++.++||++++.+|..+.
T Consensus       396 Ptn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~  475 (844)
T 1tf5_A          396 PTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIE  475 (844)
T ss_dssp             CCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHT
T ss_pred             cCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHH
Confidence            456777542     2223346888888888642 2567899999999999999999999999999999999888887777


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc--------CCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE--------RINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~--------gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++++.|  .|+|||+      .++||+|++        |+. +|||+++|.+.|.|+|+.+++|.
T Consensus       476 ~ag~~g--~VlIATd------mAgRG~DI~l~~~V~~~ggl-~VIn~d~p~s~r~y~hr~GRTGR  531 (844)
T 1tf5_A          476 EAGQKG--AVTIATN------MAGRGTDIKLGEGVKELGGL-AVVGTERHESRRIDNQLRGRSGR  531 (844)
T ss_dssp             TTTSTT--CEEEEET------TSSTTCCCCCCTTSGGGTSE-EEEESSCCSSHHHHHHHHTTSSG
T ss_pred             HcCCCC--eEEEeCC------ccccCcCccccchhhhcCCc-EEEEecCCCCHHHHHhhcCcccc
Confidence            666655  6899999      889999999        888 99999999999999999987764

>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=99.62  E-value=1.3e-15  Score=116.71  Aligned_cols=88  Identities=18%  Similarity=0.118  Sum_probs=82.5

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+|+++..++.++..|...|+.+.++|+++|+..|..+.+.|++|+..|+|+       +|+|++++|+++++|.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~  110 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPD  110 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBSEEEESSCCS
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCcEEEECCCCc
Confidence            458999999999999999999999999999999999999999999999999999999       6999999999999999


Q ss_pred             CccccccccccccCCcc
Q psy437          157 IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~  173 (184)
                      +.+.|+|+++  |+||.
T Consensus       111 ~~~~~~qr~G--R~gR~  125 (212)
T 3eaq_A          111 RAEAYQHRSG--RTGRA  125 (212)
T ss_dssp             SHHHHHHHHT--TBCCC
T ss_pred             CHHHHHHHhc--ccCCC
Confidence            9999999996  55554

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

Probab=99.61  E-value=1.9e-15  Score=114.16  Aligned_cols=102  Identities=12%  Similarity=0.118  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHhc-cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           70 DKLRNEVQMKWIS-NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        70 ~~~R~~~~~~f~~-g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      ..++...+..+.. ...++||+|+++..++.++..|...|+++..+|+++++..|..+.+.|++|++.|+|+       +
T Consensus        39 ~~~K~~~L~~~l~~~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gl  118 (191)
T 2p6n_A           39 EEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGL  118 (191)
T ss_dssp             GGGHHHHHHHHHTTSCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTC
T ss_pred             hHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCC
Confidence            3455555555543 2347999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|+++++|.+.+.|+|+++  |+||.
T Consensus       119 di~~v~~VI~~d~p~~~~~~~qr~G--R~gR~  148 (191)
T 2p6n_A          119 DFPAIQHVINYDMPEEIENYVHRIG--RTGCS  148 (191)
T ss_dssp             CCCCCSEEEESSCCSSHHHHHHHHT--TSCC-
T ss_pred             CcccCCEEEEeCCCCCHHHHHHHhC--ccccC
Confidence            9999999999999999999999996  55554

>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=99.61  E-value=1.6e-15  Score=112.61  Aligned_cols=101  Identities=17%  Similarity=0.208  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           71 KLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        71 ~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      .++...+..+..  ...++||+|+++..|+.++..|...|+++..+|+++|+..|..+.+.|++|++.|+++       +
T Consensus        16 ~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl   95 (172)
T 1t5i_A           16 NEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGM   95 (172)
T ss_dssp             GGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTC
T ss_pred             HHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCchhcCc
Confidence            344444444432  2347999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|+++++|.+.+.|+|+++  |+||.
T Consensus        96 di~~~~~Vi~~d~p~~~~~~~qr~G--R~~R~  125 (172)
T 1t5i_A           96 DIERVNIAFNYDMPEDSDTYLHRVA--RAGRF  125 (172)
T ss_dssp             CGGGCSEEEESSCCSSHHHHHHHHH--HHTGG
T ss_pred             chhhCCEEEEECCCCCHHHHHHHhc--ccccC
Confidence            9999999999999999999999996  55553

>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=99.61  E-value=1.3e-16  Score=140.98  Aligned_cols=94  Identities=18%  Similarity=0.215  Sum_probs=82.8

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC------CCeeEEecCC--------CCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE------RINAISYHAG--------LADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~------gi~~~~~hg~--------l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      +.++||||+|+..++.+++.|...      |+++..+||+        |++.+|.+++++|++|+.+|||||+      .
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~------~  473 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATT------V  473 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEEC------S
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEcc------c
Confidence            689999999999999999999987      8999999999        9999999999999999999999999      5


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +++|||.++++ +|||+|+|.+...|+|+.+|.|.
T Consensus       474 ~~~GIDip~v~-~VI~~d~p~s~~~~~Qr~GRArr  507 (699)
T 4gl2_A          474 AEEGLDIKECN-IVIRYGLVTNEIAMVQARGRARA  507 (699)
T ss_dssp             CCTTSCCCSCC-CCEEESCCCCHHHHHHHHTTSCS
T ss_pred             cccCCccccCC-EEEEeCCCCCHHHHHHHcCCCCC
Confidence            57799999999 99999999999999999987553

>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=99.60  E-value=5.7e-17  Score=137.59  Aligned_cols=108  Identities=17%  Similarity=0.172  Sum_probs=0.0

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .+...|..++... ...++||||+|+..|+.++..|...++.+..+||+|++.+|..+++.|++|+.+|||||+      
T Consensus       319 ~~~~~l~~~~~~~-~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~------  391 (479)
T 3fmp_B          319 EKFQALCNLYGAI-TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN------  391 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHhhc-cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEcc------
Confidence            4666666666543 567899999999999999999999999999999999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCC------hHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLA------DKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p------~~~r~~~~~~f~~~~  134 (184)
                      .+++|+|.++++ +|||+|+|      .+...|+|+.+|.|.
T Consensus       392 ~~~~GlDip~v~-~VI~~d~p~~~~~~~s~~~~~Qr~GRagR  432 (479)
T 3fmp_B          392 VCARGIDVEQVS-VVINFDLPVDKDGNPDNETYLHRIGRTGR  432 (479)
T ss_dssp             ------------------------------------------
T ss_pred             ccccCCccccCC-EEEEecCCCCCccCCCHHHHHHHhccccc
Confidence            889999999999 99999999      567899999977654

>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=99.60  E-value=4.8e-15  Score=130.90  Aligned_cols=116  Identities=16%  Similarity=0.122  Sum_probs=101.1

Q ss_pred             EEEEEccChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      +.+.+...+...|...|.+.. .+.++||||+|+..++.+++.|.+.|+++.++||++++.+|..+++.|++|+++|||+
T Consensus       422 i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVa  501 (661)
T 2d7d_A          422 IDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVG  501 (661)
T ss_dssp             EEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEE
T ss_pred             EEEecccchHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEe
Confidence            444555556667766665432 4678999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCC-----ChHHHHHHHHHhhCCC
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGL-----ADKLRNEVQMKWISNK  134 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~-----p~~~r~~~~~~f~~~~  134 (184)
                      |+      .+++|+|.++++ +|++++.     |.+.++|+|+.++.|.
T Consensus       502 T~------~l~~GlDip~v~-lVi~~d~d~~G~p~s~~~~iQr~GRagR  543 (661)
T 2d7d_A          502 IN------LLREGLDIPEVS-LVAILDADKEGFLRSERSLIQTIGRAAR  543 (661)
T ss_dssp             SC------CCSTTCCCTTEE-EEEETTTTCCTTTTSHHHHHHHHHTTTT
T ss_pred             cc------hhhCCcccCCCC-EEEEeCcccccCCCCHHHHHHHhCcccC
Confidence            99      778999999999 9999997     9999999999987653

>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=99.60  E-value=4.9e-15  Score=110.02  Aligned_cols=99  Identities=12%  Similarity=0.073  Sum_probs=85.5

Q ss_pred             HHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Eec
Q psy437           73 RNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKI  143 (184)
Q Consensus        73 R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~  143 (184)
                      +...+..+..  ...++||+++++..|+.++..|...|+.+..+|+++|+..|..+.+.|++|++.|+|+       +|+
T Consensus        21 K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~  100 (175)
T 2rb4_A           21 KYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDV  100 (175)
T ss_dssp             HHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCC
T ss_pred             HHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCc
Confidence            4444444443  2347999999999999999999999999999999999999999999999999999999       599


Q ss_pred             CCccEEEecCCC------CCccccccccccccCCcc
Q psy437          144 QWKRIIWIHSLV------LIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       144 ~~vr~v~~~~~p------~~~e~y~~~i~~~~~~r~  173 (184)
                      |++++|+++++|      .+.++|+|+++  |+||.
T Consensus       101 ~~~~~Vi~~d~p~~~~~~~~~~~~~qr~G--R~gR~  134 (175)
T 2rb4_A          101 KQVTIVVNFDLPVKQGEEPDYETYLHRIG--RTGRF  134 (175)
T ss_dssp             TTEEEEEESSCCC--CCSCCHHHHHHHHC--BC---
T ss_pred             ccCCEEEEeCCCCCccccCCHHHHHHHhc--ccccC
Confidence            999999999999      99999999995  66664

>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=99.59  E-value=6.1e-15  Score=130.27  Aligned_cols=122  Identities=13%  Similarity=0.104  Sum_probs=102.9

Q ss_pred             EEEEEccChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      +.+.+...+...|...|.+.. .+.++||||+|+..++.+++.|.+.|+++.++||++++.+|..++++|++|+++||||
T Consensus       416 i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLva  495 (664)
T 1c4o_A          416 VRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVG  495 (664)
T ss_dssp             EEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEE
T ss_pred             EEEecccchHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEc
Confidence            334444456666666665432 5679999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCC-----ChHHHHHHHHHhhCC---CceEEEE
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGL-----ADKLRNEVQMKWISN---KVHLYNV  140 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~-----p~~~r~~~~~~f~~~---~~~v~va  140 (184)
                      |+      .+++|+|.++++ +|+|++.     |.+.++|+|+.++.|   ...+++.
T Consensus       496 T~------~l~~GlDip~v~-lVI~~d~d~~G~p~s~~~~iQr~GRagR~~~G~~i~~  546 (664)
T 1c4o_A          496 IN------LLREGLDIPEVS-LVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLY  546 (664)
T ss_dssp             SC------CCCTTCCCTTEE-EEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEE
T ss_pred             cC------hhhcCccCCCCC-EEEEeCCcccCCCCCHHHHHHHHCccCcCCCCEEEEE
Confidence            99      668899999999 9999997     999999999997654   3344444

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

Probab=99.58  E-value=2.7e-16  Score=138.84  Aligned_cols=108  Identities=9%  Similarity=0.114  Sum_probs=64.8

Q ss_pred             ChHHHHHHHHHhhc---CCCcEEEEeccHHHHHHHHHHHHhCC----CeeEEe--------cCCCCHHHHHHHHHHHhc-
Q psy437           19 NVLKEVISLIKAKY---SGQSGIVYCLTRKECDSVAAALAQER----INAISY--------HAGLADKLRNEVQMKWIS-   82 (184)
Q Consensus        19 ~k~~~L~~~l~~~~---~~~~~IIf~~tr~~~e~la~~L~~~g----i~~~~~--------hg~l~~~~R~~~~~~f~~-   82 (184)
                      .|...|.++|.+..   .+.++||||+++..++.+++.|...|    +++..+        ||+|++++|.+++++|++ 
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            47888888886542   46789999999999999999999988    888888        559999999999999998 


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+.+|||||+      .+++|||.++++ +|||+|+|.+...|+||.+| |.
T Consensus       460 g~~~vLVaT~------v~~~GiDip~v~-~VI~~d~p~s~~~~~Qr~GR-GR  503 (696)
T 2ykg_A          460 GDHNILIATS------VADEGIDIAQCN-LVILYEYVGNVIKMIQTRGR-GR  503 (696)
T ss_dssp             -CCSCSEEEE------SSCCC---CCCS-EEEEESCC--CCCC---------
T ss_pred             CCccEEEEec------hhhcCCcCccCC-EEEEeCCCCCHHHHHHhhcc-Cc
Confidence            9999999999      556788888888 88888888888888888877 54

>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=99.58  E-value=3.9e-15  Score=111.85  Aligned_cols=88  Identities=20%  Similarity=0.158  Sum_probs=73.8

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+|+++..++.++..|...|+.+..+|+++|+..|..+.+.|++|++.|+|+       +|+|++++|+++++|.
T Consensus        46 ~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~  125 (185)
T 2jgn_A           46 DSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPS  125 (185)
T ss_dssp             CSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC------CCCSBSEEEESSCCS
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCC
Confidence            357999999999999999999999999999999999999999999999999999998       6999999999999999


Q ss_pred             CccccccccccccCCcc
Q psy437          157 IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~  173 (184)
                      +.+.|+|+++  |+||.
T Consensus       126 s~~~~~Qr~G--R~~R~  140 (185)
T 2jgn_A          126 DIEEYVHRIG--RTGRV  140 (185)
T ss_dssp             SHHHHHHHHT--TBCCT
T ss_pred             CHHHHHHHcc--ccCCC
Confidence            9999999996  55554

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

Probab=99.58  E-value=4.7e-15  Score=126.74  Aligned_cols=109  Identities=14%  Similarity=0.128  Sum_probs=67.3

Q ss_pred             ChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhCC----C--------eeEEecCCCCHHHHHHHHHHHhc-
Q psy437           19 NVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQER----I--------NAISYHAGLADKLRNEVQMKWIS-   82 (184)
Q Consensus        19 ~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~g----i--------~~~~~hg~l~~~~R~~~~~~f~~-   82 (184)
                      .|...|.++|.+.   ....++||||+++..++.++..|...+    +        ....+||+|++++|.+++++|++ 
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            4777888777643   256899999999999999999999764    3        44455669999999999999999 


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCccccc
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYL  162 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~e~y~  162 (184)
                      |+.+|||||++      ++     .|                                +|+|++++|||||+|.++..|+
T Consensus       451 g~~~vLvaT~~------~~-----~G--------------------------------lDlp~v~~VI~~d~p~s~~~~~  487 (555)
T 3tbk_A          451 GDNNILIATSV------AD-----EG--------------------------------IDIAECNLVILYEYVGNVIKMI  487 (555)
T ss_dssp             -CCSEEEECCC------TT-----CC--------------------------------EETTSCSEEEEESCCSSCCCEE
T ss_pred             CCeeEEEEcch------hh-----cC--------------------------------CccccCCEEEEeCCCCCHHHHH
Confidence            99999999992      22     22                                3788888888889999999999


Q ss_pred             cccccccCCcc
Q psy437          163 PPILDLRLGRE  173 (184)
Q Consensus       163 ~~i~~~~~~r~  173 (184)
                      |+++  | ||.
T Consensus       488 Qr~G--R-gR~  495 (555)
T 3tbk_A          488 QTRG--R-GRA  495 (555)
T ss_dssp             CSSC--C-CTT
T ss_pred             HhcC--c-CcC
Confidence            9985  4 665

>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=99.57  E-value=6.9e-15  Score=118.28  Aligned_cols=116  Identities=15%  Similarity=0.157  Sum_probs=96.3

Q ss_pred             CCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCce
Q psy437            7 RANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH   86 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~   86 (184)
                      .+|+.+.............+.+... ...++||||+|++.++.+++.|.    .+..+||++++.+|.+++++|++|+.+
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~  268 (337)
T 2z0m_A          194 LANVEHKFVHVKDDWRSKVQALREN-KDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYD  268 (337)
T ss_dssp             GGGEEEEEEECSSSSHHHHHHHHTC-CCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             cCCceEEEEEeChHHHHHHHHHHhC-CCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCc
Confidence            4455555554444334444566543 67889999999999999999886    478899999999999999999999999


Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +||||+      .+++|+|.++++ .|+|+++|.+...|+|+..|.|.
T Consensus       269 vlv~T~------~~~~Gid~~~~~-~Vi~~~~~~s~~~~~Q~~GR~gR  309 (337)
T 2z0m_A          269 MLITTD------VASRGLDIPLVE-KVINFDAPQDLRTYIHRIGRTGR  309 (337)
T ss_dssp             EEEECH------HHHTTCCCCCBS-EEEESSCCSSHHHHHHHHTTBCG
T ss_pred             EEEEcC------ccccCCCccCCC-EEEEecCCCCHHHhhHhcCcccc
Confidence            999999      888999999999 99999999999999999976654

>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=99.56  E-value=1.8e-14  Score=120.25  Aligned_cols=109  Identities=12%  Similarity=0.162  Sum_probs=96.5

Q ss_pred             ChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecC--------CCCHHHHHHHHHHHhccCceE
Q psy437           19 NVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQERINAISYHA--------GLADKLRNEVQMKWISNKVHV   87 (184)
Q Consensus        19 ~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg--------~l~~~~R~~~~~~f~~g~~~v   87 (184)
                      .|...|.++|.+.   ..+.++||||+++..++.+++.|...|+++..+||        +|++++|..++++|.+|+.+|
T Consensus       343 ~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~v  422 (494)
T 1wp9_A          343 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNV  422 (494)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSE
T ss_pred             hHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceE
Confidence            4788888888653   36789999999999999999999999999999999        999999999999999999999


Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ||+|+      .++.|+|.++++ .|+++++|.+...|+|+..|.|.
T Consensus       423 Lv~T~------~~~~Gldl~~~~-~Vi~~d~~~~~~~~~Qr~GR~~R  462 (494)
T 1wp9_A          423 LVATS------VGEEGLDVPEVD-LVVFYEPVPSAIRSIQRRGRTGR  462 (494)
T ss_dssp             EEECG------GGGGGGGSTTCC-EEEESSCCHHHHHHHHHHTTSCS
T ss_pred             EEECC------ccccCCCchhCC-EEEEeCCCCCHHHHHHHHhhccC
Confidence            99999      668899999999 99999999999999999976543

>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=99.55  E-value=4.5e-15  Score=130.61  Aligned_cols=122  Identities=12%  Similarity=0.077  Sum_probs=98.5

Q ss_pred             CCCCCCeEEEE-----EEccChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYEI-----LPKKNVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~v-----~~~~~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||+.....     .....|...|.+.+.+.+ .+.|+||||+|++.++.++..|.+.|+++.++||+..+.++..+.
T Consensus       438 Ptnkp~~R~d~~d~vy~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~  517 (822)
T 3jux_A          438 PTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVA  517 (822)
T ss_dssp             CCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHH
T ss_pred             CCCCCcceeecCcEEEecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHH
Confidence            56777654332     122358888888886532 567999999999999999999999999999999996666666666


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhc--------CCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQE--------RINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~--------gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++++.|  .|+|||+      .++||+|++        |.. +|||+++|.+.|.|+|+.+++|.
T Consensus       518 ~ag~~g--~VtVATd------mAgRGtDI~lg~~V~~~Ggl-hVInte~Pes~r~y~qriGRTGR  573 (822)
T 3jux_A          518 KAGQKG--MVTIATN------MAGRGTDIKLGPGVAELGGL-CIIGTERHESRRIDNQLRGRAGR  573 (822)
T ss_dssp             HHHSTT--CEEEEET------TTTTTCCCCCCTTTTTTTSC-EEEESSCCSSHHHHHHHHTTSSC
T ss_pred             hCCCCC--eEEEEcc------hhhCCcCccCCcchhhcCCC-EEEecCCCCCHHHHHHhhCcccc
Confidence            666655  6999999      889999997        776 99999999999999999987654

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

Probab=99.55  E-value=8.9e-15  Score=117.84  Aligned_cols=100  Identities=17%  Similarity=0.108  Sum_probs=86.4

Q ss_pred             HHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Ee
Q psy437           72 LRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WK  142 (184)
Q Consensus        72 ~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D  142 (184)
                      +|...+..+..  ...++||+|+++..++.++..|...|+.+.++|+++|+..|..+.+.|++|+..|+||       +|
T Consensus        14 ~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gid   93 (300)
T 3i32_A           14 GRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLD   93 (300)
T ss_dssp             SHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTT
T ss_pred             HHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCcc
Confidence            34444444432  2457999999999999999999999999999999999999999999999999999999       59


Q ss_pred             cCCccEEEecCCCCCccccccccccccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|++++||++++|.+.+.|+|+++  |+||.
T Consensus        94 i~~v~~VI~~d~p~s~~~y~Qr~G--RagR~  122 (300)
T 3i32_A           94 IPQVDLVVHYRMPDRAEAYQHRSG--RTGRA  122 (300)
T ss_dssp             CCCCSEEEESSCCSSTTHHHHHHT--CCC--
T ss_pred             ccceeEEEEcCCCCCHHHHHHHcc--CcCcC
Confidence            999999999999999999999996  55554

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

Probab=99.55  E-value=6.7e-15  Score=122.50  Aligned_cols=112  Identities=11%  Similarity=0.090  Sum_probs=95.3

Q ss_pred             CCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeE-EecCCCCHHHHHHHHHHHhccCc
Q psy437            7 RANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAI-SYHAGLADKLRNEVQMKWISNKV   85 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~-~~hg~l~~~~R~~~~~~f~~g~~   85 (184)
                      .+|+...+... .+...|.+++..  .+.++||||+|+..++.++..|...|+++. .+||+    +|.  ++.|++|+.
T Consensus       228 ~~~i~~~~~~~-~~~~~l~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~  298 (414)
T 3oiy_A          228 ARNITHVRISS-RSKEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKI  298 (414)
T ss_dssp             CCSEEEEEESS-CCHHHHHHHHHH--HCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSC
T ss_pred             cccchheeecc-CHHHHHHHHHHH--cCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCC
Confidence            45565544444 567788888876  357999999999999999999999999998 99985    444  999999999


Q ss_pred             eEEEE----EeecccHHHHHHHHHhcC-CcEEEeeCCCC--hHHHHHHHHHhhCCC
Q psy437           86 HVGHW----TVVSKECDSVAAALAQER-INAISYHAGLA--DKLRNEVQMKWISNK  134 (184)
Q Consensus        86 ~vlVa----T~tr~~~e~~a~gL~~~g-i~~~vih~~~p--~~~r~~~~~~f~~~~  134 (184)
                      +||||    |+      .+++|+|.++ ++ +|||+|+|  .+...|+|+.+|.|.
T Consensus       299 ~vLvat~s~T~------~~~~GiDip~~v~-~VI~~~~p~~~~~~~y~qr~GR~gR  347 (414)
T 3oiy_A          299 NILIGVQAYYG------KLTRGVDLPERIK-YVIFWGTPSGPDVYTYIQASGRSSR  347 (414)
T ss_dssp             SEEEEECCTTC------CCCCCCCCTTTCC-EEEEESCCTTTCHHHHHHHHGGGCC
T ss_pred             eEEEEecCcCc------hhhccCccccccC-EEEEECCCCCCCHHHHHHHhCcccc
Confidence            99999    88      6688999999 99 99999999  899999999987765

>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=99.55  E-value=1.4e-14  Score=121.91  Aligned_cols=165  Identities=11%  Similarity=0.145  Sum_probs=114.6

Q ss_pred             CCeEEEEEEccCh------HHHHHHHHHhh--cCCCcEEEEeccHH-HHHHHHHHHHhC--------------CCeeEEe
Q psy437            8 ANLKYEILPKKNV------LKEVISLIKAK--YSGQSGIVYCLTRK-ECDSVAAALAQE--------------RINAISY   64 (184)
Q Consensus         8 ~Nl~y~v~~~~~k------~~~L~~~l~~~--~~~~~~IIf~~tr~-~~e~la~~L~~~--------------gi~~~~~   64 (184)
                      .++.|.|..+.+.      ...+..++...  .+..+.+.|+.|-. ..+.++..+-..              ++.-.++
T Consensus       202 ~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~  281 (434)
T 2db3_A          202 EDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIY  281 (434)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEE
T ss_pred             ccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEE
Confidence            4566777765432      23344444321  13456788888753 233333332111              1111112


Q ss_pred             cCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE----
Q psy437           65 HAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV----  140 (184)
Q Consensus        65 hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va----  140 (184)
                      .-. ....+..+.+.+.....++||++++++.|+.++..|...|+++..+|+++++..|..+.+.|++|+..|+||    
T Consensus       282 ~~~-~~~k~~~l~~~l~~~~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~  360 (434)
T 2db3_A          282 EVN-KYAKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVA  360 (434)
T ss_dssp             ECC-GGGHHHHHHHHHHHCCTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGG
T ss_pred             EeC-cHHHHHHHHHHHHhCCCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhh
Confidence            111 122334444444444445999999999999999999999999999999999999999999999999999999    


Q ss_pred             ---EecCCccEEEecCCCCCcccccccccc-ccCCcc
Q psy437          141 ---WKIQWKRIIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       141 ---~D~~~vr~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                         +|+|++++|||+++|.+.++|+|+++| +|.|+.
T Consensus       361 ~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~  397 (434)
T 2db3_A          361 SRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNN  397 (434)
T ss_dssp             TSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCC
T ss_pred             hCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCC
Confidence               699999999999999999999999965 244443

>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=99.54  E-value=6.5e-15  Score=132.40  Aligned_cols=108  Identities=8%  Similarity=0.105  Sum_probs=62.2

Q ss_pred             ChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC------------CCeeEEecCCCCHHHHHHHHHHHhc-
Q psy437           19 NVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE------------RINAISYHAGLADKLRNEVQMKWIS-   82 (184)
Q Consensus        19 ~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~------------gi~~~~~hg~l~~~~R~~~~~~f~~-   82 (184)
                      .|+..|.++|.+.   ..+.++||||+++..++.++..|.+.            |.....+||+|++.+|..++++|++ 
T Consensus       613 ~K~~~L~~lL~~~~~~~~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~  692 (797)
T 4a2q_A          613 PKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTS  692 (797)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC---------------------------
T ss_pred             hHHHHHHHHHHHHhccCCCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhcc
Confidence            4788888888642   35689999999999999999999863            5566778999999999999999999 


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+.+|||||+      .+++|||.++++ +|||+|+|.+...|+|+.+| |.
T Consensus       693 g~~~vLVaT~------~~~~GIDlp~v~-~VI~yd~p~s~~~~iQr~GR-GR  736 (797)
T 4a2q_A          693 KDNRLLIATS------VADEGIDIVQCN-LVVLYEYSGNVTKMIQVRGR-GR  736 (797)
T ss_dssp             -CCSEEEEEC------C-------CCCS-EEEEESCCSCHHHHHTC------
T ss_pred             CCceEEEEcC------chhcCCCchhCC-EEEEeCCCCCHHHHHHhcCC-CC
Confidence            9999999999      778999999999 99999999999999999988 54

>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=99.53  E-value=5.4e-15  Score=135.01  Aligned_cols=108  Identities=8%  Similarity=0.105  Sum_probs=63.9

Q ss_pred             ChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC------------CCeeEEecCCCCHHHHHHHHHHHhc-
Q psy437           19 NVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE------------RINAISYHAGLADKLRNEVQMKWIS-   82 (184)
Q Consensus        19 ~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~------------gi~~~~~hg~l~~~~R~~~~~~f~~-   82 (184)
                      .|...|.++|.+.   ..+.++||||+|++.++.++..|.+.            |.....+||+|++.+|..++++|++ 
T Consensus       613 ~K~~~L~~lL~~~~~~~~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~  692 (936)
T 4a2w_A          613 PKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTS  692 (936)
T ss_dssp             HHHHHHHHHHHHTTTSCTTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC---------------------------
T ss_pred             HHHHHHHHHHHHHhccCCCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhcc
Confidence            4888888888753   25678999999999999999999986            5566677999999999999999999 


Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+.+|||||+      .+++|||.++++ .|||+|+|.+...|+|+.+| |.
T Consensus       693 g~~~VLVaT~------~~~eGIDlp~v~-~VI~yD~p~s~~~~iQr~GR-GR  736 (936)
T 4a2w_A          693 KDNRLLIATS------VADEGIDIVQCN-LVVLYEYSGNVTKMIQVRGR-GR  736 (936)
T ss_dssp             -CCSEEEEEC------C------CCCCS-EEEEESCCSCSHHHHCC------
T ss_pred             CCeeEEEEeC------chhcCCcchhCC-EEEEeCCCCCHHHHHHhcCC-CC
Confidence            9999999999      778999999999 99999999999999999987 53

>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=99.53  E-value=6.5e-16  Score=126.93  Aligned_cols=107  Identities=12%  Similarity=0.210  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHH
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDS   99 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~   99 (184)
                      +...+.+++... ...++||||+|++.++.+++.|.+.++.+..+||++++++|..+++.|++|+.+|||||+      .
T Consensus       246 ~~~~l~~~~~~~-~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~------~  318 (394)
T 1fuu_A          246 KYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD------L  318 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhcC-CCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECC------h
Confidence            566666666543 567899999999999999999999999999999999999999999999999999999999      7


Q ss_pred             HHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437          100 VAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       100 ~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +++|+|.++++ .|+|+++|.+...|+|+..|.|.
T Consensus       319 ~~~Gldi~~~~-~Vi~~~~p~s~~~~~Qr~GR~~R  352 (394)
T 1fuu_A          319 LARGIDVQQVS-LVINYDLPANKENYIHRIGRGGR  352 (394)
T ss_dssp             -----------------------------------
T ss_pred             hhcCCCcccCC-EEEEeCCCCCHHHHHHHcCcccC
Confidence            89999999999 99999999999999999976543

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

Probab=99.52  E-value=1e-14  Score=122.85  Aligned_cols=118  Identities=9%  Similarity=-0.019  Sum_probs=94.8

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHH
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSV  100 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~  100 (184)
                      ...+.+.+.+  .++++||||+|++.++.+++.|.+.++++..+||+    +|.+++++|++|+.+|||||+      .+
T Consensus       160 ~~~~~~~l~~--~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~------v~  227 (431)
T 2v6i_A          160 WNSGYEWITE--FDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTD------IS  227 (431)
T ss_dssp             CSSCCHHHHS--CSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECG------GG
T ss_pred             HHHHHHHHHc--CCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECc------hH
Confidence            3444556655  46789999999999999999999999999999997    688999999999999999999      77


Q ss_pred             HHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          101 AAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       101 a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ++|+|.+ +. .|++++.                 .....+|  +.+.|++++.|.+..+|+|++  +|+||.
T Consensus       228 e~GiDip-~~-~VI~~g~-----------------~~~~v~d--~~~~vi~~~~p~~~~~~~Qr~--GR~GR~  277 (431)
T 2v6i_A          228 EMGANFK-AD-RVIDPRK-----------------TIKPILL--DGRVSMQGPIAITPASAAQRR--GRIGRN  277 (431)
T ss_dssp             GTSCCCC-CS-EEEECCE-----------------EEEEEEE--TTEEEEEEEEECCHHHHHHHH--TTSSCC
T ss_pred             HcCcccC-Cc-EEEecCc-----------------cccceec--ccceeecccccCCHHHHHHhh--hccCCC
Confidence            8999998 76 7777762                 2222246  567888888888888888888  466664

>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=99.52  E-value=5.2e-15  Score=124.92  Aligned_cols=117  Identities=11%  Similarity=-0.012  Sum_probs=83.5

Q ss_pred             HHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHH
Q psy437           24 VISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAA  103 (184)
Q Consensus        24 L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~g  103 (184)
                      +...+.+  .+.++||||+|++.++.+++.|.+.|+++..+||    ++|..+++.|++|+.+|||||+      .+++|
T Consensus       169 ~~~~l~~--~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~------v~e~G  236 (440)
T 1yks_A          169 GHDWILA--DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATD------IAEMG  236 (440)
T ss_dssp             SCHHHHH--CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESS------STTCC
T ss_pred             HHHHHHh--cCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECC------hhhee
Confidence            3344544  4679999999999999999999999999999999    4688999999999999999999      77899


Q ss_pred             HHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          104 LAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       104 L~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|.+ ++ .|||.|.                 .+--.++.+.-+.+++++.|.+..+|+|+++  |+||.
T Consensus       237 iDip-v~-~VI~~g~-----------------~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~G--R~GR~  285 (440)
T 1yks_A          237 ANLC-VE-RVLDCRT-----------------AFKPVLVDEGRKVAIKGPLRISASSAAQRRG--RIGRN  285 (440)
T ss_dssp             TTCC-CS-EEEECCE-----------------EEEEEEETTTTEEEEEEEEECCHHHHHHHHT--TSSCC
T ss_pred             eccC-ce-EEEeCCc-----------------cceeeecccccceeeccccccCHHHHHHhcc--ccCCC
Confidence            9999 99 8888652                 1111133333367777777777777777773  55553

>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=99.52  E-value=2.7e-13  Score=111.26  Aligned_cols=85  Identities=18%  Similarity=0.223  Sum_probs=77.7

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccc
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPD  160 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~  160 (184)
                      ||+++++..++.++..|...|+.+..+|+++|+..|..+.+.|++|+..|+++       +|+|++++|+++++|.+...
T Consensus       254 lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~  333 (391)
T 1xti_A          254 VIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDT  333 (391)
T ss_dssp             EEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHH
T ss_pred             EEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHH
Confidence            66666667899999999999999999999999999999999999999999999       69999999999999999999


Q ss_pred             cccccccccCCccc
Q psy437          161 YLPPILDLRLGRED  174 (184)
Q Consensus       161 y~~~i~~~~~~r~~  174 (184)
                      |+|+++  |+||.+
T Consensus       334 ~~Qr~G--R~~R~g  345 (391)
T 1xti_A          334 YLHRVA--RAGRFG  345 (391)
T ss_dssp             HHHHHC--BCSSSC
T ss_pred             HHHhcc--cccCCC
Confidence            999995  777753

>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=99.51  E-value=1.4e-14  Score=127.09  Aligned_cols=120  Identities=11%  Similarity=-0.036  Sum_probs=97.9

Q ss_pred             HHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHH
Q psy437           23 EVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAA  102 (184)
Q Consensus        23 ~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~  102 (184)
                      .+...+.+  ...++||||+|++.|+.+++.|.+.|+++..+||+    +|.+++++|++|+.+|||||+      .+++
T Consensus       346 ~ll~~l~~--~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTd------v~~r  413 (618)
T 2whx_A          346 TGFDWITD--YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTD------ISEM  413 (618)
T ss_dssp             SSCHHHHH--CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECG------GGGT
T ss_pred             HHHHHHHh--CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECc------HHHc
Confidence            34445544  46799999999999999999999999999999985    788999999999999999999      8899


Q ss_pred             HHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCccccccccccccCCccc
Q psy437          103 ALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       103 gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                      |+|.+ ++ .||+++++.+              +++  .|..+-+.+++++.|.+.++|+|+++  |+||.+
T Consensus       414 GiDi~-v~-~VId~g~~~~--------------P~~--~~~~~~~~~i~~d~P~s~~~yiQR~G--RaGR~g  465 (618)
T 2whx_A          414 GANFR-AG-RVIDPRRCLK--------------PVI--LTDGPERVILAGPIPVTPASAAQRRG--RIGRNP  465 (618)
T ss_dssp             TCCCC-CS-EEEECCEEEE--------------EEE--ECSSSCEEEEEEEEECCHHHHHHHHT--TSSCCT
T ss_pred             CcccC-ce-EEEECcceec--------------cee--cccCCCceEEcccccCCHHHHHHhcc--ccCCCC
Confidence            99996 98 8988873211              111  24555578899999999999999994  666653

>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=99.51  E-value=1.5e-14  Score=128.87  Aligned_cols=123  Identities=15%  Similarity=0.072  Sum_probs=100.2

Q ss_pred             CCCCCCeEEE-----EEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKYE-----ILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y~-----v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      |.+||...-.     ......|...|.+.+... ..+.|+||||+|++.++.++..|.+.|+++.++||++++.++..+.
T Consensus       405 Ptn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia  484 (853)
T 2fsf_A          405 PTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVA  484 (853)
T ss_dssp             CCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHH
T ss_pred             CCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHH
Confidence            4567765322     223346899999888653 2567899999999999999999999999999999999988888888


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcCC--------------------------------c----EEEeeCCCChH
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQERI--------------------------------N----AISYHAGLADK  121 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi--------------------------------~----~~vih~~~p~~  121 (184)
                      ++|+.|  .|+|||+      .++||+|++..                                .    .+||++++|.+
T Consensus       485 ~agr~G--~VtIATn------mAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes  556 (853)
T 2fsf_A          485 QAGYPA--AVTIATN------MAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHES  556 (853)
T ss_dssp             TTTSTT--CEEEEES------CCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSS
T ss_pred             hcCCCC--eEEEecc------cccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCC
Confidence            999887  6999999      77889888763                                1    28999999999


Q ss_pred             HHHHHHHHhhCCC
Q psy437          122 LRNEVQMKWISNK  134 (184)
Q Consensus       122 ~r~~~~~~f~~~~  134 (184)
                      .|.|+|+.+++|.
T Consensus       557 ~riy~qr~GRTGR  569 (853)
T 2fsf_A          557 RRIDNQLRGRSGR  569 (853)
T ss_dssp             HHHHHHHHTTSSG
T ss_pred             HHHHHhhcccccc
Confidence            9999999877663

>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=99.50  E-value=1.1e-14  Score=127.96  Aligned_cols=97  Identities=21%  Similarity=0.203  Sum_probs=79.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEE
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAI  112 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~  112 (184)
                      ...++||||+|++.++.+++.|.+.|+++..+||+|++++       |.+++.+|||||+      .+++|||.+ ++ .
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATd------VaerGIDId-V~-~  459 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATD------ALMTGYTGD-FD-S  459 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECT------THHHHCCCC-BS-E
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECC------hHHccCCCC-Cc-E
Confidence            5678999999999999999999999999999999999876       4567779999999      889999986 98 8


Q ss_pred             EeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecC-----------CCCCccccccccccccCCc
Q psy437          113 SYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHS-----------LVLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       113 vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~-----------~p~~~e~y~~~i~~~~~~r  172 (184)
                      |||.|+                          .+++|+|||           +|.+.++|+||++  |+||
T Consensus       460 VI~~Gl--------------------------~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiG--RtGR  502 (666)
T 3o8b_A          460 VIDCNT--------------------------CVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRG--RTGR  502 (666)
T ss_dssp             EEECCE--------------------------EEEEEEECCCSSSCEEEEEEEECBHHHHHHHHT--TBCS
T ss_pred             EEecCc--------------------------ccccccccccccccccccccCcCCHHHHHHHhc--cCCC
Confidence            887662                          235666666           7777777777774  5555

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

Probab=99.49  E-value=5.7e-14  Score=130.01  Aligned_cols=100  Identities=9%  Similarity=0.073  Sum_probs=86.5

Q ss_pred             CCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeE-EecCCCCHHHHHHHHHHHhcc
Q psy437            5 FNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAI-SYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus         5 ~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~-~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      ...+|+...+... ++...|.+++..  .+.++||||+|+..++.++..|...|+++. .+||.     |.+ +++|++|
T Consensus       283 ~~~~~i~~~~~~~-~k~~~L~~ll~~--~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G  353 (1104)
T 4ddu_A          283 SVARNITHVRISS-RSKEKLVELLEI--FRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVG  353 (1104)
T ss_dssp             CCCCCEEEEEESC-CCHHHHHHHHHH--HCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHT
T ss_pred             CCcCCceeEEEec-CHHHHHHHHHHh--cCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCC
Confidence            4456776555544 567888888876  358999999999999999999999999998 99992     555 9999999


Q ss_pred             CceEEEE----EeecccHHHHHHHHHhcC-CcEEEeeCCCCh
Q psy437           84 KVHVGHW----TVVSKECDSVAAALAQER-INAISYHAGLAD  120 (184)
Q Consensus        84 ~~~vlVa----T~tr~~~e~~a~gL~~~g-i~~~vih~~~p~  120 (184)
                      +.+||||    |+      .+++|||.++ |+ +|||+|+|.
T Consensus       354 ~~~VLVatas~Td------vlarGIDip~~V~-~VI~~d~P~  388 (1104)
T 4ddu_A          354 KINILIGVQAYYG------KLTRGVDLPERIK-YVIFWGTPS  388 (1104)
T ss_dssp             SCSEEEEETTTHH------HHCCSCCCTTTCC-EEEEESCCE
T ss_pred             CCCEEEEecCCCC------eeEecCcCCCCCC-EEEEECCCC
Confidence            9999999    88      8899999999 99 999999998

>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=99.21  E-value=3.6e-15  Score=110.33  Aligned_cols=87  Identities=16%  Similarity=0.129  Sum_probs=81.5

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLI  157 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~  157 (184)
                      .++||+|+++..++.++..|...|+.+..+|+++++..|..+.+.|++|++.|+++       +|+|++++|+++++|.+
T Consensus        31 ~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~  110 (170)
T 2yjt_D           31 TRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRS  110 (170)
Confidence            47999999999999999999999999999999999999999999999999999998       59999999999999999


Q ss_pred             ccccccccccccCCcc
Q psy437          158 KPDYLPPILDLRLGRE  173 (184)
Q Consensus       158 ~e~y~~~i~~~~~~r~  173 (184)
                      ...|+|+++  |+||.
T Consensus       111 ~~~~~qr~G--R~~R~  124 (170)
T 2yjt_D          111 GDTYLHRIG--RTARA  124 (170)
Confidence            999999995  55553

>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=99.47  E-value=6.9e-14  Score=125.15  Aligned_cols=98  Identities=9%  Similarity=0.001  Sum_probs=79.0

Q ss_pred             CCCCCCeEE-----EEEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHH
Q psy437            4 SFNRANLKY-----EILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQ   77 (184)
Q Consensus         4 s~~R~Nl~y-----~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~   77 (184)
                      +.+||.+.-     .......|...|.+.+.+. ..+.|+||||+|++.++.++..|.+.|+++.++||++.+.++..+.
T Consensus       424 Ptn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia  503 (922)
T 1nkt_A          424 PTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIA  503 (922)
T ss_dssp             CCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHH
T ss_pred             CCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHH
Confidence            456676542     2223345888888888653 2567899999999999999999999999999999999888888888


Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcCC
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQERI  109 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi  109 (184)
                      +.|+.|  .|+|||+      .++||+|++..
T Consensus       504 ~agr~G--~VtIATn------mAgRGtDI~l~  527 (922)
T 1nkt_A          504 VAGRRG--GVTVATN------MAGRGTDIVLG  527 (922)
T ss_dssp             TTTSTT--CEEEEET------TCSTTCCCCTT
T ss_pred             hcCCCC--eEEEecc------hhhcCccccCC
Confidence            888877  6899999      77889888865

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

Probab=99.46  E-value=1.6e-13  Score=125.92  Aligned_cols=110  Identities=15%  Similarity=0.230  Sum_probs=95.7

Q ss_pred             EccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCC------------------------------------
Q psy437           16 PKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI------------------------------------   59 (184)
Q Consensus        16 ~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi------------------------------------   59 (184)
                      +...+...|.+.+.+. ...++||||+|++.|+.++..|...++                                    
T Consensus       319 ~~~~~~~~li~~l~~~-~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~  397 (997)
T 4a4z_A          319 PSKKTWPEIVNYLRKR-ELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSL  397 (997)
T ss_dssp             CCTTHHHHHHHHHHHT-TCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHhC-CCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHH
Confidence            4445788888888764 667999999999999999999987665                                    


Q ss_pred             ---eeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh---------HHHHHHH
Q psy437           60 ---NAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD---------KLRNEVQ  127 (184)
Q Consensus        60 ---~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~---------~~r~~~~  127 (184)
                         .+.++||+|++.+|..+++.|.+|..+|||||+      .++.|+|.++ . .|++.++|+         +..+|+|
T Consensus       398 l~~gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~------~~a~GIDiP~-~-~VVi~~~~k~dg~~~~~~s~~~y~Q  469 (997)
T 4a4z_A          398 LERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATE------TFAMGLNLPT-R-TVIFSSIRKHDGNGLRELTPGEFTQ  469 (997)
T ss_dssp             HTTTEEEECTTSCHHHHHHHHHHHHTTCCSEEEECT------HHHHSCCCCC-S-EEEESCSEEEETTEEEECCHHHHHH
T ss_pred             hhcCeeeecCCCCHHHHHHHHHHHHCCCCcEEEEch------HhhCCCCCCC-c-eEEEeccccccCccCCCCCHHHHhH
Confidence               468999999999999999999999999999999      8899999999 4 677777777         9999999


Q ss_pred             HHhhCCC
Q psy437          128 MKWISNK  134 (184)
Q Consensus       128 ~~f~~~~  134 (184)
                      +.++.|.
T Consensus       470 r~GRAGR  476 (997)
T 4a4z_A          470 MAGRAGR  476 (997)
T ss_dssp             HHGGGCC
T ss_pred             Hhccccc
Confidence            9987664

>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=99.45  E-value=2.4e-13  Score=117.33  Aligned_cols=89  Identities=10%  Similarity=0.132  Sum_probs=82.6

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhc---CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEec
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQE---RINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIH  152 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~---gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~  152 (184)
                      ...++||++++++.|+.++..|...   ++.+..+|+++++..|..+.+.|++|+..|+||       +|+|++++||++
T Consensus       338 ~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiDip~v~~VI~~  417 (563)
T 3i5x_A          338 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQI  417 (563)
T ss_dssp             TCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEE
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCCcccCCEEEEE
Confidence            3558999999999999999999765   999999999999999999999999999999999       699999999999


Q ss_pred             CCCCCccccccccccccCCcc
Q psy437          153 SLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       153 ~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ++|.+.++|+|+++  |+||.
T Consensus       418 ~~p~s~~~y~Qr~G--RagR~  436 (563)
T 3i5x_A          418 GVPSELANYIHRIG--RTARS  436 (563)
T ss_dssp             SCCSSTTHHHHHHT--TSSCT
T ss_pred             CCCCchhhhhhhcC--ccccC
Confidence            99999999999995  66665

>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=99.45  E-value=7e-14  Score=125.35  Aligned_cols=95  Identities=8%  Similarity=0.012  Sum_probs=89.3

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh-----------CCCeeEEecCCCCHHHHHHHHHHHh-----ccCceEEEEEeeccc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ-----------ERINAISYHAGLADKLRNEVQMKWI-----SNKVHVGHWTVVSKE   96 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~-----------~gi~~~~~hg~l~~~~R~~~~~~f~-----~g~~~vlVaT~tr~~   96 (184)
                      .++++||||++++.++.+++.|.+           .++.+..+||+|++++|..+++.|.     +|..+|||||+    
T Consensus       302 ~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~----  377 (773)
T 2xau_A          302 EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTN----  377 (773)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECT----
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCc----
Confidence            578999999999999999999985           5888999999999999999999999     99999999999    


Q ss_pred             HHHHHHHHHhcCCcEEEeeCCC------------------ChHHHHHHHHHhhCCC
Q psy437           97 CDSVAAALAQERINAISYHAGL------------------ADKLRNEVQMKWISNK  134 (184)
Q Consensus        97 ~e~~a~gL~~~gi~~~vih~~~------------------p~~~r~~~~~~f~~~~  134 (184)
                        .+++|+|+++++ +||++|+                  |.+..+|+||.++.|.
T Consensus       378 --iae~GidIp~v~-~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR  430 (773)
T 2xau_A          378 --IAETSLTIDGIV-YVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGR  430 (773)
T ss_dssp             --HHHHTCCCTTEE-EEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGS
T ss_pred             --HHHhCcCcCCeE-EEEeCCCccceeeccccCccccccccCCHHHHHhhccccCC
Confidence              889999999999 9999999                  8899999999988775

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

Probab=99.45  E-value=2.6e-13  Score=117.88  Aligned_cols=89  Identities=10%  Similarity=0.132  Sum_probs=82.5

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhc---CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEec
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQE---RINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIH  152 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~---gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~  152 (184)
                      ...++||+|+++..|+.++..|...   ++.+..+|+++++..|..+++.|++|+..|+||       +|+|++++||++
T Consensus       287 ~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiDip~v~~VI~~  366 (579)
T 3sqw_A          287 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQI  366 (579)
T ss_dssp             TCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCCCTTCCEEEEE
T ss_pred             CCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCCcccCCEEEEc
Confidence            3568999999999999999999766   999999999999999999999999999999999       699999999999


Q ss_pred             CCCCCccccccccccccCCcc
Q psy437          153 SLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       153 ~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ++|.+.+.|+|+++  |+||.
T Consensus       367 ~~p~s~~~y~Qr~G--RagR~  385 (579)
T 3sqw_A          367 GVPSELANYIHRIG--RTARS  385 (579)
T ss_dssp             SCCSSTTHHHHHHT--TSSCT
T ss_pred             CCCCCHHHhhhhcc--ccccC
Confidence            99999999999995  66664

>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=99.44  E-value=4.9e-13  Score=110.51  Aligned_cols=84  Identities=14%  Similarity=0.170  Sum_probs=69.2

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccc
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPD  160 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~  160 (184)
                      ||+++++..++.++..|...++.+..+|+++++..|..+.+.|++|+..|+|+       +|+|++++||++++|.+..+
T Consensus       284 lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~  363 (414)
T 3eiq_A          284 VIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNREN  363 (414)
T ss_dssp             EEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHH
T ss_pred             EEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHH
Confidence            56666667899999999999999999999999999999999999999999999       69999999999999999999


Q ss_pred             cccccccccCCcc
Q psy437          161 YLPPILDLRLGRE  173 (184)
Q Consensus       161 y~~~i~~~~~~r~  173 (184)
                      |+|+++  |+||.
T Consensus       364 ~~Qr~G--R~gR~  374 (414)
T 3eiq_A          364 YIHRIG--RGGRF  374 (414)
T ss_dssp             HHHHSC--CC---
T ss_pred             hhhhcC--cccCC
Confidence            999995  66664

>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=99.44  E-value=1.2e-13  Score=126.53  Aligned_cols=107  Identities=12%  Similarity=0.042  Sum_probs=98.2

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHh-CCCeeEEecCCCCHHHHHHHHHHHhccC--ceEEEEEeecc
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQ-ERINAISYHAGLADKLRNEVQMKWISNK--VHVGHWTVVSK   95 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~-~gi~~~~~hg~l~~~~R~~~~~~f~~g~--~~vlVaT~tr~   95 (184)
                      .|...|.+++... .+.++||||+++..++.++..|.+ .|+++..+||+|++.+|..++++|++|+  .+|||||+   
T Consensus       489 ~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~---  564 (968)
T 3dmq_A          489 PRVEWLMGYLTSH-RSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSE---  564 (968)
T ss_dssp             HHHHHHHHHHHHT-SSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSC---
T ss_pred             HHHHHHHHHHHhC-CCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecc---
Confidence            3888899988763 778999999999999999999995 5999999999999999999999999998  99999999   


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                         .+++|+|.++++ .||++++|.+...|+|+..|.+
T Consensus       565 ---v~~~GlDl~~~~-~VI~~d~p~~~~~~~Q~~GR~~  598 (968)
T 3dmq_A          565 ---IGSEGRNFQFAS-HMVMFDLPFNPDLLEQRIGRLD  598 (968)
T ss_dssp             ---CTTCSSCCTTCC-EEECSSCCSSHHHHHHHHHTTS
T ss_pred             ---hhhcCCCcccCc-EEEEecCCCCHHHHHHHhhccc
Confidence               678899999999 9999999999999999996643

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.43  E-value=9.8e-13  Score=104.42  Aligned_cols=106  Identities=12%  Similarity=0.044  Sum_probs=80.2

Q ss_pred             cChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhC-CCeeEEecCCCCHHHHHHHHHHHhcc-Cce-EEEEEee
Q psy437           18 KNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISN-KVH-VGHWTVV   93 (184)
Q Consensus        18 ~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~hg~l~~~~R~~~~~~f~~g-~~~-vlVaT~t   93 (184)
                      ..|+..|.++|.+. ..+.++||||+++..++.+...|... |+++..+||++++++|..++++|.++ ..+ +|++|. 
T Consensus        95 s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~-  173 (271)
T 1z5z_A           95 SGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK-  173 (271)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECC-
T ss_pred             CHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehh-
Confidence            35888888888653 15679999999999999999999885 99999999999999999999999998 677 677888 


Q ss_pred             cccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHh
Q psy437           94 SKECDSVAAALAQERINAISYHAGLADKLRNEVQMKW  130 (184)
Q Consensus        94 r~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f  130 (184)
                           ..+.||+..+.+ .|||+|+|-+...+.|+..
T Consensus       174 -----~~g~Glnl~~a~-~VI~~d~~wnp~~~~Q~~g  204 (271)
T 1z5z_A          174 -----AGGFGINLTSAN-RVIHFDRWWNPAVEDQATD  204 (271)
T ss_dssp             -----TTCCCCCCTTCS-EEEECSCCSCTTTC-----
T ss_pred             -----hhcCCcCcccCC-EEEEECCCCChhHHHHHHH
Confidence                 334566666655 5666666655555555553

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

Probab=99.42  E-value=5.6e-13  Score=110.34  Aligned_cols=101  Identities=18%  Similarity=0.154  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHhc---cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           71 KLRNEVQMKWIS---NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        71 ~~R~~~~~~f~~---g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      ..+...+..+..   ...++||+++++..++.++..|...|+.+..+|+++++..|..+.+.|++|+..|+|+       
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            444444444443   2457999999999999999999999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|+|++++|+++++|.+...|+|+++  |+||.
T Consensus       340 idip~v~~Vi~~~~p~s~~~~~Qr~G--R~gR~  370 (417)
T 2i4i_A          340 LDISNVKHVINFDLPSDIEEYVHRIG--RTGRV  370 (417)
T ss_dssp             SCCCCEEEEEESSCCSSHHHHHHHHT--TBCC-
T ss_pred             CCcccCCEEEEEcCCCCHHHHHHhcC--ccccC
Confidence            69999999999999999999999995  66664

>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=99.41  E-value=1.7e-13  Score=126.51  Aligned_cols=98  Identities=14%  Similarity=0.183  Sum_probs=79.4

Q ss_pred             CCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCc
Q psy437            6 NRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV   85 (184)
Q Consensus         6 ~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~   85 (184)
                      ..+|+...+. ...+...|.+++..  .+.++||||+|++.|+.+++.|... +++..+||+++     .++++|++|+.
T Consensus       250 ~~~~i~~~~~-~~~k~~~L~~ll~~--~~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~  320 (1054)
T 1gku_B          250 TVRNVEDVAV-NDESISTLSSILEK--LGTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEI  320 (1054)
T ss_dssp             CCCCEEEEEE-SCCCTTTTHHHHTT--SCSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSC
T ss_pred             CcCCceEEEe-chhHHHHHHHHHhh--cCCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCC
Confidence            3566665555 34567777777755  3678999999999999999999988 99999999983     78899999999


Q ss_pred             eEEEE----EeecccHHHHHHHHHhcC-CcEEEeeCCCC
Q psy437           86 HVGHW----TVVSKECDSVAAALAQER-INAISYHAGLA  119 (184)
Q Consensus        86 ~vlVa----T~tr~~~e~~a~gL~~~g-i~~~vih~~~p  119 (184)
                      +||||    |+      .+++|||.++ ++ +|||+|+|
T Consensus       321 ~VLVaTas~Td------v~~rGIDip~VI~-~VI~~~~P  352 (1054)
T 1gku_B          321 DHLIGTAHYYG------TLVRGLDLPERIR-FAVFVGCP  352 (1054)
T ss_dssp             SEEEEECC------------CCSCCTTTCC-EEEEESCC
T ss_pred             cEEEEecCCCC------eeEeccccCCccc-EEEEeCCC
Confidence            99999    78      8899999999 59 99999999

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

Probab=99.40  E-value=6.2e-13  Score=122.18  Aligned_cols=106  Identities=15%  Similarity=0.206  Sum_probs=91.6

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe---------------------------------------e
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN---------------------------------------A   61 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~---------------------------------------~   61 (184)
                      +..|+..+... ...++||||+|+..|+.++..|...++.                                       +
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            44566666543 5568999999999999999999775543                                       6


Q ss_pred             EEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee----CCC----ChHHHHHHHHHhhCC
Q psy437           62 ISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYH----AGL----ADKLRNEVQMKWISN  133 (184)
Q Consensus        62 ~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih----~~~----p~~~r~~~~~~f~~~  133 (184)
                      .++||+|++.+|..+++.|++|.++|||||+      .++.|+|.++++ +|||    +|.    |.+..+|+|+.+|.|
T Consensus       410 ~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~------~la~GIDiP~~~-vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAG  482 (1010)
T 2xgj_A          410 GIHHSGLLPILKEVIEILFQEGFLKVLFATE------TFSIGLNMPAKT-VVFTSVRKWDGQQFRWVSGGEYIQMSGRAG  482 (1010)
T ss_dssp             EEESTTSCHHHHHHHHHHHHTTCCSEEEEEG------GGGGSTTCCBSE-EEESCSEEECSSCEEECCHHHHHHHHTTBC
T ss_pred             eEECCCCCHHHHHHHHHHHhcCCCcEEEEeh------HhhccCCCCCce-EEEeCCcccCCcCCccCCHHHHhHhhhhcc
Confidence            7899999999999999999999999999999      678899999998 8999    898    889999999998766


Q ss_pred             C
Q psy437          134 K  134 (184)
Q Consensus       134 ~  134 (184)
                      .
T Consensus       483 R  483 (1010)
T 2xgj_A          483 R  483 (1010)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=99.39  E-value=4.5e-13  Score=118.42  Aligned_cols=93  Identities=11%  Similarity=0.110  Sum_probs=85.4

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcE
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINA  111 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~  111 (184)
                      ....||||+|++.++.+++.|.+.++.+..+||+|++++|..+++.|.+  |+.+|||||+      .+++|||. +++ 
T Consensus       320 ~~g~iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATd------i~e~GlDi-~v~-  391 (677)
T 3rc3_A          320 RPGDCIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATD------AIGMGLNL-SIR-  391 (677)
T ss_dssp             CTTEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECG------GGGSSCCC-CBS-
T ss_pred             CCCCEEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCc------HHHCCcCc-Ccc-
Confidence            3456999999999999999999999999999999999999999999999  8899999999      77889999 999 


Q ss_pred             EEeeCCC--------------ChHHHHHHHHHhhCCC
Q psy437          112 ISYHAGL--------------ADKLRNEVQMKWISNK  134 (184)
Q Consensus       112 ~vih~~~--------------p~~~r~~~~~~f~~~~  134 (184)
                      .||++|+              |.+..+|+|+.+|.|.
T Consensus       392 ~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR  428 (677)
T 3rc3_A          392 RIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGR  428 (677)
T ss_dssp             EEEESCSBC-----------CBCCHHHHHHHHTTBTC
T ss_pred             EEEECCccccccccCCccccccCCHHHHHHHhcCCCC
Confidence            9999999              6678999999977664

>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=99.39  E-value=5.2e-13  Score=110.53  Aligned_cols=87  Identities=15%  Similarity=0.164  Sum_probs=82.4

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLI  157 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~  157 (184)
                      .++||++++++.++.++..|...|+.+..+|+++++..|..+.+.|++|+..|+|+       +|+|++++|+++++|.+
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s  356 (410)
T 2j0s_A          277 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN  356 (410)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSS
T ss_pred             CcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCC
Confidence            48999999999999999999999999999999999999999999999999999999       69999999999999999


Q ss_pred             ccccccccccccCCcc
Q psy437          158 KPDYLPPILDLRLGRE  173 (184)
Q Consensus       158 ~e~y~~~i~~~~~~r~  173 (184)
                      .+.|+|+++  |+||.
T Consensus       357 ~~~~~Qr~G--R~gR~  370 (410)
T 2j0s_A          357 RELYIHRIG--RSGRY  370 (410)
T ss_dssp             HHHHHHHHT--TSSGG
T ss_pred             HHHHHHhcc--cccCC
Confidence            999999995  66664

>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=99.38  E-value=7.7e-13  Score=118.56  Aligned_cols=139  Identities=10%  Similarity=0.046  Sum_probs=118.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .+.++++.+||+..+.++++.+.+.    |+++..+||+++..+|...++.+.+|+.+|+|+|+..              
T Consensus       416 ~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVV  495 (780)
T 1gm5_A          416 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVI  495 (780)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEE
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEE
Confidence            3578999999999999998887653    7899999999999999999999999999999999876              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       496 IDEaHr~g~~qr~~l~~~~~~~~vL~mSATp~p~tl~~~~~g~~~~s~i~~~p~~r~~i~~~~~~~~~~~~l~~~i~~~l  575 (780)
T 1gm5_A          496 IDEQHRFGVKQREALMNKGKMVDTLVMSATPIPRSMALAFYGDLDVTVIDEMPPGRKEVQTMLVPMDRVNEVYEFVRQEV  575 (780)
T ss_dssp             EESCCCC-----CCCCSSSSCCCEEEEESSCCCHHHHHHHTCCSSCEEECCCCSSCCCCEECCCCSSTHHHHHHHHHHHT
T ss_pred             ecccchhhHHHHHHHHHhCCCCCEEEEeCCCCHHHHHHHHhCCcceeeeeccCCCCcceEEEEeccchHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ---------------------ccHHHHHHHHHh---cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Eec
Q psy437           95 ---------------------KECDSVAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKI  143 (184)
Q Consensus        95 ---------------------~~~e~~a~gL~~---~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~  143 (184)
                                           ..++.++..|..   +++++..+|+++++..|..+.+.|++|++.|+||       +|+
T Consensus       576 ~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVaT~vie~GIDi  655 (780)
T 1gm5_A          576 MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDV  655 (780)
T ss_dssp             TTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCC
T ss_pred             hcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECCCCCccccC
Confidence                                 024667777766   6888899999999999999999999999999999       599


Q ss_pred             CCccEEEecCCCC-CccccccccccccCCcc
Q psy437          144 QWKRIIWIHSLVL-IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       144 ~~vr~v~~~~~p~-~~e~y~~~i~~~~~~r~  173 (184)
                      |++++|++++.|. +...|.|++  +|+||.
T Consensus       656 P~v~~VIi~d~~r~~l~~l~Qr~--GRaGR~  684 (780)
T 1gm5_A          656 PRANVMVIENPERFGLAQLHQLR--GRVGRG  684 (780)
T ss_dssp             TTCCEEEBCSCSSSCTTHHHHHH--HTSCCS
T ss_pred             CCCCEEEEeCCCCCCHHHHHHHh--cccCcC
Confidence            9999999999997 566667888  477774

>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=99.38  E-value=3.1e-13  Score=114.29  Aligned_cols=96  Identities=8%  Similarity=-0.070  Sum_probs=84.9

Q ss_pred             HHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHH
Q psy437           25 ISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAAL  104 (184)
Q Consensus        25 ~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL  104 (184)
                      ...+.+  ..+++||||+|++.++.+++.|.+.|+++..+||++    +.++++.|++|+.+|||||+      .+++|+
T Consensus       181 ~~~l~~--~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~----~~~~~~~f~~g~~~vLVaT~------v~~~Gi  248 (451)
T 2jlq_A          181 FDWITD--YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKT----FDTEYPKTKLTDWDFVVTTD------ISEMGA  248 (451)
T ss_dssp             CHHHHH--CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTT----HHHHGGGGGSSCCSEEEECG------GGGSSC
T ss_pred             HHHHHh--CCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHH----HHHHHHhhccCCceEEEECC------HHHhCc
Confidence            344544  456999999999999999999999999999999974    46799999999999999999      789999


Q ss_pred             HhcCCcEEEeeCC--------------------CChHHHHHHHHHhhCCC
Q psy437          105 AQERINAISYHAG--------------------LADKLRNEVQMKWISNK  134 (184)
Q Consensus       105 ~~~gi~~~vih~~--------------------~p~~~r~~~~~~f~~~~  134 (184)
                      |.++ + .|||+|                    +|.+..+|+|+.++.|.
T Consensus       249 Dip~-~-~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR  296 (451)
T 2jlq_A          249 NFRA-G-RVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR  296 (451)
T ss_dssp             CCCC-S-EEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSC
T ss_pred             CCCC-C-EEEECCCcccccccccccceeeecccccCCHHHHHHhccccCC
Confidence            9999 7 999999                    99999999999977553

>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=99.37  E-value=2.1e-12  Score=105.75  Aligned_cols=102  Identities=14%  Similarity=0.092  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           70 DKLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        70 ~~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      ...+...+..+..  ...++||+++++..++.++..|...|+++..+|+++|+..|..+.+.|++|+..|+|+       
T Consensus       227 ~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G  306 (395)
T 3pey_A          227 EADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARG  306 (395)
T ss_dssp             HHHHHHHHHHHHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSS
T ss_pred             hHHHHHHHHHHHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcC
Confidence            3455555555543  2358999999999999999999999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCC------CccccccccccccCCcc
Q psy437          141 WKIQWKRIIWIHSLVL------IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~------~~e~y~~~i~~~~~~r~  173 (184)
                      +|+|++++|+++++|.      +...|+|+++  |+||.
T Consensus       307 idip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~G--R~gR~  343 (395)
T 3pey_A          307 IDIPTVSMVVNYDLPTLANGQADPATYIHRIG--RTGRF  343 (395)
T ss_dssp             CCCTTEEEEEESSCCBCTTSSBCHHHHHHHHT--TSSCT
T ss_pred             CCcccCCEEEEcCCCCCCcCCCCHHHhhHhcc--ccccC
Confidence            6999999999999999      9999999995  66664

>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=99.37  E-value=2e-12  Score=106.67  Aligned_cols=101  Identities=15%  Similarity=0.113  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           71 KLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        71 ~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      ..+...+..+..  ...++||+++++..++.++..|...|+.+..+|+++|+..|..+.+.|++|+..|+|+       +
T Consensus       251 ~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gi  330 (412)
T 3fht_A          251 DEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGI  330 (412)
T ss_dssp             HHHHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSC
T ss_pred             HHHHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCC
Confidence            344444444443  3458999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCC------CccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVL------IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~------~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|+++++|.      +..+|+|+++  |+||.
T Consensus       331 dip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~G--R~gR~  366 (412)
T 3fht_A          331 DVEQVSVVINFDLPVDKDGNPDNETYLHRIG--RTGRF  366 (412)
T ss_dssp             CCTTEEEEEESSCCBCSSSSBCHHHHHHHHT--TSSCT
T ss_pred             CccCCCEEEEECCCCCCCCCcchheeecccC--cccCC
Confidence            999999999999994      6689999995  66764

>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=99.37  E-value=3.1e-13  Score=125.13  Aligned_cols=106  Identities=15%  Similarity=0.227  Sum_probs=85.7

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe---------------------------------------e
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN---------------------------------------A   61 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~---------------------------------------~   61 (184)
                      +..++..+.+. ...++||||+|+..|+.++..|...++.                                       +
T Consensus       429 l~~li~~l~~~-~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV  507 (1108)
T 3l9o_A          429 IYKIVKMIWKK-KYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGI  507 (1108)
T ss_dssp             HHHHHHHHHHT-TCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTE
T ss_pred             HHHHHHHHHhc-CCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCe
Confidence            34455555443 5679999999999999999998654332                                       6


Q ss_pred             EEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCC--------hHHHHHHHHHhhCC
Q psy437           62 ISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLA--------DKLRNEVQMKWISN  133 (184)
Q Consensus        62 ~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p--------~~~r~~~~~~f~~~  133 (184)
                      .++||+|++.+|..+++.|.+|.++|||||+      .+++|+|.++++ +|||++.|        -+..+|+|+.+|.|
T Consensus       508 ~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~------vla~GIDiP~v~-~VI~~~~~~d~~~~r~iS~~eyiQr~GRAG  580 (1108)
T 3l9o_A          508 GIHHSGLLPILKEVIEILFQEGFLKVLFATE------TFSIGLNMPAKT-VVFTSVRKWDGQQFRWVSGGEYIQMSGRAG  580 (1108)
T ss_dssp             EEECSCSCHHHHHHHHHHHHHTCCCEEEEES------CCCSCCCC--CE-EEESCSEEESSSCEEECCHHHHHHHHHHSC
T ss_pred             eeecCCCCHHHHHHHHHHHhCCCCeEEEECc------HHhcCCCCCCce-EEEecCcccCccccccCCHHHHHHhhcccC
Confidence            8899999999999999999999999999999      568899999999 89988774        36778999998765


Q ss_pred             C
Q psy437          134 K  134 (184)
Q Consensus       134 ~  134 (184)
                      .
T Consensus       581 R  581 (1108)
T 3l9o_A          581 R  581 (1108)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.36  E-value=2.4e-12  Score=104.34  Aligned_cols=102  Identities=16%  Similarity=0.157  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHHh-ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           70 DKLRNEVQMKWI-SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        70 ~~~R~~~~~~f~-~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      ..++...+..+. ....++||+++++..++.++..|...|+.+..+|+++|+..|..+.+.|++|+..|+++       +
T Consensus       223 ~~~~~~~l~~~l~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gi  302 (367)
T 1hv8_A          223 ENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGI  302 (367)
T ss_dssp             GGGHHHHHHHHHCSTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHC
T ss_pred             hHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCC
Confidence            344555544444 45668999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|+++++|.+..+|+|+++  |+||.
T Consensus       303 d~~~~~~Vi~~~~~~s~~~~~Q~~G--R~~R~  332 (367)
T 1hv8_A          303 DVNDLNCVINYHLPQNPESYMHRIG--RTGRA  332 (367)
T ss_dssp             CCSCCSEEEESSCCSCHHHHHHHST--TTCCS
T ss_pred             CcccCCEEEEecCCCCHHHhhhccc--ccccC
Confidence            9999999999999999999999995  66665

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

Probab=99.36  E-value=3.9e-12  Score=112.92  Aligned_cols=105  Identities=18%  Similarity=0.153  Sum_probs=86.3

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCC------------------------------------CeeEE
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER------------------------------------INAIS   63 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~g------------------------------------i~~~~   63 (184)
                      +...+.+.+.   .+.++||||+|++.++.++..|.+..                                    ..+.+
T Consensus       241 ~~~~~~~~~~---~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~  317 (715)
T 2va8_A          241 IIAYTLDSLS---KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAY  317 (715)
T ss_dssp             HHHHHHHHHT---TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEE
T ss_pred             HHHHHHHHHh---cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEE
Confidence            4444444442   56899999999999999999998642                                    24888


Q ss_pred             ecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee----CC-------CChHHHHHHHHHhhC
Q psy437           64 YHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYH----AG-------LADKLRNEVQMKWIS  132 (184)
Q Consensus        64 ~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih----~~-------~p~~~r~~~~~~f~~  132 (184)
                      +||+|++++|..+++.|.+|..+|||||+      .++.|+|.++++ +||+    ++       .|.+..+|.|+.+|.
T Consensus       318 ~h~~l~~~~r~~v~~~f~~g~~~vlvaT~------~l~~Gidip~~~-~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRa  390 (715)
T 2va8_A          318 HHAGLSKALRDLIEEGFRQRKIKVIVATP------TLAAGVNLPART-VIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRA  390 (715)
T ss_dssp             ECTTSCHHHHHHHHHHHHTTCSCEEEECG------GGGGSSCCCBSE-EEECCC--------------CHHHHHHHHTTB
T ss_pred             ECCCCCHHHHHHHHHHHHcCCCeEEEECh------HHhcccCCCceE-EEEeCCeeccccCCCCCCcCCHHHHHHHhhhc
Confidence            99999999999999999999999999999      778899999998 8999    77       899999999999887


Q ss_pred             CC
Q psy437          133 NK  134 (184)
Q Consensus       133 ~~  134 (184)
                      |.
T Consensus       391 GR  392 (715)
T 2va8_A          391 GR  392 (715)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.35  E-value=7.4e-13  Score=108.62  Aligned_cols=85  Identities=14%  Similarity=0.186  Sum_probs=0.0

Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcc
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKP  159 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e  159 (184)
                      +||+++++.+++.++..|...|+.+..+|+++|+..|..+.+.|++|+..|+|+       +|+|++++|+++++|.+..
T Consensus       262 ~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~  341 (394)
T 1fuu_A          262 AVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKE  341 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHH
Confidence            477777778899999999999999999999999999999999999999999998       6999999999999999999


Q ss_pred             ccccccccccCCcc
Q psy437          160 DYLPPILDLRLGRE  173 (184)
Q Consensus       160 ~y~~~i~~~~~~r~  173 (184)
                      .|+|+++  |+||.
T Consensus       342 ~~~Qr~G--R~~R~  353 (394)
T 1fuu_A          342 NYIHRIG--RGGRF  353 (394)
T ss_dssp             --------------
T ss_pred             HHHHHcC--cccCC
Confidence            9999995  66664

>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=99.35  E-value=3.1e-12  Score=105.45  Aligned_cols=102  Identities=17%  Similarity=0.135  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           70 DKLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        70 ~~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      ...+...+..+..  ...++||+++++..++.++..|...|+.+..+|+++++..|..+.+.|++|+..|+|+       
T Consensus       242 ~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~G  321 (400)
T 1s2m_A          242 ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG  321 (400)
T ss_dssp             GGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSS
T ss_pred             hhhHHHHHHHHHhhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccC
Confidence            3444444444443  2348999999999999999999999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|+|++++|+++++|.+...|+|+++  |+||.
T Consensus       322 idip~~~~Vi~~~~p~s~~~~~Qr~G--R~gR~  352 (400)
T 1s2m_A          322 IDIQAVNVVINFDFPKTAETYLHRIG--RSGRF  352 (400)
T ss_dssp             CCCTTEEEEEESSCCSSHHHHHHHHC--BSSCT
T ss_pred             CCccCCCEEEEeCCCCCHHHHHHhcc--hhcCC
Confidence            69999999999999999999999995  66665

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

Probab=99.34  E-value=3.8e-13  Score=118.92  Aligned_cols=97  Identities=9%  Similarity=-0.062  Sum_probs=83.0

Q ss_pred             HHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHH
Q psy437           24 VISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAA  103 (184)
Q Consensus        24 L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~g  103 (184)
                      +...+.+  ...++||||+|++.++.+++.|.+.++++..+||+    +|.++++.|++|+.+|||||+      .+++|
T Consensus       402 ~l~~l~~--~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTd------v~e~G  469 (673)
T 2wv9_A          402 GFEWITD--YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTD------ISEMG  469 (673)
T ss_dssp             CCHHHHS--CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECG------GGGTT
T ss_pred             HHHHHHh--CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECc------hhhcc
Confidence            3445544  56799999999999999999999999999999994    799999999999999999999      78999


Q ss_pred             HHhcCCcEEEee--------------------CCCChHHHHHHHHHhhCCC
Q psy437          104 LAQERINAISYH--------------------AGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       104 L~~~gi~~~vih--------------------~~~p~~~r~~~~~~f~~~~  134 (184)
                      +|.+ ++ .|||                    +++|.+..+|+|+..|.|.
T Consensus       470 IDip-v~-~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR  518 (673)
T 2wv9_A          470 ANFG-AS-RVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGR  518 (673)
T ss_dssp             CCCC-CS-EEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSC
T ss_pred             eeeC-Cc-EEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCC
Confidence            9999 98 8888                    4577777777777765544

>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=99.33  E-value=2.8e-12  Score=113.28  Aligned_cols=95  Identities=16%  Similarity=0.066  Sum_probs=86.8

Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEE
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRII  149 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v  149 (184)
                      +..+.....++||+|++++.++.++..|...|+++..+|+++++..|..+.+.|+.|++.|+|+       +|+|++++|
T Consensus       438 l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lV  517 (661)
T 2d7d_A          438 IQARIERNERVLVTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLV  517 (661)
T ss_dssp             HHHHHTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEE
T ss_pred             HHHHHhcCCeEEEEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEE
Confidence            3444444568999999999999999999999999999999999999999999999999999998       699999999


Q ss_pred             EecCC-----CCCccccccccccccCCcc
Q psy437          150 WIHSL-----VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       150 ~~~~~-----p~~~e~y~~~i~~~~~~r~  173 (184)
                      ++++.     |.+.++|+|++  +|+||.
T Consensus       518 i~~d~d~~G~p~s~~~~iQr~--GRagR~  544 (661)
T 2d7d_A          518 AILDADKEGFLRSERSLIQTI--GRAARN  544 (661)
T ss_dssp             EETTTTCCTTTTSHHHHHHHH--HTTTTS
T ss_pred             EEeCcccccCCCCHHHHHHHh--CcccCC
Confidence            99998     99999999999  588886

>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=99.33  E-value=1e-12  Score=116.00  Aligned_cols=88  Identities=14%  Similarity=0.102  Sum_probs=77.0

Q ss_pred             CceEEEEEeecccHHHHHHHHHhc------CCcEEEeeCC--------CChHHHHHHHHHhhCCCceEEEE-------Ee
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQE------RINAISYHAG--------LADKLRNEVQMKWISNKVHLYNV-------WK  142 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~------gi~~~vih~~--------~p~~~r~~~~~~f~~~~~~v~va-------~D  142 (184)
                      ..++||+|.++..++.++..|...      |+++..+|++        |++..|..+++.|++|++.|+||       +|
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            578999999999999999999877      8999999999        99999999999999999999999       59


Q ss_pred             cCCccEEEecCCCCCccccccccccccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|++++|||||+|.++++|+|+++  |+||.
T Consensus       480 ip~v~~VI~~d~p~s~~~~~Qr~G--RArr~  508 (699)
T 4gl2_A          480 IKECNIVIRYGLVTNEIAMVQARG--RARAD  508 (699)
T ss_dssp             CCSCCCCEEESCCCCHHHHHHHHT--TSCSS
T ss_pred             cccCCEEEEeCCCCCHHHHHHHcC--CCCCC
Confidence            999999999999999999999995  56665

>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=99.32  E-value=1.7e-12  Score=115.34  Aligned_cols=106  Identities=15%  Similarity=0.137  Sum_probs=90.7

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC------------------C---------------CeeEEec
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE------------------R---------------INAISYH   65 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~------------------g---------------i~~~~~h   65 (184)
                      .+...+.+.+.   .+.++||||+|++.++.++..|.+.                  +               ..+.++|
T Consensus       225 ~~~~~~~~~~~---~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h  301 (720)
T 2zj8_A          225 SWEELVYDAIR---KKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHH  301 (720)
T ss_dssp             STTHHHHHHHH---TTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEEC
T ss_pred             HHHHHHHHHHh---CCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeec
Confidence            35566666553   4589999999999999999999753                  1               2388999


Q ss_pred             CCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee----CC----CChHHHHHHHHHhhCCC
Q psy437           66 AGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYH----AG----LADKLRNEVQMKWISNK  134 (184)
Q Consensus        66 g~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih----~~----~p~~~r~~~~~~f~~~~  134 (184)
                      |+|++++|..+++.|.+|..+|||||+      .++.|+|.++++ +||+    ++    .|.+..+|+|+.+|.|.
T Consensus       302 ~~l~~~~R~~v~~~f~~g~~~vlvaT~------~l~~Gvdip~~~-~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR  371 (720)
T 2zj8_A          302 AGLGRDERVLVEENFRKGIIKAVVATP------TLSAGINTPAFR-VIIRDIWRYSDFGMERIPIIEVHQMLGRAGR  371 (720)
T ss_dssp             TTSCHHHHHHHHHHHHTTSSCEEEECS------TTGGGCCCCBSE-EEECCSEECCSSSCEECCHHHHHHHHTTBCC
T ss_pred             CCCCHHHHHHHHHHHHCCCCeEEEECc------HhhccCCCCceE-EEEcCCeeecCCCCccCCHHHHHHHHhhcCC
Confidence            999999999999999999999999999      778899999998 8998    54    58999999999988776

>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=99.32  E-value=3.1e-12  Score=112.98  Aligned_cols=95  Identities=12%  Similarity=0.017  Sum_probs=86.7

Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEE
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRII  149 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v  149 (184)
                      +..+.....++||+|++++.++.++..|...|+++..+|+++++..|..+.+.|+.|++.|+|+       +|+|++++|
T Consensus       432 l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lV  511 (664)
T 1c4o_A          432 IRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLV  511 (664)
T ss_dssp             HHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEE
T ss_pred             HHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEE
Confidence            3444445568999999999999999999999999999999999999999999999999999998       699999999


Q ss_pred             EecCC-----CCCccccccccccccCCcc
Q psy437          150 WIHSL-----VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       150 ~~~~~-----p~~~e~y~~~i~~~~~~r~  173 (184)
                      ++++.     |.+.++|+|++  +|+||.
T Consensus       512 I~~d~d~~G~p~s~~~~iQr~--GRagR~  538 (664)
T 1c4o_A          512 AILDADKEGFLRSERSLIQTI--GRAARN  538 (664)
T ss_dssp             EETTTTSCSGGGSHHHHHHHH--GGGTTS
T ss_pred             EEeCCcccCCCCCHHHHHHHH--CccCcC
Confidence            99998     99999999999  588886

>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=99.32  E-value=3.7e-13  Score=114.07  Aligned_cols=96  Identities=8%  Similarity=-0.071  Sum_probs=81.7

Q ss_pred             HHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHH
Q psy437           25 ISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAAL  104 (184)
Q Consensus        25 ~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL  104 (184)
                      ...+.+  ..+++||||+|++.++.+++.|...|+++..+||.    +|..+++.|++|+.+|||||+      .+++|+
T Consensus       183 ~~~l~~--~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~------v~~~Gi  250 (459)
T 2z83_A          183 YEWITE--YAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTD------ISEMGA  250 (459)
T ss_dssp             CHHHHH--CCSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESS------CC---C
T ss_pred             HHHHHh--cCCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECC------hHHhCe
Confidence            345544  46799999999999999999999999999999995    688899999999999999999      779999


Q ss_pred             HhcCCcEEEee--------------------CCCChHHHHHHHHHhhCCC
Q psy437          105 AQERINAISYH--------------------AGLADKLRNEVQMKWISNK  134 (184)
Q Consensus       105 ~~~gi~~~vih--------------------~~~p~~~r~~~~~~f~~~~  134 (184)
                      |.++ + .|||                    +++|.+..+|+||.++.|.
T Consensus       251 Dip~-~-~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR  298 (459)
T 2z83_A          251 NFGA-S-RVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGR  298 (459)
T ss_dssp             CCSC-S-EEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSC
T ss_pred             ecCC-C-EEEECCcccccccccccccccccccCCCCCHHHHHHhccccCC
Confidence            9999 7 9999                    5699999999999876654

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

Probab=99.32  E-value=3.3e-11  Score=100.09  Aligned_cols=80  Identities=10%  Similarity=-0.002  Sum_probs=69.0

Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEE-EeeCCCChHHHHHHHHHhhCCCceEEEE-----------EecCC-ccEEEecC
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAI-SYHAGLADKLRNEVQMKWISNKVHLYNV-----------WKIQW-KRIIWIHS  153 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~-vih~~~p~~~r~~~~~~f~~~~~~v~va-----------~D~~~-vr~v~~~~  153 (184)
                      +||+|+++..|+.++..|...|+++. .+|++    .|.  .+.|++|++.|+||           +|+|+ +++||+++
T Consensus       255 ~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~  328 (414)
T 3oiy_A          255 ILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWG  328 (414)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEES
T ss_pred             EEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCchhhccCccccccCEEEEEC
Confidence            37777777899999999999999977 78885    444  89999999999998           39999 99999999


Q ss_pred             CC--CCccccccccccccCCccc
Q psy437          154 LV--LIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       154 ~p--~~~e~y~~~i~~~~~~r~~  174 (184)
                      +|  .+.+.|+|+++  |+||.+
T Consensus       329 ~p~~~~~~~y~qr~G--R~gR~g  349 (414)
T 3oiy_A          329 TPSGPDVYTYIQASG--RSSRIL  349 (414)
T ss_dssp             CCTTTCHHHHHHHHG--GGCCEE
T ss_pred             CCCCCCHHHHHHHhC--ccccCC
Confidence            99  99999999995  777754

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.30  E-value=4.8e-12  Score=107.94  Aligned_cols=103  Identities=8%  Similarity=-0.096  Sum_probs=87.0

Q ss_pred             HHHHHHHHHhhc--CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE-eecccH
Q psy437           21 LKEVISLIKAKY--SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT-VVSKEC   97 (184)
Q Consensus        21 ~~~L~~~l~~~~--~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT-~tr~~~   97 (184)
                      ...+.+.+.+..  .+.+.||||+ .+.++.+++.|.+.+.++..+||++++.+|.++++.|.+|+.+||||| +     
T Consensus       333 ~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~-----  406 (510)
T 2oca_A          333 NKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYG-----  406 (510)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHH-----
T ss_pred             HHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcC-----
Confidence            334555554321  2334556666 888899999999988899999999999999999999999999999999 8     


Q ss_pred             HHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           98 DSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        98 e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                       .++.|+|.++++ .|++++.|.+...++|+..|
T Consensus       407 -~~~~GiDip~v~-~vi~~~~~~s~~~~~Q~~GR  438 (510)
T 2oca_A          407 -VFSTGISVKNLH-HVVLAHGVKSKIIVLQTIGR  438 (510)
T ss_dssp             -HHHHSCCCCSEE-EEEESSCCCSCCHHHHHHHH
T ss_pred             -hhhcccccccCc-EEEEeCCCCCHHHHHHHHhc
Confidence             889999999999 99999999999999999854

>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=99.29  E-value=2e-12  Score=114.66  Aligned_cols=105  Identities=20%  Similarity=0.140  Sum_probs=89.9

Q ss_pred             hHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC------------------------------CCeeEEecCCCC
Q psy437           20 VLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE------------------------------RINAISYHAGLA   69 (184)
Q Consensus        20 k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~------------------------------gi~~~~~hg~l~   69 (184)
                      +...+.+.+.   .+.++||||+|++.++.++..|.+.                              +..+.++||+|+
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            4556666553   5689999999999999999998753                              135788999999


Q ss_pred             HHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee----CC---CChHHHHHHHHHhhCCC
Q psy437           70 DKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYH----AG---LADKLRNEVQMKWISNK  134 (184)
Q Consensus        70 ~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih----~~---~p~~~r~~~~~~f~~~~  134 (184)
                      +++|..+++.|.+|..+|||||+      .++.|+|.++++ +||+    |+   .|.+..+|.|+.+|.|.
T Consensus       308 ~~~R~~v~~~f~~g~~~vlvaT~------~l~~Gidip~~~-~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR  372 (702)
T 2p6r_A          308 NGQRRVVEDAFRRGNIKVVVATP------TLAAGVNLPARR-VIVRSLYRFDGYSKRIKVSEYKQMAGRAGR  372 (702)
T ss_dssp             HHHHHHHHHHHHTTSCCEEEECS------TTTSSSCCCBSE-EEECCSEEESSSEEECCHHHHHHHHTTBSC
T ss_pred             HHHHHHHHHHHHCCCCeEEEECc------HHhccCCCCceE-EEEcCceeeCCCCCcCCHHHHHHHhhhcCC
Confidence            99999999999999999999999      678899999998 8988    44   78899999999988765

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

Probab=99.28  E-value=2.5e-12  Score=113.51  Aligned_cols=87  Identities=8%  Similarity=0.027  Sum_probs=49.9

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcC----CcEEEe--------eCCCChHHHHHHHHHhhC-CCceEEEE-------Eec
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQER----INAISY--------HAGLADKLRNEVQMKWIS-NKVHLYNV-------WKI  143 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~g----i~~~vi--------h~~~p~~~r~~~~~~f~~-~~~~v~va-------~D~  143 (184)
                      ..++||+|+++..++.++..|...|    +++..+        |+++|+..|..+.+.|++ |+..|+||       +|+
T Consensus       398 ~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~GiDi  477 (696)
T 2ykg_A          398 ETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDI  477 (696)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC---
T ss_pred             CCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcCCcC
Confidence            4589999999999999999999887    888888        569999999999999998 99999999       699


Q ss_pred             CCccEEEecCCCCCccccccccccccCCcc
Q psy437          144 QWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       144 ~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |++++|||||+|.+.++|+|+++  | ||.
T Consensus       478 p~v~~VI~~d~p~s~~~~~Qr~G--R-GR~  504 (696)
T 2ykg_A          478 AQCNLVILYEYVGNVIKMIQTRG--R-GRA  504 (696)
T ss_dssp             CCCSEEEEESCC--CCCC------------
T ss_pred             ccCCEEEEeCCCCCHHHHHHhhc--c-CcC
Confidence            99999999999999999999995  6 885

>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=99.27  E-value=1.5e-11  Score=114.39  Aligned_cols=123  Identities=11%  Similarity=0.024  Sum_probs=95.0

Q ss_pred             CCCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHHh
Q psy437            4 SFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus         4 s~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f~   81 (184)
                      +..|.++...+..... ......++.....+.+++|||++++.++.+++.|.+.  ++++..+||+|++.+|.+++++|.
T Consensus       783 ~~~r~~i~~~~~~~~~-~~i~~~il~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~  861 (1151)
T 2eyq_A          783 PARRLAVKTFVREYDS-MVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFH  861 (1151)
T ss_dssp             CCBCBCEEEEEEECCH-HHHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHH
T ss_pred             CCCccccEEEEecCCH-HHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHH
Confidence            3445566555554432 2222222333335688999999999999999999987  889999999999999999999999


Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCC-ChHHHHHHHHHhhCCC
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGL-ADKLRNEVQMKWISNK  134 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~-p~~~r~~~~~~f~~~~  134 (184)
                      +|+.+|||||+      .+++|+|.++++ .||..+. +-+...++|+.+|.|.
T Consensus       862 ~g~~~VLVaT~------v~e~GiDip~v~-~VIi~~~~~~~l~~l~Qr~GRvgR  908 (1151)
T 2eyq_A          862 HQRFNVLVCTT------IIETGIDIPTAN-TIIIERADHFGLAQLHQLRGRVGR  908 (1151)
T ss_dssp             TTSCCEEEESS------TTGGGSCCTTEE-EEEETTTTSSCHHHHHHHHTTCCB
T ss_pred             cCCCcEEEECC------cceeeecccCCc-EEEEeCCCCCCHHHHHHHHhccCc
Confidence            99999999999      778999999999 5554444 4567789999876554

>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=99.27  E-value=5.4e-13  Score=112.81  Aligned_cols=103  Identities=7%  Similarity=0.037  Sum_probs=91.4

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .|...|.+++.+ ..+.++||||++++.++.+++.|.     +..+||++++.+|.+++++|.+|+.+|||+|+      
T Consensus       335 ~k~~~l~~~l~~-~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~------  402 (472)
T 2fwr_A          335 NKIRKLREILER-HRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQ------  402 (472)
T ss_dssp             HHHHHHHHHHHH-TSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSS------
T ss_pred             HHHHHHHHHHHh-CCCCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcC------
Confidence            367788888876 377899999999999999999884     56799999999999999999999999999999      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .++.|+|.++++ .|++++.|.+...|+|+..|.+.
T Consensus       403 ~~~~Gldlp~~~-~Vi~~~~~~s~~~~~Q~~GR~~R  437 (472)
T 2fwr_A          403 VLDEGIDVPDAN-VGVIMSGSGSAREYIQRLGRILR  437 (472)
T ss_dssp             CCCSSSCSCCBS-EEEEECCSSCCHHHHHHHHHSBC
T ss_pred             chhcCcccccCc-EEEEECCCCCHHHHHHHHhhccC
Confidence            667899999999 99999999999999999976543

>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=99.26  E-value=1.1e-10  Score=108.55  Aligned_cols=139  Identities=12%  Similarity=0.017  Sum_probs=120.2

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec--------------
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS--------------   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr--------------   94 (184)
                      .+.+++|.|||+..+.++++.+.+.    ++++..++|..+..++...++.+.+|..+|+|+|...              
T Consensus       651 ~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvI  730 (1151)
T 2eyq_A          651 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI  730 (1151)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEE
T ss_pred             hCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEE
Confidence            5678999999999999999888742    6788899999998888888888888888888777544              


Q ss_pred             --------------------------------------------------------------------------------
Q psy437           95 --------------------------------------------------------------------------------   94 (184)
Q Consensus        95 --------------------------------------------------------------------------------   94 (184)
                                                                                                      
T Consensus       731 iDEaH~~g~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~~~r~~i~~~~~~~~~~~i~~~il~~l~  810 (1151)
T 2eyq_A          731 VDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREIL  810 (1151)
T ss_dssp             EESGGGSCHHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCCCBCBCEEEEEEECCHHHHHHHHHHHHT
T ss_pred             EechHhcChHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCCCCccccEEEEecCCHHHHHHHHHHHHh
Confidence                                                                                            


Q ss_pred             ------------ccHHHHHHHHHhc--CCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecC
Q psy437           95 ------------KECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHS  153 (184)
Q Consensus        95 ------------~~~e~~a~gL~~~--gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~  153 (184)
                                  ..++.++..|...  ++++.++|+++++..|..+.+.|++|+..|+||       +|+|++++|+.++
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                        4789999999765  888899999999999999999999999999999       6999999999888


Q ss_pred             C-CCCccccccccccccCCcc
Q psy437          154 L-VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       154 ~-p~~~e~y~~~i~~~~~~r~  173 (184)
                      . +.+..+|+|+++  |+||.
T Consensus       891 ~~~~~l~~l~Qr~G--RvgR~  909 (1151)
T 2eyq_A          891 ADHFGLAQLHQLRG--RVGRS  909 (1151)
T ss_dssp             TTSSCHHHHHHHHT--TCCBT
T ss_pred             CCCCCHHHHHHHHh--ccCcC
Confidence            7 457889999995  66664

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

Probab=99.25  E-value=1e-10  Score=103.37  Aligned_cols=85  Identities=14%  Similarity=0.065  Sum_probs=78.2

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC--CCceEEEE-------EecCCccEEEecCC----
Q psy437           88 GHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS--NKVHLYNV-------WKIQWKRIIWIHSL----  154 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~--~~~~v~va-------~D~~~vr~v~~~~~----  154 (184)
                      +|++.++++|+.++..|...|+.+.++|+++|+..|..+.+.|++  |+..|+||       +|+ ++++||++++    
T Consensus       324 iIf~~s~~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~  402 (677)
T 3rc3_A          324 CIVCFSKNDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPS  402 (677)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC--
T ss_pred             EEEEcCHHHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccc
Confidence            667888899999999999999999999999999999999999999  88999999       699 8999999999    


Q ss_pred             ----------CCCccccccccccccCCcccc
Q psy437          155 ----------VLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       155 ----------p~~~e~y~~~i~~~~~~r~~~  175 (184)
                                |.+..+|+|++  +|+||.+.
T Consensus       403 ~~~~G~~~~~p~s~~~~~QR~--GRAGR~g~  431 (677)
T 3rc3_A          403 INEKGERELEPITTSQALQIA--GRAGRFSS  431 (677)
T ss_dssp             ---------CBCCHHHHHHHH--TTBTCTTS
T ss_pred             cccCCccccccCCHHHHHHHh--cCCCCCCC
Confidence                      77899999999  58888754

>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=99.24  E-value=2e-11  Score=109.52  Aligned_cols=138  Identities=8%  Similarity=-0.020  Sum_probs=104.2

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHHH-HH----HHHHHHhc-cCceEEEEEeecccHH
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADKL-RN----EVQMKWIS-NKVHVGHWTVVSKECD   98 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~~-R~----~~~~~f~~-g~~~vlVaT~tr~~~e   98 (184)
                      +..+.|+++.|- ..+.+++++...        ..++..++-.....+ ..    .+++.... ...++||+++++++++
T Consensus       239 ~~~~iIl~SAT~-~~~~l~~~~~~~~vi~v~gr~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~  317 (773)
T 2xau_A          239 PDLKIIIMSATL-DAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIE  317 (773)
T ss_dssp             TTCEEEEEESCS-CCHHHHHHTTSCCEEECCCCCCCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHH
T ss_pred             CCceEEEEeccc-cHHHHHHHhcCCCcccccCcccceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHH
Confidence            456778887787 456777777532        123333332222111 11    22222222 4568999999999999


Q ss_pred             HHHHHHHh-----------cCCcEEEeeCCCChHHHHHHHHHhh-----CCCceEEEE-------EecCCccEEEecCC-
Q psy437           99 SVAAALAQ-----------ERINAISYHAGLADKLRNEVQMKWI-----SNKVHLYNV-------WKIQWKRIIWIHSL-  154 (184)
Q Consensus        99 ~~a~gL~~-----------~gi~~~vih~~~p~~~r~~~~~~f~-----~~~~~v~va-------~D~~~vr~v~~~~~-  154 (184)
                      .++..|..           .++.+..+|+++|+..|..+.+.|.     .|...|+||       +|+|+|++||++++ 
T Consensus       318 ~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~  397 (773)
T 2xau_A          318 DAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFS  397 (773)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEE
T ss_pred             HHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCc
Confidence            99999974           6888899999999999999999999     999999999       69999999999888 


Q ss_pred             -----------------CCCccccccccccccCCcc
Q psy437          155 -----------------VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       155 -----------------p~~~e~y~~~i~~~~~~r~  173 (184)
                                       |.+..+|+|++  +|+||.
T Consensus       398 k~~~yd~~~g~~~L~~~p~S~~s~~QR~--GRaGR~  431 (773)
T 2xau_A          398 KQKVYNPRIRVESLLVSPISKASAQQRA--GRAGRT  431 (773)
T ss_dssp             EEEEEETTTTEEEEEEEECCHHHHHHHH--HGGGSS
T ss_pred             cceeeccccCccccccccCCHHHHHhhc--cccCCC
Confidence                             88999999999  588886

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.24  E-value=1.1e-11  Score=107.82  Aligned_cols=103  Identities=10%  Similarity=0.103  Sum_probs=84.2

Q ss_pred             HHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe--------eEEecCCCCHHHHHHHHHHHhccCce---EEEEEe
Q psy437           24 VISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN--------AISYHAGLADKLRNEVQMKWISNKVH---VGHWTV   92 (184)
Q Consensus        24 L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~--------~~~~hg~l~~~~R~~~~~~f~~g~~~---vlVaT~   92 (184)
                      |.+.+.......++||||+++..|+.+++.|.+.+..        +..+||+++ ++|..++++|++|+.+   |||+|+
T Consensus       429 l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~-~~r~~~l~~F~~~~~~~~~ilvtt~  507 (590)
T 3h1t_A          429 LTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEG-KIGKGHLSRFQELETSTPVILTTSQ  507 (590)
T ss_dssp             HHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTH-HHHHHHHHHHHCTTCCCCCEEEESS
T ss_pred             HHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCCh-HHHHHHHHHHhCCCCCCCEEEEECC
Confidence            3344444334578999999999999999999875432        677899875 4799999999998765   778888


Q ss_pred             ecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           93 VSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        93 tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                            .+++|+|.++++ .||+++.|.+...|+|+.+|.+.
T Consensus       508 ------~l~~GiDip~v~-~Vi~~~~~~s~~~~~Q~iGR~~R  542 (590)
T 3h1t_A          508 ------LLTTGVDAPTCK-NVVLARVVNSMSEFKQIVGRGTR  542 (590)
T ss_dssp             ------TTTTTCCCTTEE-EEEEESCCCCHHHHHHHHTTSCC
T ss_pred             ------hhhcCccchhee-EEEEEecCCChHHHHHHHhhhcc
Confidence                  678899999998 89999999999999999977664

>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=99.23  E-value=7.7e-13  Score=112.11  Aligned_cols=88  Identities=17%  Similarity=0.125  Sum_probs=0.0

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCC-
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLV-  155 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p-  155 (184)
                      ..++||+|++++.|+.++..|...++.+.++|+++++..|..+.+.|++|+..|+|+       +|+|++++||++++| 
T Consensus       333 ~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI~~d~p~  412 (479)
T 3fmp_B          333 IAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPV  412 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEEEecCCC
Confidence            347999999999999999999999999999999999999999999999999999998       699999999999999 


Q ss_pred             -----CCccccccccccccCCcc
Q psy437          156 -----LIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       156 -----~~~e~y~~~i~~~~~~r~  173 (184)
                           .+.+.|+|+++  |+||.
T Consensus       413 ~~~~~~s~~~~~Qr~G--RagR~  433 (479)
T 3fmp_B          413 DKDGNPDNETYLHRIG--RTGRF  433 (479)
T ss_dssp             -----------------------
T ss_pred             CCccCCCHHHHHHHhc--ccccC
Confidence                 46789999995  66664

>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=99.23  E-value=7.1e-12  Score=107.22  Aligned_cols=89  Identities=8%  Similarity=0.019  Sum_probs=46.2

Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhc------------CCcEEEeeCCCChHHHHHHHHHhhC-CCceEEEE-------E
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQE------------RINAISYHAGLADKLRNEVQMKWIS-NKVHLYNV-------W  141 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~------------gi~~~vih~~~p~~~r~~~~~~f~~-~~~~v~va-------~  141 (184)
                      ....++||+|+++..++.++..|...            |.....+|+++|+..|..+.+.|++ |++.|+|+       +
T Consensus       388 ~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~Gi  467 (556)
T 4a2p_A          388 NPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGI  467 (556)
T ss_dssp             CTTCCEEEEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC------
T ss_pred             CCCceEEEEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCC
Confidence            34568999999999999999999765            4555667889999999999999999 99999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|||||+|.++..|+|+++  | ||.
T Consensus       468 Dip~v~~VI~~d~p~s~~~~~Qr~G--R-gR~  496 (556)
T 4a2p_A          468 DIVQCNLVVLYEYSGNVTKMIQVRG--R-GRA  496 (556)
T ss_dssp             -----CEEEEETCCSCHHHHHHC---------
T ss_pred             CchhCCEEEEeCCCCCHHHHHHhcC--C-CCC
Confidence            9999999999999999999999996  5 776

>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=99.20  E-value=2.4e-11  Score=97.40  Aligned_cols=86  Identities=15%  Similarity=0.120  Sum_probs=78.5

Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCC
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSL  154 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~  154 (184)
                      ....++||+++++.+++.++..|.    .+..+|+++|+..|..+.+.|++|+..|+|+       +|+|++++|+++++
T Consensus       218 ~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~  293 (337)
T 2z0m_A          218 NKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDA  293 (337)
T ss_dssp             CCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEESSC
T ss_pred             CCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEecC
Confidence            345679999999999999998887    4689999999999999999999999999999       69999999999999


Q ss_pred             CCCccccccccccccCCcc
Q psy437          155 VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       155 p~~~e~y~~~i~~~~~~r~  173 (184)
                      |.+...|+|+++  |+||.
T Consensus       294 ~~s~~~~~Q~~G--R~gR~  310 (337)
T 2z0m_A          294 PQDLRTYIHRIG--RTGRM  310 (337)
T ss_dssp             CSSHHHHHHHHT--TBCGG
T ss_pred             CCCHHHhhHhcC--ccccC
Confidence            999999999995  77775

>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=99.16  E-value=4.4e-11  Score=106.93  Aligned_cols=88  Identities=10%  Similarity=-0.136  Sum_probs=77.6

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC--------CccE
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ--------WKRI  148 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~--------~vr~  148 (184)
                      .-++||+|.+...+|.++..|...|+++.++|+++++..+..+.+.|+.|  .|+||       .|++        ++.+
T Consensus       432 ~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~  509 (844)
T 1tf5_A          432 GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLA  509 (844)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcE
Confidence            34799999999999999999999999999999999999888777777666  57888       6999        7889


Q ss_pred             EEecCCCCCcccccccccc-ccCCcc
Q psy437          149 IWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       149 v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      |||+++|.+.+.|+|++++ +|.|+.
T Consensus       510 VIn~d~p~s~r~y~hr~GRTGRqG~~  535 (844)
T 1tf5_A          510 VVGTERHESRRIDNQLRGRSGRQGDP  535 (844)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSGGGCC
T ss_pred             EEEecCCCCHHHHHhhcCccccCCCC
Confidence            9999999999999999976 366665

>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=99.16  E-value=3.4e-11  Score=102.42  Aligned_cols=107  Identities=12%  Similarity=0.033  Sum_probs=89.0

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhC-CCeeEEecCCCCHHHHHHHHHHHhcc-Cce-EEEEEeec
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISN-KVH-VGHWTVVS   94 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~hg~l~~~~R~~~~~~f~~g-~~~-vlVaT~tr   94 (184)
                      .|...+.+++.+. ..+.++||||+++..++.++..|... |+++..+||++++++|.+++++|.++ ..+ +|++|.  
T Consensus       325 ~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~--  402 (500)
T 1z63_A          325 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK--  402 (500)
T ss_dssp             HHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECC--
T ss_pred             hhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecc--
Confidence            4777777777653 25678999999999999999999885 99999999999999999999999998 555 688888  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                          ..+.||+.++++ .||++++|-+...+.|+..|.
T Consensus       403 ----~~~~Glnl~~~~-~vi~~d~~~~~~~~~Q~~gR~  435 (500)
T 1z63_A          403 ----AGGFGINLTSAN-RVIHFDRWWNPAVEDQATDRV  435 (500)
T ss_dssp             ----CC-CCCCCTTCS-EEEESSCCSCC---CHHHHTT
T ss_pred             ----cccCCCchhhCC-EEEEeCCCCCcchHHHHHHHH
Confidence                557799999999 999999999999999998654

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

Probab=99.15  E-value=3.5e-10  Score=100.42  Aligned_cols=141  Identities=16%  Similarity=0.105  Sum_probs=103.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC-------CCee--EEecCC------------CC------HHHHHHHHHHHhccCc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE-------RINA--ISYHAG------------LA------DKLRNEVQMKWISNKV   85 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~-------gi~~--~~~hg~------------l~------~~~R~~~~~~f~~g~~   85 (184)
                      +..+.|.++.|-..++.++++|...       .++.  ..+..+            .+      .......+........
T Consensus       174 ~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  253 (715)
T 2va8_A          174 KRRNLLALSATISNYKQIAKWLGAEPVATNWRPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNG  253 (715)
T ss_dssp             HTSEEEEEESCCTTHHHHHHHHTCEEEECCCCSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHTTTC
T ss_pred             ccCcEEEEcCCCCCHHHHHHHhCCCccCCCCCCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHhcCC
Confidence            3567788889987789999999632       1111  111111            00      1233444444445567


Q ss_pred             eEEEEEeecccHHHHHHHHHhcC------------------------------------CcEEEeeCCCChHHHHHHHHH
Q psy437           86 HVGHWTVVSKECDSVAAALAQER------------------------------------INAISYHAGLADKLRNEVQMK  129 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~g------------------------------------i~~~vih~~~p~~~r~~~~~~  129 (184)
                      ++||+++++++|+.+|..|....                                    ..+.++|+++|+..|..+.+.
T Consensus       254 ~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~  333 (715)
T 2va8_A          254 QVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEG  333 (715)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHH
T ss_pred             CEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHH
Confidence            89999999999999999996431                                    236889999999999999999


Q ss_pred             hhCCCceEEEE-------EecCCccEEEe----cC-------CCCCccccccccccccCCcccc
Q psy437          130 WISNKVHLYNV-------WKIQWKRIIWI----HS-------LVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       130 f~~~~~~v~va-------~D~~~vr~v~~----~~-------~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      |++|.++|+||       +|+|+++.||+    |+       .|.+..+|+|++  +|+||.+.
T Consensus       334 f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~--GRaGR~g~  395 (715)
T 2va8_A          334 FRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMS--GRAGRPGF  395 (715)
T ss_dssp             HHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHH--TTBCCTTT
T ss_pred             HHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHh--hhcCCCCC
Confidence            99999999999       59999999999    98       899999999999  58888654

>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=99.14  E-value=4.9e-11  Score=99.36  Aligned_cols=90  Identities=11%  Similarity=0.134  Sum_probs=81.3

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeC--------CCChHHHHHHHHHhhCCCceEEEE-------EecCCcc
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHA--------GLADKLRNEVQMKWISNKVHLYNV-------WKIQWKR  147 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~--------~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr  147 (184)
                      ...++||+|+++..++.++..|...|+++..+|+        +++...|..+.+.|++|+..|+++       +|+|+++
T Consensus       360 ~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~  439 (494)
T 1wp9_A          360 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVD  439 (494)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCC
T ss_pred             CCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCC
Confidence            4668999999999999999999999999999999        999999999999999999999999       6999999


Q ss_pred             EEEecCCCCCccccccccccccCCccc
Q psy437          148 IIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                      +|+++++|.++..|+|++  +|+||.+
T Consensus       440 ~Vi~~d~~~~~~~~~Qr~--GR~~R~g  464 (494)
T 1wp9_A          440 LVVFYEPVPSAIRSIQRR--GRTGRHM  464 (494)
T ss_dssp             EEEESSCCHHHHHHHHHH--TTSCSCC
T ss_pred             EEEEeCCCCCHHHHHHHH--hhccCCC
Confidence            999999999999999999  5777753

>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=99.13  E-value=2e-10  Score=101.79  Aligned_cols=153  Identities=16%  Similarity=0.168  Sum_probs=109.5

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC-------CCeeE--EecCCC---CH-H-------HHHHHHHHH
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE-------RINAI--SYHAGL---AD-K-------LRNEVQMKW   80 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~-------gi~~~--~~hg~l---~~-~-------~R~~~~~~f   80 (184)
                      .+.++..++...+..+.|.++.|-..++.++++|...       .++..  .+..+.   .. .       .....+.+.
T Consensus       159 ~~~ll~~l~~~~~~~~ii~lSATl~n~~~~~~~l~~~~~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (702)
T 2p6r_A          159 LEILVTKMRRMNKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEEC  238 (702)
T ss_dssp             HHHHHHHHHHHCTTCEEEEEECCCTTHHHHHHHTTCEEEECCCCSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHH
T ss_pred             HHHHHHHHHhcCcCceEEEECCCcCCHHHHHHHhCCCcccCCCCCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHH
Confidence            3444444543324567788889988788999988631       11111  111110   00 0       033344444


Q ss_pred             hccCceEEEEEeecccHHHHHHHHHhc------------------------------CCcEEEeeCCCChHHHHHHHHHh
Q psy437           81 ISNKVHVGHWTVVSKECDSVAAALAQE------------------------------RINAISYHAGLADKLRNEVQMKW  130 (184)
Q Consensus        81 ~~g~~~vlVaT~tr~~~e~~a~gL~~~------------------------------gi~~~vih~~~p~~~r~~~~~~f  130 (184)
                      .+...++||+++++++|+.+|..|...                              +..+..+|+++|++.|..+.+.|
T Consensus       239 ~~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f  318 (702)
T 2p6r_A          239 VAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAF  318 (702)
T ss_dssp             HHTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHH
T ss_pred             HhcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHH
Confidence            445668999999999999999988642                              12357899999999999999999


Q ss_pred             hCCCceEEEE-------EecCCccEEEe----cC---CCCCccccccccccccCCcccc
Q psy437          131 ISNKVHLYNV-------WKIQWKRIIWI----HS---LVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       131 ~~~~~~v~va-------~D~~~vr~v~~----~~---~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      ++|.++|+||       +|+|+++.||+    ||   .|.+..+|+|++  +|+||.+.
T Consensus       319 ~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~--GRaGR~g~  375 (702)
T 2p6r_A          319 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMA--GRAGRPGM  375 (702)
T ss_dssp             HTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHH--TTBSCTTT
T ss_pred             HCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHh--hhcCCCCC
Confidence            9999999999       59999999999    65   789999999999  58888654

>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=99.12  E-value=4.9e-11  Score=108.97  Aligned_cols=88  Identities=8%  Similarity=0.015  Sum_probs=51.0

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhc------------CCcEEEeeCCCChHHHHHHHHHhhC-CCceEEEE-------Ee
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQE------------RINAISYHAGLADKLRNEVQMKWIS-NKVHLYNV-------WK  142 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~------------gi~~~vih~~~p~~~r~~~~~~f~~-~~~~v~va-------~D  142 (184)
                      ...++||+|.++.+++.++..|...            |.....+|+++++..|..+.+.|++ |.+.|+|+       +|
T Consensus       630 ~~~rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGID  709 (936)
T 4a2w_A          630 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID  709 (936)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCc
Confidence            3468999999999999999999876            5555677999999999999999999 99999999       69


Q ss_pred             cCCccEEEecCCCCCccccccccccccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|++++|||||+|.++..|+|+++  | ||.
T Consensus       710 lp~v~~VI~yD~p~s~~~~iQr~G--R-GR~  737 (936)
T 4a2w_A          710 IVQCNLVVLYEYSGNVTKMIQVRG--R-GRA  737 (936)
T ss_dssp             CCCCSEEEEESCCSCSHHHHCC---------
T ss_pred             chhCCEEEEeCCCCCHHHHHHhcC--C-CCC
Confidence            999999999999999999999996  5 776

>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=99.12  E-value=4.5e-12  Score=113.58  Aligned_cols=121  Identities=12%  Similarity=0.187  Sum_probs=93.3

Q ss_pred             CCCCeEEEEEEccChHHHHHHHHHhh-cCCCcEEEEeccH--------HHHHHHHHHHHh---CCCeeEEecCCCCHHHH
Q psy437            6 NRANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTR--------KECDSVAAALAQ---ERINAISYHAGLADKLR   73 (184)
Q Consensus         6 ~R~Nl~y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr--------~~~e~la~~L~~---~gi~~~~~hg~l~~~~R   73 (184)
                      .|.++...+.+. .+...+.+.+.+. ..+.+++|||++.        ..++.+++.|.+   .++.+..+||+|++++|
T Consensus       550 ~r~~i~~~~~~~-~~~~~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR  628 (780)
T 1gm5_A          550 GRKEVQTMLVPM-DRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEK  628 (780)
T ss_dssp             SCCCCEECCCCS-STHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCS
T ss_pred             CCcceEEEEecc-chHHHHHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHH
Confidence            345554433333 3445566666543 2567899999865        457888899988   57889999999999999


Q ss_pred             HHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh-HHHHHHHHHhhCCC
Q psy437           74 NEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD-KLRNEVQMKWISNK  134 (184)
Q Consensus        74 ~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~-~~r~~~~~~f~~~~  134 (184)
                      ..++++|++|+.+|||||+      .+++|+|.++++ +|++++.|. +...+.|+.+|.|.
T Consensus       629 ~~v~~~F~~G~~~ILVaT~------vie~GIDiP~v~-~VIi~d~~r~~l~~l~Qr~GRaGR  683 (780)
T 1gm5_A          629 DRVMLEFAEGRYDILVSTT------VIEVGIDVPRAN-VMVIENPERFGLAQLHQLRGRVGR  683 (780)
T ss_dssp             HHHHHHHTTTSSSBCCCSS------CCCSCSCCTTCC-EEEBCSCSSSCTTHHHHHHHTSCC
T ss_pred             HHHHHHHHCCCCeEEEECC------CCCccccCCCCC-EEEEeCCCCCCHHHHHHHhcccCc
Confidence            9999999999999999999      778899999999 999999996 57778888877654

>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=99.12  E-value=5.6e-11  Score=106.84  Aligned_cols=88  Identities=8%  Similarity=0.015  Sum_probs=49.6

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhc------------CCcEEEeeCCCChHHHHHHHHHhhC-CCceEEEE-------Ee
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQE------------RINAISYHAGLADKLRNEVQMKWIS-NKVHLYNV-------WK  142 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~------------gi~~~vih~~~p~~~r~~~~~~f~~-~~~~v~va-------~D  142 (184)
                      ...++||+|.++..++.++..|...            |..+..+|+++++..|..+.+.|++ |.+.|+|+       +|
T Consensus       630 ~~~kvLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GID  709 (797)
T 4a2q_A          630 PQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGID  709 (797)
T ss_dssp             SSCCEEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC------
T ss_pred             CCCeEEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCC
Confidence            3478999999999999999999763            5555678999999999999999999 99999999       69


Q ss_pred             cCCccEEEecCCCCCccccccccccccCCcc
Q psy437          143 IQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       143 ~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|++++||||++|.++..|+|+++  | ||.
T Consensus       710 lp~v~~VI~yd~p~s~~~~iQr~G--R-GR~  737 (797)
T 4a2q_A          710 IVQCNLVVLYEYSGNVTKMIQVRG--R-GRA  737 (797)
T ss_dssp             -CCCSEEEEESCCSCHHHHHTC---------
T ss_pred             chhCCEEEEeCCCCCHHHHHHhcC--C-CCC
Confidence            999999999999999999999996  5 776

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

Probab=99.12  E-value=5.3e-10  Score=103.64  Aligned_cols=63  Identities=6%  Similarity=-0.010  Sum_probs=55.0

Q ss_pred             EEEEeecccHHHHHHHHHhcCCcEE-EeeCCCChHHHHHHHHHhhCCCceEEEE-----------EecCC-ccEEEecCC
Q psy437           88 GHWTVVSKECDSVAAALAQERINAI-SYHAGLADKLRNEVQMKWISNKVHLYNV-----------WKIQW-KRIIWIHSL  154 (184)
Q Consensus        88 lVaT~tr~~~e~~a~gL~~~gi~~~-vih~~~p~~~r~~~~~~f~~~~~~v~va-----------~D~~~-vr~v~~~~~  154 (184)
                      ||++++++.|+.++..|...|+++. .+|++     |.. .+.|++|+..|+|+           +|+|+ |++|||+|+
T Consensus       313 LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~~VLVatas~TdvlarGIDip~~V~~VI~~d~  386 (1104)
T 4ddu_A          313 LIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGT  386 (1104)
T ss_dssp             EEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSCSEEEEETTTHHHHCCSCCCTTTCCEEEEESC
T ss_pred             EEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCCCEEEEecCCCCeeEecCcCCCCCCEEEEECC
Confidence            6677777889999999999999987 88883     444 89999999999999           39999 999999999


Q ss_pred             CC
Q psy437          155 VL  156 (184)
Q Consensus       155 p~  156 (184)
                      |+
T Consensus       387 P~  388 (1104)
T 4ddu_A          387 PS  388 (1104)
T ss_dssp             CE
T ss_pred             CC
Confidence            99

>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=99.10  E-value=1.1e-10  Score=112.04  Aligned_cols=96  Identities=17%  Similarity=0.091  Sum_probs=82.1

Q ss_pred             cCCCcEEEEeccHHHHHHHHHHHHhC-------------------------------------CCeeEEecCCCCHHHHH
Q psy437           32 YSGQSGIVYCLTRKECDSVAAALAQE-------------------------------------RINAISYHAGLADKLRN   74 (184)
Q Consensus        32 ~~~~~~IIf~~tr~~~e~la~~L~~~-------------------------------------gi~~~~~hg~l~~~~R~   74 (184)
                      ..+.++||||+||+.|+.+|..|.+.                                     ...++++||||++++|.
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~  394 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRT  394 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHH
Confidence            35678999999999999999888531                                     12378899999999999


Q ss_pred             HHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeC----------CCChHHHHHHHHHhhCCC
Q psy437           75 EVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHA----------GLADKLRNEVQMKWISNK  134 (184)
Q Consensus        75 ~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~----------~~p~~~r~~~~~~f~~~~  134 (184)
                      .+.+.|++|..+|||||+      .+|.|++.+.++ +|+++          ..|-+..+|.|+.+|.|.
T Consensus       395 ~vE~~F~~G~i~vlvaTs------TLa~GVNlPa~~-vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR  457 (1724)
T 4f92_B          395 LVEDLFADKHIQVLVSTA------TLAWGVNLPAHT-VIIKGTQVYSPEKGRWTELGALDILQMLGRAGR  457 (1724)
T ss_dssp             HHHHHHHTTCCCEEEECH------HHHHHSCCCBSE-EEEECCEEEETTTTEEEECCHHHHHHHHTTBSC
T ss_pred             HHHHHHHCCCCeEEEEcc------hhHhhCCCCCce-EEEeCCEEecCcCCCcccCCHHHHHHhhhhccC
Confidence            999999999999999999      889999999998 77763          246688999999988775

>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=99.09  E-value=4.2e-10  Score=104.36  Aligned_cols=98  Identities=13%  Similarity=0.205  Sum_probs=77.9

Q ss_pred             HHHHHhc-cCceEEEEEeecccHHHHHHHHHhcCCc---------------------------------------EEEee
Q psy437           76 VQMKWIS-NKVHVGHWTVVSKECDSVAAALAQERIN---------------------------------------AISYH  115 (184)
Q Consensus        76 ~~~~f~~-g~~~vlVaT~tr~~~e~~a~gL~~~gi~---------------------------------------~~vih  115 (184)
                      ++..+.. +..++||+++++..|+.++..|...++.                                       +.++|
T Consensus       432 li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~H  511 (1108)
T 3l9o_A          432 IVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHH  511 (1108)
T ss_dssp             HHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEEC
T ss_pred             HHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeec
Confidence            4444433 4458999999999999999988543322                                       58899


Q ss_pred             CCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCcc--------ccccccccccCCcccc
Q psy437          116 AGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKP--------DYLPPILDLRLGREDI  175 (184)
Q Consensus       116 ~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e--------~y~~~i~~~~~~r~~~  175 (184)
                      ++|++..|..+.+.|++|.+.|+||       +|+|++++||+++.|.+.+        +|+|++  +|+||.+.
T Consensus       512 g~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~--GRAGR~G~  584 (1108)
T 3l9o_A          512 SGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMS--GRAGRRGL  584 (1108)
T ss_dssp             SCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHH--HHSCCSSS
T ss_pred             CCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhh--cccCCCCC
Confidence            9999999999999999999999999       5999999999888755544        599999  47777653

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

Probab=99.09  E-value=2.4e-11  Score=107.42  Aligned_cols=156  Identities=9%  Similarity=0.016  Sum_probs=106.7

Q ss_pred             CCeEEEEEEccChH----HHHHHHHHhhc--CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHh
Q psy437            8 ANLKYEILPKKNVL----KEVISLIKAKY--SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus         8 ~Nl~y~v~~~~~k~----~~L~~~l~~~~--~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~   81 (184)
                      .|+.+.|..+...+    .....++.+..  ...+.|.|+.|....  + ..+.....+...+....+.......+....
T Consensus       331 ~~l~lvViDEaH~~~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~--i-~~~~~~~~~i~~v~~~~~~~~~~~~l~~l~  407 (673)
T 2wv9_A          331 PNYNLFVMDEAHFTDPASIAARGYIATRVEAGEAAAIFMTATPPGT--S-DPFPDTNSPVHDVSSEIPDRAWSSGFEWIT  407 (673)
T ss_dssp             CCCSEEEEESTTCCCHHHHHHHHHHHHHHHTTSCEEEEECSSCTTC--C-CSSCCCSSCEEEEECCCCSSCCSSCCHHHH
T ss_pred             ccceEEEEeCCcccCccHHHHHHHHHHhccccCCcEEEEcCCCChh--h-hhhcccCCceEEEeeecCHHHHHHHHHHHH
Confidence            56777777765432    12223332221  346777888776411  1 011111223333333233222233344444


Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEe---
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWI---  151 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~---  151 (184)
                      ....++||+++++..|+.++..|...|+++..+|+    +.|..+.+.|++|+..|+||       +|+| +++|||   
T Consensus       408 ~~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg----~eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g~  482 (673)
T 2wv9_A          408 DYAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNR----KSYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCRK  482 (673)
T ss_dssp             SCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECS----SSHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECCE
T ss_pred             hCCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeCh----HHHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECCC
Confidence            55668999999999999999999999999999999    37888999999999999999       6999 999998   


Q ss_pred             -----------------cCCCCCccccccccccccCCcc
Q psy437          152 -----------------HSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       152 -----------------~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                                       +++|.+.++|+|+++  |+||.
T Consensus       483 ~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~G--RaGR~  519 (673)
T 2wv9_A          483 SVKPTILDEGEGRVILSVPSAITSASAAQRRG--RVGRN  519 (673)
T ss_dssp             ECCEEEECSTTCEEEECCSEECCHHHHHHHHT--TSSCC
T ss_pred             cccceeeecccccceecccCCCCHHHHHHHhh--ccCCC
Confidence                             679999999999995  77775

>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=99.08  E-value=3e-10  Score=99.95  Aligned_cols=106  Identities=8%  Similarity=-0.076  Sum_probs=90.1

Q ss_pred             hHHHHHHHHHhh--cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCce---EEEEEeec
Q psy437           20 VLKEVISLIKAK--YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH---VGHWTVVS   94 (184)
Q Consensus        20 k~~~L~~~l~~~--~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~---vlVaT~tr   94 (184)
                      |+..|..++...  ..+.++||||+++..++.+...|...|+++..+||++++++|..++++|.++...   +|++|.  
T Consensus       400 K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~--  477 (644)
T 1z3i_X          400 KMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK--  477 (644)
T ss_dssp             HHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG--
T ss_pred             HHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecc--
Confidence            555555544321  1567999999999999999999999999999999999999999999999998764   788888  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                          ..+.||+..+.+ .|||+++|-+...+.|+..|.
T Consensus       478 ----a~g~Glnl~~a~-~Vi~~d~~wnp~~~~Qa~gR~  510 (644)
T 1z3i_X          478 ----AGGCGLNLIGAN-RLVMFDPDWNPANDEQAMARV  510 (644)
T ss_dssp             ----GSCTTCCCTTEE-EEEECSCCSSHHHHHHHHTTS
T ss_pred             ----cccCCcccccCC-EEEEECCCCCccHHHHHHHhh
Confidence                446799999998 999999999999999998543

>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=99.08  E-value=1.2e-10  Score=111.66  Aligned_cols=104  Identities=19%  Similarity=0.133  Sum_probs=85.6

Q ss_pred             HHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC----------------------------------CCeeEEecCCCC
Q psy437           24 VISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE----------------------------------RINAISYHAGLA   69 (184)
Q Consensus        24 L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~----------------------------------gi~~~~~hg~l~   69 (184)
                      +...+.+.....++||||+||+.|+.+|..|...                                  ...++++||||+
T Consensus      1145 ~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~ 1224 (1724)
T 4f92_B         1145 VYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLS 1224 (1724)
T ss_dssp             HHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSC
T ss_pred             HHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCC
Confidence            3444545456789999999999999998777421                                  124788999999


Q ss_pred             HHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEe----------eCCCChHHHHHHHHHhhCCC
Q psy437           70 DKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISY----------HAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        70 ~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vi----------h~~~p~~~r~~~~~~f~~~~  134 (184)
                      +++|..+.+.|++|.++|||||+      .+|.|++.+... +||          |+..|-+..+|+|+.+|.|.
T Consensus      1225 ~~~R~~VE~lF~~G~i~VLvaT~------tlA~GVnlPa~~-VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR 1292 (1724)
T 4f92_B         1225 PMERRLVEQLFSSGAIQVVVASR------SLCWGMNVAAHL-VIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANR 1292 (1724)
T ss_dssp             HHHHHHHHHHHHHTSBCEEEEEG------GGSSSCCCCBSE-EEEECSEEEETTTTEEEECCHHHHHHHHTTBCC
T ss_pred             HHHHHHHHHHHHCCCCeEEEECh------HHHcCCCCCccE-EEEecCccccCcccccCCCCHHHHHHhhccccC
Confidence            99999999999999999999999      678999999988 666          55567889999999987764

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

Probab=99.07  E-value=1.5e-09  Score=99.80  Aligned_cols=98  Identities=13%  Similarity=0.208  Sum_probs=83.6

Q ss_pred             HHHHHhc-cCceEEEEEeecccHHHHHHHHHhcCCc---------------------------------------EEEee
Q psy437           76 VQMKWIS-NKVHVGHWTVVSKECDSVAAALAQERIN---------------------------------------AISYH  115 (184)
Q Consensus        76 ~~~~f~~-g~~~vlVaT~tr~~~e~~a~gL~~~gi~---------------------------------------~~vih  115 (184)
                      +++.+.. +..++||+++++..|+.++..|...++.                                       +.++|
T Consensus       334 l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~H  413 (1010)
T 2xgj_A          334 IVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHH  413 (1010)
T ss_dssp             HHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEES
T ss_pred             HHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEEC
Confidence            4444443 3448999999999999999999764432                                       57899


Q ss_pred             CCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEe----cCC----CCCccccccccccccCCcccc
Q psy437          116 AGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWI----HSL----VLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       116 ~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~----~~~----p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      +++++..|..+.+.|++|.+.|+||       +|+|+++.||+    |+.    |.+..+|+|++  +|+||.+.
T Consensus       414 ggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~--GRAGR~G~  486 (1010)
T 2xgj_A          414 SGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMS--GRAGRRGL  486 (1010)
T ss_dssp             TTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHH--TTBCCTTT
T ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhh--hhcccCCC
Confidence            9999999999999999999999999       59999999999    999    89999999999  57777654

>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=99.05  E-value=4.2e-10  Score=99.37  Aligned_cols=88  Identities=13%  Similarity=-0.132  Sum_probs=75.0

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC--------CccE
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ--------WKRI  148 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~--------~vr~  148 (184)
                      .-++||+|.++..+|.++..|...|+++.++|++..+..+..+.+.|+.|  .|+||       .|++        +..+
T Consensus       474 gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAgRGtDI~lg~~V~~~Gglh  551 (822)
T 3jux_A          474 GQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAGRGTDIKLGPGVAELGGLC  551 (822)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTTTTCCCCCCTTTTTTTSCE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhhCCcCccCCcchhhcCCCE
Confidence            45799999999999999999999999999999997777777777777766  57888       5997        5569


Q ss_pred             EEecCCCCCcccccccccc-ccCCcc
Q psy437          149 IWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       149 v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                      ||++++|.+.+.|+|++++ +|.|..
T Consensus       552 VInte~Pes~r~y~qriGRTGRqG~~  577 (822)
T 3jux_A          552 IIGTERHESRRIDNQLRGRAGRQGDP  577 (822)
T ss_dssp             EEESSCCSSHHHHHHHHTTSSCSSCC
T ss_pred             EEecCCCCCHHHHHHhhCccccCCCC
Confidence            9999999999999999975 355554

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

Probab=99.05  E-value=3.3e-10  Score=104.12  Aligned_cols=102  Identities=14%  Similarity=0.167  Sum_probs=85.6

Q ss_pred             HHHHHHHHHHhcc-CceEEEEEeecccHHHHHHHHHhcCC---------------------------------------c
Q psy437           71 KLRNEVQMKWISN-KVHVGHWTVVSKECDSVAAALAQERI---------------------------------------N  110 (184)
Q Consensus        71 ~~R~~~~~~f~~g-~~~vlVaT~tr~~~e~~a~gL~~~gi---------------------------------------~  110 (184)
                      .....+++.+... ..++||++.+++.|+.++..|...|+                                       .
T Consensus       322 ~~~~~li~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~g  401 (997)
T 4a4z_A          322 KTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERG  401 (997)
T ss_dssp             THHHHHHHHHHHTTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcC
Confidence            3344555555543 46899999999999999999976655                                       3


Q ss_pred             EEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC---------CccccccccccccCCccc
Q psy437          111 AISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL---------IKPDYLPPILDLRLGRED  174 (184)
Q Consensus       111 ~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~---------~~e~y~~~i~~~~~~r~~  174 (184)
                      +.++|+++++..|..+++.|..|.+.|+||       +|+|+ +.|+++++|+         +..+|+|++  +|+||.+
T Consensus       402 i~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~--GRAGR~G  478 (997)
T 4a4z_A          402 IAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMA--GRAGRRG  478 (997)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHH--GGGCCTT
T ss_pred             eeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHh--cccccCC
Confidence            589999999999999999999999999999       69999 8888888887         999999999  5888865


Q ss_pred             c
Q psy437          175 I  175 (184)
Q Consensus       175 ~  175 (184)
                      +
T Consensus       479 ~  479 (997)
T 4a4z_A          479 L  479 (997)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.04  E-value=6.8e-10  Score=102.59  Aligned_cols=64  Identities=8%  Similarity=-0.008  Sum_probs=56.8

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----------EecCCc-cEEEecC
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----------WKIQWK-RIIWIHS  153 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----------~D~~~v-r~v~~~~  153 (184)
                      ++||+|+++..|+.++..|... +++..+|+++.     .+.+.|++|++.|+||           +|+|+| ++|||++
T Consensus       277 ~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~  350 (1054)
T 1gku_B          277 GGIIYARTGEEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVG  350 (1054)
T ss_dssp             CEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEES
T ss_pred             CEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeC
Confidence            4588888889999999999887 99999999984     6677899999999998           499995 9999999


Q ss_pred             CC
Q psy437          154 LV  155 (184)
Q Consensus       154 ~p  155 (184)
                      +|
T Consensus       351 ~P  352 (1054)
T 1gku_B          351 CP  352 (1054)
T ss_dssp             CC
T ss_pred             CC
Confidence            99

>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=99.02  E-value=3.7e-10  Score=103.57  Aligned_cols=103  Identities=17%  Similarity=0.176  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHH-hcCCcEEEeeCCCChHHHHHHHHHhhCCC--ceEEEE-----
Q psy437           71 KLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALA-QERINAISYHAGLADKLRNEVQMKWISNK--VHLYNV-----  140 (184)
Q Consensus        71 ~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~-~~gi~~~vih~~~p~~~r~~~~~~f~~~~--~~v~va-----  140 (184)
                      ..|...+..+..  ...++||+|.++..++.++..|. ..|+++.++|+++++..|..+.+.|++|+  +.|+|+     
T Consensus       488 ~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~  567 (968)
T 3dmq_A          488 DPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGS  567 (968)
T ss_dssp             SHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTT
T ss_pred             cHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhh
Confidence            356666665553  35689999999999999999998 46999999999999999999999999998  999999     


Q ss_pred             --EecCCccEEEecCCCCCccccccccccc-cCCcc
Q psy437          141 --WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       141 --~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                        +|+|++.+|+++++|.++..|+|++++. |.|+.
T Consensus       568 ~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~  603 (968)
T 3dmq_A          568 EGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQA  603 (968)
T ss_dssp             CSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSC
T ss_pred             cCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCC
Confidence              6999999999999999999999999753 55544

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.00  E-value=7.3e-10  Score=94.40  Aligned_cols=88  Identities=11%  Similarity=-0.019  Sum_probs=78.5

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE--------EecCCccEEEecCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV--------WKIQWKRIIWIHSL  154 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va--------~D~~~vr~v~~~~~  154 (184)
                      +...+||++. ...++.++..|...+.++..+|+++++..|..+.+.|.+|+..|+|+        +|+|+++.|++++.
T Consensus       347 ~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~~~  425 (510)
T 2oca_A          347 DENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLAHG  425 (510)
T ss_dssp             TCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEESSC
T ss_pred             CCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEeCC
Confidence            4556677777 78888999999998889999999999999999999999999999998        59999999999999


Q ss_pred             CCCccccccccccccCCcc
Q psy437          155 VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       155 p~~~e~y~~~i~~~~~~r~  173 (184)
                      |.+...|+|+++  |+||.
T Consensus       426 ~~s~~~~~Q~~G--R~gR~  442 (510)
T 2oca_A          426 VKSKIIVLQTIG--RVLRK  442 (510)
T ss_dssp             CCSCCHHHHHHH--HHHTT
T ss_pred             CCCHHHHHHHHh--ccccc
Confidence            999999999996  55554

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=98.99  E-value=4.3e-10  Score=95.03  Aligned_cols=84  Identities=10%  Similarity=-0.027  Sum_probs=75.5

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecC---
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHS---  153 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~---  153 (184)
                      ..++||++++++.|+.++..|...|+.+..+|++++    ..+.+.|++|+..|+||       +|+|+ ++|||++   
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~  262 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCL  262 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEE
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcc
Confidence            448999999999999999999999999999999765    46778899999999999       69999 9999999   


Q ss_pred             -----------------CCCCccccccccccccCCccc
Q psy437          154 -----------------LVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       154 -----------------~p~~~e~y~~~i~~~~~~r~~  174 (184)
                                       .|.+.++|+|+++  |+||.+
T Consensus       263 ~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~G--RaGR~g  298 (451)
T 2jlq_A          263 KPVILTDGPERVILAGPIPVTPASAAQRRG--RIGRNP  298 (451)
T ss_dssp             EEEEECSSSCEEEEEEEEECCHHHHHHHHT--TSSCCT
T ss_pred             cccccccccceeeecccccCCHHHHHHhcc--ccCCCC
Confidence                             9999999999995  666654

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=98.98  E-value=5.5e-10  Score=99.29  Aligned_cols=140  Identities=16%  Similarity=0.072  Sum_probs=103.6

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC-------CCeeE--EecC------C-CC--HHHHHHHHHHHhccCceEEEEEeecc
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE-------RINAI--SYHA------G-LA--DKLRNEVQMKWISNKVHVGHWTVVSK   95 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~-------gi~~~--~~hg------~-l~--~~~R~~~~~~f~~g~~~vlVaT~tr~   95 (184)
                      ..+.|.++.|-..++.++++|...       .++..  .+..      . ..  .......+........++||++++++
T Consensus       169 ~~~ii~lSATl~n~~~~~~~l~~~~~~~~~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LVF~~sr~  248 (720)
T 2zj8_A          169 KAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRR  248 (720)
T ss_dssp             TBEEEEEECCCSCHHHHHHHTTEEEEECCCCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHHHTTCCEEEECSCHH
T ss_pred             CCeEEEEcCCcCCHHHHHHHhCCcccCCCCCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHHhCCCCEEEEecCHH
Confidence            456777888877788999988531       11111  1111      0 00  11223333443444578999999999


Q ss_pred             cHHHHHHHHHhc------------------CC---------------cEEEeeCCCChHHHHHHHHHhhCCCceEEEE--
Q psy437           96 ECDSVAAALAQE------------------RI---------------NAISYHAGLADKLRNEVQMKWISNKVHLYNV--  140 (184)
Q Consensus        96 ~~e~~a~gL~~~------------------gi---------------~~~vih~~~p~~~r~~~~~~f~~~~~~v~va--  140 (184)
                      +|+.+|..|...                  ++               .+..+|+++|++.|..+.+.|++|.+.|+||  
T Consensus       249 ~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~  328 (720)
T 2zj8_A          249 KAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATP  328 (720)
T ss_dssp             HHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTSSCEEEECS
T ss_pred             HHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCCCeEEEECc
Confidence            999999998642                  22               3689999999999999999999999999999  


Q ss_pred             -----EecCCccEEEe----cC----CCCCccccccccccccCCcccc
Q psy437          141 -----WKIQWKRIIWI----HS----LVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       141 -----~D~~~vr~v~~----~~----~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                           +|+|+++.||+    |+    .|.+..+|+|++  +|+||.+.
T Consensus       329 ~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~--GRaGR~g~  374 (720)
T 2zj8_A          329 TLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQML--GRAGRPKY  374 (720)
T ss_dssp             TTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHH--TTBCCTTT
T ss_pred             HhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHH--hhcCCCCC
Confidence                 69999999999    76    689999999999  58888653

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=98.93  E-value=1.8e-09  Score=96.56  Aligned_cols=103  Identities=12%  Similarity=-0.096  Sum_probs=84.2

Q ss_pred             CHHHHHHHHHHHh----ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE----
Q psy437           69 ADKLRNEVQMKWI----SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV----  140 (184)
Q Consensus        69 ~~~~R~~~~~~f~----~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va----  140 (184)
                      +..++...+-...    ...-++||+|.+...+|.++..|...|+++.++|++..+..+..+.+.|+.|  .|+||    
T Consensus       422 ~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmA  499 (853)
T 2fsf_A          422 TEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMA  499 (853)
T ss_dssp             SHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCC
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccc
Confidence            4455554444332    2234799999999999999999999999999999999988888888889888  57777    


Q ss_pred             ---EecCC--------------------------------c-----cEEEecCCCCCcccccccccc-ccCCcc
Q psy437          141 ---WKIQW--------------------------------K-----RIIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       141 ---~D~~~--------------------------------v-----r~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                         .|++.                                |     .+||++++|.+.+.|.|++++ +|.|+.
T Consensus       500 gRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~  573 (853)
T 2fsf_A          500 GRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDA  573 (853)
T ss_dssp             SSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCC
T ss_pred             cCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCC
Confidence               59987                                4     699999999999999999976 366655

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.93  E-value=2.5e-09  Score=96.28  Aligned_cols=107  Identities=9%  Similarity=-0.023  Sum_probs=93.4

Q ss_pred             ChHHHHHHHHHhhc-CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCce---EEEEEeec
Q psy437           19 NVLKEVISLIKAKY-SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH---VGHWTVVS   94 (184)
Q Consensus        19 ~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~---vlVaT~tr   94 (184)
                      .|+..|.++|.... .+.++||||.....++.+...|...|+++..+||+++..+|..++++|.++...   +|++|.  
T Consensus       556 ~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~--  633 (800)
T 3mwy_W          556 GKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTR--  633 (800)
T ss_dssp             HHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHH--
T ss_pred             hHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecc--
Confidence            47777777776532 456899999999999999999999999999999999999999999999986654   788888  


Q ss_pred             ccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           95 KECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                          ....||+.+..+ .|||++.|-+...+.|+..|.
T Consensus       634 ----agg~GlNL~~a~-~VI~~D~~wnp~~~~Qa~gR~  666 (800)
T 3mwy_W          634 ----AGGLGINLMTAD-TVVIFDSDWNPQADLQAMARA  666 (800)
T ss_dssp             ----HHTTTCCCTTCC-EEEESSCCSCSHHHHHHHTTT
T ss_pred             ----cccCCCCccccc-eEEEecCCCChhhHHHHHHHH
Confidence                667899999998 999999999999999998553

>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=98.84  E-value=6.2e-10  Score=94.25  Aligned_cols=84  Identities=10%  Similarity=-0.020  Sum_probs=75.0

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEe-----
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWI-----  151 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~-----  151 (184)
                      ..++||++++++.|+.++..|...|+.+..+|++    .|..+.+.|++|+..|+|+       +|+|+ ++||+     
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~  264 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSV  264 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEEC
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCccc
Confidence            4579999999999999999999999999999985    5667778899999999999       59999 99999     


Q ss_pred             ---------------cCCCCCccccccccccccCCccc
Q psy437          152 ---------------HSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       152 ---------------~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                                     ++.|.+..+|+|+++  |+||.+
T Consensus       265 ~~~~~~~~~~~~~~~~d~p~s~~~~~QR~G--RaGR~g  300 (459)
T 2z83_A          265 KPTILEEGEGRVILGNPSPITSASAAQRRG--RVGRNP  300 (459)
T ss_dssp             CEEEECSSSCEEEECSCEECCHHHHHHHHT--TSSCCT
T ss_pred             ccccccccccccccccCCCCCHHHHHHhcc--ccCCCC
Confidence                           789999999999995  666654

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=98.83  E-value=6.9e-09  Score=93.21  Aligned_cols=87  Identities=9%  Similarity=-0.118  Sum_probs=76.2

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCc-----------
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWK-----------  146 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~v-----------  146 (184)
                      -++||+|.+...+|.++..|...|+++.++|++..+..+..+.+.|+.|  .|+||       .|++.+           
T Consensus       461 qpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~  538 (922)
T 1nkt_A          461 QPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRL  538 (922)
T ss_dssp             CCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHH
T ss_pred             CcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHH
Confidence            4799999999999999999999999999999999888888888888877  56777       599875           


Q ss_pred             -----------------------------------------cEEEecCCCCCcccccccccc-ccCCcc
Q psy437          147 -----------------------------------------RIIWIHSLVLIKPDYLPPILD-LRLGRE  173 (184)
Q Consensus       147 -----------------------------------------r~v~~~~~p~~~e~y~~~i~~-~~~~r~  173 (184)
                                                               -+||++++|.+.+.|.|++++ +|.|+.
T Consensus       539 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRqGdp  607 (922)
T 1nkt_A          539 RERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQGDP  607 (922)
T ss_dssp             HHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGGGCC
T ss_pred             hhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccCCCC
Confidence                                                     599999999999999999975 355554

>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=98.81  E-value=1.1e-08  Score=86.96  Aligned_cols=97  Identities=10%  Similarity=0.060  Sum_probs=79.0

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhc-CCcEEEeeCCCChHHHHHHHHHhhCC-Cce-EEEE-------EecCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISN-KVH-LYNV-------WKIQW  145 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~-gi~~~vih~~~p~~~r~~~~~~f~~~-~~~-v~va-------~D~~~  145 (184)
                      .+..+.....++||+|.....++.++..|... |+.+..+|+++|+..|..+.+.|+++ .+. ++++       +|.+.
T Consensus       333 ~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Glnl~~  412 (500)
T 1z63_A          333 IIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTS  412 (500)
T ss_dssp             HHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCCCCTT
T ss_pred             HHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCCchhh
Confidence            34444455668999999999999999999875 99989999999999999999999988 555 4544       69999


Q ss_pred             ccEEEecCCCCCccccccccccc-cCCc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~-~~~r  172 (184)
                      +..|+++++|.++..|.|+++|. |.|.
T Consensus       413 ~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq  440 (500)
T 1z63_A          413 ANRVIHFDRWWNPAVEDQATDRVYRIGQ  440 (500)
T ss_dssp             CSEEEESSCCSCC---CHHHHTTTTTTT
T ss_pred             CCEEEEeCCCCCcchHHHHHHHHHHcCC
Confidence            99999999999999999999653 4443

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=98.71  E-value=2.5e-09  Score=90.23  Aligned_cols=84  Identities=11%  Similarity=0.022  Sum_probs=76.7

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+|++...++.++..|.     +.++|+++|...|..+.+.|++|++.|+|+       +|+|++..|++++.|.
T Consensus       349 ~~k~lvF~~~~~~~~~l~~~l~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~  423 (472)
T 2fwr_A          349 KDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSG  423 (472)
T ss_dssp             SSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSS
T ss_pred             CCcEEEEECCHHHHHHHHHHhC-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCC
Confidence            4589999999999999999884     367999999999999999999999999998       6999999999999999


Q ss_pred             CccccccccccccCCccc
Q psy437          157 IKPDYLPPILDLRLGRED  174 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~~  174 (184)
                      +...|+|+++  |+||.+
T Consensus       424 s~~~~~Q~~G--R~~R~g  439 (472)
T 2fwr_A          424 SAREYIQRLG--RILRPS  439 (472)
T ss_dssp             CCHHHHHHHH--HSBCCC
T ss_pred             CHHHHHHHHh--hccCCC
Confidence            9999999994  777765

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.70  E-value=5.9e-08  Score=85.38  Aligned_cols=90  Identities=8%  Similarity=-0.006  Sum_probs=80.1

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCce---EEEE-------EecCCccEEEec
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH---LYNV-------WKIQWKRIIWIH  152 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~---v~va-------~D~~~vr~v~~~  152 (184)
                      +.-++||+|.....++.++..|...|+.+..+||++|.+.|..+.+.|.++...   ++++       +|.+.+.+||++
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            456899999999999999999999999999999999999999999999998654   5555       699999999999


Q ss_pred             CCCCCccccccccccc-cCCc
Q psy437          153 SLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       153 ~~p~~~e~y~~~i~~~-~~~r  172 (184)
                      |+|.++..|.|++.+. |.|.
T Consensus       495 d~~wnp~~~~Qa~gR~~R~Gq  515 (644)
T 1z3i_X          495 DPDWNPANDEQAMARVWRDGQ  515 (644)
T ss_dssp             SCCSSHHHHHHHHTTSSSTTC
T ss_pred             CCCCCccHHHHHHHhhhhcCC
Confidence            9999999999999653 5553

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.70  E-value=1.5e-08  Score=87.88  Aligned_cols=86  Identities=8%  Similarity=0.018  Sum_probs=73.4

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCc--------EEEeeCCCChHHHHHHHHHhhCCCce---EEEE-------EecCCc
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERIN--------AISYHAGLADKLRNEVQMKWISNKVH---LYNV-------WKIQWK  146 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~--------~~vih~~~p~~~r~~~~~~f~~~~~~---v~va-------~D~~~v  146 (184)
                      .++||+|+++..|+.++..|...+..        +..+|+++|+ .|..+.+.|++++..   |+++       +|+|++
T Consensus       440 ~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v  518 (590)
T 3h1t_A          440 AKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTC  518 (590)
T ss_dssp             SEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTE
T ss_pred             ccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccchhe
Confidence            58999999999999999999765432        5789999875 788999999997755   6666       699999


Q ss_pred             cEEEecCCCCCccccccccccccCCcc
Q psy437          147 RIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       147 r~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ..|+++++|.+...|+|+++  |+||.
T Consensus       519 ~~Vi~~~~~~s~~~~~Q~iG--R~~R~  543 (590)
T 3h1t_A          519 KNVVLARVVNSMSEFKQIVG--RGTRL  543 (590)
T ss_dssp             EEEEEESCCCCHHHHHHHHT--TSCCC
T ss_pred             eEEEEEecCCChHHHHHHHh--hhccc
Confidence            99999999999999999995  66663

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.50  E-value=3.3e-07  Score=82.50  Aligned_cols=97  Identities=11%  Similarity=0.055  Sum_probs=83.4

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCce---EEEE-------EecCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH---LYNV-------WKIQW  145 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~---v~va-------~D~~~  145 (184)
                      ++..+....-++||+|.....++.++..|...|+++..+||++|...|..+.+.|.++...   ++++       +|.+.
T Consensus       564 lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~agg~GlNL~~  643 (800)
T 3mwy_W          564 LLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMT  643 (800)
T ss_dssp             HHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHHHHTTTCCCTT
T ss_pred             HHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecccccCCCCccc
Confidence            3444555566899999999999999999999999999999999999999999999986543   5555       69999


Q ss_pred             ccEEEecCCCCCccccccccccc-cCCc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~-~~~r  172 (184)
                      ...||++|+|.++..+.|++.|. |.|-
T Consensus       644 a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ  671 (800)
T 3mwy_W          644 ADTVVIFDSDWNPQADLQAMARAHRIGQ  671 (800)
T ss_dssp             CCEEEESSCCSCSHHHHHHHTTTSCSSC
T ss_pred             cceEEEecCCCChhhHHHHHHHHHhcCC
Confidence            99999999999999999999753 5554

>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=98.48  E-value=2.4e-07  Score=85.39  Aligned_cols=93  Identities=5%  Similarity=0.057  Sum_probs=75.5

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhCC------------Cee-EEecCC----------C----------CH----------
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQER------------INA-ISYHAG----------L----------AD----------   70 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~g------------i~~-~~~hg~----------l----------~~----------   70 (184)
                      +.++||||+|+..|..+++.|.+.+            +++ .++||+          +          ++          
T Consensus       537 g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I  616 (1038)
T 2w00_A          537 GFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAI  616 (1038)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHH
Confidence            3579999999999999999998654            555 456653          2          22          


Q ss_pred             -------------------HHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           71 -------------------KLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        71 -------------------~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                                         ..|..++++|++|+.++||+|+      .+++|+|.|.+.  +++.+.|-+...++|+..|
T Consensus       617 ~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd------~lltGfDiP~l~--tlylDkpl~~~~liQaIGR  688 (1038)
T 2w00_A          617 REYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVG------MFLTGFDAPTLN--TLFVDKNLRYHGLMQAFSR  688 (1038)
T ss_dssp             HHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESS------TTSSSCCCTTEE--EEEEESCCCHHHHHHHHHT
T ss_pred             HHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcc------hHHhCcCccccc--EEEEccCCCccceeehhhc
Confidence                               1478899999999999999999      888999999984  5678899999999999977


Q ss_pred             CCC
Q psy437          132 SNK  134 (184)
Q Consensus       132 ~~~  134 (184)
                      .++
T Consensus       689 tnR  691 (1038)
T 2w00_A          689 TNR  691 (1038)
T ss_dssp             TCC
T ss_pred             cCc
Confidence            654

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

Probab=98.33  E-value=2e-06  Score=62.49  Aligned_cols=88  Identities=14%  Similarity=0.178  Sum_probs=81.6

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+++++..++.++..|...|+.+..+|+++|+..|..+.+.|++|+..|+++       +|+|++++|+++++|.
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~  109 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPA  109 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCS
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhcCCCcccCCEEEEeCCCC
Confidence            357999999999999999999999999999999999999999999999999999999       6999999999999999


Q ss_pred             CccccccccccccCCcc
Q psy437          157 IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~  173 (184)
                      +.+.|+|+++  |+||.
T Consensus       110 ~~~~~~qr~G--R~gR~  124 (165)
T 1fuk_A          110 NKENYIHRIG--RGGRF  124 (165)
T ss_dssp             SGGGGGGSSC--SCC--
T ss_pred             CHHHHHHHhc--ccccC
Confidence            9999999995  66664

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=98.11  E-value=4.3e-07  Score=76.38  Aligned_cols=137  Identities=9%  Similarity=0.016  Sum_probs=81.2

Q ss_pred             CCeEEEEEEccChH--------HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHH
Q psy437            8 ANLKYEILPKKNVL--------KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMK   79 (184)
Q Consensus         8 ~Nl~y~v~~~~~k~--------~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~   79 (184)
                      .|+.+.|..+...+        ..+...+..  ...+.|.++.|....  + ..+.....+........+.......+..
T Consensus        98 ~~l~~vViDEah~~~~~~~~~~~~~~~~~~~--~~~~~l~~SAT~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (440)
T 1yks_A           98 VNWEVIIMDEAHFLDPASIAARGWAAHRARA--NESATILMTATPPGT--S-DEFPHSNGEIEDVQTDIPSEPWNTGHDW  172 (440)
T ss_dssp             CCCSEEEETTTTCCSHHHHHHHHHHHHHHHT--TSCEEEEECSSCTTC--C-CSSCCCSSCEEEEECCCCSSCCSSSCHH
T ss_pred             cCccEEEEECccccCcchHHHHHHHHHHhcc--CCceEEEEeCCCCch--h-hhhhhcCCCeeEeeeccChHHHHHHHHH
Confidence            56777777665432        223332321  446677788775321  1 1111111222222222222222233344


Q ss_pred             HhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEec
Q psy437           80 WISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIH  152 (184)
Q Consensus        80 f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~  152 (184)
                      +.....++||+++++..|+.++..|...|+++..+|+    +.|..+.+.|++|+..|+|+       +|+| +++|||+
T Consensus       173 l~~~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~  247 (440)
T 1yks_A          173 ILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDC  247 (440)
T ss_dssp             HHHCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEEC
T ss_pred             HHhcCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeC
Confidence            4444568999999999999999999999999999999    45788899999999999999       5999 9999997


Q ss_pred             CC
Q psy437          153 SL  154 (184)
Q Consensus       153 ~~  154 (184)
                      +.
T Consensus       248 g~  249 (440)
T 1yks_A          248 RT  249 (440)
T ss_dssp             CE
T ss_pred             Cc
Confidence            65

>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=97.99  E-value=4.3e-06  Score=73.29  Aligned_cols=75  Identities=8%  Similarity=-0.110  Sum_probs=64.3

Q ss_pred             HHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEE
Q psy437           78 MKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIW  150 (184)
Q Consensus        78 ~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~  150 (184)
                      +.+.+...++||++++++.|+.++..|...|+++..+|++    .|..+.+.|++|+..|+||       +|+| +++||
T Consensus       349 ~~l~~~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~VI  423 (618)
T 2whx_A          349 DWITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AGRVI  423 (618)
T ss_dssp             HHHHHCCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEEE
T ss_pred             HHHHhCCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ceEEE
Confidence            3333445689999999999999999999999999999974    6777999999999999999       6997 99999


Q ss_pred             ecCCCCC
Q psy437          151 IHSLVLI  157 (184)
Q Consensus       151 ~~~~p~~  157 (184)
                      ++.++..
T Consensus       424 d~g~~~~  430 (618)
T 2whx_A          424 DPRRCLK  430 (618)
T ss_dssp             ECCEEEE
T ss_pred             ECcceec
Confidence            9987433

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

Probab=97.94  E-value=4.7e-06  Score=69.83  Aligned_cols=142  Identities=11%  Similarity=0.026  Sum_probs=90.6

Q ss_pred             CCCeEEEEEEccChH----HHHHHHHHhh--cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHH
Q psy437            7 RANLKYEILPKKNVL----KEVISLIKAK--YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKW   80 (184)
Q Consensus         7 R~Nl~y~v~~~~~k~----~~L~~~l~~~--~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f   80 (184)
                      -.|+.+.|..+...+    ......+...  ....+.|.++.|....  + ..+.....+...+....+......+++..
T Consensus        91 ~~~l~~vViDEaH~~~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~--~-~~~~~~~~~i~~~~~~~~~~~~~~~~~~l  167 (431)
T 2v6i_A           91 VPNYNLYIMDEAHFLDPASVAARGYIETRVSMGDAGAIFMTATPPGT--T-EAFPPSNSPIIDEETRIPDKAWNSGYEWI  167 (431)
T ss_dssp             CCCCSEEEEESTTCCSHHHHHHHHHHHHHHHTTSCEEEEEESSCTTC--C-CSSCCCSSCCEEEECCCCSSCCSSCCHHH
T ss_pred             ccCCCEEEEeCCccCCccHHHHHHHHHHHhhCCCCcEEEEeCCCCcc--h-hhhcCCCCceeeccccCCHHHHHHHHHHH
Confidence            356777777665432    2333333322  1356677788776531  1 11111122222222222222222233333


Q ss_pred             hccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecC
Q psy437           81 ISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHS  153 (184)
Q Consensus        81 ~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~  153 (184)
                      .....++||++++++.++.++..|...|+++..+|++    .|..+.+.|++|+..|+|+       +|+| +.+||++.
T Consensus       168 ~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g  242 (431)
T 2v6i_A          168 TEFDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPR  242 (431)
T ss_dssp             HSCSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECC
T ss_pred             HcCCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecC
Confidence            4445589999999999999999999999999999987    5677899999999999999       6999 99999886


Q ss_pred             CCC
Q psy437          154 LVL  156 (184)
Q Consensus       154 ~p~  156 (184)
                      .+.
T Consensus       243 ~~~  245 (431)
T 2v6i_A          243 KTI  245 (431)
T ss_dssp             EEE
T ss_pred             ccc
Confidence            544

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=97.93  E-value=2.1e-05  Score=72.56  Aligned_cols=87  Identities=6%  Similarity=0.003  Sum_probs=68.5

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcC------------CcE-EEeeCC----------C----------ChH----------
Q psy437           85 VHVGHWTVVSKECDSVAAALAQER------------INA-ISYHAG----------L----------ADK----------  121 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~g------------i~~-~vih~~----------~----------p~~----------  121 (184)
                      .++||+|+++..|..++..|...+            +++ .++|++          +          ++.          
T Consensus       538 ~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~  617 (1038)
T 2w00_A          538 FNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIR  617 (1038)
T ss_dssp             CEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHH
T ss_pred             CcEEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHHH
Confidence            479999999999999999996533            554 567753          2          222          


Q ss_pred             -------------------HHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccc-cCCc
Q psy437          122 -------------------LRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       122 -------------------~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~-~~~r  172 (184)
                                         .|..+.+.|++|+++|+++       ||.|.+ .++++|.|.+...|+|+++|+ |++.
T Consensus       618 dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~  694 (1038)
T 2w00_A          618 EYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYD  694 (1038)
T ss_dssp             HHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCC
T ss_pred             HHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCC
Confidence                               2556677799999999999       799999 889999999999999999652 4443

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=97.92  E-value=0.00074  Score=45.61  Aligned_cols=106  Identities=13%  Similarity=0.102  Sum_probs=75.7

Q ss_pred             EEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC---------------------------ceEEEE
Q psy437           38 IVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK---------------------------VHVGHW   90 (184)
Q Consensus        38 IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~---------------------------~~vlVa   90 (184)
                      ++|.+..+-...+...+...|+.+..++++-+.+.|.+.++.|.+..                           +-+||.
T Consensus         6 vvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgvdvrtvedkedfrenireiwerypqldvvvivt   85 (162)
T 2l82_A            6 VVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVRTVEDKEDFRENIREIWERYPQLDVVVIVT   85 (162)
T ss_dssp             EEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCEEEECCSHHHHHHHHHHHHHHCTTCCEEEEEE
T ss_pred             EEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCceeeeccHHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            45666666666677777777777777777777666666666665433                           234677


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEec
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKI  143 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~  143 (184)
                      |+.+.........-...|+.++|+--+...+.|...|+.|++..+.+-...|+
T Consensus        86 tddkewikdfieeakergvevfvvynnkdddrrkeaqqefrsdgvdvrtvsdk  138 (162)
T 2l82_A           86 TDDKEWIKDFIEEAKERGVEVFVVYNNKDDDRRKEAQQEFRSDGVDVRTVSDK  138 (162)
T ss_dssp             CCCHHHHHHHHHHHHHTTCEEEEEEECSCHHHHHHHHHHHCCSSCEEEEESSH
T ss_pred             cCcHHHHHHHHHHHHhcCcEEEEEecCCCchhHHHHHHHhhhcCceeeecCCH
Confidence            77666655555555778999888777888999999999999998877665443

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=97.67  E-value=6.3e-05  Score=66.30  Aligned_cols=65  Identities=18%  Similarity=0.125  Sum_probs=57.2

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLI  157 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~  157 (184)
                      .++||+++++++|+.++..|...|+++..+|+++++..       |.++...|+||       +|+| +++||++.+...
T Consensus       397 ~~vLVFv~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~  468 (666)
T 3o8b_A          397 GRHLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVT  468 (666)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEE
T ss_pred             CcEEEEeCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccc
Confidence            37899999999999999999999999999999999875       55566699999       6987 999999987653

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=97.35  E-value=0.00024  Score=61.17  Aligned_cols=75  Identities=17%  Similarity=0.088  Sum_probs=48.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEE--EEeecccHHHHHHHHHhcC--
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGH--WTVVSKECDSVAAALAQER--  108 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlV--aT~tr~~~e~~a~gL~~~g--  108 (184)
                      .++.++||++|.+.++.+++.|..  .+ ...+|..  .+|..++++|+++. .|++  +|.      ..++|+|.+|  
T Consensus       383 ~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~------~~~EGiD~~~~~  450 (540)
T 2vl7_A          383 SSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRA------KESEGVEFREKE  450 (540)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC--------------------
T ss_pred             CCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecC------ceecceecCCCc
Confidence            567899999999999999988864  22 3455553  46889999999864 5776  678      6799999998  


Q ss_pred             --CcEEEeeCCCCh
Q psy437          109 --INAISYHAGLAD  120 (184)
Q Consensus       109 --i~~~vih~~~p~  120 (184)
                        ++ +|+..++|.
T Consensus       451 ~~~~-~Vii~~lPf  463 (540)
T 2vl7_A          451 NLFE-SLVLAGLPY  463 (540)
T ss_dssp             -CEE-EEEEESCCC
T ss_pred             cccc-EEEEECCCC
Confidence              66 777799993

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=97.24  E-value=0.00078  Score=52.94  Aligned_cols=97  Identities=10%  Similarity=0.057  Sum_probs=75.0

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHhc-CCcEEEeeCCCChHHHHHHHHHhhCC-CceE-EEE-------EecCC
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISN-KVHL-YNV-------WKIQW  145 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~-gi~~~vih~~~p~~~r~~~~~~f~~~-~~~v-~va-------~D~~~  145 (184)
                      ++..+....-++||+|.....++.++..|... |+++..+||++|+..|..+.+.|.++ ++.| +++       +|.+.
T Consensus       104 ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~st~~~g~Glnl~~  183 (271)
T 1z5z_A          104 IIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTS  183 (271)
T ss_dssp             HHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTT
T ss_pred             HHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEehhhhcCCcCccc
Confidence            34444445568999999999999999999885 99989999999999999999999988 7774 444       59999


Q ss_pred             ccEEEecCCCCCccccccccccc-cCCc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDL-RLGR  172 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~-~~~r  172 (184)
                      +.+||++|+|.++..|.|++.+. |.|.
T Consensus       184 a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq  211 (271)
T 1z5z_A          184 ANRVIHFDRWWNPAVEDQATDRVYRIGQ  211 (271)
T ss_dssp             CSEEEECSCCSCTTTC------------
T ss_pred             CCEEEEECCCCChhHHHHHHHhccccCC
Confidence            99999999999999999999753 5554

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

Probab=96.59  E-value=0.0017  Score=54.87  Aligned_cols=61  Identities=5%  Similarity=0.013  Sum_probs=31.2

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcC------------CcEEEeeCCCChHHHHHHHHHhhC-CCceEEEEEecC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQER------------INAISYHAGLADKLRNEVQMKWIS-NKVHLYNVWKIQ  144 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~g------------i~~~vih~~~p~~~r~~~~~~f~~-~~~~v~va~D~~  144 (184)
                      ..++||+|+++..++.++..|...+            .....+|+++|+..|..+.+.|++ |++.|+|+-|.-
T Consensus       389 ~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~  462 (555)
T 3tbk_A          389 ETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVA  462 (555)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCT
T ss_pred             CceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchh
Confidence            4689999999999999999998763            233556679999999999999999 999999986654

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=96.03  E-value=0.055  Score=40.97  Aligned_cols=57  Identities=18%  Similarity=0.088  Sum_probs=44.4

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      +..+||.|+|++.+.++.+.+.+    .++.+..++|+.+.......+.    ...+|+|+|+.+
T Consensus       102 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~I~v~Tp~~  162 (242)
T 3fe2_A          102 GPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLE----RGVEICIATPGR  162 (242)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH----HCCSEEEECHHH
T ss_pred             CCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhc----CCCCEEEECHHH
Confidence            55689999999999999887765    3889999999988765544433    257899999854

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=95.55  E-value=0.048  Score=41.74  Aligned_cols=57  Identities=12%  Similarity=0.042  Sum_probs=43.8

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ..++||.++|++.+.++++.+.+.    ++.+..++|+.+.......+    .+..+|+|+|+.+
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~  171 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGR  171 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHH
Confidence            456999999999999999888754    78899999998765443322    3567899999843

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=95.48  E-value=0.12  Score=38.48  Aligned_cols=58  Identities=21%  Similarity=0.097  Sum_probs=39.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh---CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~---~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .+.++||.++|++.+.++++.+..   .++.+..++|+.+...+...   + ....+|+|+|+.+
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~iiv~Tp~~  153 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIED---I-SKGVDIIIATPGR  153 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHH---H-HSCCSEEEECHHH
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHH---h-cCCCCEEEECHHH
Confidence            456689999999999999999887   37788889998765433322   2 2357899999844

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=95.37  E-value=0.055  Score=40.17  Aligned_cols=56  Identities=20%  Similarity=0.144  Sum_probs=44.8

Q ss_pred             CcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           35 QSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        35 ~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      .++||.|+|+..++++++.+.+.     ++++..++|+.+.....   +.+.++..+|+|+|+.
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~~~~~~~~i~v~T~~  143 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE---EVLKKNCPHIVVGTPG  143 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHH---HHHHHSCCSEEEECHH
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHH---HHHhcCCCCEEEeCHH
Confidence            47899999999999999888764     78899999998865543   3445566789999993

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=95.05  E-value=0.048  Score=47.63  Aligned_cols=78  Identities=14%  Similarity=0.072  Sum_probs=51.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcC--Cc
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQER--IN  110 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~g--i~  110 (184)
                      .++.++||++|....+.+++.|.  .+... ..-|++..+|..++++|+ ++..||++|.+-    ..++|+|.+|  .+
T Consensus       447 ~~g~~lvlF~Sy~~l~~v~~~l~--~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~g----sf~EGiD~~g~~l~  518 (620)
T 4a15_A          447 VKKNTIVYFPSYSLMDRVENRVS--FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGG----RLSEGINFPGNELE  518 (620)
T ss_dssp             HCSCEEEEESCHHHHHHHTSSCC--SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTS----CC--------CCCC
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHH--hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecC----ceeccccCCCCceE
Confidence            45679999999999999998886  22222 445566778999999999 888899997411    2378999887  44


Q ss_pred             EEEeeCCCC
Q psy437          111 AISYHAGLA  119 (184)
Q Consensus       111 ~~vih~~~p  119 (184)
                       .|+=.++|
T Consensus       519 -~viI~~lP  526 (620)
T 4a15_A          519 -MIILAGLP  526 (620)
T ss_dssp             -EEEESSCC
T ss_pred             -EEEEEcCC
Confidence             66667776

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=94.92  E-value=0.05  Score=40.90  Aligned_cols=56  Identities=9%  Similarity=0.061  Sum_probs=44.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      ...++||.|+|++.+.++++.+.+.     ++++..++|+.+..++...+     ...+|+|+|+.
T Consensus        91 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~  151 (230)
T 2oxc_A           91 LSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPG  151 (230)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHH
Confidence            3467899999999999999988763     67889999998866544332     35789999994

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=94.70  E-value=0.45  Score=34.55  Aligned_cols=57  Identities=18%  Similarity=0.040  Sum_probs=42.7

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ..++||.|+|+..++++++.+.+.     ++.+..++|+.+..+....    ..+..+|+|+|+.+
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~i~v~T~~~  132 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR----LDDTVHVVIATPGR  132 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH----TTSCCSEEEECHHH
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh----cCCCCCEEEeCHHH
Confidence            457999999999999999888653     6788889999875543221    23567899999843

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=94.57  E-value=0.2  Score=37.48  Aligned_cols=56  Identities=18%  Similarity=0.051  Sum_probs=41.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      .+.++||.|+|+..+.++++.+.+.    ++.+..++|+.+.......+     +..+|+|+|+.
T Consensus        96 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~  155 (236)
T 2pl3_A           96 DGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPG  155 (236)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHH
Confidence            3567899999999999999988764    47888999997755433322     46789999983

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=94.32  E-value=0.2  Score=37.67  Aligned_cols=59  Identities=12%  Similarity=0.047  Sum_probs=37.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ...++||.++|++.+.++++.+...    ++.+..++|+.+..   .....+..+..+|+|+|+.+
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~---~~~~~l~~~~~~Ilv~Tp~~  159 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVR---NEMQKLQAEAPHIVVGTPGR  159 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHH
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchH---HHHHHHhcCCCCEEEECHHH
Confidence            3467899999999999999988764    56778888886533   23344556668899999843

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=94.16  E-value=0.065  Score=39.83  Aligned_cols=57  Identities=14%  Similarity=0.011  Sum_probs=40.9

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC--------CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE--------RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~--------gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      +.++||.|+|++.+.++++.+.+.        ++.+..++|+.+..+...    ...+..+|+|+|+.+
T Consensus        72 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~Iiv~Tp~~  136 (219)
T 1q0u_A           72 EVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALE----KLNVQPHIVIGTPGR  136 (219)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTC----CCSSCCSEEEECHHH
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHH----HcCCCCCEEEeCHHH
Confidence            457899999999999999887653        678888899865432211    112456899999843

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=93.88  E-value=0.67  Score=35.47  Aligned_cols=58  Identities=12%  Similarity=-0.006  Sum_probs=42.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .+.++||.+||+..++++++.+.+    .++.+..+.|+........   .+.. ..+|+|+|+.+
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~-~~~Iiv~Tp~~  186 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQ---KLGN-GINIIVATPGR  186 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHH---HHHH-CCSEEEECHHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHH---HhcC-CCCEEEEcHHH
Confidence            356789999999999999998876    3667788888876544332   2333 47899999843

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=93.55  E-value=0.14  Score=38.91  Aligned_cols=56  Identities=9%  Similarity=-0.015  Sum_probs=42.2

Q ss_pred             CcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           35 QSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        35 ~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .++||.|+|++.+.++++.+.+.    ++.+..++|+.+.......    .....+|+|+|+.+
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~Ivv~Tp~~  160 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIRE----VQMGCHLLVATPGR  160 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHH----HSSCCSEEEECHHH
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH----hCCCCCEEEECHHH
Confidence            57999999999999998888753    5778888998875543322    23467899999954

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=93.53  E-value=0.22  Score=36.28  Aligned_cols=58  Identities=16%  Similarity=0.059  Sum_probs=43.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC--CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE--RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~--gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ...+++|.|+|+..+.++++.+...  ++++..++|+.+.......+    ....+|+|+|+.+
T Consensus        71 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~i~v~T~~~  130 (207)
T 2gxq_A           71 RKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEAL----LRGADAVVATPGR  130 (207)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHH----HHCCSEEEECHHH
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHh----hCCCCEEEECHHH
Confidence            3567899999999999999999875  46788899988755433322    2357899999843

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=93.16  E-value=0.3  Score=44.61  Aligned_cols=56  Identities=11%  Similarity=-0.047  Sum_probs=46.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .+.+++|.|+|+..|.+.++++..    .|+++..+.||++.++|....      ...|+|+|+++
T Consensus       119 ~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~i~Gg~~~~~r~~ay------~~DIvyGTpgr  178 (997)
T 2ipc_A          119 TGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAY------LADVTYVTNSE  178 (997)
T ss_dssp             TCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEECCTTCCHHHHHHHH------TSSEEEEEHHH
T ss_pred             hCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHc------CCCEEEECchh
Confidence            567899999999999998888764    599999999999987776654      37899999954

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=92.85  E-value=0.15  Score=38.42  Aligned_cols=58  Identities=14%  Similarity=0.001  Sum_probs=39.7

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      +.++||.+||++.+.++++.+.+.    ++.+..++|+.....   .......+..+|+|+|+.+
T Consensus        98 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~I~v~Tp~~  159 (245)
T 3dkp_A           98 GFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAK---KFGPKSSKKFDILVTTPNR  159 (245)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHT---TTSTTSCCCCCEEEECHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHH---HhhhhhcCCCCEEEECHHH
Confidence            446899999999999999988764    667777776532211   1122234567899999743

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=92.61  E-value=0.084  Score=39.20  Aligned_cols=57  Identities=11%  Similarity=-0.023  Sum_probs=37.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ...++||.++|+..+.++++.+..    .++.+..++|+.+..+....   +.  ..+|+|+|+.+
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~--~~~iiv~Tp~~  141 (224)
T 1qde_A           81 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---LR--DAQIVVGTPGR  141 (224)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC-------------CT--TCSEEEECHHH
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---CC--CCCEEEECHHH
Confidence            345789999999999999988875    36788889998765443322   22  27899999843

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=91.86  E-value=0.18  Score=33.44  Aligned_cols=49  Identities=16%  Similarity=0.210  Sum_probs=37.4

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      ...|.+.+.+..+..+.++||.+-..+...+..|...|+++..+.||+.
T Consensus        42 ~~~l~~~~~~l~~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           42 ISELREKWKILERDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             HHHHHHHGGGSCTTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHH
T ss_pred             HHHHHHHHHhCCCCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHH
Confidence            3445555544324567889999988899999999999998888999864

>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=91.69  E-value=0.24  Score=33.56  Aligned_cols=48  Identities=13%  Similarity=0.214  Sum_probs=35.5

Q ss_pred             HHHHHHHhhcCC-CcEEEEe-ccHHHHHHHHHHHHhCCCeeEEecCCCCH
Q psy437           23 EVISLIKAKYSG-QSGIVYC-LTRKECDSVAAALAQERINAISYHAGLAD   70 (184)
Q Consensus        23 ~L~~~l~~~~~~-~~~IIf~-~tr~~~e~la~~L~~~gi~~~~~hg~l~~   70 (184)
                      .+...+....+. .+.|+|| .+-..+...+..|...|+++..+.||+..
T Consensus        77 ~~~~~~~~~~~~~~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~~  126 (134)
T 3g5j_A           77 DIYLQAAELALNYDNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYKA  126 (134)
T ss_dssp             HHHHHHHHHHTTCSEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHHH
T ss_pred             HHHHHHHHhccCCCeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHHH
Confidence            344444332244 6788899 57777889999999999998999999754

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=91.62  E-value=0.13  Score=40.45  Aligned_cols=79  Identities=9%  Similarity=-0.079  Sum_probs=48.9

Q ss_pred             CeEEEEEEccChHH-HHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHH
Q psy437            9 NLKYEILPKKNVLK-EVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMK   79 (184)
Q Consensus         9 Nl~y~v~~~~~k~~-~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~   79 (184)
                      |+.........|.. .++.++...   .....+||.+||++.|.++...+...     ++.+..+.|+.+.....     
T Consensus       133 ~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----  207 (300)
T 3fmo_B          133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ-----  207 (300)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC-----
T ss_pred             eEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh-----
Confidence            44333333345543 344444321   13346999999999999998888753     56777777776532211     


Q ss_pred             HhccCceEEEEEeec
Q psy437           80 WISNKVHVGHWTVVS   94 (184)
Q Consensus        80 f~~g~~~vlVaT~tr   94 (184)
                        ....+|+|+|+.+
T Consensus       208 --~~~~~IlV~TP~~  220 (300)
T 3fmo_B          208 --KISEQIVIGTPGT  220 (300)
T ss_dssp             --CCCCSEEEECHHH
T ss_pred             --cCCCCEEEECHHH
Confidence              3456899999954

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=90.27  E-value=0.51  Score=43.08  Aligned_cols=52  Identities=19%  Similarity=0.245  Sum_probs=38.7

Q ss_pred             CCCCCCeEEEEE---E--ccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHH
Q psy437            4 SFNRANLKYEIL---P--KKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALA   55 (184)
Q Consensus         4 s~~R~Nl~y~v~---~--~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~   55 (184)
                      |.+||.+.....   .  ...|...+++.+.+. ..+.|+||+|.|.+..|.+++.|.
T Consensus       407 PTn~p~~R~D~~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE~LS~~L~  464 (997)
T 2ipc_A          407 PTNRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLK  464 (997)
T ss_dssp             CCSSCCCCEEEEEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHHHHHHHHh
Confidence            677888754322   1  224788877777543 257899999999999999999998

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=90.06  E-value=0.69  Score=28.84  Aligned_cols=47  Identities=21%  Similarity=0.271  Sum_probs=33.3

Q ss_pred             HHHHHHHHhh--cCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           22 KEVISLIKAK--YSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        22 ~~L~~~l~~~--~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      ..+.+.+.+.  .+..+.++||.+-..+...+..|.+.|+. +..+ ||+.
T Consensus        27 ~~l~~~~~~l~~~~~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           27 KEVKERIATAVPDKNDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             HHHHHHHHHHCCCTTSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             HHHHHHHHHhCCCCCCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHH
Confidence            3344444332  24567888999988889999999999996 4445 8765

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=89.67  E-value=1  Score=38.35  Aligned_cols=71  Identities=14%  Similarity=-0.019  Sum_probs=49.8

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEE--E-------EecCC----ccEE
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYN--V-------WKIQW----KRII  149 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~v--a-------~D~~~----vr~v  149 (184)
                      ...++||.+++...++.++..|..  .. ..+++..  ..+..+.+.|+.+. .|++  +       +|.|+    ++.|
T Consensus       383 ~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~V  456 (540)
T 2vl7_A          383 SSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFESL  456 (540)
T ss_dssp             CSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccEE
Confidence            345799999999999999888854  55 5566554  45777888888765 3444  3       49987    8999


Q ss_pred             EecCCCCCcc
Q psy437          150 WIHSLVLIKP  159 (184)
Q Consensus       150 ~~~~~p~~~e  159 (184)
                      |+..+|....
T Consensus       457 ii~~lPf~~~  466 (540)
T 2vl7_A          457 VLAGLPYPNV  466 (540)
T ss_dssp             EEESCCCCCT
T ss_pred             EEECCCCCCC
Confidence            9999997666

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=88.92  E-value=2.4  Score=31.93  Aligned_cols=59  Identities=7%  Similarity=-0.034  Sum_probs=46.0

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .|.......+..  ...+++|+|+++..++++.+.+.+.++. +..++|+...             ..+|+|+|.
T Consensus       120 GKT~~a~~~~~~--~~~~~liv~P~~~L~~q~~~~~~~~~~~~v~~~~g~~~~-------------~~~i~v~T~  179 (237)
T 2fz4_A          120 GKTHVAMAAINE--LSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKE-------------LKPLTVSTY  179 (237)
T ss_dssp             THHHHHHHHHHH--SCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCBC-------------CCSEEEEEH
T ss_pred             CHHHHHHHHHHH--cCCCEEEEeCCHHHHHHHHHHHHhCCCCeEEEEeCCCCC-------------cCCEEEEeH
Confidence            466655555544  3678999999999999999999888888 8888887542             457899997

>3ipz_A Monothiol glutaredoxin-S14, chloroplastic; electron transport, PL redox-active center, transit peptide, transport, oxidoreduc; 2.40A {Arabidopsis thaliana} PDB: 2lku_A

Probab=88.85  E-value=3  Score=27.38  Aligned_cols=56  Identities=7%  Similarity=-0.065  Sum_probs=38.0

Q ss_pred             CCCcEEEEec------cHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEE
Q psy437           33 SGQSGIVYCL------TRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVG   88 (184)
Q Consensus        33 ~~~~~IIf~~------tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vl   88 (184)
                      ...+.+||..      .+..|....+.|.+.|++...+.=..+++.+..+.+..-...++.|
T Consensus        16 ~~~~Vvvy~k~t~~~p~Cp~C~~ak~~L~~~gi~~~~~dI~~~~~~~~~l~~~~g~~tvP~i   77 (109)
T 3ipz_A           16 NSEKVVLFMKGTRDFPMCGFSNTVVQILKNLNVPFEDVNILENEMLRQGLKEYSNWPTFPQL   77 (109)
T ss_dssp             TSSSEEEEESBCSSSBSSHHHHHHHHHHHHTTCCCEEEEGGGCHHHHHHHHHHHTCSSSCEE
T ss_pred             ccCCEEEEEecCCCCCCChhHHHHHHHHHHcCCCcEEEECCCCHHHHHHHHHHHCCCCCCeE
Confidence            5578999987      4999999999999999887666543344444444443333345543

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=88.68  E-value=0.36  Score=31.27  Aligned_cols=37  Identities=19%  Similarity=0.362  Sum_probs=31.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      +..+.++||.+-..+...+..|...|+++..+.||+.
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            4467888999988899999999999998888999864

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=88.16  E-value=0.53  Score=30.85  Aligned_cols=48  Identities=15%  Similarity=0.239  Sum_probs=36.0

Q ss_pred             HHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           22 KEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        22 ~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      ..+...+.+..+..+.++||.+-..+...+..|...|+. +..+.||+.
T Consensus        46 ~~l~~~~~~l~~~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           46 DTLGAFMRDNDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHHHSCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             HHHHHHHHhcCCCCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHH
Confidence            444445544324567888999988889999999999995 778889864

>3zyw_A Glutaredoxin-3; metal binding protein; 1.84A {Homo sapiens}

Probab=87.76  E-value=3.4  Score=27.30  Aligned_cols=56  Identities=7%  Similarity=-0.011  Sum_probs=38.0

Q ss_pred             CCCcEEEEe------ccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEE
Q psy437           33 SGQSGIVYC------LTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVG   88 (184)
Q Consensus        33 ~~~~~IIf~------~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vl   88 (184)
                      ...+.+||.      +++..|....+.|.+.|++...+.=..+++.+..+.+..-...++.|
T Consensus        14 ~~~~Vvlf~kg~~~~~~Cp~C~~ak~~L~~~gi~y~~~di~~d~~~~~~l~~~~g~~tvP~i   75 (111)
T 3zyw_A           14 HAAPCMLFMKGTPQEPRCGFSKQMVEILHKHNIQFSSFDIFSDEEVRQGLKAYSSWPTYPQL   75 (111)
T ss_dssp             TSSSEEEEESBCSSSBSSHHHHHHHHHHHHTTCCCEEEEGGGCHHHHHHHHHHHTCCSSCEE
T ss_pred             hcCCEEEEEecCCCCCcchhHHHHHHHHHHcCCCeEEEECcCCHHHHHHHHHHHCCCCCCEE
Confidence            457899998      68899999999999999887666544455555544433223345544

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=87.54  E-value=0.49  Score=30.20  Aligned_cols=35  Identities=23%  Similarity=0.268  Sum_probs=30.6

Q ss_pred             CcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           35 QSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        35 ~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      .+.++||.+-..+...+..|...|+.+..+.||+.
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            67888999988888999999999999777889875

>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=87.47  E-value=0.38  Score=31.67  Aligned_cols=36  Identities=17%  Similarity=0.291  Sum_probs=31.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGL   68 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l   68 (184)
                      +..+.++||.+-..+...+..|.+.|+.+..+.||+
T Consensus        55 ~~~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~   90 (103)
T 3iwh_A           55 KNEIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGM   90 (103)
T ss_dssp             TTSEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHH
T ss_pred             CCCeEEEECCCCHHHHHHHHHHHHcCCCEEEecChH
Confidence            456788899998888899999999999988888886

>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=87.34  E-value=0.33  Score=32.88  Aligned_cols=49  Identities=16%  Similarity=0.148  Sum_probs=35.5

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHH--HHHHHHHHHhCCCeeEEecCCCC
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKE--CDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~--~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      ...|...+....+..+.|+||.+-..  +...+..|...|+++..+.||+.
T Consensus        58 ~~~l~~~~~~l~~~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~~  108 (124)
T 3flh_A           58 AKDLATRIGELDPAKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGALE  108 (124)
T ss_dssp             HHHHHHHGGGSCTTSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHHH
T ss_pred             HHHHHHHHhcCCCCCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcHH
Confidence            34455555433245568889988765  78899999999999888889864

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=87.19  E-value=0.66  Score=33.71  Aligned_cols=55  Identities=9%  Similarity=-0.049  Sum_probs=36.5

Q ss_pred             CCcEEEEeccHHHHHH-HHHHHHh---CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           34 GQSGIVYCLTRKECDS-VAAALAQ---ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~-la~~L~~---~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      ..++||.|+|+..+++ +.+.+..   .++.+..++|+.+...+...+.    +..+|+|+|+
T Consensus        82 ~~~~lil~p~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~----~~~~i~v~T~  140 (216)
T 3b6e_A           82 PGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVV----KSCDIIISTA  140 (216)
T ss_dssp             CCCEEEEESSHHHHHHHHHHTHHHHHTTTSCEEECCC---CCCCHHHHH----HHCSEEEEEH
T ss_pred             CCcEEEEECHHHHHHHHHHHHHHHHhccCceEEEEeCCcccchhHHhhc----cCCCEEEECH
Confidence            5689999999999888 6555554   3678888998865433222211    2468999998

>3jy6_A Transcriptional regulator, LACI family; NYSGXRC, PSI-II, protein S initiative, structural genomics; 1.97A {Lactobacillus brevis}

Probab=87.16  E-value=6.6  Score=29.46  Aligned_cols=16  Identities=13%  Similarity=0.248  Sum_probs=9.4

Q ss_pred             ccHHHHHHHHHhcCCc
Q psy437           95 KECDSVAAALAQERIN  110 (184)
Q Consensus        95 ~~~e~~a~gL~~~gi~  110 (184)
                      .....+++.|-..|.+
T Consensus       109 ~~g~~a~~~L~~~G~~  124 (276)
T 3jy6_A          109 EAAKAATTAFRQQGYQ  124 (276)
T ss_dssp             HHHHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHcCCC
Confidence            3455666666666655

>3ipz_A Monothiol glutaredoxin-S14, chloroplastic; electron transport, PL redox-active center, transit peptide, transport, oxidoreduc; 2.40A {Arabidopsis thaliana} PDB: 2lku_A

Probab=86.89  E-value=4.8  Score=26.32  Aligned_cols=72  Identities=11%  Similarity=-0.007  Sum_probs=51.6

Q ss_pred             CCCCHHHHHHHHHHHhccCceEEEEEee------cccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEE
Q psy437           66 AGLADKLRNEVQMKWISNKVHVGHWTVV------SKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYN  139 (184)
Q Consensus        66 g~l~~~~R~~~~~~f~~g~~~vlVaT~t------r~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~v  139 (184)
                      ++|+++.+..+.+...+.  +|+|++.+      -..|..+-+.|+..|++...++.+-....+.++.+......++.+.
T Consensus         1 ~~~s~~~~~~v~~~i~~~--~Vvvy~k~t~~~p~Cp~C~~ak~~L~~~gi~~~~~dI~~~~~~~~~l~~~~g~~tvP~if   78 (109)
T 3ipz_A            1 SALTPQLKDTLEKLVNSE--KVVLFMKGTRDFPMCGFSNTVVQILKNLNVPFEDVNILENEMLRQGLKEYSNWPTFPQLY   78 (109)
T ss_dssp             CCCCHHHHHHHHHHHTSS--SEEEEESBCSSSBSSHHHHHHHHHHHHTTCCCEEEEGGGCHHHHHHHHHHHTCSSSCEEE
T ss_pred             CCCCHHHHHHHHHHHccC--CEEEEEecCCCCCCChhHHHHHHHHHHcCCCcEEEECCCCHHHHHHHHHHHCCCCCCeEE
Confidence            367887777666655543  57888764      6789999999999999977777776667777776654445565554

>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=85.49  E-value=0.79  Score=30.00  Aligned_cols=37  Identities=16%  Similarity=0.207  Sum_probs=31.2

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +..+.|+||.+-..+...+..|...|+. +..+.||+.
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            4467888999988899999999999995 777888854

>3h75_A Periplasmic sugar-binding domain protein; protein structure initiative II (PSI II), sugar binding PROT alpha/beta fold; 1.60A {Pseudomonas fluorescens pf-5}

Probab=85.14  E-value=8.2  Score=30.13  Aligned_cols=73  Identities=8%  Similarity=-0.098  Sum_probs=52.3

Q ss_pred             HHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChH
Q psy437           49 SVAAALAQERINAISYHAGLADKLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADK  121 (184)
Q Consensus        49 ~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~  121 (184)
                      -+.+.+.+.|+.+..+.++-+.......++.+..  ..+..||.++.....+.+...+...|++++.+....+..
T Consensus        25 g~~~~a~~~g~~~~~~~~~~~~~~~~~~i~~~i~~~~~vDgiIi~~~~~~~~~~~~~~~~~giPvV~~~~~~~~~   99 (350)
T 3h75_A           25 FMQAAARDLGLDLRILYAERDPQNTLQQARELFQGRDKPDYLMLVNEQYVAPQILRLSQGSGIKLFIVNSPLTLD   99 (350)
T ss_dssp             HHHHHHHHHTCEEEEEECTTCHHHHHHHHHHHHHSSSCCSEEEEECCSSHHHHHHHHHTTSCCEEEEEESCCCTT
T ss_pred             HHHHHHHHcCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEeCchhhHHHHHHHHHhCCCcEEEEcCCCChH
Confidence            3444455669998888877777766777888887  478877777644455566677788899987788777654

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=84.91  E-value=8.3  Score=29.95  Aligned_cols=75  Identities=4%  Similarity=-0.093  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           46 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        46 ~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                      ....+.+.+.+.|+.+..+.+.-+.+.-...++.+....+..||..+.....+.+...+...++++.++....+.
T Consensus        81 ~~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~iPvV~~~~~~~~  155 (338)
T 3dbi_A           81 LLFHAARMAEEKGRQLLLADGKHSAEEERQAIQYLLDLRCDAIMIYPRFLSVDEIDDIIDAHSQPIMVLNRRLRK  155 (338)
T ss_dssp             HHHHHHHHHHHTTCEEEEEECTTSHHHHHHHHHHHHHTTCSEEEECCSSSCHHHHHHHHHHCSSCEEEESSCCSS
T ss_pred             HHHHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHhCCCCEEEEeCCCCChHHHHHHHHcCCCCEEEEcCCCCC
Confidence            344455566677888877776666665566777787777877777665544455566666777875556555543

>2yan_A Glutaredoxin-3; oxidoreductase; HET: GSH; 1.90A {Homo sapiens}

Probab=84.84  E-value=5.3  Score=25.68  Aligned_cols=55  Identities=5%  Similarity=-0.041  Sum_probs=37.1

Q ss_pred             CCcEEEEe------ccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEE
Q psy437           34 GQSGIVYC------LTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVG   88 (184)
Q Consensus        34 ~~~~IIf~------~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vl   88 (184)
                      ..+.+||+      +++..|..+...|.+.+++...+.-..++..+..+.+.+-...++.|
T Consensus        16 ~~~vvvf~~g~~~~~~C~~C~~~~~~L~~~~i~~~~vdi~~~~~~~~~l~~~~g~~~vP~v   76 (105)
T 2yan_A           16 KASVMLFMKGNKQEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKAYSNWPTYPQL   76 (105)
T ss_dssp             SSSEEEEESBCSSSBCTTHHHHHHHHHHHHTCCCEEEEGGGCHHHHHHHHHHHTCCSSCEE
T ss_pred             cCCEEEEEecCCCCCCCccHHHHHHHHHHCCCCeEEEECCCCHHHHHHHHHHHCCCCCCeE
Confidence            45688887      57889999999999988876666555455555555444433455554

>3l49_A ABC sugar (ribose) transporter, periplasmic substrate-binding subunit; sugar binding/transporter, structural genomics, PSI; HET: UNL; 2.30A {Rhodobacter sphaeroides}

Probab=84.59  E-value=9.6  Score=28.61  Aligned_cols=10  Identities=10%  Similarity=0.116  Sum_probs=4.4

Q ss_pred             HHHHHHHHHh
Q psy437           97 CDSVAAALAQ  106 (184)
Q Consensus        97 ~e~~a~gL~~  106 (184)
                      ...+++.|-.
T Consensus       111 g~~~~~~l~~  120 (291)
T 3l49_A          111 GAELALQMVA  120 (291)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            3444444444

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*

Probab=84.56  E-value=5.1  Score=29.82  Aligned_cols=25  Identities=16%  Similarity=0.114  Sum_probs=14.3

Q ss_pred             EEeecccHHHHHHHHHhcCCcEEEe
Q psy437           90 WTVVSKECDSVAAALAQERINAISY  114 (184)
Q Consensus        90 aT~tr~~~e~~a~gL~~~gi~~~vi  114 (184)
                      .++.......+++.|-..|.+-.++
T Consensus       101 ~~d~~~~~~~a~~~L~~~G~~~i~~  125 (272)
T 3o74_A          101 ISDDRDASRQLAASLLSSAPRSIAL  125 (272)
T ss_dssp             EECHHHHHHHHHHHHHTTCCSEEEE
T ss_pred             EEchHHHHHHHHHHHHHCCCcEEEE
Confidence            3344445666777777777653333

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=84.31  E-value=1.1  Score=29.42  Aligned_cols=37  Identities=5%  Similarity=0.105  Sum_probs=31.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      +..+.++||.+-..+...+..|...|+....+.||+.
T Consensus        55 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~~~~l~GG~~   91 (110)
T 2k0z_A           55 KDKKVLLHCRAGRRALDAAKSMHELGYTPYYLEGNVY   91 (110)
T ss_dssp             SSSCEEEECSSSHHHHHHHHHHHHTTCCCEEEESCGG
T ss_pred             CCCEEEEEeCCCchHHHHHHHHHHCCCCEEEecCCHH
Confidence            4567889999988899999999999997677889975

>3tb6_A Arabinose metabolism transcriptional repressor; transcription regulation, arabinose binding, DNA binding Pro; HET: ARB; 2.21A {Bacillus subtilis}

Probab=84.27  E-value=9.8  Score=28.59  Aligned_cols=72  Identities=8%  Similarity=-0.038  Sum_probs=35.7

Q ss_pred             HHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc----cHHHHHHHHHhcCCcEEEeeCCCC
Q psy437           48 DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK----ECDSVAAALAQERINAISYHAGLA  119 (184)
Q Consensus        48 e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~----~~e~~a~gL~~~gi~~~vih~~~p  119 (184)
                      +.+.+.+.+.|+.+..+...-+.+.-...++.+.+..+..||..+...    ........+...|++++.+....+
T Consensus        35 ~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~~~~~iPvV~~~~~~~  110 (298)
T 3tb6_A           35 RGIESYLSEQGYSMLLTSTNNNPDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINASYA  110 (298)
T ss_dssp             HHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHHHHTCCSEEEECCSSTTSCCTTHHHHHHHHHTTCCEEEESSCCT
T ss_pred             HHHHHHHHHCCCEEEEEeCCCChHHHHHHHHHHHHCCCCEEEEecccccccCCcHHHHHHHHhcCCCEEEEecCcC
Confidence            334444445566665555554444445555555555565555544321    222334445555666444444433

>3m9w_A D-xylose-binding periplasmic protein; xylose binding protein, conformational changes, SUGA protein; 2.15A {Escherichia coli} PDB: 3m9x_A* 3ma0_A*

Probab=83.30  E-value=12  Score=28.48  Aligned_cols=26  Identities=15%  Similarity=-0.198  Sum_probs=13.4

Q ss_pred             EEEeecccHHHHHHHHH-hcCCcEEEe
Q psy437           89 HWTVVSKECDSVAAALA-QERINAISY  114 (184)
Q Consensus        89 VaT~tr~~~e~~a~gL~-~~gi~~~vi  114 (184)
                      |.++.......+++.|- ..|.+..++
T Consensus       102 V~~D~~~~g~~a~~~L~~~~G~~~i~~  128 (313)
T 3m9w_A          102 ISFDNEKVGELQAKALVDIVPQGNYFL  128 (313)
T ss_dssp             EEECHHHHHHHHHHHHHHHCSSEEEEE
T ss_pred             EecCHHHHHHHHHHHHHHhCCCCcEEE
Confidence            33344445556666665 566653333

>3gx8_A Monothiol glutaredoxin-5, mitochondrial; TRX fold, electron transport, mitochondrion, redox-active center, transit peptide, transport; 1.67A {Saccharomyces cerevisiae}

Probab=82.72  E-value=8.2  Score=25.81  Aligned_cols=56  Identities=7%  Similarity=0.016  Sum_probs=36.6

Q ss_pred             CCCcEEEEec------cHHHHHHHHHHHHhCCCe---eEEecCCCCHHHHHHHHHHHhccCceEE
Q psy437           33 SGQSGIVYCL------TRKECDSVAAALAQERIN---AISYHAGLADKLRNEVQMKWISNKVHVG   88 (184)
Q Consensus        33 ~~~~~IIf~~------tr~~~e~la~~L~~~gi~---~~~~hg~l~~~~R~~~~~~f~~g~~~vl   88 (184)
                      ...+.+||..      .+..|..+.+.|.+.|++   ...+.-..+.+.+..+.+..-...++.|
T Consensus        14 ~~~~Vvvfsk~t~~~p~Cp~C~~ak~lL~~~gv~~~~~~~~dv~~~~~~~~~l~~~sg~~tvP~v   78 (121)
T 3gx8_A           14 ESAPVVLFMKGTPEFPKCGFSRATIGLLGNQGVDPAKFAAYNVLEDPELREGIKEFSEWPTIPQL   78 (121)
T ss_dssp             HSCSEEEEESBCSSSBCTTHHHHHHHHHHHHTBCGGGEEEEECTTCHHHHHHHHHHHTCCSSCEE
T ss_pred             ccCCEEEEEeccCCCCCCccHHHHHHHHHHcCCCcceEEEEEecCCHHHHHHHHHHhCCCCCCeE
Confidence            3468999988      488999999999999987   5445444455555544443323344443

>3uug_A Multiple sugar-binding periplasmic receptor CHVE; periplasmic binding protein, sugar-binding protein, sugar binding protein; HET: BDP; 1.75A {Agrobacterium tumefaciens} PDB: 3urm_A*

Probab=82.53  E-value=12  Score=28.69  Aligned_cols=74  Identities=11%  Similarity=0.043  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc-cHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           47 CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK-ECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        47 ~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~-~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                      ..-+.+.+.+.|+.+..+.+.-+.+.-...++.+.+.++..||.++... ........+...|+++..+....|.
T Consensus        22 ~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~i~~~~~~~vdgiIi~~~~~~~~~~~~~~~~~~giPvV~~~~~~~~   96 (330)
T 3uug_A           22 GNNIVKQLQEAGYKTDLQYADDDIPNQLSQIENMVTKGVKVLVIASIDGTTLSDVLKQAGEQGIKVIAYDRLIRN   96 (330)
T ss_dssp             HHHHHHHHHHTTCEEEEEECTTCHHHHHHHHHHHHHHTCSEEEECCSSGGGGHHHHHHHHHTTCEEEEESSCCCS
T ss_pred             HHHHHHHHHHcCCEEEEeeCCCCHHHHHHHHHHHHHcCCCEEEEEcCCchhHHHHHHHHHHCCCCEEEECCCCCC
Confidence            4445566667899988887777777777888888888888888777553 3455566778889997667665543

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=82.08  E-value=0.94  Score=31.53  Aligned_cols=37  Identities=22%  Similarity=0.285  Sum_probs=30.8

Q ss_pred             CCCcEEEEeccH--HHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           33 SGQSGIVYCLTR--KECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr--~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      +..+.|+||.+-  ..+...+..|...|+++..+.||+.
T Consensus        71 ~~~~ivvyC~~g~~~rs~~aa~~L~~~G~~v~~l~GG~~  109 (144)
T 3nhv_A           71 KEKVIITYCWGPACNGATKAAAKFAQLGFRVKELIGGIE  109 (144)
T ss_dssp             TTSEEEEECSCTTCCHHHHHHHHHHHTTCEEEEEESHHH
T ss_pred             CCCeEEEEECCCCccHHHHHHHHHHHCCCeEEEeCCcHH
Confidence            345678899987  5788899999999999888999964

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=81.75  E-value=1.3  Score=30.86  Aligned_cols=37  Identities=16%  Similarity=0.223  Sum_probs=30.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +..+.|+||.+-..+...+..|...|+. +..+.||+.
T Consensus        79 ~~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           79 HERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             --CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            4567899999877788899999999995 888999985

>2xw6_A MGS, methylglyoxal synthase; lyase; 1.08A {Thermus SP} PDB: 2x8w_A 1wo8_A

Probab=81.08  E-value=11  Score=26.08  Aligned_cols=78  Identities=8%  Similarity=0.033  Sum_probs=48.3

Q ss_pred             CCCCeEEEEEEccChHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHh-CCCeeEEecCCCCHHHHHHHHHHHh
Q psy437            6 NRANLKYEILPKKNVLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQ-ERINAISYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus         6 ~R~Nl~y~v~~~~~k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~-~gi~~~~~hg~l~~~~R~~~~~~f~   81 (184)
                      ++-||-+++.... | ..++.+.++.   ..+. .|+  .|..++    +.|++ .|+++..+..+ +.+-+..+.+..+
T Consensus         2 ~~~~ialsv~D~d-K-~~~v~~a~~~~~ll~Gf-~l~--AT~gTa----~~L~e~~Gl~v~~v~k~-~~eG~p~I~d~I~   71 (134)
T 2xw6_A            2 HMRALALIAHDAK-K-EEMVAFCQRHREVLARF-PLV--ATGTTG----RRIEEATGLTVEKLLSG-PLGGDQQMGARVA   71 (134)
T ss_dssp             CSCEEEEEECGGG-H-HHHHHHHHHTHHHHTTS-CEE--ECHHHH----HHHHHHHCCCCEECSCG-GGTHHHHHHHHHH
T ss_pred             CccEEEEEEeccc-H-HHHHHHHHHHHHHhCCC-EEE--EccHHH----HHHHHhhCceEEEEEec-CCCCcchHHHHHH
Confidence            3556777766552 3 3444444332   1222 333  354444    45555 69998887643 2135778999999


Q ss_pred             ccCceEEEEEee
Q psy437           82 SNKVHVGHWTVV   93 (184)
Q Consensus        82 ~g~~~vlVaT~t   93 (184)
                      +|+++.+|.|+.
T Consensus        72 ~geIdlVInt~~   83 (134)
T 2xw6_A           72 EGRILAVIFFRD   83 (134)
T ss_dssp             TTCEEEEEEECC
T ss_pred             CCCccEEEEccC
Confidence            999999999997

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=80.99  E-value=0.96  Score=30.70  Aligned_cols=37  Identities=14%  Similarity=0.154  Sum_probs=31.4

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +..+.|+||.+-..+...+..|...|+. +..+.||+.
T Consensus        81 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~  118 (129)
T 1tq1_A           81 QSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYS  118 (129)
T ss_dssp             TTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             CCCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcHH
Confidence            4567899999988888999999999996 778999974

>3l6u_A ABC-type sugar transport system periplasmic compo; structural genomics, nysgrc, target 11006S, PSI-2, protein S initiative; 1.90A {Exiguobacterium sibiricum}

Probab=80.65  E-value=15  Score=27.45  Aligned_cols=74  Identities=11%  Similarity=0.076  Sum_probs=52.5

Q ss_pred             HHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecc-cHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           47 CDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSK-ECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        47 ~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~-~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                      ..-+.+.+.+.|+.+..+..+-+.+.-...++.+.+..+..||..+... ........+...|++++++....|.
T Consensus        27 ~~gi~~~a~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~vdgiI~~~~~~~~~~~~~~~~~~~~iPvV~~~~~~~~  101 (293)
T 3l6u_A           27 INAFKAEAKANKYEALVATSQNSRISEREQILEFVHLKVDAIFITTLDDVYIGSAIEEAKKAGIPVFAIDRMIRS  101 (293)
T ss_dssp             HHHHHHHHHHTTCEEEEEECSSCHHHHHHHHHHHHHTTCSEEEEECSCTTTTHHHHHHHHHTTCCEEEESSCCCC
T ss_pred             HHHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEecCChHHHHHHHHHHHHcCCCEEEecCCCCC
Confidence            3445556667799988888777777677788888888888777766443 3335566777889997777766664

---

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	184
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	2e-12
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	2e-11
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-09
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-05

>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 = 60.8 bits (146), Expect = 2e-12
 Identities = 30/97 (30%), Positives = 57/97 (58%), Gaps = 1/97 (1%)

Query: 4   SFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAIS 63
           SF+R N++Y ++ K   L +++  ++ +  G+SGI+YC +R + +  AA L  + I+A +
Sbjct: 1   SFDRPNIRYMLMEKFKPLDQLMRYVQ-EQRGKSGIIYCNSRAKVEDTAARLQSKGISAAA 59

Query: 64  YHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSV 100
           YHAGL + +R +VQ K+  + + +   TV      + 
Sbjct: 60  YHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINK 96

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 4  SFNRANLKYEILPKKNVLKEVISLIK-AKYSGQSGIVYCLTRKECDSVAAALAQERINAI 62
          +    N++   L     +      I      G   +++C ++K+CD +AA L    INA+
Sbjct: 4  TVPHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAV 63

Query: 63 SYHAGLADKLRNEVQMKWISN 83
          +Y+ GL   +        +  
Sbjct: 64 AYYRGLDVSVIPTNGDVVVVA 84

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 53.0 bits (127), Expect = 2e-09
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 7  RANLKYEILPKKNVLKEVISLIK-AKYSGQSGIVYCLTRKECDSVAAALAQERINAISYH 65
            N++   L     +      I      G   +++C ++K+CD +AA L    INA++Y+
Sbjct: 8  HPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYY 67

Query: 66 AGLADKLRNEVQMKWI 81
           GL   +        +
Sbjct: 68 RGLDVSVIPTSGDVVV 83

>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 = 41.7 bits (97), Expect = 2e-05
 Identities = 10/76 (13%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 12 YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADK 71
           ++      +  + S+++    G  GI+Y  T +E + +  +L  +      +  G+   
Sbjct: 5  EDVAVNDESISTLSSILEKL--GTGGIIYARTGEEAEEIYESLKNK------FRIGIVTA 56

Query: 72 LRNEVQMKWISNKVHV 87
           +     K++  ++  
Sbjct: 57 TKKGDYEKFVEGEIDH 72

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	184
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.91
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.9
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.89
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.89
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.89
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.89
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.87
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.86
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.79
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.76
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.74
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.74
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.73
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.7
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.7
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.69
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.68
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.68
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.65
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.59
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.58
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.51
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.37
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.37
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.28
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.26
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.24
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.18
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.15
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.9
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.87
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	98.83
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.58
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	98.44
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.22
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.1
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	97.34
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	97.27
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.23
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	97.15
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.97
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.85
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	96.24
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	95.98
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	95.69
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	95.63
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.49
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	95.47
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	94.98
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	94.84
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.66
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	94.33
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	93.69
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	93.4
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	92.43
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	91.61
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	91.56
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	90.62
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	89.55
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	89.19
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	88.84
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	88.83
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	86.58
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	84.33
d1e5da1	152	Rubredoxin oxygen:oxidoreductase (ROO), C-terminal	84.14
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	83.83
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	83.4
d2b2na1	308	Transcription-repair coupling factor, TRCF {Escher	82.99
d1ycga1	149	Nitric oxide reductase C-terminal domain {Moorella	82.75
d2dria_	271	D-ribose-binding protein {Escherichia coli, strain	81.97
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	81.8
d1vmea1	148	ROO-like flavoprotein TM0755, C-terminal domain {T	81.22
d1jyea_	271	Lac-repressor (lacR) core (C-terminal domain) {Esc	80.99
d1dbqa_	282	Purine repressor (PurR), C-terminal domain {Escher	80.14

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.97  E-value=3.3e-30  Score=195.19  Aligned_cols=123  Identities=26%  Similarity=0.503  Sum_probs=116.0

Q ss_pred             CCCCCCeEEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhcc
Q psy437            4 SFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN   83 (184)
Q Consensus         4 s~~R~Nl~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g   83 (184)
                      |||||||+|.|.+..+|++.|..+|... .+.++||||+|++.++.++..|...|+.+..+||++++++|..+++.|++|
T Consensus         1 s~~RpNi~y~v~~~~~k~~~L~~~l~~~-~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g   79 (200)
T d1oywa3           1 SFDRPNIRYMLMEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRD   79 (200)
T ss_dssp             CCCCTTEEEEEEECSSHHHHHHHHHHHT-TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCCCCCcEEEEEcCCcHHHHHHHHHHhc-CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcc
Confidence            8999999999999999999999999764 677899999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      +.++||||+      .+++|+|.++|+ +|||+|+|.+..+|+||.++.|.
T Consensus        80 ~~~ilvaTd------~~~~GiD~p~v~-~VI~~~~P~~~~~y~qr~GR~gR  123 (200)
T d1oywa3          80 DLQIVVATV------AFGMGINKPNVR-FVVHFDIPRNIESYYQETGRAGR  123 (200)
T ss_dssp             SCSEEEECT------TSCTTTCCTTCC-EEEESSCCSSHHHHHHHHTTSCT
T ss_pred             cceEEEecc------hhhhccCCCCCC-EEEECCCccchHHHHHHhhhhhc
Confidence            999999999      557899999999 99999999999999999977654

>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=99.91  E-value=1.3e-23  Score=153.60  Aligned_cols=112  Identities=12%  Similarity=0.192  Sum_probs=89.1

Q ss_pred             EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      +.+...+.|++.|.+++... +..++||||+|+..++.++..|...|+++..+||+|++++|..+++.|+.|+.++||+|
T Consensus         6 ~~v~~~e~K~~~L~~ll~~~-~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~T   84 (162)
T d1fuka_           6 VNVEEEEYKYECLTDLYDSI-SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILIST   84 (162)
T ss_dssp             EEEESGGGHHHHHHHHHHHT-TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEE
T ss_pred             EEeCCcHHHHHHHHHHHHhC-CCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeecc
Confidence            33434456999999998764 77899999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhh
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI  131 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~  131 (184)
                      +      .+++|+|.++++ +|||+|+|.+...|+||..+
T Consensus        85 d------v~~rGiDi~~v~-~VI~~d~P~~~~~yihR~GR  117 (162)
T d1fuka_          85 D------LLARGIDVQQVS-LVINYDLPANKENYIHRIGR  117 (162)
T ss_dssp             G------GGTTTCCCCSCS-EEEESSCCSSGGGGGGSSCS
T ss_pred             c------cccccccCCCce-EEEEeccchhHHHHHhhccc
Confidence            9      556666555555 44444444444444444433

>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=99.90  E-value=6.7e-24  Score=154.05  Aligned_cols=118  Identities=17%  Similarity=0.251  Sum_probs=107.0

Q ss_pred             CCeE--EEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCc
Q psy437            8 ANLK--YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV   85 (184)
Q Consensus         8 ~Nl~--y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~   85 (184)
                      +||.  |..++..+|++.|.++|+.  .+.++||||+|++.|+.+++.|++.|+.+..+||++++.+|..++++|++|+.
T Consensus         2 ~nI~~~~i~v~~~~K~~~L~~ll~~--~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~   79 (155)
T d1hv8a2           2 ANIEQSYVEVNENERFEALCRLLKN--KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI   79 (155)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHCS--TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSS
T ss_pred             CCeEEEEEEeChHHHHHHHHHHHcc--CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccc
Confidence            4664  4445566799999999865  56789999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++||||+      .+++|+|.++++ +|+|+|+|.+...|+||.++.|.
T Consensus        80 ~ilv~T~------~~~~Gid~~~v~-~Vi~~d~p~~~~~y~qr~GR~gR  121 (155)
T d1hv8a2          80 RILIATD------VMSRGIDVNDLN-CVINYHLPQNPESYMHRIGRTGR  121 (155)
T ss_dssp             SEEEECT------THHHHCCCSCCS-EEEESSCCSCHHHHHHHSTTTCC
T ss_pred             eeeeehh------HHhhhhhhccCc-EEEEecCCCCHHHHHHHHHhcCc
Confidence            9999999      889999999999 99999999999999999976653

>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=99.89  E-value=1.8e-23  Score=153.76  Aligned_cols=119  Identities=13%  Similarity=0.198  Sum_probs=107.2

Q ss_pred             CCeE--EEEEEcc-ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC
Q psy437            8 ANLK--YEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK   84 (184)
Q Consensus         8 ~Nl~--y~v~~~~-~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~   84 (184)
                      .|+.  |..++.. .|+..|.+++.+. ...++||||+|+..++.++..|...|+++..+||++++++|..+++.|++|+
T Consensus         6 ~~i~q~~v~v~~~~~K~~~L~~ll~~~-~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~   84 (168)
T d2j0sa2           6 EGIKQFFVAVEREEWKFDTLCDLYDTL-TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGA   84 (168)
T ss_dssp             TTEEEEEEEESSTTHHHHHHHHHHHHH-TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTS
T ss_pred             CCcEEEEEEecChHHHHHHHHHHHHhC-CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCC
Confidence            4664  5555544 4999999999765 7789999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      .++||||+      .+++|+|.++++ +|||+|+|.+...|+||.++.|.
T Consensus        85 ~~iLv~Td------~~~rGiDi~~v~-~VIn~d~P~~~~~yihR~GR~gR  127 (168)
T d2j0sa2          85 SRVLISTD------VWARGLDVPQVS-LIINYDLPNNRELYIHRIGRSGR  127 (168)
T ss_dssp             SCEEEECG------GGSSSCCCTTEE-EEEESSCCSSHHHHHHHHTTSSG
T ss_pred             ccEEeccc------hhcccccccCcc-eEEEecCCcCHHHHHhhhccccc
Confidence            99999999      779999999999 99999999999999999977654

>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=2.4e-23  Score=154.72  Aligned_cols=116  Identities=16%  Similarity=0.151  Sum_probs=102.7

Q ss_pred             EEEEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           12 YEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        12 y~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      -.|.|.....+.|+..+.+. ..+.++||||+|+..++.++..|...|+++.++||+|++.+|.+++++|++|+.+||||
T Consensus         8 ievrp~~~qvd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVa   87 (181)
T d1t5la2           8 IDVRPTKGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVG   87 (181)
T ss_dssp             EEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEE
T ss_pred             EEEEECCCcHHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEe
Confidence            34667666677777766543 25678999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCCh-----HHHHHHHHHhhCCC
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLAD-----KLRNEVQMKWISNK  134 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~-----~~r~~~~~~f~~~~  134 (184)
                      |+      .+++|+|.++++ +|+|+++|.     +.+.|+||..++|+
T Consensus        88 Td------v~~rGiDip~v~-~VI~~d~p~~~~~~s~~~yi~R~GRagR  129 (181)
T d1t5la2          88 IN------LLREGLDIPEVS-LVAILDADKEGFLRSERSLIQTIGRAAR  129 (181)
T ss_dssp             SC------CCSSSCCCTTEE-EEEETTTTSCSGGGSHHHHHHHHGGGTT
T ss_pred             hh------HHHccCCCCCCC-EEEEecCCcccccccHHHHHHHHHhhcc
Confidence            99      778999999999 999999995     68999999987765

>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=99.89  E-value=1.6e-23  Score=154.38  Aligned_cols=116  Identities=13%  Similarity=0.185  Sum_probs=106.5

Q ss_pred             EEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           11 KYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        11 ~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      +|.+++..+|...|.++|++. +..++||||+|++.++.++..|...|+.+..+||+|++++|..++++|++|+.++|||
T Consensus        10 ~yi~v~~~~K~~~L~~ll~~~-~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~   88 (171)
T d1s2ma2          10 YYAFVEERQKLHCLNTLFSKL-QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVC   88 (171)
T ss_dssp             EEEECCGGGHHHHHHHHHHHS-CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEE
T ss_pred             EEEEcCHHHHHHHHHHHHHhC-CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccc
Confidence            466666667999999999764 7789999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCC
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~  134 (184)
                      |+      .+++|+|.++++ .|||+|+|.+.+.|+||..+.|+
T Consensus        89 Td------~~~~Gid~~~v~-~VI~~d~p~~~~~y~qr~GR~gR  125 (171)
T d1s2ma2          89 SD------LLTRGIDIQAVN-VVINFDFPKTAETYLHRIGRSGR  125 (171)
T ss_dssp             SS------CSSSSCCCTTEE-EEEESSCCSSHHHHHHHHCBSSC
T ss_pred             hh------HhhhccccceeE-EEEecCCcchHHHHHHHhhhccc
Confidence            99      678999999999 99999999999999999966543

>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=99.89  E-value=2.7e-23  Score=152.91  Aligned_cols=115  Identities=14%  Similarity=0.119  Sum_probs=101.2

Q ss_pred             EEEEccChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEE
Q psy437           13 EILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWT   91 (184)
Q Consensus        13 ~v~~~~~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT   91 (184)
                      .+.+..+..+.|++.+.+. ..+.++||||+|++.|+.++..|.+.|+++.++||+|++.+|.+++++|++|+++|||||
T Consensus         9 ev~p~~~qv~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT   88 (174)
T d1c4oa2           9 RVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI   88 (174)
T ss_dssp             EEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEES
T ss_pred             EEEeCCCCHHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEee
Confidence            4667766777777777543 367899999999999999999999999999999999999999999999999999999999


Q ss_pred             eecccHHHHHHHHHhcCCcEEEeeCCCC-----hHHHHHHHHHhhCCC
Q psy437           92 VVSKECDSVAAALAQERINAISYHAGLA-----DKLRNEVQMKWISNK  134 (184)
Q Consensus        92 ~tr~~~e~~a~gL~~~gi~~~vih~~~p-----~~~r~~~~~~f~~~~  134 (184)
                      +      .+++|+|.|+++ +|+|++.|     .+.+.|+|+..+.|.
T Consensus        89 ~------v~~~GiDip~V~-~Vi~~~~~~~~~~~~~~~~iq~~GR~gR  129 (174)
T d1c4oa2          89 N------LLREGLDIPEVS-LVAILDADKEGFLRSERSLIQTIGRAAR  129 (174)
T ss_dssp             C------CCCTTCCCTTEE-EEEETTTTSCSGGGSHHHHHHHHGGGTT
T ss_pred             e------eeeeeccCCCCc-EEEEeccccccccchhHHHHHHhhhhhh
Confidence            9      668899999999 99999955     467999999977654

>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=99.87  E-value=1e-22  Score=149.70  Aligned_cols=115  Identities=14%  Similarity=0.206  Sum_probs=105.7

Q ss_pred             EEEEEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEE
Q psy437           11 KYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        11 ~y~v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      +|..+..++|.+.|.++|... ...++||||+|++.++.+++.|.+.|+++..+||+|++++|..++++|.+|+.++||+
T Consensus         5 ~~v~~~~~~K~~~L~~ll~~~-~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~   83 (168)
T d1t5ia_           5 YYVKLKDNEKNRKLFDLLDVL-EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVA   83 (168)
T ss_dssp             EEEECCGGGHHHHHHHHHHHS-CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEE
T ss_pred             EEEEeChHHHHHHHHHHHHhC-CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeec
Confidence            566666778999999999764 7789999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           91 TVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        91 T~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      |+      .+++|+|.+.++ .|+|+++|.+...|+||..+.|
T Consensus        84 T~------~~~~Gid~~~~~-~vi~~~~p~~~~~yiqr~GR~g  119 (168)
T d1t5ia_          84 TN------LFGRGMDIERVN-IAFNYDMPEDSDTYLHRVARAG  119 (168)
T ss_dssp             SS------CCSTTCCGGGCS-EEEESSCCSSHHHHHHHHHHHT
T ss_pred             cc------cccchhhcccch-hhhhhhcccchhhHhhhhhhcc
Confidence            99      668899999999 9999999999999999986643

>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=99.79  E-value=2.2e-21  Score=138.01  Aligned_cols=115  Identities=17%  Similarity=0.237  Sum_probs=88.0

Q ss_pred             CCCCCCeEEEEEEccChHHHHHHH--HHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHh
Q psy437            4 SFNRANLKYEILPKKNVLKEVISL--IKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWI   81 (184)
Q Consensus         4 s~~R~Nl~y~v~~~~~k~~~L~~~--l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~   81 (184)
                      +.-+|||...+.+...+...+...  |.. ..++++||||+|++.|+.+++.|...|+++..|||+|++++       |+
T Consensus         4 t~~~p~I~~~~~~~~~~~~~~~~~i~l~~-~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~-------~~   75 (138)
T d1jr6a_           4 TVPHPNIEEVALSTTGEIPFYGKAIPLEV-IKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSV-------IP   75 (138)
T ss_dssp             CCCCTTEEEEECCBCSSEECSSCEECHHH-HTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCC-------CT
T ss_pred             CCcCCCeEEEEeccCChhHHHHhhChHhh-cCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhh-------hh
Confidence            556899998877665422222111  222 26689999999999999999999999999999999998654       67


Q ss_pred             ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCC----CChHHHHHHHHHhhCCC
Q psy437           82 SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAG----LADKLRNEVQMKWISNK  134 (184)
Q Consensus        82 ~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~----~p~~~r~~~~~~f~~~~  134 (184)
                      +|+.++||||+      .+++|+| ++++ .|+|++    +|.+.++|+||..+.|.
T Consensus        76 ~~~~~vlvaTd------~~~~GiD-~~v~-~Vi~~~~~~~~P~~~~~y~qr~GR~gR  124 (138)
T d1jr6a_          76 TNGDVVVVATD------ALMTGFT-GDFD-SVIDCNTSDGKPQDAVSRTQRRGRTGR  124 (138)
T ss_dssp             TSSCEEEEESS------SSCSSSC-CCBS-EEEECSEETTEECCHHHHHHHHTTBCS
T ss_pred             hhhcceeehhH------HHHhccc-cccc-eEEEEEecCCCCCCHHHHHhHhccccC
Confidence            89999999999      6678888 8888 787754    47777777777655543

>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=99.76  E-value=1.6e-18  Score=127.19  Aligned_cols=88  Identities=13%  Similarity=0.002  Sum_probs=81.8

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      .-++||+|.++++|+.++..|...|+++..||+++|++.|..+++.|++|+++|+||       +|+|+|++|+|+++|+
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~~  110 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADK  110 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTS
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEecccc
Confidence            347999999999999999999999999999999999999999999999999999999       6999999999999887


Q ss_pred             Cc-----cccccccccccCCcc
Q psy437          157 IK-----PDYLPPILDLRLGRE  173 (184)
Q Consensus       157 ~~-----e~y~~~i~~~~~~r~  173 (184)
                      +.     ++|+|++  +|+||.
T Consensus       111 ~~~~~~~~~~iq~~--GR~gR~  130 (174)
T d1c4oa2         111 EGFLRSERSLIQTI--GRAARN  130 (174)
T ss_dssp             CSGGGSHHHHHHHH--GGGTTS
T ss_pred             ccccchhHHHHHHh--hhhhhc
Confidence            54     7799999  577775

>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=99.74  E-value=1.7e-19  Score=139.81  Aligned_cols=107  Identities=12%  Similarity=0.191  Sum_probs=82.9

Q ss_pred             EEEccChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           14 ILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        14 v~~~~~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      |...++|++.|..+|++  -+.++||||+|++.|+.+++.|...      +||++++.+|.+++++|++|+++|||||++
T Consensus         7 ~~~~~~~~~~l~~~l~~--~~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a   78 (248)
T d1gkub2           7 VAVNDESISTLSSILEK--LGTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAH   78 (248)
T ss_dssp             EEESCCCTTTTHHHHTT--SCSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC
T ss_pred             EecCchHHHHHHHHHHH--hCCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEecc
Confidence            33456788999999965  4568999999999999999999753      899999999999999999999999999985


Q ss_pred             cccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEEecCC-ccEEEecCCCCCccccccccccccCCc
Q psy437           94 SKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVWKIQW-KRIIWIHSLVLIKPDYLPPILDLRLGR  172 (184)
Q Consensus        94 r~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~-vr~v~~~~~p~~~e~y~~~i~~~~~~r  172 (184)
                      +.+  .+     ..|+                                |+|+ |++|||||+|+    |+|+++  |+||
T Consensus        79 ~~~--v~-----~rGl--------------------------------Dip~~v~~VI~~d~P~----~~~r~g--R~~R  113 (248)
T d1gkub2          79 YYG--TL-----VRGL--------------------------------DLPERIRFAVFVGCPS----FRVTIE--DIDS  113 (248)
T ss_dssp             -------------CCS--------------------------------CCTTTCCEEEEESCCE----EEEECS--CGGG
T ss_pred             ccc--hh-----hhcc--------------------------------CccccccEEEEeCCCc----chhhhh--hhhc
Confidence            432  22     3333                                6775 78888888884    888885  4444


Q ss_pred             c
Q psy437          173 E  173 (184)
Q Consensus       173 ~  173 (184)
                      .
T Consensus       114 ~  114 (248)
T d1gkub2         114 L  114 (248)
T ss_dssp             S
T ss_pred             c
Confidence            3

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.74  E-value=2.5e-18  Score=129.24  Aligned_cols=88  Identities=22%  Similarity=0.269  Sum_probs=83.4

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLI  157 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~  157 (184)
                      .++||+++++..|+.++..|...|+.+..+|+++++..|..+++.|++|++.++||       +|+|+|++|||+++|.+
T Consensus        31 ~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~  110 (200)
T d1oywa3          31 KSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRN  110 (200)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSS
T ss_pred             CCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEEECCCccc
Confidence            46899999999999999999999999999999999999999999999999999999       59999999999999999


Q ss_pred             ccccccccccccCCccc
Q psy437          158 KPDYLPPILDLRLGRED  174 (184)
Q Consensus       158 ~e~y~~~i~~~~~~r~~  174 (184)
                      +++|+|+++  |+||.+
T Consensus       111 ~~~y~qr~G--R~gR~g  125 (200)
T d1oywa3         111 IESYYQETG--RAGRDG  125 (200)
T ss_dssp             HHHHHHHHT--TSCTTS
T ss_pred             hHHHHHHhh--hhhcCC
Confidence            999999995  777753

>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=99.73  E-value=4.8e-18  Score=125.72  Aligned_cols=88  Identities=15%  Similarity=0.062  Sum_probs=82.0

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      ..++||+|+++..++.++..|...|+++..+|++++++.|..+++.|++|++.|+||       +|+|+|++|||||+|+
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~  110 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADK  110 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTTS
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCCc
Confidence            347999999999999999999999999999999999999999999999999999999       6999999999999997


Q ss_pred             -----CccccccccccccCCcc
Q psy437          157 -----IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 -----~~e~y~~~i~~~~~~r~  173 (184)
                           +.+.|+||++  |+||.
T Consensus       111 ~~~~~s~~~yi~R~G--RagR~  130 (181)
T d1t5la2         111 EGFLRSERSLIQTIG--RAARN  130 (181)
T ss_dssp             CSGGGSHHHHHHHHG--GGTTS
T ss_pred             ccccccHHHHHHHHH--hhccc
Confidence                 5788999994  77775

>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=99.70  E-value=3.7e-17  Score=117.95  Aligned_cols=102  Identities=16%  Similarity=0.155  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHHhc-cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------E
Q psy437           70 DKLRNEVQMKWIS-NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------W  141 (184)
Q Consensus        70 ~~~R~~~~~~f~~-g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~  141 (184)
                      .++|...+.++.+ ...++||+|+++.+|+.++..|...|+.+..+|+++++..|..+.+.|++|+..++++       +
T Consensus        13 ~~~K~~~L~~ll~~~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gi   92 (155)
T d1hv8a2          13 ENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGI   92 (155)
T ss_dssp             GGGHHHHHHHHHCSTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHC
T ss_pred             hHHHHHHHHHHHccCCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhh
Confidence            3445555555553 3457999999999999999999999999999999999999999999999999999999       6


Q ss_pred             ecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          142 KIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       142 D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+|++++|+|+++|.+++.|+|+++  |+||.
T Consensus        93 d~~~v~~Vi~~d~p~~~~~y~qr~G--R~gR~  122 (155)
T d1hv8a2          93 DVNDLNCVINYHLPQNPESYMHRIG--RTGRA  122 (155)
T ss_dssp             CCSCCSEEEESSCCSCHHHHHHHST--TTCCS
T ss_pred             hhccCcEEEEecCCCCHHHHHHHHH--hcCcC
Confidence            9999999999999999999999995  66664

>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=99.70  E-value=2.7e-17  Score=120.29  Aligned_cols=87  Identities=15%  Similarity=0.164  Sum_probs=82.5

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCC
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLI  157 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~  157 (184)
                      .++||+|+++..|+.++..|...|+.+..+|++++++.|..+++.|++|+..++++       +|+|++++|+|||+|.+
T Consensus        35 ~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~  114 (168)
T d2j0sa2          35 TQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNN  114 (168)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSS
T ss_pred             CceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchhcccccccCcceEEEecCCcC
Confidence            47999999999999999999999999999999999999999999999999999999       69999999999999999


Q ss_pred             ccccccccccccCCcc
Q psy437          158 KPDYLPPILDLRLGRE  173 (184)
Q Consensus       158 ~e~y~~~i~~~~~~r~  173 (184)
                      .+.|+||++  |.||.
T Consensus       115 ~~~yihR~G--R~gR~  128 (168)
T d2j0sa2         115 RELYIHRIG--RSGRY  128 (168)
T ss_dssp             HHHHHHHHT--TSSGG
T ss_pred             HHHHHhhhc--ccccc
Confidence            999999995  66654

>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=99.69  E-value=4.9e-17  Score=119.14  Aligned_cols=102  Identities=17%  Similarity=0.135  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------
Q psy437           70 DKLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------  140 (184)
Q Consensus        70 ~~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------  140 (184)
                      ..+|...+..+.+  ...++||+|+++.+|+.++..|...|+.+..+|+++++..|..+.+.|+.|...++++       
T Consensus        16 ~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~G   95 (171)
T d1s2ma2          16 ERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRG   95 (171)
T ss_dssp             GGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSS
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHhhhc
Confidence            3445555555543  2348999999999999999999999999999999999999999999999999999999       


Q ss_pred             EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 ~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +|+|++++||||++|.+++.|+|+++  |+||-
T Consensus        96 id~~~v~~VI~~d~p~~~~~y~qr~G--R~gR~  126 (171)
T d1s2ma2          96 IDIQAVNVVINFDFPKTAETYLHRIG--RSGRF  126 (171)
T ss_dssp             CCCTTEEEEEESSCCSSHHHHHHHHC--BSSCT
T ss_pred             cccceeEEEEecCCcchHHHHHHHhh--hcccC
Confidence            69999999999999999999999995  55553

>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=99.68  E-value=9.8e-17  Score=126.18  Aligned_cols=107  Identities=12%  Similarity=0.159  Sum_probs=92.3

Q ss_pred             hHHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecC--------CCCHHHHHHHHHHHhccCceEE
Q psy437           20 VLKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQERINAISYHA--------GLADKLRNEVQMKWISNKVHVG   88 (184)
Q Consensus        20 k~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg--------~l~~~~R~~~~~~f~~g~~~vl   88 (184)
                      |++.|.++|.+.   ..+.++||||+++..++.+++.|.+.|+++..+||        ++++.+|..+++.|++|+++||
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            666666666432   36778999999999999999999999999988876        5667789999999999999999


Q ss_pred             EEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           89 HWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        89 VaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                      |+|+      .+++|||.++++ .|||+|+|.+...|+||.+|.|
T Consensus       224 v~T~------~~~~Gld~~~~~-~Vi~~d~~~~~~~~~Qr~GR~g  261 (286)
T d1wp9a2         224 VATS------VGEEGLDVPEVD-LVVFYEPVPSAIRSIQRRGRTG  261 (286)
T ss_dssp             EECG------GGGGGGGSTTCC-EEEESSCCHHHHHHHHHHTTSC
T ss_pred             EEcc------ceeccccCCCCC-EEEEeCCCCCHHHHHHHHHhCC
Confidence            9999      778999999999 9999999999999999997753

>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=99.65  E-value=1.2e-16  Score=116.86  Aligned_cols=103  Identities=17%  Similarity=0.218  Sum_probs=90.3

Q ss_pred             CHHHHHHHHHHHhc--cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE------
Q psy437           69 ADKLRNEVQMKWIS--NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV------  140 (184)
Q Consensus        69 ~~~~R~~~~~~f~~--g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va------  140 (184)
                      ..++|...+.++..  ...++||+|+++..++.++..|...|+.+..+|+++|+..|..+.+.|++|++.++++      
T Consensus        10 ~~~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~   89 (168)
T d1t5ia_          10 KDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR   89 (168)
T ss_dssp             CGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCST
T ss_pred             ChHHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccccc
Confidence            34556666555543  2347999999999999999999999999999999999999999999999999999999      


Q ss_pred             -EecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          141 -WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       141 -~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                       +|+|++++|++|++|.+++.|+|+++  |+||.
T Consensus        90 Gid~~~~~~vi~~~~p~~~~~yiqr~G--R~gR~  121 (168)
T d1t5ia_          90 GMDIERVNIAFNYDMPEDSDTYLHRVA--RAGRF  121 (168)
T ss_dssp             TCCGGGCSEEEESSCCSSHHHHHHHHH--HHTGG
T ss_pred             hhhcccchhhhhhhcccchhhHhhhhh--hcccC
Confidence             59999999999999999999999995  55653

>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=99.59  E-value=7.6e-18  Score=131.93  Aligned_cols=118  Identities=17%  Similarity=0.248  Sum_probs=79.1

Q ss_pred             CCCCCeEEEEEEccChH---HH-H-HHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHH------
Q psy437            5 FNRANLKYEILPKKNVL---KE-V-ISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLR------   73 (184)
Q Consensus         5 ~~R~Nl~y~v~~~~~k~---~~-L-~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R------   73 (184)
                      .-+|||.+.+.+.+...   .. + .+.+    ++.++||||+|++.|+.++..|.+.|+++..+||+++++.|      
T Consensus         6 ~pHPnI~ev~l~~egEi~f~~k~I~le~~----kggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~   81 (299)
T d1a1va2           6 VPHPNIEEVALSTTGEIPFYGKAIPLEVI----KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDV   81 (299)
T ss_dssp             CCCTTEEEEECCSCSSEEETTEEECTHHH----HSSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSE
T ss_pred             CCCCCeEEEecCCccchhhhhhhchhhhh----cCCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccch
Confidence            45899998877654311   11 1 1222    45789999999999999999999999999999999999887      


Q ss_pred             ----HHHHHHHhccCceEEEEEeecccHHHHHHHHH---hcCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           74 ----NEVQMKWISNKVHVGHWTVVSKECDSVAAALA---QERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        74 ----~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~---~~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                          ...++.|.+|+.+++|+|++.      +++++   .+.+. .|+|+++|.+.++|+||..|.|
T Consensus        82 ~i~~~~aLe~f~~G~~dvVVaT~~~------a~g~~giDid~V~-~VI~~d~P~SvesyIQRiGRTG  141 (299)
T d1a1va2          82 VVVATDALMTGFTGDFDSVIDCNTC------VTQTVDFSLDPTF-TIETTTLPQDAVSRTQRRGRTG  141 (299)
T ss_dssp             EEEECTTC---CCCCBSEEEECCEE------EEEEEECCCSSSC-EEEEEEEECBHHHHHHHHTTBC
T ss_pred             HHHHHHHHHHHhcCCCcEEEEEeeh------hccCCCCCCCcce-EEEeCCCCCCHHHHHhhccccC
Confidence                467899999999999999932      23222   22222 4445555555555555544443

>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=99.58  E-value=3.9e-16  Score=117.13  Aligned_cols=104  Identities=19%  Similarity=0.126  Sum_probs=85.7

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCC------------------------------CeeEEecCCCCH
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQER------------------------------INAISYHAGLAD   70 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~g------------------------------i~~~~~hg~l~~   70 (184)
                      .+.+.+.++   .+.++||||+||+.|+.+|..|....                              ..++++||+|++
T Consensus        30 ~~l~~~~i~---~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          30 EELVEECVA---ENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHH---TTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHH---cCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            344555554   45799999999999999998886410                              126889999999


Q ss_pred             HHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEee-------CCCChHHHHHHHHHhhCCC
Q psy437           71 KLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYH-------AGLADKLRNEVQMKWISNK  134 (184)
Q Consensus        71 ~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih-------~~~p~~~r~~~~~~f~~~~  134 (184)
                      ++|..+.+.|++|.++|||||+      .++.|++.+... +||+       ++.|.+..+|+|+.++.|.
T Consensus       107 ~~r~~ie~~f~~g~i~vlvaT~------~l~~Gin~p~~~-vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR  170 (201)
T d2p6ra4         107 GQRRVVEDAFRRGNIKVVVATP------TLAAGVNLPARR-VIVRSLYRFDGYSKRIKVSEYKQMAGRAGR  170 (201)
T ss_dssp             HHHHHHHHHHHTTSCCEEEECS------TTTSSSCCCBSE-EEECCSEEESSSEEECCHHHHHHHHTTBSC
T ss_pred             hhHHHHHHHHhCCCceEEEech------HHHhhcCCCCce-EEEecceeccCCcCCCCHHHHHHHhcccCC
Confidence            9999999999999999999999      678899999888 7776       6778888889998877664

>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=99.51  E-value=2.9e-15  Score=105.93  Aligned_cols=77  Identities=21%  Similarity=0.086  Sum_probs=69.7

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEec----CC
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIH----SL  154 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~----~~  154 (184)
                      ++||+|+++++|+.+|..|...|+++..||++++++       .|++|+..++||       +| |++++|+|+    ++
T Consensus        37 k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~~  108 (138)
T d1jr6a_          37 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSDGK  108 (138)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEETTE
T ss_pred             CEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEEecCCC
Confidence            689999999999999999999999999999999854       588999999999       59 999999985    46


Q ss_pred             CCCccccccccccccCCc
Q psy437          155 VLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       155 p~~~e~y~~~i~~~~~~r  172 (184)
                      |.+.++|+||++  |+||
T Consensus       109 P~~~~~y~qr~G--R~gR  124 (138)
T d1jr6a_         109 PQDAVSRTQRRG--RTGR  124 (138)
T ss_dssp             ECCHHHHHHHHT--TBCS
T ss_pred             CCCHHHHHhHhc--cccC
Confidence            999999999995  6666

>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=99.37  E-value=5.3e-14  Score=109.93  Aligned_cols=85  Identities=20%  Similarity=0.141  Sum_probs=72.9

Q ss_pred             eEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHH----------HHHHHHhhCCCceEEEE----------EecCC
Q psy437           86 HVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLR----------NEVQMKWISNKVHLYNV----------WKIQW  145 (184)
Q Consensus        86 ~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r----------~~~~~~f~~~~~~v~va----------~D~~~  145 (184)
                      ++||+|++|..||.+|..|...|+++.++|++++++.+          ....+.|.+|+..++|+          +|++.
T Consensus        38 k~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDid~  117 (299)
T d1a1va2          38 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDP  117 (299)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCCSS
T ss_pred             CEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCCCc
Confidence            68999999999999999999999999999999999886          33556788999999998          27777


Q ss_pred             ccEEEecCCCCCccccccccccccCCc
Q psy437          146 KRIIWIHSLVLIKPDYLPPILDLRLGR  172 (184)
Q Consensus       146 vr~v~~~~~p~~~e~y~~~i~~~~~~r  172 (184)
                      +..|+++++|.+.++|+||++|  .||
T Consensus       118 V~~VI~~d~P~SvesyIQRiGR--TGR  142 (299)
T d1a1va2         118 TFTIETTTLPQDAVSRTQRRGR--TGR  142 (299)
T ss_dssp             SCEEEEEEEECBHHHHHHHHTT--BCS
T ss_pred             ceEEEeCCCCCCHHHHHhhccc--cCC
Confidence            8899999999999999999965  444

>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=99.37  E-value=2.9e-14  Score=106.36  Aligned_cols=101  Identities=7%  Similarity=0.048  Sum_probs=83.1

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHH
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECD   98 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e   98 (184)
                      .|+..|.+++.+. .+.++||||++...++.+++.|.     +..+||++++.+|..++++|.+|+.+|||+|+      
T Consensus        79 ~K~~~l~~ll~~~-~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~------  146 (200)
T d2fwra1          79 NKIRKLREILERH-RKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQ------  146 (200)
T ss_dssp             HHHHHHHHHHHHT-SSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSS------
T ss_pred             HHHHHHHHHHHhC-CCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeeecc------
Confidence            4788888888764 67899999999999999988773     45689999999999999999999999999998      


Q ss_pred             HHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhC
Q psy437           99 SVAAALAQERINAISYHAGLADKLRNEVQMKWIS  132 (184)
Q Consensus        99 ~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~  132 (184)
                      .++.|+|.++++ .|++++.|.+...++|+..|.
T Consensus       147 ~~~~Gidl~~~~-~vi~~~~~~s~~~~~Q~iGR~  179 (200)
T d2fwra1         147 VLDEGIDVPDAN-VGVIMSGSGSAREYIQRLGRI  179 (200)
T ss_dssp             CCCSSSCSCCBS-EEEEECCSSCCHHHHHHHHHS
T ss_pred             hhhcccCCCCCC-EEEEeCCCCCHHHHHHHHHhc
Confidence            445677777777 677777777777777777554

>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=99.28  E-value=1.9e-12  Score=101.25  Aligned_cols=89  Identities=11%  Similarity=0.147  Sum_probs=78.6

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeC--------CCChHHHHHHHHHhhCCCceEEEE-------EecCCcc
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHA--------GLADKLRNEVQMKWISNKVHLYNV-------WKIQWKR  147 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~--------~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr  147 (184)
                      ...++||+|.++..++.++..|...|+++..+|+        ++++..+..+.+.|++|++.|+++       +|+|+++
T Consensus       160 ~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~~~~Gld~~~~~  239 (286)
T d1wp9a2         160 QNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVD  239 (286)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCC
T ss_pred             CCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccceeccccCCCCC
Confidence            3458999999999999999999999999888866        566668899999999999999999       6999999


Q ss_pred             EEEecCCCCCccccccccccccCCcc
Q psy437          148 IIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       148 ~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      +||+||+|.++..|+|++  +|+||.
T Consensus       240 ~Vi~~d~~~~~~~~~Qr~--GR~gR~  263 (286)
T d1wp9a2         240 LVVFYEPVPSAIRSIQRR--GRTGRH  263 (286)
T ss_dssp             EEEESSCCHHHHHHHHHH--TTSCSC
T ss_pred             EEEEeCCCCCHHHHHHHH--HhCCCC
Confidence            999999999999999998  577775

>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=99.26  E-value=4.5e-12  Score=94.57  Aligned_cols=96  Identities=18%  Similarity=0.190  Sum_probs=80.8

Q ss_pred             HHHHHhccCceEEEEEeecccHHHHHHHHHh--------------------------------cCCcEEEeeCCCChHHH
Q psy437           76 VQMKWISNKVHVGHWTVVSKECDSVAAALAQ--------------------------------ERINAISYHAGLADKLR  123 (184)
Q Consensus        76 ~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~--------------------------------~gi~~~vih~~~p~~~r  123 (184)
                      +..+..+...++||++++|++|+.+|..|..                                .|  +.++|+|||+..|
T Consensus        32 l~~~~i~~~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~G--Ia~hh~~l~~~~r  109 (201)
T d2p6ra4          32 LVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKG--AAFHHAGLLNGQR  109 (201)
T ss_dssp             HHHHHHHTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTT--CCEECTTSCHHHH
T ss_pred             HHHHHHHcCCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhcc--HHHHHHHhhhhhH
Confidence            3444444456899999999999999988753                                23  3789999999999


Q ss_pred             HHHHHHhhCCCceEEEE-------EecCCccEEEe-------cCCCCCccccccccccccCCcccc
Q psy437          124 NEVQMKWISNKVHLYNV-------WKIQWKRIIWI-------HSLVLIKPDYLPPILDLRLGREDI  175 (184)
Q Consensus       124 ~~~~~~f~~~~~~v~va-------~D~~~vr~v~~-------~~~p~~~e~y~~~i~~~~~~r~~~  175 (184)
                      ..+.+.|++|.+.|+||       +|.|..+.||+       ++.|.+..+|+|.+  +|+||.+.
T Consensus       110 ~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~--GRAGR~g~  173 (201)
T d2p6ra4         110 RVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMA--GRAGRPGM  173 (201)
T ss_dssp             HHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHH--TTBSCTTT
T ss_pred             HHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHh--cccCCCCC
Confidence            99999999999999999       59999999997       67888999999999  58888754

>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=99.24  E-value=6e-13  Score=99.69  Aligned_cols=95  Identities=14%  Similarity=0.216  Sum_probs=62.3

Q ss_pred             ChHHHHHHHHHhhc-CCCcEEEEeccHHHHH--------HHHHHHHhC---CCeeEEecCCCCHHHHHHHHHHHhccCce
Q psy437           19 NVLKEVISLIKAKY-SGQSGIVYCLTRKECD--------SVAAALAQE---RINAISYHAGLADKLRNEVQMKWISNKVH   86 (184)
Q Consensus        19 ~k~~~L~~~l~~~~-~~~~~IIf~~tr~~~e--------~la~~L~~~---gi~~~~~hg~l~~~~R~~~~~~f~~g~~~   86 (184)
                      ++...+.+.|++.. .+.++-+.||..+..+        ...+.|.+.   ++++..+||+|++++|++++.+|++|+++
T Consensus        13 ~~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~   92 (206)
T d1gm5a4          13 DRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYD   92 (206)
T ss_dssp             STHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSS
T ss_pred             ccHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEE
Confidence            46677777776543 4556666787654333        334444332   66788899999999999999999999999


Q ss_pred             EEEEEeecccHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           87 VGHWTVVSKECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        87 vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                      |||||+      .++.|+|.|+++ .+++++.|.
T Consensus        93 iLVaTt------ViE~GIDip~a~-~iii~~a~~  119 (206)
T d1gm5a4          93 ILVSTT------VIEVGIDVPRAN-VMVIENPER  119 (206)
T ss_dssp             BCCCSS------CCCSCSCCTTCC-EEEBCSCSS
T ss_pred             EEEEeh------hhhccccccCCc-EEEEEccCC
Confidence            999999      444555555544 333444443

>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=99.18  E-value=9.7e-12  Score=97.06  Aligned_cols=111  Identities=13%  Similarity=0.003  Sum_probs=85.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEE
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQERINAI  112 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~  112 (184)
                      .+.+++|||+|++.++.+++.|.+.|+.+..+||++.+..+    ..|++|..+++|+|+      .+++|++. +++ .
T Consensus       177 ~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~~----~~~~~~~~~~lvaT~------~~~~G~~~-~~~-~  244 (305)
T d2bmfa2         177 FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTD------ISEMGANF-KAE-R  244 (305)
T ss_dssp             SCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHHG----GGGGTSCCSEEEECG------GGGTTCCC-CCS-E
T ss_pred             hCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHHH----hhhhccchhhhhhhH------HHHhcCCC-Ccc-E
Confidence            56789999999999999999999999999999999865543    467899999999999      55677776 566 5


Q ss_pred             EeeCCCChHHHHHHHHHhhCCCceEEEEEecCCccEEEecCCCCCccccccccccccCCcc
Q psy437          113 SYHAGLADKLRNEVQMKWISNKVHLYNVWKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       113 vih~~~p~~~r~~~~~~f~~~~~~v~va~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |+..+.               .......+|.+. +.+.+...|-+..+|+|++  +|+||.
T Consensus       245 Vi~~~~---------------~~~~~~~~~~~~-~~~~~~~~~~s~~~~~Qr~--GR~GR~  287 (305)
T d2bmfa2         245 VIDPRR---------------CMKPVILTDGEE-RVILAGPMPVTHSSAAQRR--GRVGRN  287 (305)
T ss_dssp             EEECCE---------------EEEEEEECSSSC-EEEEEEEEECCHHHHHHHH--TTSSCS
T ss_pred             EEEcCC---------------ceeeeEecCCCC-ceEEeccccCCHHHHhhhh--cCcCcC
Confidence            554331               112222245554 6777888999999999999  588886

>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=99.15  E-value=1.6e-10  Score=86.12  Aligned_cols=103  Identities=14%  Similarity=0.066  Sum_probs=81.0

Q ss_pred             CCCCCCeEEEEEEccChHHHHHHHHHh-hcCCCcEEEEeccHHHHHHHHHHHHh--CCCeeEEecCCCCHHHHHHHHHHH
Q psy437            4 SFNRANLKYEILPKKNVLKEVISLIKA-KYSGQSGIVYCLTRKECDSVAAALAQ--ERINAISYHAGLADKLRNEVQMKW   80 (184)
Q Consensus         4 s~~R~Nl~y~v~~~~~k~~~L~~~l~~-~~~~~~~IIf~~tr~~~e~la~~L~~--~gi~~~~~hg~l~~~~R~~~~~~f   80 (184)
                      |..|..+.=.+.+.+ +. .+.+.|.+ ...+.++-+.||..+..+.+++.|.+  .++++..+||.|+++++++++.+|
T Consensus         2 P~gR~pI~T~v~~~~-~~-~i~~~I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F   79 (211)
T d2eyqa5           2 PARRLAVKTFVREYD-SM-VVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDF   79 (211)
T ss_dssp             CCBCBCEEEEEEECC-HH-HHHHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHH
T ss_pred             cccCcCeEEEEeCCC-HH-HHHHHHHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHH
Confidence            456777764455543 22 34444433 23677888889999999999999887  478899999999999999999999


Q ss_pred             hccCceEEEEEeecccHHHHHHHHHhcCCcEEEe
Q psy437           81 ISNKVHVGHWTVVSKECDSVAAALAQERINAISY  114 (184)
Q Consensus        81 ~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vi  114 (184)
                      .+|+.+|||||.      .+..|+|.|+.++.||
T Consensus        80 ~~g~~~ILv~Tt------vIEvGiDvpnA~~iiI  107 (211)
T d2eyqa5          80 HHQRFNVLVCTT------IIETGIDIPTANTIII  107 (211)
T ss_dssp             HTTSCCEEEESS------TTGGGSCCTTEEEEEE
T ss_pred             HcCCcceEEEeh------hhhhccCCCCCcEEEE
Confidence            999999999999      7788888888885444

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.90  E-value=9.1e-09  Score=78.15  Aligned_cols=104  Identities=13%  Similarity=0.069  Sum_probs=73.7

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhC-CCeeEEecCCCCHHHHHHHHHHHhccC-ceEEEEEeecc
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISNK-VHVGHWTVVSK   95 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~hg~l~~~~R~~~~~~f~~g~-~~vlVaT~tr~   95 (184)
                      .|+..|.+++.+. ..+.++||||+.+...+.+...|... |+++..+||++++.+|..+++.|.++. ..+++++..- 
T Consensus        69 ~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~-  147 (244)
T d1z5za1          69 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA-  147 (244)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT-
T ss_pred             hHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccc-
Confidence            4888888888642 25678999999999999999888654 899999999999999999999999874 5777776511 


Q ss_pred             cHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHH
Q psy437           96 ECDSVAAALAQERINAISYHAGLADKLRNEVQM  128 (184)
Q Consensus        96 ~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~  128 (184)
                          .+.||+....+ .+++++.|-+...+.|.
T Consensus       148 ----~g~Glnl~~a~-~vi~~~~~wn~~~~~Qa  175 (244)
T d1z5za1         148 ----GGFGINLTSAN-RVIHFDRWWNPAVEDQA  175 (244)
T ss_dssp             ----TCCCCCCTTCS-EEEECSCCSCTTTC---
T ss_pred             ----cccccccchhh-hhhhcCchhhhHHHhhh
Confidence                12344444444 45555555444444433

>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=98.87  E-value=1.9e-10  Score=85.12  Aligned_cols=83  Identities=11%  Similarity=0.016  Sum_probs=73.8

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVL  156 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~  156 (184)
                      .-++||+|.....++.+++.|..     ..+|+++|+..|..+.+.|++|++.|+++       +|.|.++.|+.+++|.
T Consensus        93 ~~k~lvf~~~~~~~~~l~~~l~~-----~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~~  167 (200)
T d2fwra1          93 KDKIIIFTRHNELVYRISKVFLI-----PAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSG  167 (200)
T ss_dssp             SSCBCCBCSCHHHHHHHHHHTTC-----CBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSS
T ss_pred             CCcEEEEeCcHHHHHHHHhhcCc-----ceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhhcccCCCCCCEEEEeCCCC
Confidence            34789999999999999988843     45799999999999999999999999988       6999999999999999


Q ss_pred             CccccccccccccCCcc
Q psy437          157 IKPDYLPPILDLRLGRE  173 (184)
Q Consensus       157 ~~e~y~~~i~~~~~~r~  173 (184)
                      ++..|+|+++  |++|.
T Consensus       168 s~~~~~Q~iG--R~~R~  182 (200)
T d2fwra1         168 SAREYIQRLG--RILRP  182 (200)
T ss_dssp             CCHHHHHHHH--HSBCC
T ss_pred             CHHHHHHHHH--hcCCC
Confidence            9999999995  66664

>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=98.83  E-value=2.2e-09  Score=84.16  Aligned_cols=79  Identities=10%  Similarity=-0.018  Sum_probs=62.1

Q ss_pred             HHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccHHHHHHHHHh
Q psy437           27 LIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAAALAQ  106 (184)
Q Consensus        27 ~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~  106 (184)
                      +|.+  ..++++|||++...++.++..|.+.|.++..+||.+..+++    ++|.+|+.++||||+      .+..|++.
T Consensus        31 ~i~~--~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~----~~~~~~~~~~~~~t~------~~~~~~~~   98 (299)
T d1yksa2          31 WILA--DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREY----PTIKQKKPDFILATD------IAEMGANL   98 (299)
T ss_dssp             HHHH--CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESS------STTCCTTC
T ss_pred             HHHh--cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHH----hhhhcCCcCEEEEec------hhhhceec
Confidence            4444  46789999999999999999999999999999999887764    457899999999999      66679999


Q ss_pred             cCCcEEEeeCCCC
Q psy437          107 ERINAISYHAGLA  119 (184)
Q Consensus       107 ~gi~~~vih~~~p  119 (184)
                       +|. .||..|++
T Consensus        99 -~~~-~vid~g~~  109 (299)
T d1yksa2          99 -CVE-RVLDCRTA  109 (299)
T ss_dssp             -CCS-EEEECCEE
T ss_pred             -Cce-EEEecCce
Confidence             688 88887753

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=98.58  E-value=8.5e-08  Score=76.49  Aligned_cols=105  Identities=8%  Similarity=-0.059  Sum_probs=86.0

Q ss_pred             ChHHHHHHHHHhh--cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCce--EEE-EEee
Q psy437           19 NVLKEVISLIKAK--YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVH--VGH-WTVV   93 (184)
Q Consensus        19 ~k~~~L~~~l~~~--~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~--vlV-aT~t   93 (184)
                      .|+..|..+|...  ..+.++|||++.+...+.+...|...|++...++|+++..+|..+++.|.++...  |++ .|. 
T Consensus       101 ~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~-  179 (346)
T d1z3ix1         101 GKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK-  179 (346)
T ss_dssp             HHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG-
T ss_pred             HHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecch-
Confidence            3777777666431  2567999999999999999999999999999999999999999999999987543  444 444 


Q ss_pred             cccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHh
Q psy437           94 SKECDSVAAALAQERINAISYHAGLADKLRNEVQMKW  130 (184)
Q Consensus        94 r~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f  130 (184)
                           ..+.||+-.+.+ .||+++.+-+.....|...
T Consensus       180 -----agg~GlnL~~a~-~vi~~d~~wnp~~~~Qa~~  210 (346)
T d1z3ix1         180 -----AGGCGLNLIGAN-RLVMFDPDWNPANDEQAMA  210 (346)
T ss_dssp             -----GSCTTCCCTTEE-EEEECSCCSSHHHHHHHHT
T ss_pred             -----hhhhccccccce-EEEEecCCCccchHhHhhh
Confidence                 234588888888 8999999999998888873

>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=98.44  E-value=5.6e-07  Score=64.05  Aligned_cols=99  Identities=13%  Similarity=0.169  Sum_probs=85.9

Q ss_pred             HHHHHHHHhcc--CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------Eec
Q psy437           73 RNEVQMKWISN--KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKI  143 (184)
Q Consensus        73 R~~~~~~f~~g--~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~  143 (184)
                      +...+..+.+.  ..++||+|+++..|+.++..|...|+.+..+|++++++.|..+.+.|+.|+..++++       +|+
T Consensus        14 K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi   93 (162)
T d1fuka_          14 KYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDV   93 (162)
T ss_dssp             HHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCC
T ss_pred             HHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccC
Confidence            44444444321  247999999999999999999999999999999999999999999999999999999       699


Q ss_pred             CCccEEEecCCCCCccccccccccccCCcc
Q psy437          144 QWKRIIWIHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       144 ~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      |++++|||||+|.+++.|+||++  |+||-
T Consensus        94 ~~v~~VI~~d~P~~~~~yihR~G--R~gR~  121 (162)
T d1fuka_          94 QQVSLVINYDLPANKENYIHRIG--RGGRF  121 (162)
T ss_dssp             CSCSEEEESSCCSSGGGGGGSSC--SCC--
T ss_pred             CCceEEEEeccchhHHHHHhhcc--ccccC
Confidence            99999999999999999999995  55553

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.22  E-value=3.5e-06  Score=60.35  Aligned_cols=106  Identities=13%  Similarity=0.034  Sum_probs=77.2

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeecccH
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKEC   97 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr~~~   97 (184)
                      .|+..+.+.+.+. ..+.|+||+|.|.+..+.++..|.+.|++..++++....++-.-+.+.  -....|.|||+     
T Consensus        18 eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~A--g~~g~VtIATN-----   90 (175)
T d1tf5a4          18 GKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEA--GQKGAVTIATN-----   90 (175)
T ss_dssp             HHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTT--TSTTCEEEEET-----
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhc--cCCCceeehhh-----
Confidence            5888888777543 257899999999999999999999999999999987543333222222  22346899999     


Q ss_pred             HHHHHHHHh--------cCCcEEEeeCCCChHHHHHHHHHhhCC
Q psy437           98 DSVAAALAQ--------ERINAISYHAGLADKLRNEVQMKWISN  133 (184)
Q Consensus        98 e~~a~gL~~--------~gi~~~vih~~~p~~~r~~~~~~f~~~  133 (184)
                       .+.+|-|+        .|- -+||....|.+.|-..|-..++|
T Consensus        91 -mAGRGtDikl~~~v~~~GG-LhVI~t~~~~s~Rid~Ql~GR~g  132 (175)
T d1tf5a4          91 -MAGRGTDIKLGEGVKELGG-LAVVGTERHESRRIDNQLRGRSG  132 (175)
T ss_dssp             -TSSTTCCCCCCTTSGGGTS-EEEEESSCCSSHHHHHHHHTTSS
T ss_pred             -HHHcCCCccchHHHHhCCC-cEEEEeccCcchhHHHHHhcchh
Confidence             33444322        121 38999999999999999886654

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=98.10  E-value=8.3e-06  Score=64.68  Aligned_cols=98  Identities=7%  Similarity=0.018  Sum_probs=82.0

Q ss_pred             HHHHHh-ccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCc--eEEEE--------EecC
Q psy437           76 VQMKWI-SNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKV--HLYNV--------WKIQ  144 (184)
Q Consensus        76 ~~~~f~-~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~--~v~va--------~D~~  144 (184)
                      ++..++ ...-++||++......+.+...|...|+.+..++|++|...|..+.+.|.++..  .|++.        +|..
T Consensus       109 ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~agg~GlnL~  188 (346)
T d1z3ix1         109 ILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLI  188 (346)
T ss_dssp             HHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCT
T ss_pred             HHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecchhhhhccccc
Confidence            344443 234589999999999999999999999998999999999999999999987643  34444        5999


Q ss_pred             CccEEEecCCCCCccccccccccc-cCCcc
Q psy437          145 WKRIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       145 ~vr~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                      ...+||++|++.++..+.|.+.|. |.|..
T Consensus       189 ~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~  218 (346)
T d1z3ix1         189 GANRLVMFDPDWNPANDEQAMARVWRDGQK  218 (346)
T ss_dssp             TEEEEEECSCCSSHHHHHHHHTTSSSTTCC
T ss_pred             cceEEEEecCCCccchHhHhhhcccccCCC
Confidence            999999999999999999999764 66653

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.34  E-value=1.6e-05  Score=59.78  Aligned_cols=65  Identities=8%  Similarity=0.034  Sum_probs=52.8

Q ss_pred             ceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEEE----ecCCccEEEecCCCCCcc
Q psy437           85 VHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNVW----KIQWKRIIWIHSLVLIKP  159 (184)
Q Consensus        85 ~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va~----D~~~vr~v~~~~~p~~~e  159 (184)
                      .++||+|.+++.++.++..|...      +|++++++.|..+++.|++|.+.|+||-    |.-    ..-.|+|+...
T Consensus        26 ~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~~v~----~rGlDip~~v~   94 (248)
T d1gkub2          26 TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTL----VRGLDLPERIR   94 (248)
T ss_dssp             SCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEEEECC----------CCSCCTTTCC
T ss_pred             CCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccccchh----hhccCcccccc
Confidence            46899999999999999999643      8999999999999999999999999994    442    12458887543

>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=97.27  E-value=0.00011  Score=56.85  Aligned_cols=74  Identities=7%  Similarity=-0.028  Sum_probs=56.1

Q ss_pred             cCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCC
Q psy437           83 NKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLV  155 (184)
Q Consensus        83 g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p  155 (184)
                      .+.+++|++++..+++.+|..|...|..++++|+.++.....    .+.+++..++||       +++ +|++||...++
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~  109 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTA  109 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCce
Confidence            455799999999999999999999999999999999987743    577899999999       488 59999987765


Q ss_pred             CCcccc
Q psy437          156 LIKPDY  161 (184)
Q Consensus       156 ~~~e~y  161 (184)
                      -.+..|
T Consensus       110 ~~~~~~  115 (299)
T d1yksa2         110 FKPVLV  115 (299)
T ss_dssp             EEEEEE
T ss_pred             eceeee
Confidence            333333

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.23  E-value=0.00056  Score=51.82  Aligned_cols=60  Identities=8%  Similarity=-0.062  Sum_probs=54.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .+.++++-+||.-.+++..+.+.+    .|+.+..+||+++..+|..+.....+|+.+|||+|-
T Consensus       131 ~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGTh  194 (264)
T d1gm5a3         131 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH  194 (264)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT
T ss_pred             cccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeeh
Confidence            467899999999999988777764    478999999999999999999999999999999998

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=97.15  E-value=0.00018  Score=54.69  Aligned_cols=94  Identities=14%  Similarity=-0.025  Sum_probs=69.9

Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecC-----
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQ-----  144 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~-----  144 (184)
                      +........++||+++++++|+.++..|...|+++..+|+++++..+    ..|.++...++++       +|++     
T Consensus       171 ~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~~~----~~~~~~~~~~lvaT~~~~~G~~~~~~~Vi  246 (305)
T d2bmfa2         171 HEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTDISEMGANFKAERVI  246 (305)
T ss_dssp             CHHHHSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHHHG----GGGGTSCCSEEEECGGGGTTCCCCCSEEE
T ss_pred             HHHHHhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHHHH----hhhhccchhhhhhhHHHHhcCCCCccEEE
Confidence            34444555678999999999999999999999999999999976544    3578899999999       4663     


Q ss_pred             ----CccEEEecCCCCCcccccccccc-----ccCCccc
Q psy437          145 ----WKRIIWIHSLVLIKPDYLPPILD-----LRLGRED  174 (184)
Q Consensus       145 ----~vr~v~~~~~p~~~e~y~~~i~~-----~~~~r~~  174 (184)
                          .++.+++++.|.....|...-.+     =|+||-+
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~G  285 (305)
T d2bmfa2         247 DPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVG  285 (305)
T ss_dssp             ECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSS
T ss_pred             EcCCceeeeEecCCCCceEEeccccCCHHHHhhhhcCcC
Confidence                23445667777766666543322     2788886

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.97  E-value=0.0028  Score=46.96  Aligned_cols=60  Identities=8%  Similarity=-0.092  Sum_probs=55.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .+.++++.+||.-.+.+..+.+++    .++++..+||+++..+|..+...+.+|+.+|||.|-
T Consensus       103 ~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGth  166 (233)
T d2eyqa3         103 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH  166 (233)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT
T ss_pred             cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeeh
Confidence            567899999999999999999986    477899999999999999999999999999999998

>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=96.85  E-value=0.0044  Score=45.08  Aligned_cols=89  Identities=15%  Similarity=0.058  Sum_probs=75.8

Q ss_pred             CceEEEEEeecccHHHHHHHHH--hcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCC
Q psy437           84 KVHVGHWTVVSKECDSVAAALA--QERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSL  154 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~--~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~  154 (184)
                      .-+|.+-++.-.+.+.++..+.  .+++++.++||.|+++.++.++..|.+|++.|+||       +|+|+...++..+.
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~iiI~~a  110 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERA  110 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEEETTT
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEEEecc
Confidence            3456666676677778887775  47889899999999999999999999999999999       59999999999888


Q ss_pred             CCCccccccccccccCCcc
Q psy437          155 VLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       155 p~~~e~y~~~i~~~~~~r~  173 (184)
                      ..---+.+|.. ++|+||-
T Consensus       111 ~rfGLaQLhQL-RGRVGR~  128 (211)
T d2eyqa5         111 DHFGLAQLHQL-RGRVGRS  128 (211)
T ss_dssp             TSSCHHHHHHH-HTTCCBT
T ss_pred             hhccccccccc-cceeeec
Confidence            87667778875 6899996

>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=96.24  E-value=0.013  Score=42.36  Aligned_cols=83  Identities=12%  Similarity=0.118  Sum_probs=61.5

Q ss_pred             ChHHHHHHHHHhh-cCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccC-ceEEEEEeeccc
Q psy437           19 NVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNK-VHVGHWTVVSKE   96 (184)
Q Consensus        19 ~k~~~L~~~l~~~-~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~-~~vlVaT~tr~~   96 (184)
                      .|...+++.+.+. ..+.|.+|-+.|.+..|.++..|.+.|++..++++.-.  +|+.-+-. ..|+ ..|-|||+    
T Consensus        18 ~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~h--erEAeIIA-qAG~~GaVTIATN----   90 (219)
T d1nkta4          18 AKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYH--EQEATIIA-VAGRRGGVTVATN----   90 (219)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCH--HHHHHHHH-TTTSTTCEEEEET----
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhH--HHHHHHHH-hcccCCcEEeecc----
Confidence            5888888877643 36789999999999999999999999999999999743  33332222 2233 36789999    


Q ss_pred             HHHHHHHHHhcCCcEEEeeC
Q psy437           97 CDSVAAALAQERINAISYHA  116 (184)
Q Consensus        97 ~e~~a~gL~~~gi~~~vih~  116 (184)
                             |...|.+ .++-+
T Consensus        91 -------MAGRGTD-I~LGg  102 (219)
T d1nkta4          91 -------MAGRGTD-IVLGG  102 (219)
T ss_dssp             -------TCSTTCC-CCTTC
T ss_pred             -------ccCCCCc-eeecC
Confidence                   7777766 44433

>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=95.98  E-value=0.0097  Score=43.76  Aligned_cols=97  Identities=10%  Similarity=0.060  Sum_probs=71.1

Q ss_pred             HHHHhccCceEEEEEeecccHHHHHHHHHhc-CCcEEEeeCCCChHHHHHHHHHhhCC-CceEEEE--------EecCCc
Q psy437           77 QMKWISNKVHVGHWTVVSKECDSVAAALAQE-RINAISYHAGLADKLRNEVQMKWISN-KVHLYNV--------WKIQWK  146 (184)
Q Consensus        77 ~~~f~~g~~~vlVaT~tr~~~e~~a~gL~~~-gi~~~vih~~~p~~~r~~~~~~f~~~-~~~v~va--------~D~~~v  146 (184)
                      +.......-++||+|.-....+.+...|... |+++..+||++|++.|..+.+.|.++ ...++++        ++.+..
T Consensus        78 l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~~g~Glnl~~a  157 (244)
T d1z5za1          78 IEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSA  157 (244)
T ss_dssp             HHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCTTCCCCCCTTC
T ss_pred             HHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccccccccccchh
Confidence            3333344558999999999988888888654 88878899999999999999999866 4667766        588999


Q ss_pred             cEEEecCCCCCccccccccccc-cCCcc
Q psy437          147 RIIWIHSLVLIKPDYLPPILDL-RLGRE  173 (184)
Q Consensus       147 r~v~~~~~p~~~e~y~~~i~~~-~~~r~  173 (184)
                      .+|+++++|.++..+.|.+.+. |.|..
T Consensus       158 ~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~  185 (244)
T d1z5za1         158 NRVIHFDRWWNPAVEDQATDRVYRIGQT  185 (244)
T ss_dssp             SEEEECSCCSCTTTC-------------
T ss_pred             hhhhhcCchhhhHHHhhhcceeeecCCC
Confidence            9999999999999999999875 77764

>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=95.69  E-value=0.01  Score=41.84  Aligned_cols=88  Identities=13%  Similarity=-0.065  Sum_probs=68.7

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----EecC--------CccEEE
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----WKIQ--------WKRIIW  150 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----~D~~--------~vr~v~  150 (184)
                      .-+|||.|.+-...|.++..|...|++..|+|+.........+.+....|.+.|-.-     -|+.        .=-|||
T Consensus        34 grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~~Ag~~g~VtIATNmAGRGtDikl~~~v~~~GGLhVI  113 (175)
T d1tf5a4          34 GQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVV  113 (175)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTTCEEEEETTSSTTCCCCCCTTSGGGTSEEEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHHhccCCCceeehhhHHHcCCCccchHHHHhCCCcEEE
Confidence            458999999999999999999999999899999988887777777777775444443     2442        235888


Q ss_pred             ecCCCCCccccccccccccCCcc
Q psy437          151 IHSLVLIKPDYLPPILDLRLGRE  173 (184)
Q Consensus       151 ~~~~p~~~e~y~~~i~~~~~~r~  173 (184)
                      ....|.+..-..|-  .+|.||.
T Consensus       114 ~t~~~~s~Rid~Ql--~GR~gRQ  134 (175)
T d1tf5a4         114 GTERHESRRIDNQL--RGRSGRQ  134 (175)
T ss_dssp             ESSCCSSHHHHHHH--HTTSSGG
T ss_pred             EeccCcchhHHHHH--hcchhhh
Confidence            88888887665554  4788886

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.63  E-value=0.0077  Score=43.98  Aligned_cols=70  Identities=13%  Similarity=0.016  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEee
Q psy437           21 LKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVV   93 (184)
Q Consensus        21 ~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~t   93 (184)
                      ...++-.+...   .....++|.|+|++.+.++.+.+..    .++++..+.|+.+..+....+    .....|||+|+.
T Consensus        69 layllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l----~~~~~Ilv~TPg  144 (222)
T d2j0sa1          69 ATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKL----DYGQHVVAGTPG  144 (222)
T ss_dssp             HHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHH----HHCCSEEEECHH
T ss_pred             hhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHh----ccCCeEEeCCCC
Confidence            34555555421   2455689999999999999988865    367888888988755443333    234679999995


Q ss_pred             c
Q psy437           94 S   94 (184)
Q Consensus        94 r   94 (184)
                      |
T Consensus       145 r  145 (222)
T d2j0sa1         145 R  145 (222)
T ss_dssp             H
T ss_pred             c
Confidence            5

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.49  E-value=0.037  Score=39.54  Aligned_cols=71  Identities=17%  Similarity=0.107  Sum_probs=47.8

Q ss_pred             HHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           21 LKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        21 ~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      ...++-.+...   ....+++|.|+|++.+.++.+.+...     .+......|+.+.....   ..+.++...|||+|+
T Consensus        53 la~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~ilI~TP  129 (207)
T d1t6na_          53 AVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE---EVLKKNCPHIVVGTP  129 (207)
T ss_dssp             HHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHH---HHHHHSCCSEEEECH
T ss_pred             cccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHH---HHHHhcCCCEEEeCc
Confidence            34455555432   13456899999999999998888753     34567778887654432   334456778999999


Q ss_pred             ec
Q psy437           93 VS   94 (184)
Q Consensus        93 tr   94 (184)
                      .|
T Consensus       130 ~r  131 (207)
T d1t6na_         130 GR  131 (207)
T ss_dssp             HH
T ss_pred             ch
Confidence            54

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.47  E-value=0.078  Score=37.69  Aligned_cols=70  Identities=17%  Similarity=0.045  Sum_probs=47.9

Q ss_pred             HHHHHHHHHhh---cCCCcEEEEeccHHHHHHHHHHHHhC-----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           21 LKEVISLIKAK---YSGQSGIVYCLTRKECDSVAAALAQE-----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        21 ~~~L~~~l~~~---~~~~~~IIf~~tr~~~e~la~~L~~~-----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      +..++-.+...   .....++|.|+|++.+.++.+.+...     +.......|+.+.......    ......+||+|+
T Consensus        55 layllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----l~~~~~ivv~TP  130 (206)
T d1veca_          55 GAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR----LDDTVHVVIATP  130 (206)
T ss_dssp             HHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH----TTSCCSEEEECH
T ss_pred             cccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHH----HHhccCeEEeCC
Confidence            44555555421   24567899999999999998887642     4566677777665544333    345778999999


Q ss_pred             ec
Q psy437           93 VS   94 (184)
Q Consensus        93 tr   94 (184)
                      .|
T Consensus       131 gr  132 (206)
T d1veca_         131 GR  132 (206)
T ss_dssp             HH
T ss_pred             cc
Confidence            76

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=94.98  E-value=0.11  Score=37.79  Aligned_cols=57  Identities=9%  Similarity=-0.030  Sum_probs=43.0

Q ss_pred             CCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           34 GQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        34 ~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ..+++|.|+|++.|.++...+..    .++++..+.|+........    .......|||+|+.+
T Consensus        98 ~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~~~~~~~ivV~TP~~  158 (238)
T d1wrba1          98 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIR----EVQMGCHLLVATPGR  158 (238)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHH----HHSSCCSEEEECHHH
T ss_pred             CceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHh----hcccCCceeecCHHH
Confidence            45689999999999999887754    3677888888766544322    344567899999976

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.84  E-value=0.021  Score=41.29  Aligned_cols=59  Identities=12%  Similarity=0.023  Sum_probs=38.6

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ....++|+++|++.|.++.+.+..    .++......++....+   .......+...|+|+|+.|
T Consensus        79 ~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~IvV~TP~r  141 (218)
T d2g9na1          79 KATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA---EVQKLQMEAPHIIVGTPGR  141 (218)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCS---TTTSSSSCCCSEEEECHHH
T ss_pred             cCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhH---HHHHHhcCCCEEEEeCChh
Confidence            456799999999999999887765    3555555555433221   1122333566899999976

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.66  E-value=0.094  Score=37.25  Aligned_cols=57  Identities=16%  Similarity=0.066  Sum_probs=43.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .+..++|.|+|++.|.++.+.+..    .+..+..++|+.+..+..+.+   .  ..+|+|+|+.+
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~--~~~IlV~TP~~  131 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL---K--NANIVVGTPGR  131 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH---H--TCSEEEECHHH
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc---C--CCCEEEEChHH
Confidence            456799999999999999888765    367788899988766544433   2  36799999853

>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=94.33  E-value=0.0021  Score=46.76  Aligned_cols=67  Identities=12%  Similarity=0.179  Sum_probs=58.1

Q ss_pred             cCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-------EecCCccEEEecCCCCCccccccccccccCCccc
Q psy437          107 ERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-------WKIQWKRIIWIHSLVLIKPDYLPPILDLRLGRED  174 (184)
Q Consensus       107 ~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-------~D~~~vr~v~~~~~p~~~e~y~~~i~~~~~~r~~  174 (184)
                      +++++.++||.|+++.++.++..|++|++.|+||       .|+|++++|++++.|..-.+|+|.. ++|+||.+
T Consensus        63 p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQl-rGRvGR~~  136 (206)
T d1gm5a4          63 PEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQL-RGRVGRGG  136 (206)
T ss_dssp             ---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHH-HHTSCCSS
T ss_pred             CCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhh-hhheeecc
Confidence            4777789999999999999999999999999999       5999999999999999888888774 47888863

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.69  E-value=0.16  Score=36.16  Aligned_cols=57  Identities=11%  Similarity=-0.017  Sum_probs=35.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ....++|.|+|++.+.++...+...    ++.....+++-+..++...+     ....|+|+|+.+
T Consensus        77 ~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~IvI~TP~~  137 (212)
T d1qdea_          77 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL-----RDAQIVVGTPGR  137 (212)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C-----TTCSEEEECHHH
T ss_pred             CCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh-----cCCcEEEECCCc
Confidence            4567999999999999998888643    44556666654443332221     246899999976

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=93.40  E-value=0.62  Score=34.36  Aligned_cols=106  Identities=4%  Similarity=0.012  Sum_probs=67.4

Q ss_pred             HHHHHHHHhCCCeeEEecCCCCHHH---HHHHHHHHhccCceEEEEEeecc----cHHHHHHHHHhcCCcEEEeeCCCCh
Q psy437           48 DSVAAALAQERINAISYHAGLADKL---RNEVQMKWISNKVHVGHWTVVSK----ECDSVAAALAQERINAISYHAGLAD  120 (184)
Q Consensus        48 e~la~~L~~~gi~~~~~hg~l~~~~---R~~~~~~f~~g~~~vlVaT~tr~----~~e~~a~gL~~~gi~~~vih~~~p~  120 (184)
                      +.+...|.....-...++|+.....   -..+.........++++-++|--    ..+.+...+...|+.+.++|++++.
T Consensus        93 ~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~  172 (264)
T d1gm5a3          93 QEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTP  172 (264)
T ss_dssp             HHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCH
T ss_pred             HHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccch
Confidence            3344444433333556787665432   22222233334456777777552    2223334445558888999999999


Q ss_pred             HHHHHHHHHhhCCCceEEEE-----E-ecC--CccEEEecC
Q psy437          121 KLRNEVQMKWISNKVHLYNV-----W-KIQ--WKRIIWIHS  153 (184)
Q Consensus       121 ~~r~~~~~~f~~~~~~v~va-----~-D~~--~vr~v~~~~  153 (184)
                      +.|..+.+...+|++.|+|.     + +.+  ++..||...
T Consensus       173 ~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDE  213 (264)
T d1gm5a3         173 SEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDE  213 (264)
T ss_dssp             HHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEES
T ss_pred             HHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeecc
Confidence            99999999999999999998     2 444  788887544

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=92.43  E-value=0.49  Score=32.86  Aligned_cols=62  Identities=8%  Similarity=-0.034  Sum_probs=53.9

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ....+++.++++..+.+....|...+.......+................+...+++.|+.+
T Consensus        64 ~~~~~~~v~P~~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~  125 (206)
T d1oywa2          64 LNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPER  125 (206)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHH
T ss_pred             ccCceEEeccchhhhhhHHHHHHhhcccccccccccccccchhHHHHHhcCCceEEEEechh
Confidence            55788999999999999999999999888888888888888888888888899999888744

>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=91.61  E-value=0.17  Score=36.33  Aligned_cols=56  Identities=11%  Similarity=0.016  Sum_probs=46.5

Q ss_pred             CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEE
Q psy437           84 KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYN  139 (184)
Q Consensus        84 ~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~v  139 (184)
                      .-+|||.|.+-...|.++..|...||+..|+|+--....-.-+-+..+.|.++|-.
T Consensus        34 GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIAqAG~~GaVTIAT   89 (219)
T d1nkta4          34 GQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRGGVTVAT   89 (219)
T ss_dssp             TCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTTCEEEEE
T ss_pred             CCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHHhcccCCcEEeec
Confidence            44799999999999999999999999999999986666666666677777666554

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.56  E-value=0.69  Score=32.30  Aligned_cols=58  Identities=12%  Similarity=0.025  Sum_probs=44.0

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      ....+++.+++...+......+..    .++++...+|+.+......    .......|||+|+.+
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~----~l~~~~~Ili~TP~~  129 (206)
T d1s2ma1          68 NKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDIL----RLNETVHILVGTPGR  129 (206)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHH----HTTSCCSEEEECHHH
T ss_pred             ccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHH----HhcccceEEEECCcc
Confidence            456688999999998888777654    4788999999987655433    335568899999965

>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=90.62  E-value=0.13  Score=32.57  Aligned_cols=49  Identities=14%  Similarity=0.214  Sum_probs=38.6

Q ss_pred             HHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           21 LKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        21 ~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      ...|...+.+..+..+.|+||.+-..+...+..|...|++ +..+.||+.
T Consensus        45 ~~~l~~~~~~~~~~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          45 NDTLGAFMRDNDFDTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHHHHSCTTSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             chhHHHHhhhccccCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHH
Confidence            4556666655446677899999988999999999999995 777899864

>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=89.55  E-value=0.18  Score=33.03  Aligned_cols=37  Identities=14%  Similarity=-0.053  Sum_probs=32.8

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCeeEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~hg~l~   69 (184)
                      +..+.++||.+-..+...+..|.+.|+.+..+.||+.
T Consensus        79 ~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          79 RGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             BTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCG
T ss_pred             ccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchH
Confidence            4567888999988899999999999999999999975

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.19  E-value=0.85  Score=32.35  Aligned_cols=58  Identities=12%  Similarity=0.094  Sum_probs=42.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHh----CCCe----eEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQ----ERIN----AISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~----~gi~----~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      ++.++|+.+||+..++++.+.|++    .+++    ...++++.+..++...+....  ...|+|+|+
T Consensus        85 ~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~Ilv~Tp  150 (237)
T d1gkub1          85 KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR--NFKIVITTT  150 (237)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG--GCSEEEEEH
T ss_pred             hcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc--ccceeccCh
Confidence            567899999999999999988875    2333    455677777777666655443  457899998

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=88.84  E-value=3  Score=29.89  Aligned_cols=103  Identities=7%  Similarity=-0.046  Sum_probs=67.9

Q ss_pred             HHHHHHhCCCeeEEecCCCCHH---HHHHHHHHHhccCceEEEEEeecccHHHHHHHHH----hcCCcEEEeeCCCChHH
Q psy437           50 VAAALAQERINAISYHAGLADK---LRNEVQMKWISNKVHVGHWTVVSKECDSVAAALA----QERINAISYHAGLADKL  122 (184)
Q Consensus        50 la~~L~~~gi~~~~~hg~l~~~---~R~~~~~~f~~g~~~vlVaT~tr~~~e~~a~gL~----~~gi~~~vih~~~p~~~  122 (184)
                      +...+.........++|.....   .=..+.........++++-+|+---+....+.+.    .-++.+..+|...+...
T Consensus        67 i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~  146 (233)
T d2eyqa3          67 VLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKE  146 (233)
T ss_dssp             HHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHH
T ss_pred             HHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchh
Confidence            3344444444566788866542   2233344444455678888886643333333333    35778788999999999


Q ss_pred             HHHHHHHhhCCCceEEEE-----E---ecCCccEEEec
Q psy437          123 RNEVQMKWISNKVHLYNV-----W---KIQWKRIIWIH  152 (184)
Q Consensus       123 r~~~~~~f~~~~~~v~va-----~---D~~~vr~v~~~  152 (184)
                      +..+.+...+|++.|++.     +   ..+++..||..
T Consensus       147 ~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIiD  184 (233)
T d2eyqa3         147 QTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVD  184 (233)
T ss_dssp             HHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEE
T ss_pred             HHHHHHHHhCCCCCEEEeehhhhccCCccccccceeee
Confidence            999999999999999997     2   44577777654

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=88.83  E-value=1  Score=30.69  Aligned_cols=55  Identities=11%  Similarity=0.004  Sum_probs=43.5

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhC----CCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQE----RINAISYHAGLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~----gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .+.++++.+|++..+++.++.+.+.    +..+..+|++....+|......     .+++++|+
T Consensus        51 ~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~-----~~i~i~t~  109 (200)
T d1wp9a1          51 YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWAR-----AKVIVATP  109 (200)
T ss_dssp             SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHH-----CSEEEECH
T ss_pred             cCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeecccchhHHHHhhhc-----cccccccc
Confidence            4567889999999999988888763    5668889999888887766543     36888887

>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=86.58  E-value=0.19  Score=32.32  Aligned_cols=37  Identities=14%  Similarity=0.154  Sum_probs=31.3

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      +..+.|+||++-..+...+..|.+.|+. +..+.||+.
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            4466888999988899999999999995 778899973

>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=84.33  E-value=0.3  Score=31.39  Aligned_cols=44  Identities=9%  Similarity=0.104  Sum_probs=35.8

Q ss_pred             ChHHHHHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhCCCeeEEe
Q psy437           19 NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISY   64 (184)
Q Consensus        19 ~k~~~L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~gi~~~~~   64 (184)
                      +.+..|..++++  ...+.|+.|.|....+.+.+.|...++++..+
T Consensus        21 ~p~~~L~~~i~~--~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~   64 (117)
T d2eyqa2          21 APLDALRKFLET--FDGPVVFSVESEGRREALGELLARIKIAPQRI   64 (117)
T ss_dssp             STTHHHHHHHTT--CCSCCCEEESSHHHHHHHHHHHGGGTCCCEEC
T ss_pred             cHHHHHHHHHHh--CCCeEEEEECCccHHHHHHHHHHHcCCCceEe
Confidence            467888888855  45577888899999999999999999887554

>d1e5da1 c.23.5.1 (A:251-402) Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain {Desulfovibrio gigas [TaxId: 879]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain
species: Desulfovibrio gigas [TaxId: 879]

Probab=84.14  E-value=3.4  Score=26.84  Aligned_cols=55  Identities=13%  Similarity=0.003  Sum_probs=35.2

Q ss_pred             EEEEe----ccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           37 GIVYC----LTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        37 ~IIf~----~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .|||.    +|++.++.+++.|...|+.+..++-.-.  ........+..-+ -++++|++-
T Consensus         6 ~IiY~S~tGnTe~~A~~Ia~~l~~~g~ev~~~~~~~~--~~~~~~~~l~~~d-~vi~Gspt~   64 (152)
T d1e5da1           6 VIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKAC--HHSQIMSEISDAG-AVIVGSPTH   64 (152)
T ss_dssp             EEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEETTTS--CHHHHHHHHHTCS-EEEEECCCB
T ss_pred             EEEEECCCcHHHHHHHHHHHHHhhCCCEEEEeecccC--ChhhhccchhhCC-EEEEecccc
Confidence            45663    6788888999999999998888764322  2233444444322 467777753

>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=83.83  E-value=1.1  Score=28.61  Aligned_cols=68  Identities=12%  Similarity=-0.003  Sum_probs=47.5

Q ss_pred             HHHHHHHhcc-CceEEEEEeecccHHHHHHHHHhcCCcEEEeeCCCChHHHHHHHHHhhCCCceEEEE-----EecCCcc
Q psy437           74 NEVQMKWISN-KVHVGHWTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHLYNV-----WKIQWKR  147 (184)
Q Consensus        74 ~~~~~~f~~g-~~~vlVaT~tr~~~e~~a~gL~~~gi~~~vih~~~p~~~r~~~~~~f~~~~~~v~va-----~D~~~vr  147 (184)
                      ...+..|.+. ..+||+++.+.+..|.+..-|...|+. ..+.-+.+         .+..+++.|+++     |-.++.+
T Consensus        23 ~~~L~~~i~~~~~~Vli~a~s~g~~erl~e~L~~~~i~-~~~~~~~~---------~~~~~~~~i~~~~l~~GF~~~~~~   92 (117)
T d2eyqa2          23 LDALRKFLETFDGPVVFSVESEGRREALGELLARIKIA-PQRIMRLD---------EASDRGRYLMIGAAEHGFVDTVRN   92 (117)
T ss_dssp             THHHHHHHTTCCSCCCEEESSHHHHHHHHHHHGGGTCC-CEECSSGG---------GCCTTCCEEEECCCCSCEEETTTT
T ss_pred             HHHHHHHHHhCCCeEEEEECCccHHHHHHHHHHHcCCC-ceEecChh---------hhcCceEEEEEecCccccccCCCC
Confidence            3456777654 568999999999999999999999998 34433332         244566777776     5555555


Q ss_pred             EEEe
Q psy437          148 IIWI  151 (184)
Q Consensus       148 ~v~~  151 (184)
                      +++.
T Consensus        93 l~vI   96 (117)
T d2eyqa2          93 LALI   96 (117)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            5554

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=83.40  E-value=0.51  Score=29.88  Aligned_cols=48  Identities=19%  Similarity=0.179  Sum_probs=35.9

Q ss_pred             HHHHHHHHhh--cCCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCCC
Q psy437           22 KEVISLIKAK--YSGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGLA   69 (184)
Q Consensus        22 ~~L~~~l~~~--~~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l~   69 (184)
                      ..+...+...  .+..+.|+||.|=..+...+..|+..|++ +..|.|+++
T Consensus        68 ~~~~~~~~~~g~~~~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~  118 (120)
T d1urha2          68 DELDAIFFGRGVSYDKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWS  118 (120)
T ss_dssp             HHHHHHHHTTTCCSSSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCC
T ss_pred             HHhhhhhhhcccCccCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChh
Confidence            4445555432  24567889999988888888999999995 888999986

>d2b2na1 c.37.1.19 (A:26-333) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=82.99  E-value=5.3  Score=29.68  Aligned_cols=67  Identities=7%  Similarity=-0.036  Sum_probs=45.9

Q ss_pred             HHHHHHhhcCCCcEEEEeccHHHHHHHHHHHHhC-CCeeEEe-------cCCCC-----HHHHHHHHHHHhccCceEEEE
Q psy437           24 VISLIKAKYSGQSGIVYCLTRKECDSVAAALAQE-RINAISY-------HAGLA-----DKLRNEVQMKWISNKVHVGHW   90 (184)
Q Consensus        24 L~~~l~~~~~~~~~IIf~~tr~~~e~la~~L~~~-gi~~~~~-------hg~l~-----~~~R~~~~~~f~~g~~~vlVa   90 (184)
                      +.+++.+  ...|.+|.|++...|+.+++.|... +-.+..+       +-..+     ..+|..++..+.+++..++|+
T Consensus         6 ~a~~~~~--~~~p~lvv~~~~~~A~~l~~~L~~~~~~~v~~fP~~e~lpyd~~s~~~~i~~~R~~~L~~l~~~~~~iiit   83 (308)
T d2b2na1           6 VAEIAER--HAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIV   83 (308)
T ss_dssp             HHHHHHH--CSSCEEEEESSHHHHHHHHHHHHTTCSSCEEECCCCCSCTTCSSCCCHHHHHHHHHHHHHGGGCCSSEEEE
T ss_pred             HHHHHHh--hCCCEEEEcCCHHHHHHHHHHHHhcCCCceEEcCCcccCccccCCCChHHHHHHHHHHHHHhhcCCceEEe
Confidence            3444433  5678999999999999999999753 2222222       11121     257999999999988777777


Q ss_pred             Ee
Q psy437           91 TV   92 (184)
Q Consensus        91 T~   92 (184)
                      |.
T Consensus        84 s~   85 (308)
T d2b2na1          84 PV   85 (308)
T ss_dssp             EH
T ss_pred             ec
Confidence            65

>d1ycga1 c.23.5.1 (A:251-399) Nitric oxide reductase C-terminal domain {Moorella thermoacetica [TaxId: 1525]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: Nitric oxide reductase C-terminal domain
species: Moorella thermoacetica [TaxId: 1525]

Probab=82.75  E-value=1.2  Score=29.14  Aligned_cols=55  Identities=16%  Similarity=0.086  Sum_probs=35.0

Q ss_pred             EEEEe----ccHHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec
Q psy437           37 GIVYC----LTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS   94 (184)
Q Consensus        37 ~IIf~----~tr~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr   94 (184)
                      .|||.    +|.+.++.+++.|.+.|+.+..++-  +......+...+..-+ -++++|++-
T Consensus         6 lIvY~S~~GnT~~vA~~Ia~~l~~~g~~v~~~~~--~~~~~~~~~~~~~~~d-~ii~Gspt~   64 (149)
T d1ycga1           6 VIAYDTMWLSTEKMAHALMDGLVAGGCEVKLFKL--SVSDRNDVIKEILDAR-AVLVGSPTI   64 (149)
T ss_dssp             EEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEEG--GGSCHHHHHHHHHHCS-EEEEECCCB
T ss_pred             EEEEECCCcHHHHHHHHHHHHHHhcCCeeEEEEc--cccchHHHhhhhhhCC-eEEEEeecc
Confidence            45564    5778888888888889998887753  2333444555554423 366777744

>d2dria_ c.93.1.1 (A:) D-ribose-binding protein {Escherichia coli, strain k-12 [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: D-ribose-binding protein
species: Escherichia coli, strain k-12 [TaxId: 562]

Probab=81.97  E-value=5.4  Score=27.73  Aligned_cols=70  Identities=6%  Similarity=-0.056  Sum_probs=41.3

Q ss_pred             HHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceEEEEEeec-ccHHHHHHHHHhcCCcEEEeeCCCC
Q psy437           50 VAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHVGHWTVVS-KECDSVAAALAQERINAISYHAGLA  119 (184)
Q Consensus        50 la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~vlVaT~tr-~~~e~~a~gL~~~gi~~~vih~~~p  119 (184)
                      +.+.+.+.|+.+..+.+.-+.....+.++.+.+..+.+++.++.. .........+...|+++.+++.+.+
T Consensus        23 i~~~a~~~g~~~~i~~~~~~~~~~~~~i~~~~~~~~d~ii~~~~~~~~~~~~~~~~~~~~ipvV~~~~~~~   93 (271)
T d2dria_          23 AQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQAT   93 (271)
T ss_dssp             HHHHHHHHTCEEEEEECTTCHHHHHHHHHHHTTTTEEEEEECCSSTTTTHHHHHHHHHTTCCEEEESSCCS
T ss_pred             HHHHHHHcCCEEEEEeCCCCHHHHHHHHHHHHhcCCcccccccccccchHHHHHHHhhcceeEEEeccccc
Confidence            334445557776666666666666677777777666666666543 2234445556667777555554443

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=81.80  E-value=0.36  Score=31.79  Aligned_cols=36  Identities=14%  Similarity=0.289  Sum_probs=30.7

Q ss_pred             CCCcEEEEeccHHHHHHHHHHHHhCCCe-eEEecCCC
Q psy437           33 SGQSGIVYCLTRKECDSVAAALAQERIN-AISYHAGL   68 (184)
Q Consensus        33 ~~~~~IIf~~tr~~~e~la~~L~~~gi~-~~~~hg~l   68 (184)
                      +..+.|+||.+-..+...+..|.+.|++ +..+.||+
T Consensus        81 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~  117 (137)
T d1qxna_          81 PEKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGM  117 (137)
T ss_dssp             TTSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCH
T ss_pred             cccceeeeecccchHHHHHHHHHHcCCCcEEEecCHH
Confidence            4567889999988899999999999995 77789995

>d1vmea1 c.23.5.1 (A:251-398) ROO-like flavoprotein TM0755, C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Flavoproteins
family: Flavodoxin-related
domain: ROO-like flavoprotein TM0755, C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.22  E-value=4.4  Score=26.15  Aligned_cols=55  Identities=7%  Similarity=0.086  Sum_probs=33.7

Q ss_pred             EEEEe----ccHHHHHHHHHHHHhCCCeeEEecC-CCCHHHHHHHHHHHhccCceEEEEEe
Q psy437           37 GIVYC----LTRKECDSVAAALAQERINAISYHA-GLADKLRNEVQMKWISNKVHVGHWTV   92 (184)
Q Consensus        37 ~IIf~----~tr~~~e~la~~L~~~gi~~~~~hg-~l~~~~R~~~~~~f~~g~~~vlVaT~   92 (184)
                      .|||.    +|+..|+.+++.|...|+.+..+.- ..+..+.......+.+-+ -++++|+
T Consensus         7 ~IiY~S~tGnTe~~A~~i~~~l~~~g~~v~~~~~~~~~~~~~~~~~~~l~~~d-~iiigsp   66 (148)
T d1vmea1           7 TVIYDSMYGFVENVMKKAIDSLKEKGFTPVVYKFSDEERPAISEILKDIPDSE-ALIFGVS   66 (148)
T ss_dssp             EEEEECSSSHHHHHHHHHHHHHHHTTCEEEEEEECSSCCCCHHHHHHHSTTCS-EEEEEEC
T ss_pred             EEEEECCCcHHHHHHHHHHHHHHhCCCeEEEEecccccccchhHhhhhHHHCC-EeEEEec
Confidence            45565    5677788888888888998877653 233333444444444433 4666666

>d1jyea_ c.93.1.1 (A:) Lac-repressor (lacR) core (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Lac-repressor (lacR) core (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=80.99  E-value=6.8  Score=27.64  Aligned_cols=84  Identities=13%  Similarity=0.121  Sum_probs=40.4

Q ss_pred             CCCcEEEEecc---HHHHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhccCceE------------EEEEeecccH
Q psy437           33 SGQSGIVYCLT---RKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV------------GHWTVVSKEC   97 (184)
Q Consensus        33 ~~~~~IIf~~t---r~~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~g~~~v------------lVaT~tr~~~   97 (184)
                      .+...+++...   .+......+.|...++....+.+.....  ......+.+..+++            -|.++.+..+
T Consensus        29 ~Gy~v~v~~~~~~~~~~~~~~l~~l~~~~vdgiIl~~~~~~~--~~~~~~~~~~~iPvV~~d~~~~~~~~~V~~D~~~~~  106 (271)
T d1jyea_          29 LGASVVVSMVERSGVEACKTAVHNLLAQRVSGLIINYPLDDQ--DAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGT  106 (271)
T ss_dssp             TTCEEEEEECCSSSHHHHHHHHHHHHTTTCSCEEEESCCCHH--HHHHHHHHTTTSCEEESSSCTTSSSCEEEECHHHHH
T ss_pred             cCCEEEEEECCCCCHHHHHHHHHHHHhcCCCEEEeccccCch--hHHHHHHHhcCCCeeeeeccccccCCccccchhhcc
Confidence            44555555432   2223333444545566554454444433  23333444444433            2344444556


Q ss_pred             HHHHHHHHhcCCc-EEEeeCCC
Q psy437           98 DSVAAALAQERIN-AISYHAGL  118 (184)
Q Consensus        98 e~~a~gL~~~gi~-~~vih~~~  118 (184)
                      ..++..|-..|.+ ..++.+..
T Consensus       107 ~~~~~~L~~~G~~~i~~i~~~~  128 (271)
T d1jyea_         107 RLGVEHLVALGHQQIALLAGPL  128 (271)
T ss_dssp             HHHHHHHHHHTCCSEEEEECCT
T ss_pred             ccceeeeecccccccccccccc
Confidence            6777777666655 34455443

>d1dbqa_ c.93.1.1 (A:) Purine repressor (PurR), C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like I
superfamily: Periplasmic binding protein-like I
family: L-arabinose binding protein-like
domain: Purine repressor (PurR), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.14  E-value=7.5  Score=27.15  Aligned_cols=72  Identities=8%  Similarity=-0.014  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHhCCCeeEEecCCCCHHHHHHHHHHHhc------------cCceEEEEEeecccHHHHHHHHHhcCCcEEE
Q psy437           46 ECDSVAAALAQERINAISYHAGLADKLRNEVQMKWIS------------NKVHVGHWTVVSKECDSVAAALAQERINAIS  113 (184)
Q Consensus        46 ~~e~la~~L~~~gi~~~~~hg~l~~~~R~~~~~~f~~------------g~~~vlVaT~tr~~~e~~a~gL~~~gi~~~v  113 (184)
                      ....+.+.|...++....+.+......+.........            ....-.|.++.+.....++..|...|.+-.+
T Consensus        44 ~~~~~~~~l~~~~vdgiIi~~~~~~~~~~~~~~~~~~iPvV~~~~~~~~~~~~~~v~~d~~~~~~~~~~~l~~~G~~~i~  123 (282)
T d1dbqa_          44 KQRAYLSMMAQKRVDGLLVMCSEYPEPLLAMLEEYRHIPMVVMDWGEAKADFTDAVIDNAFEGGYMAGRYLIERGHREIG  123 (282)
T ss_dssp             HHHHHHHHHHHTTCSEEEEECSCCCHHHHHHHHHTTTSCEEEEECSSCCSSSCEEEEECHHHHHHHHHHHHHHTTCCSEE
T ss_pred             HHHHHHHHHHhcCCCEEeeecccccchhhhhHHhhcCCCceEEEecccccccceEEEecccchhhhhhhhhccccccccc
Confidence            3345666677777776555443333333333322210            1112245555556677777888888887333


Q ss_pred             eeCC
Q psy437          114 YHAG  117 (184)
Q Consensus       114 ih~~  117 (184)
                      +-.+
T Consensus       124 ~i~~  127 (282)
T d1dbqa_         124 VIPG  127 (282)
T ss_dssp             EECC
T ss_pred             cccC
Confidence            3333