Psyllid ID: psy11948

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------
Protein Sequence
MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHccccccHHHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHccccccccccccccccccHHHHHHcccccccccEEccccEEcccccccccccccccccccccccHHHHHHHHHHHHHcHHHHHHccccccEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHccccEEEEEccccccccHHHHHccccEEEEccHHHHHHHHHccccHHHcccccccccEEEEEcccHHHHHH
Coil and Loop (DISEMBL)
maewvkfnipETIIRALYQkgfktptkiqsmvmpsaLLARKDIVgaaetgsgktlafgIPILTGIVnklenpteedendsarKDIVGaaetgsgktlafgIPILTGIVnklenpteedendsgleEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ
Flexible Loop (DISEMBL)
maewvkfnipeTIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAEtgsgktlafgiPILTGIVNKLenpteedendsaRKDIVGAaetgsgktlafgIPILTGIVNklenpteedendsgLEEEAEEVLEEleeesanttefvkkTRNKLYAlilaptrelaiq
Low Complexity Region (SEG)
MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTeedendsgleeeaeevleeleeeSANTTEFVKKTRNKLYALILAPTRELAIQ
Disordered region (IsUnstruct)
***WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNK*************************GKTLAFGIPILTGIVNK*************************************KTRNKLYALILAP*******
Disordered Region (DISOPRED)
MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI********************************AFGIPILTG*************************LEE***************RNKLYALILAPTRELAIQ
Disordered Region (DISEMBL)
MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLEN*********ARKDIVGAAETGSGKTLAFGIPILTGIVNKLEN******************************EFVKKTRNKLYALILAPTRELAIQ
Disordered Region (DISPRO)
*AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLYALILAPTRELAIQ
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	167	2.2.26 [Sep-21-2011]
Q54TD7	940	ATP-dependent RNA helicas	yes	N/A	0.497	0.088	0.433	2e-14
Q9GZR7	859	ATP-dependent RNA helicas	yes	N/A	0.982	0.190	0.288	5e-13
Q5RDL2	859	ATP-dependent RNA helicas	yes	N/A	0.982	0.190	0.288	1e-12
Q9ESV0	857	ATP-dependent RNA helicas	yes	N/A	1.0	0.194	0.279	3e-12
A3AVH5	832	DEAD-box ATP-dependent RN	yes	N/A	0.485	0.097	0.419	5e-12
A2XVF7	832	DEAD-box ATP-dependent RN	N/A	N/A	0.485	0.097	0.419	5e-12
Q93Y39	826	DEAD-box ATP-dependent RN	yes	N/A	0.419	0.084	0.428	2e-11
Q4IBS2	781	ATP-dependent RNA helicas	yes	N/A	0.365	0.078	0.5	1e-10
A5DF03	575	Pre-mRNA-splicing ATP-dep	N/A	N/A	0.371	0.107	0.492	2e-10
A7EAY2	780	ATP-dependent RNA helicas	N/A	N/A	0.347	0.074	0.525	2e-10

>sp|Q54TD7|DDX24_DICDI ATP-dependent RNA helicase ddx24 OS=Dictyostelium discoideum GN=ddx24 PE=3 SV=1

 Score = 78.6 bits (192), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/83 (43%), Positives = 55/83 (66%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           M+EW  +N+   I++ L   GF  PT+IQS V+P A+ +  D++GAA+TGSGKTLAFGIP
Sbjct: 293 MSEWNSYNLDPLILKGLRSLGFSKPTEIQSSVIPVAVSSGYDVIGAAQTGSGKTLAFGIP 352

Query: 61  ILTGIVNKLENPTEEDENDSARK 83
           ++  I+  L    +  EN + ++
Sbjct: 353 MVQRILQHLRKHGQNVENKANKQ 375

ATP-dependent RNA helicase.
Dictyostelium discoideum (taxid: 44689)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q9GZR7|DDX24_HUMAN ATP-dependent RNA helicase DDX24 OS=Homo sapiens GN=DDX24 PE=1 SV=1

 Score = 73.9 bits (180), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 99/215 (46%), Gaps = 51/215 (23%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P  ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct: 191 VSAWKDLFVPRPVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 250

Query: 61  ILTGIV-----NKLENPTE----------------------EDENDSARKDIV------- 86
           ++  ++     N    P+                       E E+D+   D V       
Sbjct: 251 MIHAVLQWQKRNAAPPPSNTEAPPGETRTEAGAETRSPGKAEAESDALPDDTVIESEALP 310

Query: 87  ------GAAETG---SGKTLAFGIPIL----TGIVNKLENPTEEDENDSGLEEEAEEVL- 132
                   A+TG   S + L FG        + ++ +   P + +  +  L++E    L 
Sbjct: 311 SDIAAEARAKTGGTVSDQALLFGDDDAGEGPSSLIREKPVPKQNENEEENLDKEQTGNLK 370

Query: 133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           +EL+++SA    + K+    L  L+L PTRELA+Q
Sbjct: 371 QELDDKSATCKAYPKRP---LLGLVLTPTRELAVQ 402

ATP-dependent RNA helicase.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RDL2|DDX24_PONAB ATP-dependent RNA helicase DDX24 OS=Pongo abelii GN=DDX24 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 98/215 (45%), Gaps = 51/215 (23%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P  ++RAL   GF  PT IQ + +  A+  + DI+GAAETGSGKTLAF IP
Sbjct: 191 VSAWKDLFVPRPVLRALSFLGFSAPTPIQVLTLAPAIRDKLDILGAAETGSGKTLAFAIP 250

Query: 61  ILTGIV-----NKLENPTE----------------------EDENDSARKDIV------- 86
           ++  ++     N    P+                       E E+D+   D V       
Sbjct: 251 MIHAVLQWQKRNAAPPPSNTEAPPGETRPEAGAETRSPGKAEAESDALPDDTVIESEALP 310

Query: 87  ------GAAETG---SGKTLAFGIPIL----TGIVNKLENPTEEDENDSGLEEEAEEVL- 132
                   A+TG   S + L FG        + ++ +   P + +  +  L++E    L 
Sbjct: 311 SDTAAEARAKTGGTVSDQALLFGDDDAGEGPSSLIREKPVPKQNENEEENLDKEQTGNLK 370

Query: 133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           +EL+++SA    + K+    L  L+L PTRELA+Q
Sbjct: 371 QELDDKSATCKTYPKRP---LLGLVLTPTRELAVQ 402

ATP-dependent RNA helicase.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9ESV0|DDX24_MOUSE ATP-dependent RNA helicase DDX24 OS=Mus musculus GN=Ddx24 PE=1 SV=2

 Score = 70.9 bits (172), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 59/211 (27%), Positives = 92/211 (43%), Gaps = 44/211 (20%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P+ ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct: 192 VSAWRDLFVPKAVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 251

Query: 61  ILTGIV--NKLENP-----------------------------------------TEEDE 77
           ++  ++  +K++ P                                         TE   
Sbjct: 252 MIHSVLQWHKMKAPPIPRSTGMPPREMRFGATAHLGSPCKDRTESGVLPEEARIETEAQP 311

Query: 78  NDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEE 137
           +DS  +     + + S +TL           + LE      +N+ G E+   E   +L++
Sbjct: 312 SDSGVQATPETSASASAQTLLVCDDDAGEGPSSLEEKPVPKQNEDGEEKFDAEQAGKLKQ 371

Query: 138 ESANTTEFVK-KTRNKLYALILAPTRELAIQ 167
           E  +     K   R  L  L+L PTRELAIQ
Sbjct: 372 ELCDQIAIYKVHPRRPLLGLVLTPTRELAIQ 402

ATP-dependent RNA helicase.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A3AVH5|RH13_ORYSJ DEAD-box ATP-dependent RNA helicase 13 OS=Oryza sativa subsp. japonica GN=Os04g0510400 PE=2 SV=2

 Score = 70.5 bits (171), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 48/81 (59%)

Query: 4   WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT 63
           W +  +   +I A+ + GFK PT IQ    P+A    KD++GAAETGSGKTLAFG+PIL 
Sbjct: 200 WRELRLHPLLITAVRRLGFKEPTPIQKACFPAAAHQGKDVIGAAETGSGKTLAFGLPILQ 259

Query: 64  GIVNKLENPTEEDENDSARKD 84
            ++ + E        D + +D
Sbjct: 260 RLLEEQEKAMRLSREDESTQD 280

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A2XVF7|RH13_ORYSI DEAD-box ATP-dependent RNA helicase 13 OS=Oryza sativa subsp. indica GN=OsI_016050 PE=2 SV=2

 Score = 70.5 bits (171), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 48/81 (59%)

Query: 4   WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT 63
           W +  +   +I A+ + GFK PT IQ    P+A    KD++GAAETGSGKTLAFG+PIL 
Sbjct: 200 WRELRLHPLLITAVRRLGFKEPTPIQKACFPAAAHQGKDVIGAAETGSGKTLAFGLPILQ 259

Query: 64  GIVNKLENPTEEDENDSARKD 84
            ++ + E        D + +D
Sbjct: 260 RLLEEQEKAMRLSREDESTQD 280

Oryza sativa subsp. indica (taxid: 39946)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q93Y39|RH13_ARATH DEAD-box ATP-dependent RNA helicase 13 OS=Arabidopsis thaliana GN=RH13 PE=2 SV=3

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 45/70 (64%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
            + W    +   +++++Y+  FK PTKIQ      A    KD++GAAETGSGKTLAFG+P
Sbjct: 189 FSAWSSMRLHPLLMKSIYRLDFKEPTKIQKACFNVAAYQGKDVIGAAETGSGKTLAFGLP 248

Query: 61  ILTGIVNKLE 70
           IL  ++++ E
Sbjct: 249 ILQRLLDERE 258

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4IBS2|MAK5_GIBZE ATP-dependent RNA helicase MAK5 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=MAK5 PE=3 SV=2

 Score = 65.9 bits (159), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/62 (50%), Positives = 42/62 (67%), Gaps = 1/62 (1%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           MA WV  N+   II A+ +  F  PTKIQ   +P  ++A  D++G A+TGSGKTLAFGIP
Sbjct: 214 MAAWVSLNLSPQIISAIAKLKFMKPTKIQKRTIPE-IVAGHDVIGKAQTGSGKTLAFGIP 272

Query: 61  IL 62
           ++
Sbjct: 273 MV 274

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DF03|PRP28_PICGU Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=PRP28 PE=3 SV=2

 Score = 65.5 bits (158), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 43/63 (68%), Gaps = 1/63 (1%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           +  W +  IP T++  + Q G+K PT IQ   +P+AL   +D+VG AETGSGKTLAF IP
Sbjct: 149 LRSWKESGIPTTLLNTIDQLGYKEPTPIQRAAIPTAL-GHRDVVGIAETGSGKTLAFLIP 207

Query: 61  ILT 63
           +L+
Sbjct: 208 LLS 210

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

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A7EAY2|MAK5_SCLS1 ATP-dependent RNA helicase mak5 OS=Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) GN=mak5 PE=3 SV=1

 Score = 65.1 bits (157), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 40/59 (67%), Gaps = 1/59 (1%)

Query: 4   WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
           WV+ ++    + AL + GF  PT IQS  +P  +LA  D+VG A TGSGKTLAFGIPI+
Sbjct: 215 WVELDLSSNTLMALSKMGFSKPTPIQSEAIPE-VLAGHDVVGKASTGSGKTLAFGIPIV 272

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) (taxid: 665079)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	167
195028797	806	GH20064 [Drosophila grimshawi] gi|193903	0.880	0.182	0.386	7e-22
195429401	823	GK19535 [Drosophila willistoni] gi|19415	0.880	0.178	0.375	2e-21
195123017	819	GI18782 [Drosophila mojavensis] gi|19391	0.868	0.177	0.390	6e-21
20130173	813	CG9143 [Drosophila melanogaster] gi|7302	0.850	0.174	0.377	9e-21
195336062	814	GM19796 [Drosophila sechellia] gi|194126	0.850	0.174	0.371	2e-20
56201305	814	unnamed protein product [Drosophila simu	0.850	0.174	0.371	2e-20
198458698	807	GA24853 [Drosophila pseudoobscura pseudo	0.856	0.177	0.371	3e-20
195154787	807	GL17630 [Drosophila persimilis] gi|19411	0.856	0.177	0.371	3e-20
195382239	819	GJ21808 [Drosophila virilis] gi|19414463	0.874	0.178	0.360	3e-20
194881539	815	GG20872 [Drosophila erecta] gi|190658075	0.850	0.174	0.365	5e-20

>gi|195028797|ref|XP_001987262.1| GH20064 [Drosophila grimshawi] gi|193903262|gb|EDW02129.1| GH20064 [Drosophila grimshawi]

 Score =  108 bits (270), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 65/168 (38%), Positives = 99/168 (58%), Gaps = 21/168 (12%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           M++W    IP +I+RAL ++G++ PT+IQ+M +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 196 MSKWQGMGIPTSIMRALAEQGYEAPTQIQAMTLPAAIHGKKDILGAAETGSGKTLAFGIP 255

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSG-KTLAFGIPILTGIVNKLENPTEEDE 119
           IL+GI+        +  ND            GSG +T A    +   +  + E PT ++ 
Sbjct: 256 ILSGIMEL------KQRND------------GSGIRTRAPKHKVEATV--EAEVPTSKEN 295

Query: 120 NDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           ++     E  + +    EE ++  ++    R  LYAL+L PTRELA+Q
Sbjct: 296 HELTPPPEELDYVSGASEEESDAEDYSSSGRRPLYALVLTPTRELAVQ 343

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195429401|ref|XP_002062751.1| GK19535 [Drosophila willistoni] gi|194158836|gb|EDW73737.1| GK19535 [Drosophila willistoni]

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 63/168 (37%), Positives = 95/168 (56%), Gaps = 21/168 (12%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P+ I+RAL +KGF+ PT+IQ+M +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 217 LSSWHGLGVPQPILRALAEKGFREPTQIQAMTLPAAIHGKKDILGAAETGSGKTLAFGIP 276

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI++  E         +A+  I  A +     +             K E P  +DE+
Sbjct: 277 MLAGIMDLKER--------NAKHGIRKAPKVKGEDS------------QKSEEPPRDDEH 316

Query: 121 D-SGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           + +   EE + V    +E+ ++           LYAL+L PTRELA+Q
Sbjct: 317 ELTPPPEELDHVSGASDEDDSDLENHSASRERPLYALVLTPTRELAVQ 364

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195123017|ref|XP_002006006.1| GI18782 [Drosophila mojavensis] gi|193911074|gb|EDW09941.1| GI18782 [Drosophila mojavensis]

 Score =  105 bits (262), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 66/169 (39%), Positives = 97/169 (57%), Gaps = 24/169 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           M +W    +PE I+RAL + G++ PT+IQ+M +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 210 MTKWHGMGVPEPIMRALAELGYEAPTQIQAMTLPAAIHGKKDILGAAETGSGKTLAFGIP 269

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLEN--PTEED 118
           IL+GI+       + +++   RK                  P + G    +E   PT+++
Sbjct: 270 ILSGIMEL----KQRNDDSGIRK-----------------APKVKGAQGPVEEAPPTKDN 308

Query: 119 ENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
              +   EE + V    +EES N  +   K R  LYA++L PTRELA+Q
Sbjct: 309 HELTPSPEELDYVSGASDEESDNEHDPEAKQR-PLYAVVLTPTRELAVQ 356

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|20130173|ref|NP_611467.1| CG9143 [Drosophila melanogaster] gi|7302399|gb|AAF57487.1| CG9143 [Drosophila melanogaster] gi|33636633|gb|AAQ23614.1| LD11580p [Drosophila melanogaster]

 Score =  105 bits (261), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 63/167 (37%), Positives = 95/167 (56%), Gaps = 25/167 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           M+ W    +P +I+RAL ++GFKTPT+IQ++ +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 214 MSAWNGLGVPASILRALGEQGFKTPTQIQALTLPAAIHGKKDILGAAETGSGKTLAFGIP 273

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI+        E +  + R  I  A +    +      P      ++L  P EE ++
Sbjct: 274 MLAGIM--------ELKQRNIRSGIRKAPKVKGQQ------PEPAADEHELTPPPEELDH 319

Query: 121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
            SG             +E ++  E  ++ +  LY L+L PTRELA+Q
Sbjct: 320 VSG-----------ASDEESDAEEQAQRVQTPLYGLVLTPTRELAVQ 355

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195336062|ref|XP_002034666.1| GM19796 [Drosophila sechellia] gi|194126636|gb|EDW48679.1| GM19796 [Drosophila sechellia]

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/167 (37%), Positives = 95/167 (56%), Gaps = 25/167 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P +I+RAL ++GFKTPT+IQ++ +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 215 VSAWNGLGVPASILRALGEQGFKTPTQIQALTLPAAIHGKKDILGAAETGSGKTLAFGIP 274

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI+        E +  + R  I  A +    +      P      ++L  P EE ++
Sbjct: 275 MLAGIM--------ELKQRNIRSGIRKAPKVKGQQ------PEPAADEHELTPPPEELDH 320

Query: 121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
            SG             +E ++  E  ++ +  LY L+L PTRELA+Q
Sbjct: 321 VSG-----------ASDEESDAEEHTQRVQTPLYGLVLTPTRELAVQ 356

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|56201305|dbj|BAD72907.1| unnamed protein product [Drosophila simulans] gi|56201324|dbj|BAD72925.1| unnamed protein product [Drosophila sechellia]

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 62/167 (37%), Positives = 95/167 (56%), Gaps = 25/167 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P +I+RAL ++GFKTPT+IQ++ +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 215 VSAWNGLGVPASILRALGEQGFKTPTQIQALTLPAAIHGKKDILGAAETGSGKTLAFGIP 274

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI+        E +  + R  I  A +    +      P      ++L  P EE ++
Sbjct: 275 MLAGIM--------ELKQRNIRSGIRKAPKVKGQQ------PEPAADEHELTPPPEELDH 320

Query: 121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
            SG             +E ++  E  ++ +  LY L+L PTRELA+Q
Sbjct: 321 VSG-----------ASDEESDAEEHTQRVQTPLYGLVLTPTRELAVQ 356

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198458698|ref|XP_002138576.1| GA24853 [Drosophila pseudoobscura pseudoobscura] gi|198136429|gb|EDY69134.1| GA24853 [Drosophila pseudoobscura pseudoobscura]

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 62/167 (37%), Positives = 93/167 (55%), Gaps = 24/167 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P  I+RAL ++GFK PT+IQSM +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 207 LSAWNGLGVPSNILRALAEQGFKAPTQIQSMTLPAAIHGKKDILGAAETGSGKTLAFGIP 266

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI+        E +  +A   I  A +         G PI          P  +DE+
Sbjct: 267 MLAGIM--------ELKQRNASSGIRKAPKVK-------GAPIA---------PPADDEH 302

Query: 121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           +     +  + +    +E ++  E  ++ +  LY L+L PTRELA+Q
Sbjct: 303 ELTPPPDELDHVSGASDEDSDAEEREQRKQTPLYGLVLTPTRELAVQ 349

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195154787|ref|XP_002018294.1| GL17630 [Drosophila persimilis] gi|194114090|gb|EDW36133.1| GL17630 [Drosophila persimilis]

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 62/167 (37%), Positives = 93/167 (55%), Gaps = 24/167 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P  I+RAL ++GFK PT+IQSM +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 207 LSAWNGLGVPSNILRALAEQGFKAPTQIQSMTLPAAIHGKKDILGAAETGSGKTLAFGIP 266

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI+        E +  +A   I  A +         G PI          P  +DE+
Sbjct: 267 MLAGIM--------ELKQRNASSGIRKAPKVK-------GAPIA---------PPADDEH 302

Query: 121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           +     +  + +    +E ++  E  ++ +  LY L+L PTRELA+Q
Sbjct: 303 ELTPPPDELDHVSGASDEDSDAEEREQRKQTPLYGLVLTPTRELAVQ 349

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195382239|ref|XP_002049838.1| GJ21808 [Drosophila virilis] gi|194144635|gb|EDW61031.1| GJ21808 [Drosophila virilis]

 Score =  103 bits (256), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 61/169 (36%), Positives = 93/169 (55%), Gaps = 23/169 (13%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           M +W    +P  I+RAL ++G++ PT+IQ+M +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 209 MTKWNGMGVPAPIMRALAEQGYEAPTQIQAMTLPAAIHGKKDILGAAETGSGKTLAFGIP 268

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           IL+GI+       + ++    RK                  P + G     E P  +D +
Sbjct: 269 ILSGIMEL----KQRNDGSCIRK-----------------APKVKGTQQVEEPPQSKDNH 307

Query: 121 DSGLEEEAEEV--LEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           +  L    EE+  +    +E ++  E  +     LYA++L PTRELA+Q
Sbjct: 308 NHELTPPPEELDYVSGASDEESDAEEHNQGMGRPLYAVVLTPTRELAVQ 356

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194881539|ref|XP_001974888.1| GG20872 [Drosophila erecta] gi|190658075|gb|EDV55288.1| GG20872 [Drosophila erecta]

 Score =  102 bits (254), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 61/167 (36%), Positives = 94/167 (56%), Gaps = 25/167 (14%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           ++ W    +P +I+RAL ++GFK PT+IQ++ +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct: 216 VSAWNGLGVPASILRALGEQGFKAPTQIQALTLPAAIHGKKDILGAAETGSGKTLAFGIP 275

Query: 61  ILTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN 120
           +L GI+        E +  + R  I  A +    +      P      ++L  P EE ++
Sbjct: 276 MLAGIM--------ELKQRNIRSGIRKAPKVKGQQ------PEPAADEHELTPPPEELDH 321

Query: 121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
            SG             +E ++  E  ++ +  LY L+L PTRELA+Q
Sbjct: 322 VSG-----------ASDEESDAEEHAQRMQTPLYGLVLTPTRELAVQ 357

Source: Drosophila erecta

Species: Drosophila erecta

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	167
FB|FBgn0034496	813	CG9143 [Drosophila melanogaste	0.395	0.081	0.590	9.6e-21
WB|WBGene00018890	746	F55F8.2 [Caenorhabditis elegan	0.485	0.108	0.433	1.6e-16
MGI|MGI:1351337	857	Ddx24 "DEAD (Asp-Glu-Ala-Asp)	0.431	0.084	0.418	1.1e-13
RGD|727929	851	Ddx24 "DEAD (Asp-Glu-Ala-Asp)	0.431	0.084	0.418	1.3e-13
GENEDB_PFALCIPARUM|PFB0860c	562	PFB0860c "RNA helicase, putati	0.359	0.106	0.516	1.9e-13
UNIPROTKB|O96264	562	PFB0860c "DEAD/DEAH box helica	0.359	0.106	0.516	1.9e-13
TAIR|locus:2086775	826	AT3G16840 [Arabidopsis thalian	0.401	0.081	0.447	2.5e-13
UNIPROTKB|A6H7B6	852	DDX24 "DDX24 protein" [Bos tau	0.485	0.095	0.397	2.7e-13
UNIPROTKB|G3V529	816	DDX24 "ATP-dependent RNA helic	0.586	0.120	0.349	3.1e-13
UNIPROTKB|Q9GZR7	859	DDX24 "ATP-dependent RNA helic	0.586	0.114	0.349	3.6e-13

FB|FBgn0034496 CG9143 [Drosophila melanogaster (taxid:7227)]

 Score = 215 (80.7 bits), Expect = 9.6e-21, Sum P(2) = 9.6e-21
 Identities = 39/66 (59%), Positives = 55/66 (83%)

Query:     1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
             M+ W    +P +I+RAL ++GFKTPT+IQ++ +P+A+  +KDI+GAAETGSGKTLAFGIP
Sbjct:   214 MSAWNGLGVPASILRALGEQGFKTPTQIQALTLPAAIHGKKDILGAAETGSGKTLAFGIP 273

Query:    61 ILTGIV 66
             +L GI+
Sbjct:   274 MLAGIM 279

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0005524 "ATP binding" evidence=IEA

WB|WBGene00018890 F55F8.2 [Caenorhabditis elegans (taxid:6239)]

 Score = 188 (71.2 bits), Expect = 1.6e-16, Sum P(2) = 1.6e-16
 Identities = 36/83 (43%), Positives = 59/83 (71%)

Query:     1 MAEWVKFN-IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI 59
             ++ W +F  +P  ++ A+ Q GF  PT+IQS V+P+A+  R+D++GAAETGSGKTLAFGI
Sbjct:   153 ISAWKQFYFLPNEVLEAIEQMGFSEPTEIQSAVLPAAVRDRQDVLGAAETGSGKTLAFGI 212

Query:    60 PILTGIVNKLENPTEEDENDSAR 82
             P++  ++   ++ ++E E+   R
Sbjct:   213 PLVARLLESSDD-SQETESTEVR 234

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040002 "collagen and cuticulin-based cuticle development" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0007276 "gamete generation" evidence=IMP

MGI|MGI:1351337 Ddx24 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24" [Mus musculus (taxid:10090)]

 Score = 158 (60.7 bits), Expect = 1.1e-13, Sum P(2) = 1.1e-13
 Identities = 31/74 (41%), Positives = 50/74 (67%)

Query:     1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
             ++ W    +P+ ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct:   192 VSAWRDLFVPKAVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 251

Query:    61 ILTGIV--NKLENP 72
             ++  ++  +K++ P
Sbjct:   252 MIHSVLQWHKMKAP 265

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

RGD|727929 Ddx24 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 24" [Rattus norvegicus (taxid:10116)]

 Score = 158 (60.7 bits), Expect = 1.3e-13, Sum P(2) = 1.3e-13
 Identities = 31/74 (41%), Positives = 50/74 (67%)

Query:     1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
             ++ W    +P+ ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct:   191 VSAWRDLFVPKAVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 250

Query:    61 ILTGIV--NKLENP 72
             ++  ++  +K++ P
Sbjct:   251 MIHSVLQWHKMKAP 264

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

GENEDB_PFALCIPARUM|PFB0860c PFB0860c "RNA helicase, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 146 (56.5 bits), Expect = 1.9e-13, Sum P(2) = 1.9e-13
 Identities = 32/62 (51%), Positives = 44/62 (70%)

Query:     8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI-V 66
             NI E I+ ++ + G+K PT+IQ  ++P A L +KDI+G +ETGSGKT  F IPIL  + V
Sbjct:   162 NICEEILESIKELGWKKPTEIQREILPHAFL-KKDIIGLSETGSGKTACFIIPILQDLKV 220

Query:    67 NK 68
             NK
Sbjct:   221 NK 222

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

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|O96264 PFB0860c "DEAD/DEAH box helicase, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 146 (56.5 bits), Expect = 1.9e-13, Sum P(2) = 1.9e-13
 Identities = 32/62 (51%), Positives = 44/62 (70%)

Query:     8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI-V 66
             NI E I+ ++ + G+K PT+IQ  ++P A L +KDI+G +ETGSGKT  F IPIL  + V
Sbjct:   162 NICEEILESIKELGWKKPTEIQREILPHAFL-KKDIIGLSETGSGKTACFIIPILQDLKV 220

Query:    67 NK 68
             NK
Sbjct:   221 NK 222

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

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2086775 AT3G16840 [Arabidopsis thaliana (taxid:3702)]

 Score = 158 (60.7 bits), Expect = 2.5e-13, Sum P(2) = 2.5e-13
 Identities = 30/67 (44%), Positives = 44/67 (65%)

Query:     4 WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT 63
             W    +   +++++Y+  FK PTKIQ      A    KD++GAAETGSGKTLAFG+PIL 
Sbjct:   192 WSSMRLHPLLMKSIYRLDFKEPTKIQKACFNVAAYQGKDVIGAAETGSGKTLAFGLPILQ 251

Query:    64 GIVNKLE 70
              ++++ E
Sbjct:   252 RLLDERE 258

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|A6H7B6 DDX24 "DDX24 protein" [Bos taurus (taxid:9913)]

 Score = 158 (60.7 bits), Expect = 2.7e-13, Sum P(2) = 2.7e-13
 Identities = 33/83 (39%), Positives = 50/83 (60%)

Query:     1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
             ++ W    +P+ ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct:   190 VSAWKDLFVPKPVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 249

Query:    61 ILTGIVN--KLENPTEEDENDSA 81
             ++  ++     + PT    N  A
Sbjct:   250 MIDAVLRWQVKKKPTPAISNTGA 272

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|G3V529 DDX24 "ATP-dependent RNA helicase DDX24" [Homo sapiens (taxid:9606)]

 Score = 157 (60.3 bits), Expect = 3.1e-13, Sum P(2) = 3.1e-13
 Identities = 36/103 (34%), Positives = 54/103 (52%)

Query:     1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
             ++ W    +P  ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct:   148 VSAWKDLFVPRPVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 207

Query:    61 ILTGIV-----NKLENPTEEDENDSARKDIVGAAETGSGKTLA 98
             ++  ++     N    P+  +      +   GA     GK  A
Sbjct:   208 MIHAVLQWQKRNAAPPPSNTEAPPGETRTEAGAETRSPGKAEA 250

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q9GZR7 DDX24 "ATP-dependent RNA helicase DDX24" [Homo sapiens (taxid:9606)]

 Score = 157 (60.3 bits), Expect = 3.6e-13, Sum P(2) = 3.6e-13
 Identities = 36/103 (34%), Positives = 54/103 (52%)

Query:     1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
             ++ W    +P  ++RAL   GF  PT IQ++ +  A+  + DI+GAAETGSGKTLAF IP
Sbjct:   191 VSAWKDLFVPRPVLRALSFLGFSAPTPIQALTLAPAIRDKLDILGAAETGSGKTLAFAIP 250

Query:    61 ILTGIV-----NKLENPTEEDENDSARKDIVGAAETGSGKTLA 98
             ++  ++     N    P+  +      +   GA     GK  A
Sbjct:   251 MIHAVLQWQKRNAAPPPSNTEAPPGETRTEAGAETRSPGKAEA 293

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016070 "RNA metabolic process" evidence=NAS

GO:0003724 "RNA helicase activity" evidence=NAS

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

GO:0005730 "nucleolus" 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

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

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	167
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-18
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-16
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-12
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-10
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-09
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-09
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-08
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-08
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	3e-08
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-08
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	4e-08
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	9e-08
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-06
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	3e-06
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	5e-06
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-05
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-05
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-05
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	6e-05
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	1e-04
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-04
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-04
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-04

>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases

 Score = 78.7 bits (195), Expect = 1e-18
 Identities = 26/62 (41%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
            +   ++R +Y  GF+ PT IQ+  +P  LL+ +D++G A+TGSGKT AF IPIL  + 
Sbjct: 4  LGLSPELLRGIYALGFEKPTPIQARAIP-PLLSGRDVIGQAQTGSGKTAAFLIPILEKLD 62

Query: 67 NK 68
            
Sbjct: 63 PS 64

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. Length = 203

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

 Score = 76.0 bits (187), Expect = 1e-16
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 1  MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
            E+    +   +++AL   GF+ PT IQ   +P  +LA +D++G A+TG+GKT AF +P
Sbjct: 28 PPEFASLGLSPELLQALKDLGFEEPTPIQLAAIP-LILAGRDVLGQAQTGTGKTAAFLLP 86

Query: 61 ILTGIVNKLENPT 73
          +L  I+  +E   
Sbjct: 87 LLQKILKSVERKY 99

Length = 513

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

 Score = 62.5 bits (152), Expect = 5e-12
 Identities = 30/64 (46%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 5   VKFN---IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
           V F     P+ I+++L   GF  PT IQ    P AL  R D++G AETGSGKTLAF +P 
Sbjct: 130 VSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGR-DMIGIAETGSGKTLAFLLPA 188

Query: 62  LTGI 65
           +  I
Sbjct: 189 IVHI 192

Length = 545

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

 Score = 57.3 bits (139), Expect = 3e-10
 Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
            + E+++ AL  KG+  PT IQ+  +P AL  R D++G+A TG+GKT AF +P L
Sbjct: 6  LELDESLLEALQDKGYTRPTAIQAEAIPPALDGR-DVLGSAPTGTGKTAAFLLPAL 60

Length = 434

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 17/46 (36%), Positives = 26/46 (56%)

Query: 17 LYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          + + GF+     Q   + + L   +D++ AA TGSGKTLA  +P L
Sbjct: 1  IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPAL 46

Length = 201

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 21/37 (56%), Positives = 28/37 (75%), Gaps = 1/37 (2%)

Query: 26 TKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          T IQ+  +P A+L+ KD++  A TGSGKTLAF +PIL
Sbjct: 1  TPIQAQAIP-AILSGKDVLVQAPTGSGKTLAFLLPIL 36

Members of this family include the DEAD and DEAH box helicases. 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. Length = 169

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

 Score = 52.7 bits (127), Expect = 1e-08
 Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F +   ++ AL +KGF   T IQ++ +P   LA +D+ G A+TG+GKT+AF    LT   
Sbjct: 13 FALHPQVVEALEKKGFHNCTPIQALALP-LTLAGRDVAGQAQTGTGKTMAF----LTATF 67

Query: 67 NKL-ENPTEED 76
          + L  +P  ED
Sbjct: 68 HYLLSHPAPED 78

Length = 423

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

 Score = 52.9 bits (127), Expect = 1e-08
 Identities = 25/60 (41%), Positives = 40/60 (66%), Gaps = 1/60 (1%)

Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENP 72
          I+ AL   G++ P+ IQ+  +P  LL  +D++G A+TGSGKT AF +P+L  +  +L+ P
Sbjct: 17 ILEALNDLGYEKPSPIQAECIPH-LLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAP 75

Length = 629

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 26/85 (30%), Positives = 33/85 (38%), Gaps = 39/85 (45%)

Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
           KD++  A TGSGKTLAF +PIL                                      
Sbjct: 15  KDVLVQAPTGSGKTLAFLLPIL-------------------------------------- 36

Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
            + +   +    AL+LAPTRELA Q
Sbjct: 37  -QALLPKKGGPQALVLAPTRELAEQ 60

Members of this family include the DEAD and DEAH box helicases. 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. Length = 169

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

 Score = 51.0 bits (122), Expect = 4e-08
 Identities = 21/50 (42%), Positives = 37/50 (74%), Gaps = 1/50 (2%)

Query: 13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          I+RA+ ++G++ PT IQ   +P A+L  +D++ +A+TG+GKT  F +P+L
Sbjct: 12 ILRAVAEQGYREPTPIQQQAIP-AVLEGRDLMASAQTGTGKTAGFTLPLL 60

Length = 456

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

 Score = 50.9 bits (122), Expect = 4e-08
 Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 8   NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
            +P  ++  L   G++ PT IQ   +P+AL + + ++ +A+TGSGKT +F +PI+
Sbjct: 127 GLPPKLLLNLETAGYEFPTPIQMQAIPAAL-SGRSLLVSADTGSGKTASFLVPII 180

Length = 518

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

 Score = 50.2 bits (121), Expect = 9e-08
 Identities = 21/42 (50%), Positives = 30/42 (71%), Gaps = 1/42 (2%)

Query: 21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          G+   T IQ+  +P A+LA KD++  A+TGSGKT AFG+ +L
Sbjct: 23 GYTEMTPIQAQSLP-AILAGKDVIAQAKTGSGKTAAFGLGLL 63

Length = 460

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 24/85 (28%), Positives = 31/85 (36%), Gaps = 40/85 (47%)

Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
           +D++ AA TGSGKTLA  +PIL                                      
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILE------------------------------------- 23

Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
              +  +      L+LAPTRELA Q
Sbjct: 24  ---LLDSLKGGQVLVLAPTRELANQ 45

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

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

 Score = 45.7 bits (108), Expect = 3e-06
 Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 5/63 (7%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F++   ++  L   GF   T IQ++ +P AL    D+ G A+TG+GKTLAF    L  ++
Sbjct: 14 FDLHPALLAGLESAGFTRCTPIQALTLPVALPGG-DVAGQAQTGTGKTLAF----LVAVM 68

Query: 67 NKL 69
          N+L
Sbjct: 69 NRL 71

Length = 572

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

 Score = 45.2 bits (108), Expect = 5e-06
 Identities = 26/85 (30%), Positives = 35/85 (41%), Gaps = 39/85 (45%)

Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
           KD++  A+TGSGKT AFG+ +L     KL                             + 
Sbjct: 42  KDVIAQAKTGSGKTAAFGLGLL----QKL-----------------------------DV 68

Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
             F      ++ AL+L PTRELA Q
Sbjct: 69  KRF------RVQALVLCPTRELADQ 87

Length = 460

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score = 43.2 bits (102), Expect = 1e-05
 Identities = 24/88 (27%), Positives = 29/88 (32%), Gaps = 40/88 (45%)

Query: 80  SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEES 139
           S  +D++ AA TGSGKTLA  +P L                                   
Sbjct: 22  SGLRDVILAAPTGSGKTLAALLPALE---------------------------------- 47

Query: 140 ANTTEFVKKTRNKLYALILAPTRELAIQ 167
                   K       L+L PTRELA Q
Sbjct: 48  ------ALKRGKGGRVLVLVPTRELAEQ 69

Length = 201

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

 Score = 43.4 bits (102), Expect = 2e-05
 Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
           FN+   ++ A++  GF   T IQ+ V+    LA  D +G A+TG+GKT AF I I+  + 
Sbjct: 92  FNLAPELMHAIHDLGFPYCTPIQAQVL-GYTLAGHDAIGRAQTGTGKTAAFLISIINQL- 149

Query: 67  NKLENPTEED 76
             L+ P  ++
Sbjct: 150 --LQTPPPKE 157

Length = 475

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

 Score = 43.3 bits (102), Expect = 2e-05
 Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 10/76 (13%)

Query: 8   NIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
            + E ++R +Y  GF+ P+ IQ   + P  +L   D +G A++G+GKT  F I  L  I 
Sbjct: 34  KLNEDLLRGIYSYGFEKPSAIQQRGIKP--ILDGYDTIGQAQSGTGKTATFVIAALQLID 91

Query: 67  NKLEN-------PTEE 75
             L         PT E
Sbjct: 92  YDLNACQALILAPTRE 107

Length = 401

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

 Score = 42.1 bits (99), Expect = 6e-05
 Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 39/85 (45%)

Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
           +D++G A+TGSGKT AF +P+L  +  +L+ P                            
Sbjct: 44  RDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQ--------------------------- 76

Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
                        L+LAPTRELA+Q
Sbjct: 77  ------------ILVLAPTRELAVQ 89

Length = 629

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 14/23 (60%), Positives = 18/23 (78%)

Query: 41 KDIVGAAETGSGKTLAFGIPILT 63
          +D++ AA TGSGKTLA  +PIL 
Sbjct: 1  RDVLLAAPTGSGKTLAALLPILE 23

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 30/86 (34%), Positives = 38/86 (44%), Gaps = 34/86 (39%)

Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLEN-PTEEDENDSGLEEEAEEVLEELEEESAN 141
            D+ G A+TG+GKTLAF    L  ++N+L + P   D       E+              
Sbjct: 47  GDVAGQAQTGTGKTLAF----LVAVMNRLLSRPALADRK----PEDPR------------ 86

Query: 142 TTEFVKKTRNKLYALILAPTRELAIQ 167
                        ALILAPTRELAIQ
Sbjct: 87  -------------ALILAPTRELAIQ 99

Length = 572

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

 Score = 40.3 bits (95), Expect = 2e-04
 Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          FNI +  +R  +++ F + T  Q   +P  + + ++++  A TGSGKT A  +P++  ++
Sbjct: 5  FNILDPRVREWFKRKFTSLTPPQRYAIP-EIHSGENVLIIAPTGSGKTEAAFLPVINELL 63

Query: 67 NKLENPTE 74
          +  +   E
Sbjct: 64 SLGKGKLE 71

Length = 814

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

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 32/85 (37%)

Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT 142
            D +G A+TG+GKT AF I I+  +   L+ P  ++                        
Sbjct: 125 HDAIGRAQTGTGKTAAFLISIINQL---LQTPPPKE------------------------ 157

Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
                +   +  ALI+APTREL +Q
Sbjct: 158 -----RYMGEPRALIIAPTRELVVQ 177

Length = 475

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	167
KOG0340|consensus	442		99.88
KOG0330|consensus	476		99.87
KOG0338|consensus	691		99.87
KOG0346|consensus	569		99.85
KOG0331|consensus	519		99.85
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.85
KOG0347|consensus	731		99.84
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.84
KOG0345|consensus	567		99.84
KOG0348|consensus	708		99.84
KOG0343|consensus	758		99.83
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.83
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.83
PTZ00110	545	helicase; Provisional	99.83
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.83
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.81
KOG0328|consensus	400		99.81
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.8
KOG0342|consensus	543		99.8
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.79
KOG0326|consensus	459		99.77
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.77
KOG0333|consensus	673		99.76
KOG0334|consensus	997		99.74
PTZ00424	401	helicase 45; Provisional	99.74
KOG0341|consensus	610		99.73
KOG0335|consensus	482		99.72
KOG0337|consensus	529		99.72
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.71
KOG0336|consensus	629		99.69
KOG0344|consensus	593		99.64
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.64
KOG0329|consensus	387		99.63
PRK02362	737	ski2-like helicase; Provisional	99.63
KOG0327|consensus	397		99.63
KOG0339|consensus	731		99.62
KOG4284|consensus	980		99.61
PRK00254	720	ski2-like helicase; Provisional	99.59
KOG0332|consensus	477		99.59
KOG0350|consensus	620		99.53
PRK01172	674	ski2-like helicase; Provisional	99.5
PRK13767	876	ATP-dependent helicase; Provisional	99.49
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.38
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.32
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.28
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.24
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.22
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.2
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.17
PRK14701	1638	reverse gyrase; Provisional	99.16
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.16
PRK09401	1176	reverse gyrase; Reviewed	99.16
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.14
COG1205	851	Distinct helicase family with a unique C-terminal	99.14
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.11
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.1
PRK10689	1147	transcription-repair coupling factor; Provisional	99.07
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.07
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.99
KOG0349|consensus	725		98.94
PHA02558	501	uvsW UvsW helicase; Provisional	98.68
COG1204	766	Superfamily II helicase [General function predicti	98.68
PRK05580	679	primosome assembly protein PriA; Validated	98.63
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.6
PHA02653	675	RNA helicase NPH-II; Provisional	98.59
COG1202	830	Superfamily II helicase, archaea-specific [General	98.57
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.55
KOG0952|consensus	1230		98.52
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.4
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.36
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.35
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.31
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.19
KOG0346|consensus	569		98.06
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.06
KOG0347|consensus	731		97.98
KOG0333|consensus	673		97.96
KOG0331|consensus	519		97.95
KOG0338|consensus	691		97.94
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	97.92
KOG0330|consensus	476		97.91
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	97.91
PRK13766	773	Hef nuclease; Provisional	97.91
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.88
KOG0343|consensus	758		97.87
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	97.77
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	97.77
KOG0348|consensus	708		97.74
KOG0345|consensus	567		97.74
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.73
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	97.73
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	97.62
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	97.57
PTZ00110	545	helicase; Provisional	97.56
KOG0335|consensus	482		97.56
KOG0336|consensus	629		97.52
KOG0341|consensus	610		97.5
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	97.5
KOG0342|consensus	543		97.46
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	97.45
COG1201	814	Lhr Lhr-like helicases [General function predictio	97.41
KOG0353|consensus	695		97.4
KOG0340|consensus	442		97.35
KOG0352|consensus	641		97.32
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.3
KOG0951|consensus	1674		97.25
KOG0337|consensus	529		97.25
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	97.25
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	97.23
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	97.22
KOG0354|consensus	746		97.2
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	97.16
PRK12904	830	preprotein translocase subunit SecA; Reviewed	97.15
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	97.15
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	97.13
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	97.12
PRK13767	876	ATP-dependent helicase; Provisional	97.11
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	97.04
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	97.02
KOG0334|consensus	997		97.01
PRK13107	908	preprotein translocase subunit SecA; Reviewed	96.95
KOG0344|consensus	593		96.92
KOG0351|consensus	941		96.86
KOG0326|consensus	459		96.86
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	96.85
PTZ00424	401	helicase 45; Provisional	96.78
PRK09694	878	helicase Cas3; Provisional	96.74
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	96.66
KOG0328|consensus	400		96.58
KOG0350|consensus	620		96.57
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	96.55
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	96.32
KOG0339|consensus	731		96.27
KOG0349|consensus	725		96.26
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	96.22
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	96.15
KOG0327|consensus	397		96.11
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	95.35
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	95.33
PRK02362	737	ski2-like helicase; Provisional	95.26
COG1205	851	Distinct helicase family with a unique C-terminal	95.0
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	95.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	94.9
PRK00254	720	ski2-like helicase; Provisional	94.75
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	94.4
KOG0332|consensus	477		94.36
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	94.34
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.3
KOG4284|consensus	980		94.2
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.14
PF13245	76	AAA_19: Part of AAA domain	94.11
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	93.97
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	93.6
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	93.6
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	93.5
PRK13833	323	conjugal transfer protein TrbB; Provisional	93.48
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	93.32
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	93.32
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	93.11
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.11
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	92.95
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	92.92
KOG0947|consensus	1248		92.89
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	92.66
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	92.61
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	92.56
KOG1803|consensus	649		92.53
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	92.47
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	92.38
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	92.17
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	91.92
TIGR00376	637	DNA helicase, putative. The gene product may repre	91.57
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	91.51
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	91.42
PRK13889	988	conjugal transfer relaxase TraA; Provisional	91.39
PRK12326	764	preprotein translocase subunit SecA; Reviewed	91.37
KOG0951|consensus	1674		91.2
PRK01172	674	ski2-like helicase; Provisional	91.14
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	91.04
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	91.03
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	91.03
PRK15483	986	type III restriction-modification system StyLTI en	91.02
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	90.94
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	90.74
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	90.59
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	90.24
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	89.98
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	89.86
PRK13826	1102	Dtr system oriT relaxase; Provisional	89.77
CHL00122	870	secA preprotein translocase subunit SecA; Validate	89.72
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	89.63
KOG0952|consensus	1230		89.43
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	89.26
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	89.24
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	89.21
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	88.85
PRK10436	462	hypothetical protein; Provisional	88.66
KOG0949|consensus	1330		88.5
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	88.2
KOG0948|consensus	1041		88.1
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	88.06
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	87.99
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	87.33
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	86.96
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	86.59
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	86.54
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	86.46
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	86.4
COG4889	1518	Predicted helicase [General function prediction on	86.37
PRK09401	1176	reverse gyrase; Reviewed	86.29
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	86.29
PRK13851	344	type IV secretion system protein VirB11; Provision	86.14
KOG0352|consensus	641		86.01
KOG0329|consensus	387		86.0
KOG0925|consensus	699		85.94
PHA02653	675	RNA helicase NPH-II; Provisional	85.87
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	85.87
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	85.65
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	85.17
COG1204	766	Superfamily II helicase [General function predicti	84.87
PRK13764	602	ATPase; Provisional	84.82
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	84.71
KOG1802|consensus	935		84.59
KOG2340|consensus	698		84.26
PRK10536	262	hypothetical protein; Provisional	84.13
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	83.98
TIGR02533	486	type_II_gspE general secretory pathway protein E.	83.97
TIGR00595	505	priA primosomal protein N'. All proteins in this f	83.59
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	83.43
KOG0950|consensus	1008		83.42
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	83.41
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	83.03
PRK09200	790	preprotein translocase subunit SecA; Reviewed	82.89
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	82.33
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	82.25
PRK13880	636	conjugal transfer coupling protein TraG; Provision	82.24
KOG1133|consensus	821		82.16
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	82.0
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	81.69
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	81.63
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	81.62
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	81.52
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	81.15
PRK13850	670	type IV secretion system protein VirD4; Provisiona	81.06
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	81.05
KOG1132|consensus	945		81.01
PRK10875	615	recD exonuclease V subunit alpha; Provisional	80.58

>KOG0340|consensus

Probab=99.88  E-value=3.1e-23  Score=164.12  Aligned_cols=65  Identities=35%  Similarity=0.595  Sum_probs=61.8

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +..|+.|||++|+.+.|+.+|+..|||||..|||.++.| +|+|.+|.||||||.+|.+|+++++.
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeG-rdcig~AkTGsGKT~AFaLPil~rLs   70 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEG-RDCIGCAKTGSGKTAAFALPILNRLS   70 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcc-cccccccccCCCcchhhhHHHHHhhc
Confidence            357999999999999999999999999999999999999 99999999999999999999988876

>KOG0330|consensus

Probab=99.87  E-value=4.5e-23  Score=164.74  Aligned_cols=64  Identities=42%  Similarity=0.699  Sum_probs=61.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|.+|++++.+++++...||..||+||+++||.++.| +|||+.|.||||||.+|.+|++++++
T Consensus        61 ~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g-~dvIglAeTGSGKT~afaLPIl~~LL  124 (476)
T KOG0330|consen   61 KSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGG-RDVIGLAETGSGKTGAFALPILQRLL  124 (476)
T ss_pred             cchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCC-CcEEEEeccCCCchhhhHHHHHHHHH
Confidence            47999999999999999999999999999999999999 99999999999999999999999888

>KOG0338|consensus

Probab=99.87  E-value=4.6e-23  Score=169.40  Aligned_cols=65  Identities=42%  Similarity=0.689  Sum_probs=62.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .+|.+|+|+..|++++..+||..|||||..+||..+.| +|++.||.||||||-+|++|+|.+++.
T Consensus       181 ~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallg-kDIca~A~TGsGKTAAF~lPiLERLlY  245 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLG-KDICACAATGSGKTAAFALPILERLLY  245 (691)
T ss_pred             hhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhc-chhhheecccCCchhhhHHHHHHHHhc
Confidence            47999999999999999999999999999999999999 999999999999999999999999883

>KOG0346|consensus

Probab=99.85  E-value=3.1e-22  Score=162.09  Aligned_cols=64  Identities=39%  Similarity=0.660  Sum_probs=62.0

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +|++|+|++.|++++.+.||+.||-||..+||.++.| +|+++.|.||||||.+|++|+++.++.
T Consensus        20 tFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEg-KDvvarArTGSGKT~AYliPllqkll~   83 (569)
T KOG0346|consen   20 TFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEG-KDVVARARTGSGKTAAYLIPLLQKLLA   83 (569)
T ss_pred             cHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcC-cceeeeeccCCCchHHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999 899999999999999999999999884

>KOG0331|consensus

Probab=99.85  E-value=4.4e-22  Score=165.94  Aligned_cols=64  Identities=41%  Similarity=0.697  Sum_probs=61.2

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .|++++|++++..+|+..||..|||||.++||.++.| +|+++.|.||||||++|++|.+.++..
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~G-rD~v~iA~TGSGKTLay~lP~i~~l~~  155 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSG-RDLVGIARTGSGKTLAYLLPAIVHLNN  155 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccC-CceEEEeccCCcchhhhhhHHHHHHHh
Confidence            4889999999999999999999999999999999999 999999999999999999999988873

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.85  E-value=1.2e-21  Score=162.58  Aligned_cols=65  Identities=32%  Similarity=0.603  Sum_probs=61.9

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ++|++|+|+++++++|.+.||..|||+|+++||.++.| +|++++|+||||||++|++|++..+..
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g-~dvi~~ApTGsGKTla~llp~l~~l~~   72 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAG-RDVAGQAQTGTGKTMAFLTATFHYLLS   72 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CcEEEECCCCchHHHHHHHHHHHHHHh
Confidence            48999999999999999999999999999999999999 999999999999999999999988763

>KOG0347|consensus

Probab=99.84  E-value=5.7e-22  Score=164.17  Aligned_cols=66  Identities=53%  Similarity=0.927  Sum_probs=59.7

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |+.|.+|.||.+++++|..+||..||+||..+||++..|..||++.|.||||||+||.+|++..+.
T Consensus       180 vsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~  245 (731)
T KOG0347|consen  180 VSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLL  245 (731)
T ss_pred             hHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhh
Confidence            467999999999999999999999999999999999999889998888888888888888877555

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

Probab=99.84  E-value=1.6e-21  Score=165.27  Aligned_cols=63  Identities=38%  Similarity=0.702  Sum_probs=60.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|++|+|++.++++|.++||..|||||..+||.++.| +|++++|+||||||++|.+|+++.+.
T Consensus        30 ~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g-~Dvi~~A~TGsGKT~Af~lP~l~~l~   92 (513)
T COG0513          30 EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAG-RDVLGQAQTGTGKTAAFLLPLLQKIL   92 (513)
T ss_pred             CHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHHh
Confidence            6999999999999999999999999999999999999 99999999999999999999998855

>KOG0345|consensus

Probab=99.84  E-value=2.2e-21  Score=158.10  Aligned_cols=64  Identities=38%  Similarity=0.542  Sum_probs=60.2

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          3 EWVKFN--IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         3 ~f~~l~--l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +|++|+  |++++++++..+||..+||+|..+||.++.+ +||++.|+||||||+||++|++..+++
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~-KDVvveavTGSGKTlAFllP~le~i~r   70 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKN-KDVVVEAVTGSGKTLAFLLPMLEIIYR   70 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcC-CceEEEcCCCCCchhhHHHHHHHHHHh
Confidence            799987  5599999999999999999999999999988 999999999999999999999998875

>KOG0348|consensus

Probab=99.84  E-value=1.7e-21  Score=161.01  Aligned_cols=65  Identities=29%  Similarity=0.511  Sum_probs=61.5

Q ss_pred             CccccCCCCHHHHHHHH-HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALY-QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~-~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +.|.+|||++.+.+.|. .++|..||.||+++||.++.| +|+++.+.||||||++|++|+++.+..
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~g-rD~lV~aQTGSGKTLAYllPiVq~Lq~  201 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEG-RDALVRAQTGSGKTLAYLLPIVQSLQA  201 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcC-cceEEEcCCCCcccHHHHHHHHHHHHh
Confidence            46999999999999999 589999999999999999998 999999999999999999999998884

>KOG0343|consensus

Probab=99.83  E-value=1.2e-21  Score=162.49  Aligned_cols=65  Identities=35%  Similarity=0.608  Sum_probs=63.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ..|++|+|+..+++.|++.+|..||.||+.+||..+.| +||++.|.||||||+||++|+|+++++
T Consensus        69 ~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G-~DvlGAAkTGSGKTLAFlvPvlE~L~r  133 (758)
T KOG0343|consen   69 KKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQG-HDVLGAAKTGSGKTLAFLVPVLEALYR  133 (758)
T ss_pred             hhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccC-cccccccccCCCceeeehHHHHHHHHH
Confidence            57999999999999999999999999999999999999 999999999999999999999999996

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.83  E-value=4.1e-21  Score=160.90  Aligned_cols=64  Identities=31%  Similarity=0.689  Sum_probs=61.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |+|++|+|+++++++|.++||..|||+|.++||.++.| +|++++++||+|||++|++|++..+.
T Consensus         1 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g-~dvlv~apTGsGKTla~~lpil~~l~   64 (456)
T PRK10590          1 MSFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEG-RDLMASAQTGTGKTAGFTLPLLQHLI   64 (456)
T ss_pred             CCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCCcHHHHHHHHHHHHhh
Confidence            58999999999999999999999999999999999998 99999999999999999999988775

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.83  E-value=5.9e-21  Score=160.03  Aligned_cols=65  Identities=34%  Similarity=0.617  Sum_probs=61.3

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +++|++|+|++.++++|.++||..|||+|.++||.++.| +|++++|+||+|||++|.+|++..+.
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g-~dvi~~a~TGsGKT~a~~lpil~~l~   67 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAG-KDVIAQAKTGSGKTAAFGLGLLQKLD   67 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcC-CCEEEECCCCCcHHHHHHHHHHHHhh
Confidence            578999999999999999999999999999999999998 99999999999999999999987654

>PTZ00110 helicase; Provisional

Probab=99.83  E-value=6.8e-21  Score=162.63  Aligned_cols=65  Identities=42%  Similarity=0.650  Sum_probs=61.5

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++++|+++++++|.++||.+|||||.++||.++.| +|+|++++||||||++|++|++..+.
T Consensus       129 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G-~dvI~~ApTGSGKTlaylLP~l~~i~  193 (545)
T PTZ00110        129 VVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSG-RDMIGIAETGSGKTLAFLLPAIVHIN  193 (545)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcC-CCEEEEeCCCChHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999999 99999999999999999999987765

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

Probab=99.83  E-value=8.4e-21  Score=161.27  Aligned_cols=65  Identities=31%  Similarity=0.575  Sum_probs=61.9

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |.+|++++|++.++++|.+.||..|||+|.++||.++.| +|++++++||||||++|++|++..+.
T Consensus       120 i~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g-~dviv~ApTGSGKTlayllPil~~l~  184 (518)
T PLN00206        120 ILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSG-RSLLVSADTGSGKTASFLVPIISRCC  184 (518)
T ss_pred             hcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcC-CCEEEEecCCCCccHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999998 99999999999999999999988776

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.81  E-value=1.8e-20  Score=160.80  Aligned_cols=64  Identities=33%  Similarity=0.618  Sum_probs=61.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.+.||..|||||.++||.++.| +|++++++||||||++|++|+++.+.
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G-~Dvi~~ApTGSGKTlafllpil~~l~   72 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPG-GDVAGQAQTGTGKTLAFLVAVMNRLL   72 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            46999999999999999999999999999999999999 99999999999999999999998876

>KOG0328|consensus

Probab=99.81  E-value=2e-20  Score=144.73  Aligned_cols=65  Identities=29%  Similarity=0.667  Sum_probs=60.6

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++|||.+++++.+++.||++|+.||+.+||.++.| +|||++|.+|+|||.+|.+.+++.+.
T Consensus        26 ~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkG-rdViaQaqSGTGKTa~~si~vlq~~d   90 (400)
T KOG0328|consen   26 IPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKG-RDVIAQAQSGTGKTATFSISVLQSLD   90 (400)
T ss_pred             ccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcc-cceEEEecCCCCceEEEEeeeeeecc
Confidence            468999999999999999999999999999999999999 99999999999999999988876543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.80  E-value=3.4e-20  Score=160.36  Aligned_cols=64  Identities=34%  Similarity=0.675  Sum_probs=60.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.++||.+|||+|.++||.++.| +|++++|+||+|||++|.+|++..+.
T Consensus         6 ~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g-~dvl~~ApTGsGKT~af~lpll~~l~   69 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNG-RDVLGMAQTGSGKTAAFSLPLLHNLD   69 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCCcHHHHHHHHHHHHhh
Confidence            57999999999999999999999999999999999988 99999999999999999999987654

>KOG0342|consensus

Probab=99.80  E-value=3.8e-20  Score=151.48  Aligned_cols=64  Identities=33%  Similarity=0.531  Sum_probs=60.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .|.++.|++.++++|+++||..+|+||+.+||.++.| +|+++.|.||+|||+||++|.++.+++
T Consensus        83 ~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~g-kDvl~~AKTGtGKTlAFLiPaie~l~k  146 (543)
T KOG0342|consen   83 RFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEG-KDVLAAAKTGTGKTLAFLLPAIELLRK  146 (543)
T ss_pred             HhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCC-ccceeeeccCCCceeeehhHHHHHHHh
Confidence            5788999999999999999999999999999999999 899999999999999999999998884

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.79  E-value=1.3e-19  Score=150.84  Aligned_cols=64  Identities=38%  Similarity=0.704  Sum_probs=61.2

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.++||..||++|.++||.++.| +|++++++||+|||++|++|+++.+.
T Consensus         1 ~~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g-~d~l~~apTGsGKT~~~~lp~l~~l~   64 (434)
T PRK11192          1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDG-RDVLGSAPTGTGKTAAFLLPALQHLL   64 (434)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999998 99999999999999999999988776

>KOG0326|consensus

Probab=99.77  E-value=4.4e-20  Score=144.91  Aligned_cols=63  Identities=35%  Similarity=0.691  Sum_probs=59.8

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|+++.|..+|+..+.+.||++|+|||.++||.++.| +|+++.|.+|+|||-+|++|++..+.
T Consensus        86 efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtG-rdiLaRaKNGTGKT~a~~IP~Lekid  148 (459)
T KOG0326|consen   86 EFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTG-RDILARAKNGTGKTAAYCIPVLEKID  148 (459)
T ss_pred             cHHHhhhhHHHHHHHHHhccCCCCCccccccceeecc-hhhhhhccCCCCCccceechhhhhcC
Confidence            6999999999999999999999999999999999999 99999999999999999999987765

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.77  E-value=3.6e-19  Score=149.88  Aligned_cols=65  Identities=34%  Similarity=0.553  Sum_probs=61.5

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .+|.+++|++.++++|.+.||..||++|.++||.++.| +|++++++||||||++|++|++..+..
T Consensus        87 ~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G-~dvi~~apTGSGKTlay~lpil~~l~~  151 (475)
T PRK01297         87 TRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAG-HDAIGRAQTGTGKTAAFLISIINQLLQ  151 (475)
T ss_pred             CCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            46899999999999999999999999999999999999 999999999999999999999988763

>KOG0333|consensus

Probab=99.76  E-value=7.4e-19  Score=145.16  Aligned_cols=65  Identities=40%  Similarity=0.679  Sum_probs=62.2

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |++|++.+||.++++.+.+.||..|||||.++||..+.. +|+|+.+.||||||.+|++|++..+.
T Consensus       244 lrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~-rD~igvaETgsGktaaf~ipLl~~Is  308 (673)
T KOG0333|consen  244 LRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQN-RDPIGVAETGSGKTAAFLIPLLIWIS  308 (673)
T ss_pred             ccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhcc-CCeeeEEeccCCccccchhhHHHHHH
Confidence            579999999999999999999999999999999999998 99999999999999999999988776

>KOG0334|consensus

Probab=99.74  E-value=1.1e-18  Score=153.05  Aligned_cols=65  Identities=35%  Similarity=0.739  Sum_probs=60.9

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|...|++..++..++++||..|||||.+|||++++| +|||++|.||||||++|+||++..+.
T Consensus       364 v~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsG-rdvIgvakTgSGKT~af~LPmirhi~  428 (997)
T KOG0334|consen  364 VTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSG-RDVIGVAKTGSGKTLAFLLPMIRHIK  428 (997)
T ss_pred             cchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccC-cceEEeeccCCccchhhhcchhhhhh
Confidence            468999999999999999999999999999999999999 99999999999999999999984443

>PTZ00424 helicase 45; Provisional

Probab=99.74  E-value=1.7e-18  Score=142.43  Aligned_cols=63  Identities=32%  Similarity=0.547  Sum_probs=59.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      .+|++|+|++.+.++|.+.||..|||+|.++|+.++.| +|++++++||+|||++|++|++..+
T Consensus        28 ~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~-~d~ii~apTGsGKT~~~~l~~l~~~   90 (401)
T PTZ00424         28 DSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDG-YDTIGQAQSGTGKTATFVIAALQLI   90 (401)
T ss_pred             CCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999999 9999999999999999999987654

>KOG0341|consensus

Probab=99.73  E-value=1.1e-18  Score=140.18  Aligned_cols=65  Identities=35%  Similarity=0.635  Sum_probs=60.4

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |.+|.+|++|..+++.|++.|+.+|||||-+.+|.+++| +|.|..|-||||||+.|.+|++--.+
T Consensus       169 IksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsG-RDmIGIAfTGSGKTlvFvLP~imf~L  233 (610)
T KOG0341|consen  169 IKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSG-RDMIGIAFTGSGKTLVFVLPVIMFAL  233 (610)
T ss_pred             hhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeec-CceeeEEeecCCceEEEeHHHHHHHH
Confidence            468999999999999999999999999999999999999 99999999999999999999875444

>KOG0335|consensus

Probab=99.72  E-value=1.3e-18  Score=143.47  Aligned_cols=65  Identities=29%  Similarity=0.514  Sum_probs=60.5

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ..|++-.+.+.+..+++..||..|||||+.+||.+..| +|+++||+||||||.+|++|++..++.
T Consensus        74 ~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~G-rdl~acAqTGsGKT~aFLiPii~~~~~  138 (482)
T KOG0335|consen   74 PTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGG-RDLMACAQTGSGKTAAFLIPIISYLLD  138 (482)
T ss_pred             ccccccchhHHHhhccccccccCCCcceeeccceeecC-CceEEEccCCCcchHHHHHHHHHHHHh
Confidence            46787788999999999999999999999999998888 999999999999999999999998885

>KOG0337|consensus

Probab=99.72  E-value=2.6e-18  Score=138.79  Aligned_cols=63  Identities=41%  Similarity=0.680  Sum_probs=60.3

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +|.+|||+..++++|.+.||..|||||+++||.++.+ +|++..+.||||||.||++|+++++.
T Consensus        22 ~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~-~dvv~martgsgktaaf~ipm~e~Lk   84 (529)
T KOG0337|consen   22 GFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEG-RDVVGMARTGSGKTAAFLIPMIEKLK   84 (529)
T ss_pred             CccccCCCHHHHHHHHHhhcCCCCchhcccccceeec-cccceeeecCCcchhhHHHHHHHHHh
Confidence            6999999999999999999999999999999999999 99999999999999999999988876

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

Probab=99.71  E-value=1e-17  Score=147.34  Aligned_cols=62  Identities=26%  Similarity=0.394  Sum_probs=56.7

Q ss_pred             cccCC--CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          4 WVKFN--IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         4 f~~l~--l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |..++  |++++.++|.+.||..||++|.++||.++.| +|++++++||||||++|.+|+++.+.
T Consensus        14 ~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G-~nvvv~apTGSGKTla~~LPiL~~l~   77 (742)
T TIGR03817        14 TAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELAHAG-RHVVVATGTASGKSLAYQLPVLSALA   77 (742)
T ss_pred             cCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCC-CCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            44443  8999999999999999999999999999999 99999999999999999999988765

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.

>KOG0336|consensus

Probab=99.69  E-value=9.1e-18  Score=135.64  Aligned_cols=64  Identities=36%  Similarity=0.573  Sum_probs=57.5

Q ss_pred             Ccccc-CCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVK-FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~-l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++ |.--+++++++++.||.+|||||.++||.+|.| .|+++.|.||+|||++|++|-+..+.
T Consensus       219 ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG-~DliGVAQTgtgKtL~~L~pg~ihi~  283 (629)
T KOG0336|consen  219 CTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQG-IDLIGVAQTGTGKTLAFLLPGFIHID  283 (629)
T ss_pred             CcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecC-cceEEEEecCCCcCHHHhccceeeee
Confidence            45655 566789999999999999999999999999999 99999999999999999999876655

>KOG0344|consensus

Probab=99.64  E-value=1.3e-16  Score=133.24  Aligned_cols=64  Identities=36%  Similarity=0.657  Sum_probs=58.6

Q ss_pred             Ccccc----CCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVK----FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~----l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|.+    ...++.+++++...+|..|||+|.++||.++.+ +|+++|++||||||++|.+|++.++.
T Consensus       132 ~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~-r~~lAcapTGsgKtlaf~~Pil~~L~  199 (593)
T KOG0344|consen  132 LSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEK-RDVLACAPTGSGKTLAFNLPILQHLK  199 (593)
T ss_pred             ccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcc-cceEEeccCCCcchhhhhhHHHHHHH
Confidence            35655    568999999999999999999999999999999 99999999999999999999988876

>cd00268 DEADc DEAD-box helicases

Probab=99.64  E-value=3.4e-16  Score=117.49  Aligned_cols=62  Identities=40%  Similarity=0.748  Sum_probs=58.9

Q ss_pred             cccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          4 WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         4 f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |+++++++.+.+.|.+.|+..|++.|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~-~~~li~~~TG~GKT~~~~~~~l~~~~   62 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSG-RDVIGQAQTGSGKTAAFLIPILEKLD   62 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcC-CcEEEECCCCCcHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999997 99999999999999999999987766

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.

>KOG0329|consensus

Probab=99.63  E-value=1.7e-16  Score=121.63  Aligned_cols=64  Identities=30%  Similarity=0.562  Sum_probs=59.5

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.|.+|-|.|+|++++-++||.+|+.+|.+|||..+.| .|++++|.+|.|||..|.+..++++-
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailg-mdvlcqaksgmgktavfvl~tlqqie  105 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLATLQQIE  105 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhc-chhheecccCCCceeeeehhhhhhcC
Confidence            46899999999999999999999999999999999999 99999999999999999888877654

>PRK02362 ski2-like helicase; Provisional

Probab=99.63  E-value=2.2e-16  Score=139.26  Aligned_cols=64  Identities=25%  Similarity=0.344  Sum_probs=58.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHH-HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPS-ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~-~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |.|++|+|+++++++|.+.||..|+|+|.+||+. ++.| +|+++++|||||||++|.+|++..+.
T Consensus         1 ~~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g-~nvlv~APTGSGKTlia~lail~~l~   65 (737)
T PRK02362          1 MKIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDG-KNLLAAIPTASGKTLIAELAMLKAIA   65 (737)
T ss_pred             CChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCC-CcEEEECCCcchHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999998 4556 99999999999999999999887653

>KOG0327|consensus

Probab=99.63  E-value=4.9e-17  Score=129.95  Aligned_cols=63  Identities=33%  Similarity=0.641  Sum_probs=59.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      -+|++|+|++.|++.++..||++|+.||+.||++...| .|++.++.+|+|||.+|++++++.+
T Consensus        26 dsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G-~dv~~qaqsgTgKt~af~i~iLq~i   88 (397)
T KOG0327|consen   26 DSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKG-HDVIAQAQSGTGKTAAFLISILQQI   88 (397)
T ss_pred             hhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccC-CceeEeeeccccchhhhHHHHHhhc
Confidence            47999999999999999999999999999999999999 9999999999999999988888765

>KOG0339|consensus

Probab=99.62  E-value=1.2e-16  Score=131.90  Aligned_cols=65  Identities=34%  Similarity=0.652  Sum_probs=60.3

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +++|+.+++++.|+.++++..|+.|||||.+++|..++| +||+..|.||||||-+|+.|++..+.
T Consensus       222 vtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsg-rdvigIAktgSgktaAfi~pm~~him  286 (731)
T KOG0339|consen  222 VTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSG-RDVIGIAKTGSGKTAAFIWPMIVHIM  286 (731)
T ss_pred             cchhhhcCchHHHHHHHhhhhcccCCccccccccccccc-ccchheeeccCcchhHHHHHHHHHhc
Confidence            578999999999999999999999999999999999999 99999999999999988888877665

>KOG4284|consensus

Probab=99.61  E-value=3.1e-16  Score=132.52  Aligned_cols=64  Identities=25%  Similarity=0.481  Sum_probs=58.2

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ..|+.|.|..+++..|+..+|..||+||..+||+++.+ .|+|+++..|+|||+.|.+-.++.+.
T Consensus        25 ~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~k-mDliVQaKSGTGKTlVfsv~av~sl~   88 (980)
T KOG4284|consen   25 PGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSK-MDLIVQAKSGTGKTLVFSVLAVESLD   88 (980)
T ss_pred             CCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcc-cceEEEecCCCCceEEEEeeeehhcC
Confidence            46889999999999999999999999999999999999 99999999999999988877765544

>PRK00254 ski2-like helicase; Provisional

Probab=99.59  E-value=9.6e-16  Score=134.90  Aligned_cols=64  Identities=28%  Similarity=0.335  Sum_probs=58.7

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHH-HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPS-ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~-~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |+|++|++++.+.+.|++.||..|+|+|.++|+. ++.| +|++++++||||||++|.+|++..+.
T Consensus         1 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g-~nvlv~apTGsGKT~~~~l~il~~l~   65 (720)
T PRK00254          1 MKVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEG-KNLVLAIPTASGKTLVAEIVMVNKLL   65 (720)
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCC-CcEEEECCCCcHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999987 5666 99999999999999999999887655

>KOG0332|consensus

Probab=99.59  E-value=3.6e-16  Score=125.00  Aligned_cols=65  Identities=25%  Similarity=0.567  Sum_probs=57.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHcc-CCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|.|++++.|+.++|++|+.||..++|.++.. .+++|.++.+|+|||.||.+.+|.++-
T Consensus        90 ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd  155 (477)
T KOG0332|consen   90 KSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVD  155 (477)
T ss_pred             ccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcC
Confidence            58999999999999999999999999999999998864 467888888888888888888877654

>KOG0350|consensus

Probab=99.53  E-value=8.3e-15  Score=120.80  Aligned_cols=83  Identities=37%  Similarity=0.493  Sum_probs=58.3

Q ss_pred             HHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhcccCCCCccccccccccceeeeeccc
Q psy11948         13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETG   92 (167)
Q Consensus        13 l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~~~a~tg   92 (167)
                      +..+|.+++++...|+|...+|-++...+.                                  +....++|+.+.|+||
T Consensus       148 ~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~----------------------------------p~~~r~rDIcV~ApTG  193 (620)
T KOG0350|consen  148 IDQLLVKMAISRLFPVQYAVLPSLLEEIRS----------------------------------PPPSRPRDICVNAPTG  193 (620)
T ss_pred             HHHHHHHhhcccccchHHHHHHHHHHhhcC----------------------------------CCCCCCCceEEecCCC
Confidence            344589999999999999999988643110                                  0012356666666666


Q ss_pred             CccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948         93 SGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus        93 sgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                      ||||++|.+|+.+.+..                                      +....+|+|||+|||||+.|
T Consensus       194 SGKTLaY~iPIVQ~L~~--------------------------------------R~v~~LRavVivPtr~L~~Q  230 (620)
T KOG0350|consen  194 SGKTLAYVIPIVQLLSS--------------------------------------RPVKRLRAVVIVPTRELALQ  230 (620)
T ss_pred             CCceeeehhHHHHHHcc--------------------------------------CCccceEEEEEeeHHHHHHH
Confidence            66666666666666542                                      23556999999999999988

>PRK01172 ski2-like helicase; Provisional

Probab=99.50  E-value=1.7e-14  Score=126.22  Aligned_cols=63  Identities=14%  Similarity=0.190  Sum_probs=57.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.+++.+.+.+|. ++++|.++++.+..| ++++++++||||||+++.++++..+.
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~-~nvlv~apTGSGKTl~a~lail~~l~   63 (674)
T PRK01172          1 MKISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKG-ENVIVSVPTAAGKTLIAYSAIYETFL   63 (674)
T ss_pred             CcHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcC-CcEEEECCCCchHHHHHHHHHHHHHH
Confidence            5799999999999999999996 999999999998887 99999999999999999888876543

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.49  E-value=3.2e-14  Score=127.46  Aligned_cols=56  Identities=27%  Similarity=0.292  Sum_probs=50.6

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |++.+.+.+.+ +|..|||+|.++||.++.| +|++++|+||||||++|++|++..+.
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g-~nvli~APTGSGKTlaa~Lpil~~l~   73 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEG-KNVLISSPTGSGKTLAAFLAIIDELF   73 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcC-CCEEEECCCCCcHHHHHHHHHHHHHH
Confidence            67777777665 7999999999999999988 89999999999999999999998776

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

Probab=99.38  E-value=4.9e-13  Score=117.43  Aligned_cols=57  Identities=25%  Similarity=0.350  Sum_probs=53.8

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      |++.+.++++.. |+.|||+|..+||.+..| +++++.||||||||++.++|++..+++
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G-~nvLiiAPTGsGKTeAAfLpil~~l~~   64 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSG-ENVLIIAPTGSGKTEAAFLPVINELLS   64 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCC-CceEEEcCCCCChHHHHHHHHHHHHHh
Confidence            699999999988 999999999999999988 999999999999999999999988874

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.32  E-value=9.2e-13  Score=111.02  Aligned_cols=43  Identities=30%  Similarity=0.483  Sum_probs=40.4

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      ..||..|+|+|.++|+.++.| +|++++++||+|||++|.+|.+
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g-~dvlv~apTGsGKTl~y~lp~l   48 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLG-RDCFVVMPTGGGKSLCYQLPAL   48 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCCcHhHHHHHHHH
Confidence            469999999999999999999 8999999999999999999875

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

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.28  E-value=3.2e-12  Score=113.12  Aligned_cols=61  Identities=18%  Similarity=0.377  Sum_probs=54.2

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---chHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          5 VKFNIPETIIRALY-----QKGFKTP---TKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         5 ~~l~l~~~l~~~l~-----~~g~~~p---t~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.|++.+++.+.+.     .+||..|   ||+|.++||.++.+ +|+++.++||+|||++|.+|++..++
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~-~gvIAeaqTGeGKTLAf~LP~l~~aL  133 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMH-KGFITEMQTGEGKTLTAVMPLYLNAL  133 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcC-CCeEEEeCCCCChHHHHHHHHHHHHh
Confidence            35778888888877     6899999   99999999999999 99999999999999999999986654

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.24  E-value=8.5e-12  Score=108.19  Aligned_cols=55  Identities=25%  Similarity=0.412  Sum_probs=47.8

Q ss_pred             CCCCHHHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          7 FNIPETIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         7 l~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      +.++....+.|++ .||..++|+|.++|+.++.| +|++++++||+|||++|.+|.+
T Consensus         7 ~~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g-~dvlv~apTGsGKTl~y~lpal   62 (607)
T PRK11057          7 LNLESLAKQVLQETFGYQQFRPGQQEIIDAVLSG-RDCLVVMPTGGGKSLCYQIPAL   62 (607)
T ss_pred             CCchhHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCchHHHHHHHHHH
Confidence            4455566666765 69999999999999999999 9999999999999999999886

>TIGR01054 rgy reverse gyrase

Probab=99.22  E-value=1.1e-11  Score=113.75  Aligned_cols=49  Identities=27%  Similarity=0.247  Sum_probs=39.2

Q ss_pred             HHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        13 l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      ..+.+.+.....||++|+.++|.++.| +|++++|+||+|||. |.+|+..
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~il~G-~d~vi~ApTGsGKT~-f~l~~~~  115 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRVLRG-DSFAIIAPTGVGKTT-FGLAMSL  115 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHHhCC-CeEEEECCCCCCHHH-HHHHHHH
Confidence            344455544558999999999999999 999999999999996 6666543

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.

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

Probab=99.20  E-value=1.6e-11  Score=110.67  Aligned_cols=59  Identities=20%  Similarity=0.344  Sum_probs=51.0

Q ss_pred             cccc--CCCCHHHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          3 EWVK--FNIPETIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         3 ~f~~--l~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .|..  ++....+...++. .||..++|+|.++|+.++.| +|++++++||+|||+||.+|.+
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~G-rDVLVimPTGSGKSLcYQLPAL  497 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSG-YDVFVLMPTGGGKSLTYQLPAL  497 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCccHHHHHHHHHH
Confidence            4765  4455667777775 69999999999999999999 9999999999999999999986

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.17  E-value=1.4e-11  Score=89.31  Aligned_cols=40  Identities=35%  Similarity=0.526  Sum_probs=36.2

Q ss_pred             chHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         26 TKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        26 t~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ||+|.++++.+..| +++++.++||+|||+++.++++..+.
T Consensus         1 t~~Q~~~~~~i~~~-~~~li~aptGsGKT~~~~~~~l~~~~   40 (169)
T PF00270_consen    1 TPLQQEAIEAIISG-KNVLISAPTGSGKTLAYILPALNRLQ   40 (169)
T ss_dssp             -HHHHHHHHHHHTT-SEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcC-CCEEEECCCCCccHHHHHHHHHhhhc
Confidence            79999999999977 99999999999999999999987766

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 ....

>PRK14701 reverse gyrase; Provisional

Probab=99.16  E-value=2.9e-11  Score=113.38  Aligned_cols=47  Identities=23%  Similarity=0.126  Sum_probs=39.2

Q ss_pred             HHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccc
Q psy11948         12 TIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP   60 (167)
Q Consensus        12 ~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp   60 (167)
                      ++.+.+++ .|| .||++|+.+||.++.| +|++++++||+|||+++.++
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G-~d~li~APTGsGKTl~~~~~  114 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRG-KSFSIVAPTGMGKSTFGAFI  114 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcC-CCEEEEEcCCCCHHHHHHHH
Confidence            44455665 799 6999999999999999 99999999999999954433

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.16  E-value=3.6e-11  Score=108.07  Aligned_cols=57  Identities=14%  Similarity=0.004  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHHH-CCCCCCchHHHhHHHHHHcc-----CCcEEEEeecCCCcccccccchhhhh
Q psy11948          8 NIPETIIRALYQ-KGFKTPTKIQSMVMPSALLA-----RKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         8 ~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~-----~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      ..+..+.+.+.+ .+| .||++|..||+.++.+     .+|++++++||+|||.+|+++++..+
T Consensus       435 ~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al  497 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAV  497 (926)
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHH
Confidence            345566666654 688 5999999999999875     36788888888888888777776543

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.16  E-value=3.5e-11  Score=110.39  Aligned_cols=40  Identities=33%  Similarity=0.415  Sum_probs=34.7

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .|+ .||++|..++|.++.| +|++++|+||+|||. |.++++
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g-~dv~i~ApTGsGKT~-f~l~~~  116 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLG-ESFAIIAPTGVGKTT-FGLVMS  116 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCC-CcEEEEcCCCCCHHH-HHHHHH
Confidence            477 8999999999999999 999999999999995 555543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.14  E-value=4.8e-11  Score=103.92  Aligned_cols=52  Identities=25%  Similarity=0.300  Sum_probs=40.3

Q ss_pred             HHHHHHHHCCCCCCchHHHhHHHHHHccC-----CcEEEEeecCCCcccccccchhhh
Q psy11948         12 TIIRALYQKGFKTPTKIQSMVMPSALLAR-----KDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        12 ~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~-----~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      .+.+.+...+| .||++|+.+|+.++.+.     .+.+++++||||||++|++|++..
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~  280 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAA  280 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHH
Confidence            34556678899 79999999999998761     256888888888888877777654

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

Probab=99.14  E-value=5.5e-11  Score=106.16  Aligned_cols=57  Identities=28%  Similarity=0.363  Sum_probs=52.0

Q ss_pred             CHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         10 PETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        10 ~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ...+..+|.+.|+..++.+|.+|+..+..| +|++++++||||||.+|++|++..+++
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G-~~vvVtTgTgSGKTe~FllPIld~~l~  112 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREG-RNVVVTTGTGSGKTESFLLPILDHLLR  112 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCC-CCEEEECCCCCchhHHHHHHHHHHHhh
Confidence            445688899999999999999999999999 999999999999999999999988873

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

Probab=99.11  E-value=4.6e-11  Score=105.64  Aligned_cols=41  Identities=20%  Similarity=0.200  Sum_probs=34.7

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccch
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      .||. |||+|.++||.++.|..+++++++||||||.+|.++.
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafl   52 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWL   52 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhh
Confidence            5897 9999999999999994478889999999998665443

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.10  E-value=6.6e-11  Score=102.36  Aligned_cols=47  Identities=26%  Similarity=0.450  Sum_probs=42.6

Q ss_pred             HHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         15 RALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        15 ~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      +.|++ .||..++|+|.++|+.++.| +|+++++|||+|||++|.+|.+
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g-~dvlv~~PTG~GKTl~y~lpal   50 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDG-RDVLVVMPTGGGKSLCYQVPAL   50 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCccHhHHHHHHHH
Confidence            34554 79999999999999999999 8999999999999999998875

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.07  E-value=1.3e-10  Score=106.54  Aligned_cols=51  Identities=20%  Similarity=0.062  Sum_probs=39.8

Q ss_pred             HHHHHHHHHCCCCCCchHHHhHHHHHHcc-----CCcEEEEeecCCCcccccccchh
Q psy11948         11 ETIIRALYQKGFKTPTKIQSMVMPSALLA-----RKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        11 ~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-----~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .+..+.....+| .||++|.++||.++.+     .+|++++++||+|||.+++.+..
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~  643 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAF  643 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHH
Confidence            344555667889 7999999999999886     36888888888888877665553

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.07  E-value=1.6e-10  Score=101.48  Aligned_cols=54  Identities=22%  Similarity=0.286  Sum_probs=40.8

Q ss_pred             HHHHHHH-HHCCCCCCchHHHhHHHHHHccC-----CcEEEEeecCCCcccccccchhhhh
Q psy11948         11 ETIIRAL-YQKGFKTPTKIQSMVMPSALLAR-----KDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        11 ~~l~~~l-~~~g~~~pt~iQ~~~ip~~l~~~-----~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      ..+.+.+ ...+| .||++|..+|+.+..+.     ++++++++||||||++|++|++..+
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~  307 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAI  307 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHH
Confidence            4455544 46788 69999999999998772     3678888888888888887776543

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.99  E-value=2.5e-10  Score=98.86  Aligned_cols=42  Identities=29%  Similarity=0.290  Sum_probs=36.5

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      .|. .||++|..++|.++.| +  |+.+.||+|||++|.+|++...
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G-~--Iae~~TGeGKTla~~lp~~~~a  141 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSG-R--LAEMQTGEGKTLTATLPAGTAA  141 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCC-C--eeeeeCCCCcHHHHHHHHHHHh
Confidence            355 8999999999999999 5  8999999999999999987543

>KOG0349|consensus

Probab=98.94  E-value=3e-10  Score=93.19  Aligned_cols=66  Identities=35%  Similarity=0.459  Sum_probs=63.1

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      |+.|++||+-|+|--+-.++.|.-||.+|.++||.++.| -|++..|.||||||-+|.+|+++.++.
T Consensus         1 m~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgg-gdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen    1 MTAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGG-GDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             CcchHhhCcchHhhhhhhhhccccccccccccccEEecC-CcEEEEeccCCCCccceehhhHHHHHH
Confidence            688999999999999999999999999999999999888 899999999999999999999998876

>PHA02558 uvsW UvsW helicase; Provisional

Probab=98.68  E-value=1.3e-08  Score=86.66  Aligned_cols=35  Identities=20%  Similarity=0.057  Sum_probs=30.9

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ...|++.|..+++.++.+ .+.+++++||+|||+.+
T Consensus       112 ~~~~r~~Q~~av~~~l~~-~~~il~apTGsGKT~i~  146 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKN-NRRLLNLPTSAGKSLIQ  146 (501)
T ss_pred             cCCCCHHHHHHHHHHHhc-CceEEEeCCCCCHHHHH
Confidence            358999999999999988 78999999999999854

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.68  E-value=1.1e-08  Score=90.49  Aligned_cols=59  Identities=25%  Similarity=0.388  Sum_probs=48.7

Q ss_pred             CCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         8 ~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+++.+.+.++..|+.+..+.|+.++...+.++.|+++|+|||||||+...+.++..+.
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~   73 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLL   73 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHH
Confidence            37889999999999988888888888665444599999999999999988877776655

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.63  E-value=4.7e-08  Score=85.96  Aligned_cols=39  Identities=26%  Similarity=0.145  Sum_probs=32.6

Q ss_pred             CCchHHHhHHHHHHcc--CCcEEEEeecCCCcccccccchh
Q psy11948         24 TPTKIQSMVMPSALLA--RKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~--~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .+|+.|+.++..+..+  ++++++.++||||||.+|+.++.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~  184 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIA  184 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHH
Confidence            5899999999998873  57899999999999998876554

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.60  E-value=2.7e-08  Score=88.02  Aligned_cols=43  Identities=23%  Similarity=0.364  Sum_probs=35.7

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|. .|+++|..+++.++.| +  |+.+.||+|||+++.+|++...+
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G-~--Iaem~TGeGKTL~a~lp~~l~al  117 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEG-N--IAEMQTGEGKTLTATMPLYLNAL  117 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCC-c--eeeecCCCcchHHHHHHHHHHHH
Confidence            366 9999999999988877 4  89999999999999988864433

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.59  E-value=4.3e-08  Score=85.80  Aligned_cols=29  Identities=28%  Similarity=0.319  Sum_probs=27.0

Q ss_pred             hHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         27 KIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        27 ~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .+|.+.++.++.| +|++++|+||+|||.+
T Consensus       167 ~iQ~qil~~i~~g-kdvIv~A~TGSGKTtq  195 (675)
T PHA02653        167 DVQLKIFEAWISR-KPVVLTGGTGVGKTSQ  195 (675)
T ss_pred             HHHHHHHHHHHhC-CCEEEECCCCCCchhH
Confidence            3899999999999 9999999999999986

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

Probab=98.57  E-value=9.7e-08  Score=80.99  Aligned_cols=63  Identities=24%  Similarity=0.373  Sum_probs=54.8

Q ss_pred             cccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          4 WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         4 f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .++|.+|+++.+.|+..|++++.|+|..|+.+-+-.+.|.++.+.|+||||+.--+.-+.+++
T Consensus       196 vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l  258 (830)
T COG1202         196 VDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLL  258 (830)
T ss_pred             ccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHH
Confidence            467899999999999999999999999999875444499999999999999977777776666

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

Probab=98.55  E-value=8e-08  Score=86.50  Aligned_cols=54  Identities=22%  Similarity=0.277  Sum_probs=40.7

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHH---HccCCcEEEEeecCCCcccccccchhh
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSA---LLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~---l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      +++...+.+...||+ +.|.|.+.+..+   +.+++++++.|+||+|||++|++|.+.
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~  287 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALY  287 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHH
Confidence            344677788888996 789999866532   333488889999999999988888754

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=98.52  E-value=5.6e-08  Score=86.72  Aligned_cols=48  Identities=35%  Similarity=0.425  Sum_probs=43.1

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .+|.+...+|..++|.+.+...+.++|||||+|||..++|.+++.+..
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~  153 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKE  153 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHh
Confidence            478899999999999999887899999999999999999999887763

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.40  E-value=1.4e-07  Score=82.72  Aligned_cols=40  Identities=28%  Similarity=0.363  Sum_probs=33.4

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      .|. .|+++|..+.+.+..| +  |+.++||+|||+++.+|++.
T Consensus        53 lg~-~p~~vQlig~~~l~~G-~--Iaem~TGeGKTLva~lpa~l   92 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKG-K--IAEMKTGEGKTLTATLPAYL   92 (745)
T ss_pred             hCC-CccchHHhhhhhhcCC-c--eeeecCCCccHHHHHHHHHH
Confidence            365 8999999999887766 3  88999999999999888853

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.

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

Probab=98.36  E-value=3.3e-07  Score=82.19  Aligned_cols=43  Identities=23%  Similarity=0.316  Sum_probs=30.7

Q ss_pred             CCCCCCchHHHh---HHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         20 KGFKTPTKIQSM---VMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        20 ~g~~~pt~iQ~~---~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      .|| ++.+-|.+   ++-..+.++..+++.|+||+|||++|++|.+.
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~  287 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLA  287 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHH
Confidence            355 67888887   44334445578888888888888888888653

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.35  E-value=2.5e-07  Score=81.53  Aligned_cols=41  Identities=24%  Similarity=0.343  Sum_probs=31.5

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      .|. .|+++|......+..|   .++.++||+|||++|.+|.+..
T Consensus        67 lgl-rpydVQlig~l~l~~G---~Iaem~TGeGKTLta~Lpa~l~  107 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVLHQG---NIAEMKTGEGKTLTATMPLYLN  107 (762)
T ss_pred             cCC-CccHHHHHHHHHhcCC---ceeEecCCcchHHHHHHHHHHH
Confidence            365 7888888877655544   5899999999999999997543

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.31  E-value=6.2e-07  Score=65.46  Aligned_cols=48  Identities=35%  Similarity=0.447  Sum_probs=39.9

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ..++..|++.|.+++..+......+++.+++|+|||.++...++..+.
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~   50 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK   50 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhc
Confidence            457889999999999988865478999999999999988877766554

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

Probab=98.19  E-value=9.6e-07  Score=76.83  Aligned_cols=25  Identities=40%  Similarity=0.347  Sum_probs=17.6

Q ss_pred             CcEEEEeecCCCcccccccchhhhh
Q psy11948         41 KDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      ..+++.|+||+|||++|++|.+..+
T Consensus        17 ~~lliEA~TGtGKTlAYLlpal~~~   41 (636)
T TIGR03117        17 RIGMLEASTGVGKTLAMIMAALTML   41 (636)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHH
Confidence            6777777777777777777776543

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.

>KOG0346|consensus

Probab=98.06  E-value=1.2e-06  Score=72.28  Aligned_cols=74  Identities=38%  Similarity=0.511  Sum_probs=61.7

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      +++.+.. +|+.||.+|+.+    ..++|+++.|.||||||++|++|+++.++......                     
T Consensus        30 llkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~---------------------   88 (569)
T KOG0346|consen   30 LLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTN---------------------   88 (569)
T ss_pred             HHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcc---------------------
Confidence            4444444 999999999765    78999999999999999999999999998654442                     


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....|.|+||+||||||.|
T Consensus        89 ------------~~e~~~sa~iLvPTkEL~qQ  108 (569)
T KOG0346|consen   89 ------------DGEQGPSAVILVPTKELAQQ  108 (569)
T ss_pred             ------------cccccceeEEEechHHHHHH
Confidence                        23467999999999999987

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.06  E-value=2.7e-06  Score=76.25  Aligned_cols=24  Identities=25%  Similarity=0.391  Sum_probs=18.9

Q ss_pred             CCcEEEEeecCCCcccccccchhh
Q psy11948         40 RKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        40 ~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      +.+++++|+||||||++|.++++.
T Consensus        20 ~~~vvv~A~TGSGKTt~~pl~lL~   43 (812)
T PRK11664         20 APQVLLKAPTGAGKSTWLPLQLLQ   43 (812)
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHH
Confidence            378888888888888888777764

>KOG0347|consensus

Probab=97.98  E-value=2.9e-06  Score=71.78  Aligned_cols=90  Identities=42%  Similarity=0.585  Sum_probs=61.9

Q ss_pred             Ccccccccchhhhhhc-ccCCCCcccccc-----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcch
Q psy11948         52 GKTLAFGIPILTGIVN-KLENPTEEDEND-----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLE  125 (167)
Q Consensus        52 GKt~~~~lp~l~~~~~-~~~~~~~~~~~~-----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~  125 (167)
                      .|-+....++|..+.. +|..||++|...     ....|++++|.||||||++|++|+++.+.....             
T Consensus       183 W~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~-------------  249 (731)
T KOG0347|consen  183 WKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSD-------------  249 (731)
T ss_pred             HhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccc-------------
Confidence            3444223367777777 999999999655     334899999999999999999999986642211             


Q ss_pred             hHHHHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        126 EEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       126 ~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                       +..+..+           .. .....+.+||++||||||+|
T Consensus       250 -~s~e~~~-----------~~-~k~~k~~~LV~tPTRELa~Q  278 (731)
T KOG0347|consen  250 -DSQELSN-----------TS-AKYVKPIALVVTPTRELAHQ  278 (731)
T ss_pred             -hHhhhhh-----------HH-hccCcceeEEecChHHHHHH
Confidence             1111111           01 11222359999999999998

>KOG0333|consensus

Probab=97.96  E-value=4.7e-06  Score=70.17  Aligned_cols=110  Identities=35%  Similarity=0.362  Sum_probs=78.3

Q ss_pred             hHHHhHHHHHHccCCc-----EEEEeecCCCccccc-------------------------ccchhhhhhc-ccCCCCcc
Q psy11948         27 KIQSMVMPSALLARKD-----IVGAAETGSGKTLAF-------------------------GIPILTGIVN-KLENPTEE   75 (167)
Q Consensus        27 ~iQ~~~ip~~l~~~~d-----~i~~a~tgsGKt~~~-------------------------~lp~l~~~~~-~~~~~~~~   75 (167)
                      -.|+.+.+....+ .|     ...-+.++.+++-.|                         ..-+|..+.+ ++..|+++
T Consensus       193 ~~qk~~k~~~k~~-~DdrhW~~k~l~Em~~rdwri~redynis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpI  271 (673)
T KOG0333|consen  193 LLQKVCKKEAKSG-WDDRHWSEKVLAEMTERDWRIFREDYNISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPI  271 (673)
T ss_pred             HHHHhhhhhhhcc-ccccchhhhhHHhcCCccceeeecceeeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchH
Confidence            5788888888877 44     334444555554443                         2335555555 88889999


Q ss_pred             cccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhcccc
Q psy11948         76 DEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRN  151 (167)
Q Consensus        76 ~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~  151 (167)
                      |..+    ...+|+++.|+||||||++|++|++..+.+--..                              ........
T Consensus       272 qR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~------------------------------~~~en~~~  321 (673)
T KOG0333|consen  272 QRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPM------------------------------ARLENNIE  321 (673)
T ss_pred             HHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCc------------------------------chhhhccc
Confidence            8665    6779999999999999999999998777532100                              00123457


Q ss_pred             ccceEEEccchhhhcC
Q psy11948        152 KLYALILAPTRELAIQ  167 (167)
Q Consensus       152 ~~~aLIl~PTRELa~Q  167 (167)
                      +|+++||.||||||.|
T Consensus       322 gpyaiilaptReLaqq  337 (673)
T KOG0333|consen  322 GPYAIILAPTRELAQQ  337 (673)
T ss_pred             CceeeeechHHHHHHH
Confidence            7999999999999987

>KOG0331|consensus

Probab=97.95  E-value=3.4e-06  Score=71.38  Aligned_cols=74  Identities=36%  Similarity=0.573  Sum_probs=60.2

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      +...+.. ++..|+.+|...    ..|+|+++.|.||||||++|++|+|..+......                      
T Consensus       102 ~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~----------------------  159 (519)
T KOG0331|consen  102 LMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGK----------------------  159 (519)
T ss_pred             HHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhcccc----------------------
Confidence            3333334 999999999765    7899999999999999999999999998742111                      


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ..+...|++|||+||||||.|
T Consensus       160 -----------~~~~~~P~vLVL~PTRELA~Q  180 (519)
T KOG0331|consen  160 -----------LSRGDGPIVLVLAPTRELAVQ  180 (519)
T ss_pred             -----------ccCCCCCeEEEEcCcHHHHHH
Confidence                       234568999999999999998

>KOG0338|consensus

Probab=97.94  E-value=2.3e-06  Score=71.89  Aligned_cols=73  Identities=41%  Similarity=0.565  Sum_probs=62.9

Q ss_pred             cchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHH
Q psy11948         59 IPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLE  133 (167)
Q Consensus        59 lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e  133 (167)
                      -|++..+-. ++..||++|...    ..|+|++++|-||+|||.+|.+|++++++-+                       
T Consensus       190 RPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYr-----------------------  246 (691)
T KOG0338|consen  190 RPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYR-----------------------  246 (691)
T ss_pred             hHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcC-----------------------
Confidence            378887777 999999999654    7899999999999999999999999999743                       


Q ss_pred             HHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        134 ELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .+.....|+||||||||||+|
T Consensus       247 -------------Pk~~~~TRVLVL~PTRELaiQ  267 (691)
T KOG0338|consen  247 -------------PKKVAATRVLVLVPTRELAIQ  267 (691)
T ss_pred             -------------cccCcceeEEEEeccHHHHHH
Confidence                         233556799999999999998

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=97.92  E-value=4.9e-06  Score=74.40  Aligned_cols=14  Identities=21%  Similarity=0.052  Sum_probs=12.6

Q ss_pred             ceEEEccchhhhcC
Q psy11948        154 YALILAPTRELAIQ  167 (167)
Q Consensus       154 ~aLIl~PTRELa~Q  167 (167)
                      .++||+||++||.|
T Consensus       125 ~V~VvTpn~yLA~q  138 (896)
T PRK13104        125 GVHIVTVNDYLAKR  138 (896)
T ss_pred             CEEEEcCCHHHHHH
Confidence            48999999999986

>KOG0330|consensus

Probab=97.91  E-value=3.9e-06  Score=68.37  Aligned_cols=69  Identities=41%  Similarity=0.649  Sum_probs=59.1

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .+++...+ .+..||.+|..+    +.++|+++.|+||||||.+|.+|+++.++.                         
T Consensus        71 ~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~-------------------------  125 (476)
T KOG0330|consen   71 ELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQ-------------------------  125 (476)
T ss_pred             HHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHc-------------------------
Confidence            45555555 899999999665    789999999999999999999999999983                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    ....+++|||+||||||.|
T Consensus       126 --------------~p~~~~~lVLtPtRELA~Q  144 (476)
T KOG0330|consen  126 --------------EPKLFFALVLTPTRELAQQ  144 (476)
T ss_pred             --------------CCCCceEEEecCcHHHHHH
Confidence                          2345999999999999987

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=97.91  E-value=7.7e-06  Score=73.38  Aligned_cols=26  Identities=31%  Similarity=0.468  Sum_probs=20.1

Q ss_pred             cCCcEEEEeecCCCcccccccchhhh
Q psy11948         39 ARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        39 ~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      .+.+++++|+||||||.+|.++++..
T Consensus        16 ~~~~vIi~a~TGSGKTT~vpl~lL~~   41 (819)
T TIGR01970        16 AHPQVVLEAPPGAGKSTAVPLALLDA   41 (819)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHh
Confidence            33788888888888888888877643

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.

>PRK13766 Hef nuclease; Provisional

Probab=97.91  E-value=8.8e-06  Score=72.66  Aligned_cols=42  Identities=21%  Similarity=0.142  Sum_probs=32.8

Q ss_pred             CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      +.-+|.+.|...+..++.+  +++++++||+|||..+++++...
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~--n~lv~~ptG~GKT~~a~~~i~~~   53 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK--NTLVVLPTGLGKTAIALLVIAER   53 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC--CeEEEcCCCccHHHHHHHHHHHH
Confidence            3447888999988777755  88999999999998777766543

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

Probab=97.88  E-value=9.1e-06  Score=68.32  Aligned_cols=35  Identities=20%  Similarity=0.125  Sum_probs=29.0

Q ss_pred             CCCchHHHhHHHHHHcc---CCcEEEEeecCCCccccc
Q psy11948         23 KTPTKIQSMVMPSALLA---RKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~---~~d~i~~a~tgsGKt~~~   57 (167)
                      ..+.+.|.+++.++...   .+..+++.+||+|||...
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va   72 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVA   72 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHH
Confidence            35889999999998883   388899999999998744

>KOG0343|consensus

Probab=97.87  E-value=3.3e-06  Score=71.52  Aligned_cols=65  Identities=45%  Similarity=0.609  Sum_probs=55.2

Q ss_pred             ccCCCCccccc----cccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEN----DSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~----~~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      .+..+|.+|..    +..|+|++++|.||||||++|++|+++.+.+..                                
T Consensus        88 ~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~k--------------------------------  135 (758)
T KOG0343|consen   88 KFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLK--------------------------------  135 (758)
T ss_pred             CCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcC--------------------------------
Confidence            67778888754    488999999999999999999999999998542                                


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                         .....++.+|||+||||||.|
T Consensus       136 ---Ws~~DGlGalIISPTRELA~Q  156 (758)
T KOG0343|consen  136 ---WSPTDGLGALIISPTRELALQ  156 (758)
T ss_pred             ---CCCCCCceeEEecchHHHHHH
Confidence               233466899999999999988

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=97.77  E-value=2.2e-05  Score=62.48  Aligned_cols=42  Identities=31%  Similarity=0.193  Sum_probs=33.8

Q ss_pred             CCchHHHhHHHH----HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         24 TPTKIQSMVMPS----ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        24 ~pt~iQ~~~ip~----~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|.|.|.+.+..    +..| .++++.+|||+|||+++++|.+....
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~-~~~~~eapTGtGKTl~~L~~al~~~~   53 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRG-KIGILESPTGTGKTLSLLCLTLTWLR   53 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcC-CcEEEECCCCcchhHHHHHHHHHHHH
Confidence            468999985543    3445 89999999999999999999987655

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=97.77  E-value=2.2e-05  Score=62.48  Aligned_cols=42  Identities=31%  Similarity=0.193  Sum_probs=33.8

Q ss_pred             CCchHHHhHHHH----HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         24 TPTKIQSMVMPS----ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        24 ~pt~iQ~~~ip~----~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|.|.|.+.+..    +..| .++++.+|||+|||+++++|.+....
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~-~~~~~eapTGtGKTl~~L~~al~~~~   53 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRG-KIGILESPTGTGKTLSLLCLTLTWLR   53 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcC-CcEEEECCCCcchhHHHHHHHHHHHH
Confidence            468999985543    3445 89999999999999999999987655

>KOG0348|consensus

Probab=97.74  E-value=8.9e-06  Score=68.72  Aligned_cols=75  Identities=37%  Similarity=0.568  Sum_probs=61.3

Q ss_pred             chhhhhhc---ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         60 PILTGIVN---KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        60 p~l~~~~~---~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      |.+..-++   ++..||.+|.++    ..++|+++.++||||||++|++|+++.+..-..+.                  
T Consensus       145 ~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki------------------  206 (708)
T KOG0348|consen  145 PHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKI------------------  206 (708)
T ss_pred             HHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccc------------------
Confidence            54444444   888999998766    67999999999999999999999999986433322                  


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                     .+..++.||||+||||||.|
T Consensus       207 ---------------~Rs~G~~ALVivPTREL~~Q  226 (708)
T KOG0348|consen  207 ---------------QRSDGPYALVIVPTRELALQ  226 (708)
T ss_pred             ---------------cccCCceEEEEechHHHHHH
Confidence                           35678999999999999988

>KOG0345|consensus

Probab=97.74  E-value=1.1e-05  Score=67.13  Aligned_cols=66  Identities=42%  Similarity=0.507  Sum_probs=56.2

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      +|...|+.|..+    ..++|+++.|+||||||+||++|+++-+.++..+.                             
T Consensus        25 GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~-----------------------------   75 (567)
T KOG0345|consen   25 GFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKT-----------------------------   75 (567)
T ss_pred             CCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCC-----------------------------
Confidence            788888888665    78899999999999999999999999997665442                             


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ....+.||||+||||||.|
T Consensus        76 -----~~~~vgalIIsPTRELa~Q   94 (567)
T KOG0345|consen   76 -----PPGQVGALIISPTRELARQ   94 (567)
T ss_pred             -----CccceeEEEecCcHHHHHH
Confidence                 2336889999999999987

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=97.73  E-value=1.7e-05  Score=57.70  Aligned_cols=35  Identities=23%  Similarity=0.218  Sum_probs=26.7

Q ss_pred             CCchHHHhHHHHHHc------cCCcEEEEeecCCCcccccc
Q psy11948         24 TPTKIQSMVMPSALL------ARKDIVGAAETGSGKTLAFG   58 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~------~~~d~i~~a~tgsGKt~~~~   58 (167)
                      .+.+.|.+++-.+..      ....+++.++||+|||...+
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~   43 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIAL   43 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhh
Confidence            478899999988874      24788888888888887554

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

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

Probab=97.73  E-value=6.4e-06  Score=70.46  Aligned_cols=72  Identities=43%  Similarity=0.638  Sum_probs=57.0

Q ss_pred             cchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHH
Q psy11948         59 IPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLE  133 (167)
Q Consensus        59 lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e  133 (167)
                      ..++..+.. ++..||++|..+    ..++|+++.|+||+|||++|++|+++.+...                       
T Consensus        38 ~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~-----------------------   94 (513)
T COG0513          38 PELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKS-----------------------   94 (513)
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcc-----------------------
Confidence            345555555 899999999765    7789999999999999999999999997532                       


Q ss_pred             HHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        134 ELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    .......+|||+||||||+|
T Consensus        95 --------------~~~~~~~aLil~PTRELA~Q  114 (513)
T COG0513          95 --------------VERKYVSALILAPTRELAVQ  114 (513)
T ss_pred             --------------cccCCCceEEECCCHHHHHH
Confidence                          00111129999999999998

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.62  E-value=1.2e-05  Score=67.03  Aligned_cols=75  Identities=33%  Similarity=0.467  Sum_probs=58.6

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+.+|..+    ..++|+++.|+||+|||++|++|+++.++......                     
T Consensus        19 l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~---------------------   77 (423)
T PRK04837         19 VVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPE---------------------   77 (423)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhccccc---------------------
Confidence            4444444 888999999765    77899999999999999999999999886432110                     


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ......+++|||+||||||.|
T Consensus        78 -----------~~~~~~~~~lil~PtreLa~Q   98 (423)
T PRK04837         78 -----------DRKVNQPRALIMAPTRELAVQ   98 (423)
T ss_pred             -----------ccccCCceEEEECCcHHHHHH
Confidence                       012346899999999999987

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

Probab=97.57  E-value=2e-05  Score=67.53  Aligned_cols=75  Identities=29%  Similarity=0.453  Sum_probs=58.0

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+.+|..+    ..++|+++.++||+|||++|++|++..+.......                     
T Consensus       132 l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~---------------------  190 (518)
T PLN00206        132 LLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGH---------------------  190 (518)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcccc---------------------
Confidence            4444444 889999999665    77899999999999999999999998876322111                     


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ......+++|||+||||||.|
T Consensus       191 -----------~~~~~~~~aLIL~PTreLa~Q  211 (518)
T PLN00206        191 -----------PSEQRNPLAMVLTPTRELCVQ  211 (518)
T ss_pred             -----------ccccCCceEEEEeCCHHHHHH
Confidence                       012356899999999999987

>PTZ00110 helicase; Provisional

Probab=97.56  E-value=1.7e-05  Score=68.37  Aligned_cols=74  Identities=41%  Similarity=0.525  Sum_probs=58.3

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.+ ++..|+.+|..+    ..++|+++.++||+|||++|++|++..+......                     
T Consensus       140 ~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~---------------------  198 (545)
T PTZ00110        140 YILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLL---------------------  198 (545)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccc---------------------
Confidence            35555555 899999999665    7789999999999999999999999877532110                     


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....+++|||+||||||.|
T Consensus       199 -------------~~~~gp~~LIL~PTreLa~Q  218 (545)
T PTZ00110        199 -------------RYGDGPIVLVLAPTRELAEQ  218 (545)
T ss_pred             -------------cCCCCcEEEEECChHHHHHH
Confidence                         11345789999999999987

>KOG0335|consensus

Probab=97.56  E-value=3.2e-05  Score=64.83  Aligned_cols=77  Identities=38%  Similarity=0.450  Sum_probs=60.1

Q ss_pred             hhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHH
Q psy11948         62 LTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELE  136 (167)
Q Consensus        62 l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~  136 (167)
                      ...+.+ ++..|+++|..+    ..++|+..+|+||+|||.+|++|++..+++........                   
T Consensus        86 ~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~-------------------  146 (482)
T KOG0335|consen   86 AGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGE-------------------  146 (482)
T ss_pred             hhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcc-------------------
Confidence            333344 788899998665    78899999999999999999999999998654433211                   


Q ss_pred             HhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        137 EESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                ......|++|||+||||||.|
T Consensus       147 ----------~~~~~~P~~lIlapTReL~~Q  167 (482)
T KOG0335|consen  147 ----------SGGGVYPRALILAPTRELVDQ  167 (482)
T ss_pred             ----------cCCCCCCceEEEeCcHHHhhH
Confidence                      112267999999999999988

>KOG0336|consensus

Probab=97.52  E-value=0.00015  Score=59.86  Aligned_cols=119  Identities=27%  Similarity=0.370  Sum_probs=86.3

Q ss_pred             HHHHHHHH--CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccc-------------cchhhhhhc-ccCCCCcc
Q psy11948         12 TIIRALYQ--KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFG-------------IPILTGIVN-KLENPTEE   75 (167)
Q Consensus        12 ~l~~~l~~--~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~-------------lp~l~~~~~-~~~~~~~~   75 (167)
                      .+.+++++  ..-..+++.|.+-|-.   . ...|-|..--.|++.-..             ..++..+.+ +|..|+++
T Consensus       171 Pi~knfYke~~e~s~ls~~q~~~~r~---e-n~~it~dd~K~gekrpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPI  246 (629)
T KOG0336|consen  171 PIKKNFYKESNETSNLSKEQLQEWRK---E-NFNITCDDLKEGEKRPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPI  246 (629)
T ss_pred             chhhhhhhcCchhccCCHHHHHHHHH---c-CCcEEecccccCCcccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcc
Confidence            44555553  3466788888886632   3 456667676777654322             235555556 89999999


Q ss_pred             cccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhcccc
Q psy11948         76 DEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRN  151 (167)
Q Consensus        76 ~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~  151 (167)
                      |.++    +.|.|+++.|+||+|||++|++|-+..+......                                 ...+.
T Consensus       247 qSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~---------------------------------~~qr~  293 (629)
T KOG0336|consen  247 QSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKR---------------------------------REQRN  293 (629)
T ss_pred             hhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchh---------------------------------hhccC
Confidence            9776    8899999999999999999999998776532211                                 12467


Q ss_pred             ccceEEEccchhhhcC
Q psy11948        152 KLYALILAPTRELAIQ  167 (167)
Q Consensus       152 ~~~aLIl~PTRELa~Q  167 (167)
                      .|++|+++||||||+|
T Consensus       294 ~p~~lvl~ptreLalq  309 (629)
T KOG0336|consen  294 GPGVLVLTPTRELALQ  309 (629)
T ss_pred             CCceEEEeccHHHHHH
Confidence            8999999999999987

>KOG0341|consensus

Probab=97.50  E-value=5.9e-05  Score=61.80  Aligned_cols=87  Identities=33%  Similarity=0.464  Sum_probs=70.9

Q ss_pred             CCCcccccccchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcc
Q psy11948         50 GSGKTLAFGIPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGL  124 (167)
Q Consensus        50 gsGKt~~~~lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~  124 (167)
                      +|-|-+-|.-|++..+.. ++..||++|-+.    .+|+|.++.|-||||||++|.+|++-..++.....          
T Consensus       170 ksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~l----------  239 (610)
T KOG0341|consen  170 KSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMML----------  239 (610)
T ss_pred             hhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcC----------
Confidence            566677777889888887 888999998665    88999999999999999999999998776433221          


Q ss_pred             hhHHHHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        125 EEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       125 ~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                           -..+...|.+|||||+||||.|
T Consensus       240 ---------------------Pf~~~EGP~gLiicPSRELArQ  261 (610)
T KOG0341|consen  240 ---------------------PFARGEGPYGLIICPSRELARQ  261 (610)
T ss_pred             ---------------------ccccCCCCeeEEEcCcHHHHHH
Confidence                                 1234677999999999999987

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

Probab=97.50  E-value=0.00014  Score=67.48  Aligned_cols=33  Identities=24%  Similarity=0.237  Sum_probs=26.1

Q ss_pred             CCchHHHhHHHHHH----ccCCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSAL----LARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l----~~~~d~i~~a~tgsGKt~~   56 (167)
                      .+.+.|..+|..+.    .|.+..+++.+||||||..
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~t  449 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRT  449 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHH
Confidence            58899999997765    3556788888888888875

>KOG0342|consensus

Probab=97.46  E-value=5.1e-05  Score=63.49  Aligned_cols=72  Identities=40%  Similarity=0.511  Sum_probs=58.2

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      .+..+.+ +|...|.+|+..    ..++|++++|.||+|||++|++|.++.+....                        
T Consensus        93 t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~------------------------  148 (543)
T KOG0342|consen   93 TLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLK------------------------  148 (543)
T ss_pred             HHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcc------------------------
Confidence            3344444 888888888765    67899999999999999999999999886432                        


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ...+..+.+||||||||||+|
T Consensus       149 -----------~~~r~~~~vlIi~PTRELA~Q  169 (543)
T KOG0342|consen  149 -----------FKPRNGTGVLIICPTRELAMQ  169 (543)
T ss_pred             -----------cCCCCCeeEEEecccHHHHHH
Confidence                       123477899999999999998

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=97.45  E-value=3e-05  Score=65.39  Aligned_cols=74  Identities=36%  Similarity=0.620  Sum_probs=57.1

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+..|..+    ..++|+++.++||+|||++|++|+++.+.......                     
T Consensus        12 l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~---------------------   70 (456)
T PRK10590         12 ILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHA---------------------   70 (456)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhccccc---------------------
Confidence            4444444 788899998665    67899999999999999999999998885321110                     


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....+++|||+||||||.|
T Consensus        71 ------------~~~~~~~aLil~PtreLa~Q   90 (456)
T PRK10590         71 ------------KGRRPVRALILTPTRELAAQ   90 (456)
T ss_pred             ------------ccCCCceEEEEeCcHHHHHH
Confidence                        12345789999999999987

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

Probab=97.41  E-value=3.3e-05  Score=68.82  Aligned_cols=77  Identities=23%  Similarity=0.311  Sum_probs=63.2

Q ss_pred             ccccchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHH
Q psy11948         56 AFGIPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEE  130 (167)
Q Consensus        56 ~~~lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (167)
                      ..+.|.+..++. ++..||+.|..+    ..|+++++.||||+|||.+.++|++..+.+...                  
T Consensus         6 ~~l~~~v~~~~~~~~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~------------------   67 (814)
T COG1201           6 NILDPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGK------------------   67 (814)
T ss_pred             hhcCHHHHHHHHHhcCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccC------------------
Confidence            345577777777 999999999665    889999999999999999999999999985430                  


Q ss_pred             HHHHHHHhhhcchhhhhccccccceEEEccchhhhc
Q psy11948        131 VLEELEEESANTTEFVKKTRNKLYALILAPTRELAI  166 (167)
Q Consensus       131 ~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~  166 (167)
                                      ......+++|||+|.|+|..
T Consensus        68 ----------------~~~~~~i~~lYIsPLkALn~   87 (814)
T COG1201          68 ----------------GKLEDGIYALYISPLKALNN   87 (814)
T ss_pred             ----------------CCCCCceEEEEeCcHHHHHH
Confidence                            12345689999999999974

>KOG0353|consensus

Probab=97.40  E-value=0.00029  Score=57.78  Aligned_cols=58  Identities=19%  Similarity=0.275  Sum_probs=50.7

Q ss_pred             ccCCCCHHHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948          5 VKFNIPETIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus         5 ~~l~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      ++|+-+.+..+.|++ ....+..|.|..+|.+.+.| .|+++.-+||.||++||-+|.+.
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~-ed~~lil~tgggkslcyqlpal~  132 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAG-EDAFLILPTGGGKSLCYQLPALC  132 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhcc-CceEEEEeCCCccchhhhhhHHh
Confidence            357778888888885 46788899999999999999 99999999999999999999864

>KOG0340|consensus

Probab=97.35  E-value=7e-05  Score=60.61  Aligned_cols=61  Identities=43%  Similarity=0.704  Sum_probs=54.5

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..||++|...    ..|+|.+++|.||||||.+|.+|+++.++                                   
T Consensus        26 ~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLs-----------------------------------   70 (442)
T KOG0340|consen   26 GIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLS-----------------------------------   70 (442)
T ss_pred             cCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhc-----------------------------------
Confidence            778899998654    88999999999999999999999999996                                   


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .....+.+||++||||||.|
T Consensus        71 ----edP~giFalvlTPTrELA~Q   90 (442)
T KOG0340|consen   71 ----EDPYGIFALVLTPTRELALQ   90 (442)
T ss_pred             ----cCCCcceEEEecchHHHHHH
Confidence                23567899999999999987

>KOG0352|consensus

Probab=97.32  E-value=0.00019  Score=59.60  Aligned_cols=52  Identities=25%  Similarity=0.427  Sum_probs=42.9

Q ss_pred             HHHHHHHH-CCCC-CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         12 TIIRALYQ-KGFK-TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        12 ~l~~~l~~-~g~~-~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      .+..+|++ .|+. .-|+.|.+++..+..+..||.++.|||+||++||-+|.|-
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~   59 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALV   59 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHH
Confidence            34556664 4654 4588999999999999899999999999999999998763

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

Probab=97.30  E-value=0.00024  Score=64.93  Aligned_cols=43  Identities=28%  Similarity=0.311  Sum_probs=32.8

Q ss_pred             CCCCCchHHHhHHHH---HHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         21 GFKTPTKIQSMVMPS---ALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~---~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      || ++-|-|.+.+..   .+..+..+++.|+||+|||++|++|.+..
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~  300 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYF  300 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHH
Confidence            44 788888885433   34455889999999999999999998643

>KOG0951|consensus

Probab=97.25  E-value=0.00027  Score=65.01  Aligned_cols=58  Identities=31%  Similarity=0.396  Sum_probs=49.1

Q ss_pred             CCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          8 NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         8 ~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .+|.|-..++.  |......||.+..++++.+..++++|||||+|||...++.+++.+.+
T Consensus       295 elP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~  352 (1674)
T KOG0951|consen  295 ELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGN  352 (1674)
T ss_pred             CCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhc
Confidence            35666666666  45669999999999999888899999999999999999999888774

>KOG0337|consensus

Probab=97.25  E-value=0.00013  Score=60.32  Aligned_cols=80  Identities=39%  Similarity=0.594  Sum_probs=69.0

Q ss_pred             CCCcccccccchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcc
Q psy11948         50 GSGKTLAFGIPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGL  124 (167)
Q Consensus        50 gsGKt~~~~lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~  124 (167)
                      |+-+++..-.+++..+.+ .+..||++|.+.    ..++|+++-+.||+|||.+|++|+++.++...             
T Consensus        21 g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s-------------   87 (529)
T KOG0337|consen   21 GGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS-------------   87 (529)
T ss_pred             CCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc-------------
Confidence            445666666788888888 899999999876    78899999999999999999999999997532             


Q ss_pred             hhHHHHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        125 EEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       125 ~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                               ....++||++||||||.|
T Consensus        88 -------------------------~~g~RalilsptreLa~q  105 (529)
T KOG0337|consen   88 -------------------------QTGLRALILSPTRELALQ  105 (529)
T ss_pred             -------------------------ccccceeeccCcHHHHHH
Confidence                                     345899999999999987

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.25  E-value=6.8e-05  Score=65.05  Aligned_cols=75  Identities=36%  Similarity=0.523  Sum_probs=57.6

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+.+|...    ..++|+++.++||+|||++|++|+++.++......                     
T Consensus        20 l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~---------------------   78 (572)
T PRK04537         20 LLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALA---------------------   78 (572)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccc---------------------
Confidence            3444444 788999999765    78899999999999999999999999886422110                     


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ......+++|||+||||||.|
T Consensus        79 -----------~~~~~~~raLIl~PTreLa~Q   99 (572)
T PRK04537         79 -----------DRKPEDPRALILAPTRELAIQ   99 (572)
T ss_pred             -----------ccccCCceEEEEeCcHHHHHH
Confidence                       011235799999999999987

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

Probab=97.23  E-value=6.9e-05  Score=66.83  Aligned_cols=69  Identities=30%  Similarity=0.515  Sum_probs=56.1

Q ss_pred             cchhhhhhc--ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         59 IPILTGIVN--KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        59 lp~l~~~~~--~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      .|.+...+.  ++..|+..|..+    ..|+|+++.++||||||++|++|+++.+..                       
T Consensus        22 ~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~-----------------------   78 (742)
T TIGR03817        22 HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALAD-----------------------   78 (742)
T ss_pred             CHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhh-----------------------
Confidence            344444444  788899999665    778999999999999999999999988852                       


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                       ...+++|||+||||||.|
T Consensus        79 -----------------~~~~~aL~l~PtraLa~q   96 (742)
T TIGR03817        79 -----------------DPRATALYLAPTKALAAD   96 (742)
T ss_pred             -----------------CCCcEEEEEcChHHHHHH
Confidence                             124689999999999986

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.

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=97.22  E-value=7.4e-05  Score=62.97  Aligned_cols=68  Identities=40%  Similarity=0.542  Sum_probs=55.2

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+++|..+    ..++|+++.++||+|||++|++|+++.+..                          
T Consensus        15 l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~--------------------------   68 (460)
T PRK11776         15 LLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDV--------------------------   68 (460)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhh--------------------------
Confidence            3444444 788899998765    678999999999999999999999987731                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   ....+++|||+||||||.|
T Consensus        69 -------------~~~~~~~lil~PtreLa~Q   87 (460)
T PRK11776         69 -------------KRFRVQALVLCPTRELADQ   87 (460)
T ss_pred             -------------ccCCceEEEEeCCHHHHHH
Confidence                         1235689999999999987

>KOG0354|consensus

Probab=97.20  E-value=0.00043  Score=60.96  Aligned_cols=37  Identities=30%  Similarity=0.334  Sum_probs=26.9

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .+-.-|......+| | +++|+++|||+|||+....-+.
T Consensus        62 ~lR~YQ~eivq~AL-g-kNtii~lPTG~GKTfIAa~Vm~   98 (746)
T KOG0354|consen   62 ELRNYQEELVQPAL-G-KNTIIALPTGSGKTFIAAVIMK   98 (746)
T ss_pred             cccHHHHHHhHHhh-c-CCeEEEeecCCCccchHHHHHH
Confidence            45557777776666 6 8999999999999985544443

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

Probab=97.16  E-value=0.00054  Score=62.52  Aligned_cols=39  Identities=21%  Similarity=0.164  Sum_probs=32.4

Q ss_pred             HHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         17 LYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        17 l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ....+| .+-++|++++-.+-.| ..|+++|+||+|||+.-
T Consensus       113 ~~~~~F-~LD~fQ~~a~~~Ler~-esVlV~ApTssGKTvVa  151 (1041)
T COG4581         113 AREYPF-ELDPFQQEAIAILERG-ESVLVCAPTSSGKTVVA  151 (1041)
T ss_pred             HHhCCC-CcCHHHHHHHHHHhCC-CcEEEEccCCCCcchHH
Confidence            345677 7889999999777777 99999999999999843

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=97.15  E-value=0.00018  Score=64.36  Aligned_cols=38  Identities=24%  Similarity=0.262  Sum_probs=23.5

Q ss_pred             CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      |. .|+++|-..-=.+..|   -|+.+.||+|||+++.+|++
T Consensus        79 g~-~~~dvQlig~l~L~~G---~Iaem~TGeGKTLva~lpa~  116 (830)
T PRK12904         79 GM-RHFDVQLIGGMVLHEG---KIAEMKTGEGKTLVATLPAY  116 (830)
T ss_pred             CC-CCCccHHHhhHHhcCC---chhhhhcCCCcHHHHHHHHH
Confidence            44 6777777665444333   26666777777776666664

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=97.15  E-value=0.0002  Score=58.66  Aligned_cols=36  Identities=33%  Similarity=0.370  Sum_probs=30.4

Q ss_pred             HHHhHHHHHHccCC-cEEEEeecCCCcccccccchhh
Q psy11948         28 IQSMVMPSALLARK-DIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        28 iQ~~~ip~~l~~~~-d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      +|.++++.+..+.. .++++++||||||.+|.+|++.
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~   37 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH   37 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            59999999998843 3788999999999998887664

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.

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=97.13  E-value=0.0001  Score=61.54  Aligned_cols=72  Identities=35%  Similarity=0.546  Sum_probs=55.5

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+..|..+    ..++|+++.++||+|||++|++|+++.++....                       
T Consensus        12 l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~-----------------------   68 (434)
T PRK11192         12 LLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR-----------------------   68 (434)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc-----------------------
Confidence            3333433 788888888665    678999999999999999999999988863210                       


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....+++|||+||||||.|
T Consensus        69 ------------~~~~~~~~lil~Pt~eLa~Q   88 (434)
T PRK11192         69 ------------RKSGPPRILILTPTRELAMQ   88 (434)
T ss_pred             ------------cCCCCceEEEECCcHHHHHH
Confidence                        11234789999999999987

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.12  E-value=0.0001  Score=62.49  Aligned_cols=75  Identities=33%  Similarity=0.450  Sum_probs=57.0

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..|+|+++.++||+|||++|++|+++.+.......                     
T Consensus        98 l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~---------------------  156 (475)
T PRK01297         98 LMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPK---------------------  156 (475)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCccc---------------------
Confidence            3344444 888899998765    77899999999999999999999999886431110                     


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ......+++|||+||||||.|
T Consensus       157 -----------~~~~~~~~aLil~PtreLa~Q  177 (475)
T PRK01297        157 -----------ERYMGEPRALIIAPTRELVVQ  177 (475)
T ss_pred             -----------ccccCCceEEEEeCcHHHHHH
Confidence                       011235789999999999987

>PRK13767 ATP-dependent helicase; Provisional

Probab=97.11  E-value=0.00011  Score=66.60  Aligned_cols=78  Identities=24%  Similarity=0.317  Sum_probs=60.6

Q ss_pred             cccchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHH
Q psy11948         57 FGIPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEV  131 (167)
Q Consensus        57 ~~lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (167)
                      .+.|.+..++. ++..++..|..+    ..++|++++||||+|||.+|++|+++.+......                  
T Consensus        17 ~l~~~v~~~~~~~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~------------------   78 (876)
T PRK13767         17 LLRPYVREWFKEKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGRE------------------   78 (876)
T ss_pred             hcCHHHHHHHHHccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccc------------------
Confidence            34577777776 778899998766    6789999999999999999999999888632111                  


Q ss_pred             HHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        132 LEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       132 ~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                     ......+++|||+||||||.|
T Consensus        79 ---------------~~~~~~~~~LyIsPtraLa~d   99 (876)
T PRK13767         79 ---------------GELEDKVYCLYVSPLRALNND   99 (876)
T ss_pred             ---------------cCCCCCeEEEEEcCHHHHHHH
Confidence                           011346889999999999975

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=97.04  E-value=0.00014  Score=63.76  Aligned_cols=69  Identities=41%  Similarity=0.635  Sum_probs=56.3

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      +++..+.. ++..|+..|...    ..++|+++.|+||+|||++|++|+++.+..                         
T Consensus        16 ~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~-------------------------   70 (629)
T PRK11634         16 PILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDP-------------------------   70 (629)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhh-------------------------
Confidence            45555555 888899998665    678999999999999999999999977631                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    ....+++|||+||||||.|
T Consensus        71 --------------~~~~~~~LIL~PTreLa~Q   89 (629)
T PRK11634         71 --------------ELKAPQILVLAPTRELAVQ   89 (629)
T ss_pred             --------------ccCCCeEEEEeCcHHHHHH
Confidence                          1234789999999999987

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

Probab=97.02  E-value=0.00077  Score=58.31  Aligned_cols=50  Identities=30%  Similarity=0.399  Sum_probs=44.1

Q ss_pred             HHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         13 IIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        13 l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      +...|+. .||...-+-|.++|..++.| +|+++.-|||.||++||-+|.+-
T Consensus         5 ~~~~L~~~fGy~~FR~gQ~evI~~~l~g-~d~lvvmPTGgGKSlCyQiPAll   55 (590)
T COG0514           5 AQQVLKQVFGYASFRPGQQEIIDALLSG-KDTLVVMPTGGGKSLCYQIPALL   55 (590)
T ss_pred             HHHHHHHHhCccccCCCHHHHHHHHHcC-CcEEEEccCCCCcchHhhhHHHh
Confidence            3455664 58999999999999999999 99999999999999999999864

>KOG0334|consensus

Probab=97.01  E-value=0.00034  Score=63.08  Aligned_cols=73  Identities=42%  Similarity=0.616  Sum_probs=57.0

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.+ ++..|+.+|..+    -+|+|+++.|.||+|||++|++|++..++.....                      
T Consensus       376 il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~----------------------  433 (997)
T KOG0334|consen  376 ILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPL----------------------  433 (997)
T ss_pred             HHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCCh----------------------
Confidence            3344433 778999999655    6899999999999999999999999666532211                      


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....|-+||++||||||.|
T Consensus       434 ------------~~gdGPi~li~aPtrela~Q  453 (997)
T KOG0334|consen  434 ------------EEGDGPIALILAPTRELAMQ  453 (997)
T ss_pred             ------------hhCCCceEEEEcCCHHHHHH
Confidence                        22457999999999999998

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=96.95  E-value=0.00036  Score=62.71  Aligned_cols=14  Identities=14%  Similarity=0.048  Sum_probs=12.2

Q ss_pred             ceEEEccchhhhcC
Q psy11948        154 YALILAPTRELAIQ  167 (167)
Q Consensus       154 ~aLIl~PTRELa~Q  167 (167)
                      .+.||+|+++||.|
T Consensus       125 ~VhIvT~ndyLA~R  138 (908)
T PRK13107        125 GVHVITVNDYLARR  138 (908)
T ss_pred             CEEEEeCCHHHHHH
Confidence            38999999999975

>KOG0344|consensus

Probab=96.92  E-value=0.00039  Score=59.32  Aligned_cols=72  Identities=42%  Similarity=0.645  Sum_probs=59.0

Q ss_pred             hhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHH
Q psy11948         62 LTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELE  136 (167)
Q Consensus        62 l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~  136 (167)
                      +..+.. .|..|+.+|..+    ..++|++.++|||+|||++|.+|++..+.....                        
T Consensus       148 l~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~------------------------  203 (593)
T KOG0344|consen  148 LENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQ------------------------  203 (593)
T ss_pred             HHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhc------------------------
Confidence            444444 899999999776    678999999999999999999999998864322                        


Q ss_pred             HhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        137 EESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                .+.....+++||.||||||.|
T Consensus       204 ----------~~~~~gl~a~Il~ptreLa~Q  224 (593)
T KOG0344|consen  204 ----------EKHKVGLRALILSPTRELAAQ  224 (593)
T ss_pred             ----------ccCccceEEEEecchHHHHHH
Confidence                      133567899999999999987

>KOG0351|consensus

Probab=96.86  E-value=0.0025  Score=58.06  Aligned_cols=50  Identities=28%  Similarity=0.292  Sum_probs=42.9

Q ss_pred             HHHHHHH-HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         12 TIIRALY-QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        12 ~l~~~l~-~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      ++...+. ..|+...-+-|.++|-+.+.| +|+++..+||.||++||-+|.+
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~G-kd~fvlmpTG~GKSLCYQlPA~  301 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSG-KDCFVLMPTGGGKSLCYQLPAL  301 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcC-CceEEEeecCCceeeEeecccc
Confidence            3444444 569999999999999988888 9999999999999999988875

>KOG0326|consensus

Probab=96.86  E-value=0.00048  Score=55.28  Aligned_cols=69  Identities=42%  Similarity=0.683  Sum_probs=60.0

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      -++-.++. +|+.|.++|+..    ..|+|++..|..|+|||.+|.+|+++.+-                          
T Consensus        95 ~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid--------------------------  148 (459)
T KOG0326|consen   95 ELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKID--------------------------  148 (459)
T ss_pred             HHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcC--------------------------
Confidence            45666666 999999999664    88999999999999999999999998874                          


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....++++||+||||||.|
T Consensus       149 -------------~~~~~IQ~~ilVPtrelALQ  168 (459)
T KOG0326|consen  149 -------------PKKNVIQAIILVPTRELALQ  168 (459)
T ss_pred             -------------ccccceeEEEEeecchhhHH
Confidence                         34567999999999999987

>TIGR00603 rad25 DNA repair helicase rad25

Probab=96.85  E-value=0.00092  Score=59.34  Aligned_cols=34  Identities=15%  Similarity=0.085  Sum_probs=23.6

Q ss_pred             CCchHHHhHHHHHHccC--CcEEEEeecCCCccccc
Q psy11948         24 TPTKIQSMVMPSALLAR--KDIVGAAETGSGKTLAF   57 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~--~d~i~~a~tgsGKt~~~   57 (167)
                      .+.|.|.+++..++..+  +.-+++.+||+|||+..
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlva  290 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVG  290 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHH
Confidence            46778888887777443  25677788888887643

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).

>PTZ00424 helicase 45; Provisional

Probab=96.78  E-value=0.00028  Score=58.09  Aligned_cols=69  Identities=42%  Similarity=0.539  Sum_probs=54.9

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.. ++..|+..|..+    ..++|+++.+|||+|||.+|++|++..+..                         
T Consensus        38 ~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~-------------------------   92 (401)
T PTZ00424         38 DLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDY-------------------------   92 (401)
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcC-------------------------
Confidence            34455555 788899998665    678999999999999999999999876531                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    .....++|||+||||||.|
T Consensus        93 --------------~~~~~~~lil~Pt~~L~~Q  111 (401)
T PTZ00424         93 --------------DLNACQALILAPTRELAQQ  111 (401)
T ss_pred             --------------CCCCceEEEECCCHHHHHH
Confidence                          1234679999999999987

>PRK09694 helicase Cas3; Provisional

Probab=96.74  E-value=0.0013  Score=59.69  Aligned_cols=39  Identities=31%  Similarity=0.171  Sum_probs=29.0

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccch
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      ...|+|+|..+..... ++.-+++.++||+|||.+.+...
T Consensus       284 ~~~p~p~Q~~~~~~~~-~pgl~ileApTGsGKTEAAL~~A  322 (878)
T PRK09694        284 GYQPRQLQTLVDALPL-QPGLTIIEAPTGSGKTEAALAYA  322 (878)
T ss_pred             CCCChHHHHHHHhhcc-CCCeEEEEeCCCCCHHHHHHHHH
Confidence            3489999998754322 33568999999999999876543

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

Probab=96.66  E-value=0.0025  Score=56.05  Aligned_cols=48  Identities=29%  Similarity=0.258  Sum_probs=37.3

Q ss_pred             HCCCCCCchHHHhHHHH---HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         19 QKGFKTPTKIQSMVMPS---ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~---~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .....+|.+.|...+-.   ++.++..+++.|+||+|||++|++|.+..-.
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~   60 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAR   60 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHH
Confidence            34456899999988744   3455466999999999999999999887654

>KOG0328|consensus

Probab=96.58  E-value=0.0012  Score=52.31  Aligned_cols=69  Identities=36%  Similarity=0.611  Sum_probs=59.7

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      -++..++. +++.|..+|..+    ..|+|++.+|++|+|||.+|.+.+++.+.                          
T Consensus        37 dlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d--------------------------   90 (400)
T KOG0328|consen   37 DLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLD--------------------------   90 (400)
T ss_pred             HHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecc--------------------------
Confidence            46667777 999999999776    78999999999999999999999987763                          


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   ...+..++|||+||||||.|
T Consensus        91 -------------~~~r~tQ~lilsPTRELa~Q  110 (400)
T KOG0328|consen   91 -------------ISVRETQALILSPTRELAVQ  110 (400)
T ss_pred             -------------cccceeeEEEecChHHHHHH
Confidence                         33566899999999999987

>KOG0350|consensus

Probab=96.57  E-value=0.001  Score=56.18  Aligned_cols=6  Identities=33%  Similarity=0.739  Sum_probs=2.4

Q ss_pred             eEEEcc
Q psy11948        155 ALILAP  160 (167)
Q Consensus       155 aLIl~P  160 (167)
                      .||-+|
T Consensus       273 IlVaTP  278 (620)
T KOG0350|consen  273 ILVATP  278 (620)
T ss_pred             eEEcCc
Confidence            343334

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=96.55  E-value=0.0038  Score=55.51  Aligned_cols=43  Identities=30%  Similarity=0.384  Sum_probs=32.3

Q ss_pred             CCCCCchHHHhHHHHH---Hcc-----CCcEEEEeecCCCcccccccchhhh
Q psy11948         21 GFKTPTKIQSMVMPSA---LLA-----RKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~---l~~-----~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      || ++-+-|.+.+-.+   +.+     +..+++-|+||+|||++|++|.+-.
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~   73 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPI   73 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHH
Confidence            55 7788888855444   343     2568899999999999999998653

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

Probab=96.32  E-value=0.0074  Score=55.00  Aligned_cols=38  Identities=29%  Similarity=0.308  Sum_probs=30.7

Q ss_pred             HHHC-CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         17 LYQK-GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        17 l~~~-g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      +++. || .|+..|..=-..++.| ...-+.||||.|||..
T Consensus        75 F~k~~G~-~~ws~QR~WakR~~rg-~SFaiiAPTGvGKTTf  113 (1187)
T COG1110          75 FKKATGF-RPWSAQRVWAKRLVRG-KSFAIIAPTGVGKTTF  113 (1187)
T ss_pred             HHHhhCC-CchHHHHHHHHHHHcC-CceEEEcCCCCchhHH
Confidence            4433 55 9999999877788888 8888999999999873

>KOG0339|consensus

Probab=96.27  E-value=0.0015  Score=55.42  Aligned_cols=93  Identities=32%  Similarity=0.443  Sum_probs=70.1

Q ss_pred             CcEEEEeecCCCcccccc---cchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccC
Q psy11948         41 KDIVGAAETGSGKTLAFG---IPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLE  112 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~~~---lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~  112 (167)
                      -.+...++.--.+++..+   -.++..+.. ++.+|+.+|..+    ..++|+++.|.||||||.+|+.|++..++...+
T Consensus       211 lrv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~e  290 (731)
T KOG0339|consen  211 LRVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPE  290 (731)
T ss_pred             ceeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhh
Confidence            344444444444444332   345555555 889999999665    789999999999999999999999999885433


Q ss_pred             CCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        113 NPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                      .                                  .....|.+||+|||||||.|
T Consensus       291 L----------------------------------~~g~gPi~vilvPTrela~Q  311 (731)
T KOG0339|consen  291 L----------------------------------KPGEGPIGVILVPTRELASQ  311 (731)
T ss_pred             h----------------------------------cCCCCCeEEEEeccHHHHHH
Confidence            2                                  34677999999999999987

>KOG0349|consensus

Probab=96.26  E-value=0.003  Score=52.79  Aligned_cols=42  Identities=40%  Similarity=0.491  Sum_probs=35.1

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      .+.-||.+|..+    ..+.|++.+|+||||||.+|.+|+++-..+
T Consensus        21 dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen   21 DWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             ccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHHHH
Confidence            455677777655    678999999999999999999999887653

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=96.22  E-value=0.0027  Score=51.57  Aligned_cols=25  Identities=40%  Similarity=0.207  Sum_probs=22.3

Q ss_pred             cEEEEeecCCCcccccccchhhhhh
Q psy11948         42 DIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        42 d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |++++++||||||.+|+++++..+.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~   25 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIK   25 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            6899999999999999999987653

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.

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

Probab=96.15  E-value=0.0052  Score=54.43  Aligned_cols=17  Identities=24%  Similarity=0.301  Sum_probs=14.1

Q ss_pred             cccceEEEccchhhhcC
Q psy11948        151 NKLYALILAPTRELAIQ  167 (167)
Q Consensus       151 ~~~~aLIl~PTRELa~Q  167 (167)
                      ..+++|||||+++|..|
T Consensus       292 ~~~~vl~lvdR~~L~~Q  308 (667)
T TIGR00348       292 KNPKVFFVVDRRELDYQ  308 (667)
T ss_pred             CCCeEEEEECcHHHHHH
Confidence            34689999999999877

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

>KOG0327|consensus

Probab=96.11  E-value=0.0022  Score=52.38  Aligned_cols=69  Identities=42%  Similarity=0.585  Sum_probs=58.9

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .+|..++. +|+.|+.+|..+    ..|.|++..+++|+|||++|++++++.+-                          
T Consensus        36 ~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD--------------------------   89 (397)
T KOG0327|consen   36 SLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQID--------------------------   89 (397)
T ss_pred             HHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcC--------------------------
Confidence            56677777 999999999776    67899999999999999999999998772                          


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   ......+|||+.||||||.|
T Consensus        90 -------------~~~ke~qalilaPtreLa~q  109 (397)
T KOG0327|consen   90 -------------MSVKETQALILAPTRELAQQ  109 (397)
T ss_pred             -------------cchHHHHHHHhcchHHHHHH
Confidence                         22345789999999999987

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=95.35  E-value=0.015  Score=51.80  Aligned_cols=46  Identities=17%  Similarity=0.092  Sum_probs=36.7

Q ss_pred             CCCCCchHHHhHHHHHH---ccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         21 GFKTPTKIQSMVMPSAL---LARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l---~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      -|..+.|.|.+.+..+.   ..+...++.+|||+|||++.+.|.+....
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~   55 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQ   55 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHH
Confidence            36666899998775543   34489999999999999999999987655

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).

>cd00268 DEADc DEAD-box helicases

Probab=95.33  E-value=0.0044  Score=46.07  Aligned_cols=63  Identities=48%  Similarity=0.661  Sum_probs=48.5

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..+...|...    ..++++++.++||+|||..|++|++..+....                                
T Consensus        18 ~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~--------------------------------   65 (203)
T cd00268          18 GFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP--------------------------------   65 (203)
T ss_pred             CCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc--------------------------------
Confidence            444555555443    45899999999999999999999998775321                                


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ....++++|++||++|+.|
T Consensus        66 -----~~~~~~viii~p~~~L~~q   84 (203)
T cd00268          66 -----KKDGPQALILAPTRELALQ   84 (203)
T ss_pred             -----ccCCceEEEEcCCHHHHHH
Confidence                 1246889999999999976

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.

>PRK02362 ski2-like helicase; Provisional

Probab=95.26  E-value=0.0042  Score=55.52  Aligned_cols=58  Identities=29%  Similarity=0.353  Sum_probs=47.6

Q ss_pred             ccCCCCcccccc-----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcc
Q psy11948         68 KLENPTEEDEND-----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT  142 (167)
Q Consensus        68 ~~~~~~~~~~~~-----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~  142 (167)
                      ++..+++.|..+     ..++|+++++|||+|||++|.+|+++.+.                                  
T Consensus        20 g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~----------------------------------   65 (737)
T PRK02362         20 GIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA----------------------------------   65 (737)
T ss_pred             CCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh----------------------------------
Confidence            566677777554     46789999999999999999999998773                                  


Q ss_pred             hhhhhccccccceEEEccchhhhcC
Q psy11948        143 TEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       143 ~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                              ...++|||+||||||.|
T Consensus        66 --------~~~kal~i~P~raLa~q   82 (737)
T PRK02362         66 --------RGGKALYIVPLRALASE   82 (737)
T ss_pred             --------cCCcEEEEeChHHHHHH
Confidence                    12479999999999976

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

Probab=95.00  E-value=0.0066  Score=55.11  Aligned_cols=42  Identities=29%  Similarity=0.450  Sum_probs=34.1

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ....+...|..+    ..|+++++.++||||||.+|++|+++.+++
T Consensus        67 g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~  112 (851)
T COG1205          67 GIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLR  112 (851)
T ss_pred             ccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhh
Confidence            444455555444    678999999999999999999999999974

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=95.00  E-value=0.027  Score=44.27  Aligned_cols=33  Identities=27%  Similarity=0.206  Sum_probs=22.7

Q ss_pred             CchHHHhHHHHHHccCCcEEEEeecCCCcccccccc
Q psy11948         25 PTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP   60 (167)
Q Consensus        25 pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp   60 (167)
                      +|+-|..+|-.  .. ..+++.|.-|||||.+...=
T Consensus         1 l~~eQ~~~i~~--~~-~~~lV~a~AGSGKT~~l~~r   33 (315)
T PF00580_consen    1 LTDEQRRIIRS--TE-GPLLVNAGAGSGKTTTLLER   33 (315)
T ss_dssp             S-HHHHHHHHS---S-SEEEEEE-TTSSHHHHHHHH
T ss_pred             CCHHHHHHHhC--CC-CCEEEEeCCCCCchHHHHHH
Confidence            46778888855  33 68999999999999855433

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

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

Probab=94.90  E-value=0.0094  Score=50.51  Aligned_cols=47  Identities=30%  Similarity=0.319  Sum_probs=36.1

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ...++.+++-|||=|||....+-+...+.                                        ...+ .+|+|+
T Consensus        27 al~~NtLvvlPTGLGKT~IA~~V~~~~l~----------------------------------------~~~~-kvlfLA   65 (542)
T COG1111          27 ALFKNTLVVLPTGLGKTFIAAMVIANRLR----------------------------------------WFGG-KVLFLA   65 (542)
T ss_pred             HhhcCeEEEecCCccHHHHHHHHHHHHHH----------------------------------------hcCC-eEEEec
Confidence            34568999999999999877766655442                                        1223 799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      ||+-|+.|
T Consensus        66 PTKPLV~Q   73 (542)
T COG1111          66 PTKPLVLQ   73 (542)
T ss_pred             CCchHHHH
Confidence            99999987

>PRK00254 ski2-like helicase; Provisional

Probab=94.75  E-value=0.0071  Score=53.95  Aligned_cols=59  Identities=27%  Similarity=0.297  Sum_probs=48.3

Q ss_pred             ccCCCCcccccc-----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcc
Q psy11948         68 KLENPTEEDEND-----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT  142 (167)
Q Consensus        68 ~~~~~~~~~~~~-----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~  142 (167)
                      ++..++..|..+     ..++|+++++|||+|||.+|.+|+++.+..                                 
T Consensus        20 g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~---------------------------------   66 (720)
T PRK00254         20 GIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR---------------------------------   66 (720)
T ss_pred             CCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh---------------------------------
Confidence            666777777544     567999999999999999999999877642                                 


Q ss_pred             hhhhhccccccceEEEccchhhhcC
Q psy11948        143 TEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       143 ~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                              ...++|||+|||+||.|
T Consensus        67 --------~~~~~l~l~P~~aLa~q   83 (720)
T PRK00254         67 --------EGGKAVYLVPLKALAEE   83 (720)
T ss_pred             --------cCCeEEEEeChHHHHHH
Confidence                    13479999999999976

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=94.40  E-value=0.01  Score=50.27  Aligned_cols=37  Identities=24%  Similarity=0.311  Sum_probs=30.3

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ++..++..|..+    ..++|+++.+|||+|||++|.+|.+
T Consensus         8 g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l   48 (470)
T TIGR00614         8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL   48 (470)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHH
Confidence            455666666543    6788999999999999999999987

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

>KOG0332|consensus

Probab=94.36  E-value=0.0081  Score=49.27  Aligned_cols=69  Identities=30%  Similarity=0.516  Sum_probs=59.6

Q ss_pred             chhhhhhc-ccCCCCcccccc------ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND------SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~------~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      -++..++. +|..|+.+|+.+      ...++++.++++|+|||.+|.+.++.+.-                        
T Consensus       100 ellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd------------------------  155 (477)
T KOG0332|consen  100 ELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVD------------------------  155 (477)
T ss_pred             HHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcC------------------------
Confidence            56777777 999999999887      56799999999999999999999987663                        


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                     .....|+++-|+||||||.|
T Consensus       156 ---------------~~~~~PQ~iCLaPtrELA~Q  175 (477)
T KOG0332|consen  156 ---------------PDVVVPQCICLAPTRELAPQ  175 (477)
T ss_pred             ---------------ccccCCCceeeCchHHHHHH
Confidence                           34567999999999999987

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=94.34  E-value=0.01  Score=42.45  Aligned_cols=47  Identities=43%  Similarity=0.598  Sum_probs=39.7

Q ss_pred             cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEcc
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP  160 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~P  160 (167)
                      .++++++.++||+|||.++.+|++..+.+.                                        ...+++|++|
T Consensus        13 ~~~~~li~aptGsGKT~~~~~~~l~~~~~~----------------------------------------~~~~~lii~P   52 (169)
T PF00270_consen   13 SGKNVLISAPTGSGKTLAYILPALNRLQEG----------------------------------------KDARVLIIVP   52 (169)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT----------------------------------------SSSEEEEEES
T ss_pred             cCCCEEEECCCCCccHHHHHHHHHhhhccC----------------------------------------CCceEEEEee
Confidence            568899999999999999999999877531                                        2348999999


Q ss_pred             chhhhcC
Q psy11948        161 TRELAIQ  167 (167)
Q Consensus       161 TRELa~Q  167 (167)
                      |++|+.|
T Consensus        53 ~~~l~~q   59 (169)
T PF00270_consen   53 TRALAEQ   59 (169)
T ss_dssp             SHHHHHH
T ss_pred             ccccccc
Confidence            9999875

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 ....

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

Probab=94.30  E-value=0.034  Score=48.80  Aligned_cols=58  Identities=21%  Similarity=0.244  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHH-HHCCCCCCchHHHhHHHHHHccC-----CcEEEEeecCCCcccccccchhhhh
Q psy11948          7 FNIPETIIRAL-YQKGFKTPTKIQSMVMPSALLAR-----KDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         7 l~l~~~l~~~l-~~~g~~~pt~iQ~~~ip~~l~~~-----~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      +..+..+++.+ ....| .+|.-|+.++..+..+-     .+=++++.-|||||...++.++..+
T Consensus       245 ~~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai  308 (677)
T COG1200         245 LPANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAI  308 (677)
T ss_pred             CCccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHH
Confidence            34455655554 57888 89999999999888551     1223455555555555555554433

>KOG4284|consensus

Probab=94.20  E-value=0.028  Score=49.34  Aligned_cols=70  Identities=27%  Similarity=0.493  Sum_probs=58.9

Q ss_pred             cchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHH
Q psy11948         59 IPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLE  133 (167)
Q Consensus        59 lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e  133 (167)
                      -+++..+.+ .|..|+.+|..+    ..+.|+++.|.+|+|||++|.+-+++.+-                         
T Consensus        34 r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~-------------------------   88 (980)
T KOG4284|consen   34 REVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLD-------------------------   88 (980)
T ss_pred             HHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcC-------------------------
Confidence            366666666 888899888654    67889999999999999999998887774                         


Q ss_pred             HHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        134 ELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    .+...+++||++||||||+|
T Consensus        89 --------------~~~~~~q~~Iv~PTREiaVQ  108 (980)
T KOG4284|consen   89 --------------SRSSHIQKVIVTPTREIAVQ  108 (980)
T ss_pred             --------------cccCcceeEEEecchhhhhH
Confidence                          44667999999999999998

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

Probab=94.14  E-value=0.082  Score=47.24  Aligned_cols=38  Identities=24%  Similarity=0.176  Sum_probs=30.4

Q ss_pred             CCchHHHhHHHHHHcc---CCcEEEEeecCCCcccccccch
Q psy11948         24 TPTKIQSMVMPSALLA---RKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~---~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      ..++-|+.++..+...   ....++.+.||||||..|+--+
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i  238 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAI  238 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHH
Confidence            5677899999887655   5778999999999998776544

>PF13245 AAA_19: Part of AAA domain

Probab=94.11  E-value=0.069  Score=33.86  Aligned_cols=15  Identities=33%  Similarity=0.372  Sum_probs=10.8

Q ss_pred             cEEEEeecCCCcccc
Q psy11948         42 DIVGAAETGSGKTLA   56 (167)
Q Consensus        42 d~i~~a~tgsGKt~~   56 (167)
                      -+++.++.|||||..
T Consensus        12 ~~vv~g~pGtGKT~~   26 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTT   26 (76)
T ss_pred             eEEEECCCCCCHHHH
Confidence            344588889998853

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=93.97  E-value=0.016  Score=52.71  Aligned_cols=29  Identities=28%  Similarity=0.483  Sum_probs=26.1

Q ss_pred             ccccceeeeecccCccceeeecchhhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIV  108 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~  108 (167)
                      ..++|+++.++||+|||++|++|++..++
T Consensus       105 ~l~~gvIAeaqTGeGKTLAf~LP~l~~aL  133 (970)
T PRK12899        105 AMHKGFITEMQTGEGKTLTAVMPLYLNAL  133 (970)
T ss_pred             hcCCCeEEEeCCCCChHHHHHHHHHHHHh
Confidence            56789999999999999999999997664

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=93.60  E-value=0.019  Score=45.78  Aligned_cols=30  Identities=30%  Similarity=0.212  Sum_probs=25.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ..+..+++.+|||+|||+++++|.+..+..
T Consensus        25 ~~~~~~~~eapTGtGKTl~~L~~al~~~~~   54 (289)
T smart00488       25 DRGKIGILESPTGTGKTLSLLCLTLTWLRS   54 (289)
T ss_pred             HcCCcEEEECCCCcchhHHHHHHHHHHHHh
Confidence            356788999999999999999999876654

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=93.60  E-value=0.019  Score=45.78  Aligned_cols=30  Identities=30%  Similarity=0.212  Sum_probs=25.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ..+..+++.+|||+|||+++++|.+..+..
T Consensus        25 ~~~~~~~~eapTGtGKTl~~L~~al~~~~~   54 (289)
T smart00489       25 DRGKIGILESPTGTGKTLSLLCLTLTWLRS   54 (289)
T ss_pred             HcCCcEEEECCCCcchhHHHHHHHHHHHHh
Confidence            356788999999999999999999876654

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=93.50  E-value=0.068  Score=48.13  Aligned_cols=42  Identities=24%  Similarity=0.369  Sum_probs=31.1

Q ss_pred             CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |. .|+++|-.+-=.+..| +  |+.-.||+|||+...+|.+...+
T Consensus        78 g~-~~~dvQlig~l~l~~G-~--iaEm~TGEGKTLvA~l~a~l~al  119 (796)
T PRK12906         78 GL-RPFDVQIIGGIVLHEG-N--IAEMKTGEGKTLTATLPVYLNAL  119 (796)
T ss_pred             CC-CCchhHHHHHHHHhcC-C--cccccCCCCCcHHHHHHHHHHHH
Confidence            54 7888998876555544 3  78888999999888887765554

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=93.48  E-value=0.083  Score=42.83  Aligned_cols=40  Identities=35%  Similarity=0.337  Sum_probs=30.6

Q ss_pred             HHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         15 RALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        15 ~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      +.+.+.|.  .++-|...+-.+...+.+++++++||||||..
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl  160 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL  160 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            34555554  55678888877777768999999999999974

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=93.32  E-value=0.024  Score=45.98  Aligned_cols=25  Identities=40%  Similarity=0.207  Sum_probs=22.0

Q ss_pred             ceeeeecccCccceeeecchhhhhh
Q psy11948         84 DIVGAAETGSGKTLAFGIPILTGIV  108 (167)
Q Consensus        84 d~~~~a~tgsgkt~~~~~p~i~~~~  108 (167)
                      |+++.+|||+|||.+|++|++..+.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~   25 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIK   25 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            5789999999999999999987653

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=93.32  E-value=0.017  Score=55.17  Aligned_cols=23  Identities=43%  Similarity=0.369  Sum_probs=21.0

Q ss_pred             EEeecCCCcccccccchhhhhhc
Q psy11948         45 GAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        45 ~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ++|+||||||++|++|++.++..
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~   23 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFR   23 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHh
Confidence            47999999999999999999875

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=93.11  E-value=0.072  Score=39.85  Aligned_cols=31  Identities=26%  Similarity=0.274  Sum_probs=24.4

Q ss_pred             CchHHHhHHHHHHccCCc-EEEEeecCCCcccc
Q psy11948         25 PTKIQSMVMPSALLARKD-IVGAAETGSGKTLA   56 (167)
Q Consensus        25 pt~iQ~~~ip~~l~~~~d-~i~~a~tgsGKt~~   56 (167)
                      +.+-|..++..++.. .+ .++.+|.|+|||..
T Consensus         2 ln~~Q~~Ai~~~~~~-~~~~~i~GpPGTGKT~~   33 (236)
T PF13086_consen    2 LNESQREAIQSALSS-NGITLIQGPPGTGKTTT   33 (236)
T ss_dssp             --HHHHHHHHHHCTS-SE-EEEE-STTSSHHHH
T ss_pred             CCHHHHHHHHHHHcC-CCCEEEECCCCCChHHH
Confidence            567899999888877 77 89999999999953

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.11  E-value=0.1  Score=41.82  Aligned_cols=43  Identities=37%  Similarity=0.429  Sum_probs=31.2

Q ss_pred             HHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         12 TIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        12 ~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ..++.|.+.|.  .++-|...+-.+..++.+++++++||||||..
T Consensus       106 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl  148 (299)
T TIGR02782       106 FTLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTL  148 (299)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH
Confidence            34455555554  45667777766666668999999999999974

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=92.95  E-value=0.12  Score=38.73  Aligned_cols=55  Identities=24%  Similarity=0.272  Sum_probs=35.5

Q ss_pred             CchHHHhHHHHHHccC-CcEEEEeecCCCcccccccchhhhhhcccCCCCccccccccccceeeeecccC
Q psy11948         25 PTKIQSMVMPSALLAR-KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGS   93 (167)
Q Consensus        25 pt~iQ~~~ip~~l~~~-~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~~~a~tgs   93 (167)
                      +++-|..++..++..+ +-++++++.|+|||...  -.+...+.            ..+..+++.++|+.
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l--~~~~~~~~------------~~g~~v~~~apT~~   57 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL--KALAEALE------------AAGKRVIGLAPTNK   57 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH--HHHHHHHH------------HTT--EEEEESSHH
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH--HHHHHHHH------------hCCCeEEEECCcHH
Confidence            6788999999887553 35778899999999742  22322221            23577888888864

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=92.92  E-value=0.12  Score=41.91  Aligned_cols=41  Identities=29%  Similarity=0.381  Sum_probs=31.3

Q ss_pred             HHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCccc
Q psy11948         13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTL   55 (167)
Q Consensus        13 l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~   55 (167)
                      .++.|.+.|+  .++.|...+..+..++.+++++++||||||.
T Consensus       123 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTT  163 (319)
T PRK13894        123 TLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTT  163 (319)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH
Confidence            3455556665  4577888887766666999999999999995

>KOG0947|consensus

Probab=92.89  E-value=0.17  Score=46.40  Aligned_cols=36  Identities=22%  Similarity=0.176  Sum_probs=31.1

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ...| +|-.+|++||-.+..| ..|+|.|.|.+|||+.
T Consensus       293 ~~pF-elD~FQk~Ai~~lerg-~SVFVAAHTSAGKTvV  328 (1248)
T KOG0947|consen  293 IYPF-ELDTFQKEAIYHLERG-DSVFVAAHTSAGKTVV  328 (1248)
T ss_pred             hCCC-CccHHHHHHHHHHHcC-CeEEEEecCCCCcchH
Confidence            3455 6778999999888888 9999999999999985

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=92.66  E-value=0.03  Score=49.12  Aligned_cols=37  Identities=24%  Similarity=0.376  Sum_probs=30.7

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ++..+++.|...    ..++|+++.+|||+|||++|.+|.+
T Consensus        22 G~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal   62 (607)
T PRK11057         22 GYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPAL   62 (607)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHH
Confidence            556666666543    6789999999999999999999987

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=92.61  E-value=0.032  Score=49.76  Aligned_cols=27  Identities=30%  Similarity=0.268  Sum_probs=22.7

Q ss_pred             ccceeeeecccCccceeeecchhhhhh
Q psy11948         82 RKDIVGAAETGSGKTLAFGIPILTGIV  108 (167)
Q Consensus        82 ~~d~~~~a~tgsgkt~~~~~p~i~~~~  108 (167)
                      +...++.|+||+|||++|++|.+-...
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~   75 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIAR   75 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHH
Confidence            356789999999999999999986543

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=92.56  E-value=0.065  Score=40.65  Aligned_cols=45  Identities=18%  Similarity=0.184  Sum_probs=31.4

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +...|+-|..++.+++.. .-+++.++.|+|||+..+...++.+..
T Consensus         2 I~p~~~~Q~~~~~al~~~-~~v~~~G~AGTGKT~LA~a~Al~~v~~   46 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNN-DLVIVNGPAGTGKTFLALAAALELVKE   46 (205)
T ss_dssp             ----SHHHHHHHHHHHH--SEEEEE--TTSSTTHHHHHHHHHHHHT
T ss_pred             ccCCCHHHHHHHHHHHhC-CeEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            345688899999998855 778899999999999777666666653

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG1803|consensus

Probab=92.53  E-value=0.17  Score=44.06  Aligned_cols=55  Identities=16%  Similarity=0.139  Sum_probs=40.1

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhcccCCCCccccccccccceeeeeccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETG   92 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~~~a~tg   92 (167)
                      ...+-|..++........-.++++|.|+|||.....-+.+.+.              .+..++++|||.
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk--------------~~k~VLVcaPSn  239 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVK--------------QKKRVLVCAPSN  239 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHH--------------cCCeEEEEcCch
Confidence            4456788888877777444678999999999876655554444              456788888874

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=92.47  E-value=0.1  Score=42.46  Aligned_cols=37  Identities=30%  Similarity=0.242  Sum_probs=32.6

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ..|...++-|...+-.+..++.++++++.||||||..
T Consensus       153 i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl  189 (355)
T COG4962         153 IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL  189 (355)
T ss_pred             HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH
Confidence            3578899999999988888867999999999999973

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

Probab=92.38  E-value=0.037  Score=50.44  Aligned_cols=28  Identities=32%  Similarity=0.413  Sum_probs=24.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGI  107 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~  107 (167)
                      ..++++++.|+||+|||.+|++|++...
T Consensus       262 ~~~~~~~~eA~TG~GKT~ayLlp~~~~~  289 (850)
T TIGR01407       262 THSEKSLIEAPTGTGKTLGYLLPALYYA  289 (850)
T ss_pred             ccCCcEEEECCCCCchhHHHHHHHHHHh
Confidence            4578899999999999999999997654

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=92.17  E-value=0.038  Score=48.23  Aligned_cols=37  Identities=24%  Similarity=0.433  Sum_probs=29.5

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ++..+...|...    ..++|+++.+|||+|||++|.+|.+
T Consensus        10 g~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal   50 (591)
T TIGR01389        10 GYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL   50 (591)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHH
Confidence            455555555443    6789999999999999999999987

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.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=91.92  E-value=0.4  Score=43.22  Aligned_cols=69  Identities=17%  Similarity=0.208  Sum_probs=44.4

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhcccCCCCccccccccccceeee
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGA   88 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~~~   88 (167)
                      +++..+......++ .+++-|..++..++.+.+-+++.+..|+|||..  +-.+...+.            ..+..+++.
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtl--l~~i~~~~~------------~~g~~V~~~  402 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTM--LKAAREAWE------------AAGYRVIGA  402 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHH--HHHHHHHHH------------hCCCeEEEE
Confidence            45544444333344 689999999998887546678999999999853  222222221            124567777


Q ss_pred             eccc
Q psy11948         89 AETG   92 (167)
Q Consensus        89 a~tg   92 (167)
                      ||||
T Consensus       403 ApTg  406 (744)
T TIGR02768       403 ALSG  406 (744)
T ss_pred             eCcH
Confidence            7775

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>TIGR00376 DNA helicase, putative

Probab=91.57  E-value=0.21  Score=44.15  Aligned_cols=34  Identities=21%  Similarity=0.210  Sum_probs=27.9

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      .+++.|..++..++.....+++.++.|+|||...
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~  190 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL  190 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH
Confidence            4588999999888765457889999999999643

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

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

Probab=91.51  E-value=0.14  Score=44.01  Aligned_cols=33  Identities=27%  Similarity=0.250  Sum_probs=25.8

Q ss_pred             CCchHHHhHHHHHHc----cCCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSALL----ARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~----~~~d~i~~a~tgsGKt~~   56 (167)
                      .|+.-|-.||..+..    |.+.-.+-+.||||||++
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT   48 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFT   48 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhH
Confidence            788888888877653    455777889999999974

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

Probab=91.42  E-value=0.091  Score=49.04  Aligned_cols=37  Identities=22%  Similarity=0.341  Sum_probs=31.6

Q ss_pred             ccCCCCccccc----cccccceeeeecccCccceeeecchh
Q psy11948         68 KLENPTEEDEN----DSARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        68 ~~~~~~~~~~~----~~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ++..+...|..    ...++|+++.+|||+|||++|.+|++
T Consensus       457 G~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL  497 (1195)
T PLN03137        457 GNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPAL  497 (1195)
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHH
Confidence            56667777754    37889999999999999999999997

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=91.39  E-value=0.4  Score=44.49  Aligned_cols=36  Identities=19%  Similarity=0.174  Sum_probs=29.6

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .|+ .+++-|..++..++.+..-+++.+..|+|||..
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~  378 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM  378 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH
Confidence            454 689999999999888734467999999999974

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=91.37  E-value=0.15  Score=45.46  Aligned_cols=43  Identities=30%  Similarity=0.236  Sum_probs=32.6

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|. .|+++|..+.-.++.|   -|+.-.||+|||+...+|.....+
T Consensus        75 lg~-r~ydvQlig~l~Ll~G---~VaEM~TGEGKTLvA~l~a~l~AL  117 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAG---DVIEMATGEGKTLAGAIAAAGYAL  117 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCC---CcccccCCCCHHHHHHHHHHHHHH
Confidence            355 8999999988777766   256788999999888887765444

>KOG0951|consensus

Probab=91.20  E-value=0.052  Score=50.78  Aligned_cols=40  Identities=28%  Similarity=0.347  Sum_probs=33.4

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      .-.|+|.++++.+...+.++++.+++|||||.+..+.++.
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~ 1182 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR 1182 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC
Confidence            3478999999988887688999999999999987776654

>PRK01172 ski2-like helicase; Provisional

Probab=91.14  E-value=0.059  Score=47.79  Aligned_cols=54  Identities=20%  Similarity=0.303  Sum_probs=42.4

Q ss_pred             CCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhh
Q psy11948         72 PTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVK  147 (167)
Q Consensus        72 ~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~  147 (167)
                      ++..|...    ..++++++++|||+|||+++.+++++.+..                                      
T Consensus        23 l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~--------------------------------------   64 (674)
T PRK01172         23 LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA--------------------------------------   64 (674)
T ss_pred             CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh--------------------------------------
Confidence            44445433    567899999999999999999998876631                                      


Q ss_pred             ccccccceEEEccchhhhcC
Q psy11948        148 KTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       148 ~~~~~~~aLIl~PTRELa~Q  167 (167)
                          ..++|||+|||+||.|
T Consensus        65 ----~~k~v~i~P~raLa~q   80 (674)
T PRK01172         65 ----GLKSIYIVPLRSLAME   80 (674)
T ss_pred             ----CCcEEEEechHHHHHH
Confidence                2478999999999976

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

Probab=91.04  E-value=0.063  Score=48.78  Aligned_cols=45  Identities=27%  Similarity=0.312  Sum_probs=37.7

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..+..+++.|+||+|||++|++|++....                                           ..++||++
T Consensus       262 ~~~~~~~~eA~tGtGKT~ayllp~l~~~~-------------------------------------------~~~vvI~t  298 (820)
T PRK07246        262 HDGPASFIEAQTGIGKTYGYLLPLLAQSD-------------------------------------------QRQIIVSV  298 (820)
T ss_pred             hCCCcEEEECCCCCcHHHHHHHHHHHhcC-------------------------------------------CCcEEEEe
Confidence            45678899999999999999999875331                                           24799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||||+.|
T Consensus       299 ~T~~Lq~Q  306 (820)
T PRK07246        299 PTKILQDQ  306 (820)
T ss_pred             CcHHHHHH
Confidence            99999987

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.03  E-value=0.17  Score=40.24  Aligned_cols=16  Identities=31%  Similarity=0.455  Sum_probs=13.3

Q ss_pred             cEEEEeecCCCccccc
Q psy11948         42 DIVGAAETGSGKTLAF   57 (167)
Q Consensus        42 d~i~~a~tgsGKt~~~   57 (167)
                      =+|+.+.|||||+...
T Consensus       129 LviiVGaTGSGKSTtm  144 (375)
T COG5008         129 LVIIVGATGSGKSTTM  144 (375)
T ss_pred             eEEEECCCCCCchhhH
Confidence            4788999999998754

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

Probab=91.03  E-value=0.065  Score=49.33  Aligned_cols=28  Identities=29%  Similarity=0.341  Sum_probs=23.9

Q ss_pred             ccccceeeeecccCccceeeecchhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGI  107 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~  107 (167)
                      ..+..+++.|+||+|||++|++|.+...
T Consensus       274 ~~~~~~~iEA~TGtGKTlaYLlpa~~~a  301 (928)
T PRK08074        274 RDSEHALIEAGTGTGKSLAYLLPAAYFA  301 (928)
T ss_pred             hcCCCEEEECCCCCchhHHHHHHHHHHh
Confidence            4567788999999999999999997544

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=91.02  E-value=0.22  Score=45.94  Aligned_cols=77  Identities=17%  Similarity=0.172  Sum_probs=41.2

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc-ccCCCCccccccccccceeeeecccCccceeee
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN-KLENPTEEDENDSARKDIVGAAETGSGKTLAFG  100 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~-~~~~~~~~~~~~~~~~d~~~~a~tgsgkt~~~~  100 (167)
                      |+. -|+|.+|+.+++.-...+-...+. .   ..|.-|++..-.. ....  ..+-......++-+..+||+|||.+|+
T Consensus         5 ~e~-l~hQ~~av~ai~~~F~~~~~~~~~-~---~~~~n~~~~~~~~~~~~~--~~~~~~~~~~n~~~~M~TGtGKT~~~~   77 (986)
T PRK15483          5 LEE-LPHQEQALAAILAAFTGIDIASAD-P---NHYANPLIKLRYENGIPG--RSRTRIDDKANIDIKMETGTGKTYVYT   77 (986)
T ss_pred             ccc-ChhHHHHHHHHHHHhcCCCccCCc-c---ccccCcccccchhhcccc--ccccccCccceEEEEeCCCCCHHHHHH
Confidence            455 799999998876432222112221 1   1344455433321 0000  011111234778889999999999888


Q ss_pred             cchhh
Q psy11948        101 IPILT  105 (167)
Q Consensus       101 ~p~i~  105 (167)
                      --+++
T Consensus        78 ~~i~~   82 (986)
T PRK15483         78 RLMYE   82 (986)
T ss_pred             HHHHH
Confidence            76653

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

Probab=90.94  E-value=0.062  Score=47.36  Aligned_cols=47  Identities=34%  Similarity=0.275  Sum_probs=38.9

Q ss_pred             cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEcc
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP  160 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~P  160 (167)
                      .++.+++.|+||+|||++|++|++.....                                        ....++||++|
T Consensus        15 ~~~~lliEA~TGtGKTlAYLlpal~~~~~----------------------------------------~~~~rvlIstp   54 (636)
T TIGR03117        15 QKRIGMLEASTGVGKTLAMIMAALTMLKE----------------------------------------RPDQKIAIAVP   54 (636)
T ss_pred             cCCeEEEEcCCCCcHHHHHHHHHHHHHHh----------------------------------------ccCceEEEECC
Confidence            45778999999999999999999876641                                        11357999999


Q ss_pred             chhhhcC
Q psy11948        161 TRELAIQ  167 (167)
Q Consensus       161 TRELa~Q  167 (167)
                      |++|+.|
T Consensus        55 T~~Lq~Q   61 (636)
T TIGR03117        55 TLALMGQ   61 (636)
T ss_pred             cHHHHHH
Confidence            9999987

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.

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=90.74  E-value=0.12  Score=46.08  Aligned_cols=30  Identities=20%  Similarity=0.226  Sum_probs=25.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ..+...+..+|||+|||++.+.|.+.....
T Consensus        27 ~~~~~~llEsPTGtGKTlslL~~aL~~~~~   56 (705)
T TIGR00604        27 DRGDEAILEMPSGTGKTISLLSLILAYQQE   56 (705)
T ss_pred             ccCCceEEeCCCCCCccHHHHHHHHHHHHh
Confidence            456788999999999999999999986653

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).

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=90.59  E-value=0.32  Score=35.95  Aligned_cols=33  Identities=39%  Similarity=0.377  Sum_probs=26.2

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ..++-|...+...+..+..+++.++||+|||..
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            356667777777666668999999999999974

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

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

Probab=90.24  E-value=0.079  Score=48.05  Aligned_cols=33  Identities=24%  Similarity=0.115  Sum_probs=23.8

Q ss_pred             CCcccccc----cccc-ceeeeecccCccceeeecchh
Q psy11948         72 PTEEDEND----SARK-DIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        72 ~~~~~~~~----~~~~-d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      |+..|...    ..|+ ++++.++||+|||.+|.++++
T Consensus        16 PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll   53 (844)
T TIGR02621        16 PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLL   53 (844)
T ss_pred             CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhc
Confidence            77777554    5566 677789999999996654444

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.

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=89.98  E-value=0.34  Score=43.60  Aligned_cols=40  Identities=33%  Similarity=0.204  Sum_probs=21.9

Q ss_pred             chHHHhHHHHHHcc--CC-cEEEEeecCCCcccccccchhhhh
Q psy11948         26 TKIQSMVMPSALLA--RK-DIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        26 t~iQ~~~ip~~l~~--~~-d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      .+.|..++..++..  .. .+++.||||.|||.+.+.+.....
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~  239 (733)
T COG1203         197 YELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALL  239 (733)
T ss_pred             hHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHh
Confidence            55666666544422  23 555666666666666655554443

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

Probab=89.86  E-value=0.61  Score=43.57  Aligned_cols=48  Identities=15%  Similarity=-0.004  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHH-CCCCCCchHHHhHHHHHHcc-----CCcEEEEeecCCCccccc
Q psy11948          9 IPETIIRALYQ-KGFKTPTKIQSMVMPSALLA-----RKDIVGAAETGSGKTLAF   57 (167)
Q Consensus         9 l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~-----~~d~i~~a~tgsGKt~~~   57 (167)
                      .+.+....+.+ .+| .-|+-|..||..+..+     .+|=++|+.-|-|||-..
T Consensus       579 ~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVA  632 (1139)
T COG1197         579 PDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVA  632 (1139)
T ss_pred             CChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHH
Confidence            34455555553 466 6799999999998854     235566666666666533

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=89.77  E-value=0.86  Score=42.78  Aligned_cols=49  Identities=14%  Similarity=0.183  Sum_probs=36.8

Q ss_pred             CCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948          7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus         7 l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .++++..++.....++ .+++-|..++..+..+.+-+++.+.-|+|||..
T Consensus       365 ~~v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~  413 (1102)
T PRK13826        365 HGVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTM  413 (1102)
T ss_pred             CCCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHH
Confidence            3455666665544444 789999999988776556788999999999963

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=89.72  E-value=0.22  Score=45.27  Aligned_cols=39  Identities=23%  Similarity=0.257  Sum_probs=25.4

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .|. .|+++|-.+-=.+.   ..-|+...||.|||++..+|..
T Consensus        73 lG~-r~ydvQlig~l~L~---~G~IaEm~TGEGKTL~a~l~ay  111 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLN---DGKIAEMKTGEGKTLVATLPAY  111 (870)
T ss_pred             hCC-CCCchHhhhhHhhc---CCccccccCCCCchHHHHHHHH
Confidence            355 57788877653332   3456777788888877777764

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

Probab=89.63  E-value=0.2  Score=43.71  Aligned_cols=26  Identities=38%  Similarity=0.551  Sum_probs=24.1

Q ss_pred             cccccceeeeecccCccceeeecchh
Q psy11948         79 DSARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        79 ~~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ...++|+++.-|||.||++.|-+|.+
T Consensus        29 ~l~g~d~lvvmPTGgGKSlCyQiPAl   54 (590)
T COG0514          29 LLSGKDTLVVMPTGGGKSLCYQIPAL   54 (590)
T ss_pred             HHcCCcEEEEccCCCCcchHhhhHHH
Confidence            36789999999999999999999987

>KOG0952|consensus

Probab=89.43  E-value=0.12  Score=47.48  Aligned_cols=55  Identities=27%  Similarity=0.385  Sum_probs=43.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      .+..+.+++||||+|||..|++-+++.+......-                                .-.+...+.++|+
T Consensus       124 ~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~--------------------------------~i~k~~fKiVYIa  171 (1230)
T KOG0952|consen  124 KSNENMLICAPTGSGKTVLAELCILRTIKEHEEQG--------------------------------DIAKDDFKIVYIA  171 (1230)
T ss_pred             cCCCCEEEECCCCCCchHHHHHHHHHHHHhhcccc--------------------------------ccccCCceEEEEe
Confidence            45688999999999999999999999987521111                                1335667899999


Q ss_pred             cchhhhc
Q psy11948        160 PTRELAI  166 (167)
Q Consensus       160 PTRELa~  166 (167)
                      |+++||.
T Consensus       172 PmKALa~  178 (1230)
T KOG0952|consen  172 PMKALAA  178 (1230)
T ss_pred             chHHHHH
Confidence            9999984

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=89.26  E-value=0.077  Score=50.89  Aligned_cols=24  Identities=42%  Similarity=0.371  Sum_probs=21.5

Q ss_pred             eeecccCccceeeecchhhhhhhc
Q psy11948         87 GAAETGSGKTLAFGIPILTGIVNK  110 (167)
Q Consensus        87 ~~a~tgsgkt~~~~~p~i~~~~~~  110 (167)
                      ++||||||||++|++|+++.++..
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~   24 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFRE   24 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhc
Confidence            479999999999999999999854

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=89.24  E-value=0.17  Score=34.00  Aligned_cols=25  Identities=56%  Similarity=0.622  Sum_probs=20.0

Q ss_pred             cEEEEeecCCCcccccccchhhhhh
Q psy11948         42 DIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        42 d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+++.++||+|||..+...+.....
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~   26 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLD   26 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHh
Confidence            5789999999999988776665544

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=89.21  E-value=0.095  Score=46.33  Aligned_cols=53  Identities=21%  Similarity=0.221  Sum_probs=43.3

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+++|..+    +.|+  ++.++||+|||++|.+|++....                                      
T Consensus       103 ~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al--------------------------------------  142 (656)
T PRK12898        103 RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL--------------------------------------  142 (656)
T ss_pred             CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh--------------------------------------
Confidence            677777554    4555  89999999999999999996543                                      


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          ...+++||+||||||.|
T Consensus       143 ----~G~~v~VvTptreLA~q  159 (656)
T PRK12898        143 ----AGLPVHVITVNDYLAER  159 (656)
T ss_pred             ----cCCeEEEEcCcHHHHHH
Confidence                24689999999999987

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=88.85  E-value=0.29  Score=44.68  Aligned_cols=40  Identities=18%  Similarity=0.140  Sum_probs=24.5

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|+++|-..==.+..   --|+...||+|||+...+|++-..+
T Consensus        82 ~~ydVQliGg~~Lh~---G~iaEM~TGEGKTLvA~l~a~l~al  121 (913)
T PRK13103         82 RHFDVQLIGGMTLHE---GKIAEMRTGEGKTLVGTLAVYLNAL  121 (913)
T ss_pred             CcchhHHHhhhHhcc---CccccccCCCCChHHHHHHHHHHHH
Confidence            677777765433332   3456777777777777777654433

>PRK10436 hypothetical protein; Provisional

Probab=88.66  E-value=0.44  Score=40.56  Aligned_cols=31  Identities=32%  Similarity=0.329  Sum_probs=20.1

Q ss_pred             hHHHhHHHHHHc-cCCcEEEEeecCCCccccc
Q psy11948         27 KIQSMVMPSALL-ARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        27 ~iQ~~~ip~~l~-~~~d~i~~a~tgsGKt~~~   57 (167)
                      +-|...|..++. ..--++++++||||||...
T Consensus       204 ~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL  235 (462)
T PRK10436        204 PAQLAQFRQALQQPQGLILVTGPTGSGKTVTL  235 (462)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCChHHHH
Confidence            334444544443 2235889999999999864

>KOG0949|consensus

Probab=88.50  E-value=0.76  Score=42.49  Aligned_cols=31  Identities=29%  Similarity=0.290  Sum_probs=24.0

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTL   55 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~   55 (167)
                      .|-..|.+.+..+=.+ ...++.|||.+|||+
T Consensus       511 ~Pd~WQ~elLDsvDr~-eSavIVAPTSaGKTf  541 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRN-ESAVIVAPTSAGKTF  541 (1330)
T ss_pred             CCcHHHHHHhhhhhcc-cceEEEeeccCCcee
Confidence            6777888877655555 788888899999886

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=88.20  E-value=0.92  Score=40.79  Aligned_cols=34  Identities=21%  Similarity=0.199  Sum_probs=29.5

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCccc
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTL   55 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~   55 (167)
                      .++ .+++-|+.++..+..+ +-+++.+..|+|||.
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~-~~~iitGgpGTGKTt  353 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQH-KVVILTGGPGTGKTT  353 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhC-CeEEEECCCCCCHHH
Confidence            454 7899999999988877 789999999999996

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>KOG0948|consensus

Probab=88.10  E-value=0.48  Score=42.55  Aligned_cols=37  Identities=24%  Similarity=0.240  Sum_probs=27.3

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccch
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      .+-|+|..+|--+-.+ ..|+++|-|.+|||...--.+
T Consensus       129 ~LDpFQ~~aI~Cidr~-eSVLVSAHTSAGKTVVAeYAI  165 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRG-ESVLVSAHTSAGKTVVAEYAI  165 (1041)
T ss_pred             ccCchHhhhhhhhcCC-ceEEEEeecCCCcchHHHHHH
Confidence            4557899988655455 899999999999997544333

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=88.06  E-value=0.92  Score=36.59  Aligned_cols=35  Identities=34%  Similarity=0.295  Sum_probs=29.0

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      +..+++.|..-+-.++..+++++++++||||||..
T Consensus       125 ~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~  159 (312)
T COG0630         125 YGTISPEQAAYLWLAIEARKSIIICGGTASGKTTL  159 (312)
T ss_pred             cCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH
Confidence            45677778777777777779999999999999975

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=87.99  E-value=0.49  Score=38.16  Aligned_cols=16  Identities=38%  Similarity=0.480  Sum_probs=13.1

Q ss_pred             cEEEEeecCCCccccc
Q psy11948         42 DIVGAAETGSGKTLAF   57 (167)
Q Consensus        42 d~i~~a~tgsGKt~~~   57 (167)
                      =|+|.++|||||+...
T Consensus       127 LILVTGpTGSGKSTTl  142 (353)
T COG2805         127 LILVTGPTGSGKSTTL  142 (353)
T ss_pred             eEEEeCCCCCcHHHHH
Confidence            4778999999998753

>TIGR01054 rgy reverse gyrase

Probab=87.33  E-value=0.18  Score=47.61  Aligned_cols=55  Identities=27%  Similarity=0.288  Sum_probs=43.4

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+..|...    ..++|+++.||||+|||. |++|+...+.                                      
T Consensus        78 ~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~--------------------------------------  118 (1171)
T TIGR01054        78 EPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLA--------------------------------------  118 (1171)
T ss_pred             CCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHH--------------------------------------
Confidence            577777544    678999999999999996 7777765442                                      


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                         ...+++|||+||||||.|
T Consensus       119 ---~~g~~vLIL~PTreLa~Q  136 (1171)
T TIGR01054       119 ---KKGKRCYIILPTTLLVIQ  136 (1171)
T ss_pred             ---hcCCeEEEEeCHHHHHHH
Confidence               124689999999999987

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.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=86.96  E-value=0.66  Score=37.90  Aligned_cols=42  Identities=24%  Similarity=0.222  Sum_probs=30.8

Q ss_pred             HHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         13 IIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        13 l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .++.|.+.|+  .++-+...+..+..++.+++++++||+|||..
T Consensus       153 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl  194 (340)
T TIGR03819       153 TLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL  194 (340)
T ss_pred             CHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH
Confidence            3555666665  44566666766666768999999999999873

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=86.59  E-value=0.61  Score=38.60  Aligned_cols=17  Identities=35%  Similarity=0.200  Sum_probs=14.4

Q ss_pred             CcEEEEeecCCCccccc
Q psy11948         41 KDIVGAAETGSGKTLAF   57 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~~   57 (167)
                      .-++++++||||||...
T Consensus       150 GlilI~G~TGSGKTT~l  166 (372)
T TIGR02525       150 GLGLICGETGSGKSTLA  166 (372)
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46889999999999753

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

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

Probab=86.54  E-value=0.19  Score=44.33  Aligned_cols=28  Identities=36%  Similarity=0.479  Sum_probs=24.1

Q ss_pred             cccceeeeecccCccceeeecchhhhhh
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIV  108 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~  108 (167)
                      .+.-+++.||||+|||++|++|.+....
T Consensus        33 ~~~~~~iEapTGtGKTl~yL~~al~~~~   60 (654)
T COG1199          33 GGEGLLIEAPTGTGKTLAYLLPALAYAR   60 (654)
T ss_pred             CCCcEEEECCCCccHHHHHHHHHHHHHH
Confidence            3444899999999999999999998774

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=86.46  E-value=0.59  Score=38.04  Aligned_cols=26  Identities=27%  Similarity=0.423  Sum_probs=20.0

Q ss_pred             hHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         31 MVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        31 ~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ..+..+..++.+++++++||||||..
T Consensus       151 ~~L~~~v~~~~nili~G~tgSGKTTl  176 (332)
T PRK13900        151 EFLEHAVISKKNIIISGGTSTGKTTF  176 (332)
T ss_pred             HHHHHHHHcCCcEEEECCCCCCHHHH
Confidence            33444455669999999999999974

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=86.40  E-value=0.2  Score=45.50  Aligned_cols=45  Identities=22%  Similarity=0.211  Sum_probs=37.3

Q ss_pred             cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEcc
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP  160 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~P  160 (167)
                      .++++++.++||+|||..|.+++++...                                          ...+++|++|
T Consensus        19 ~~~~vvv~A~TGSGKTt~~pl~lL~~~~------------------------------------------~~~~ilvlqP   56 (812)
T PRK11664         19 TAPQVLLKAPTGAGKSTWLPLQLLQHGG------------------------------------------INGKIIMLEP   56 (812)
T ss_pred             hCCCEEEEcCCCCCHHHHHHHHHHHcCC------------------------------------------cCCeEEEECC
Confidence            5679999999999999999998885431                                          1247999999


Q ss_pred             chhhhcC
Q psy11948        161 TRELAIQ  167 (167)
Q Consensus       161 TRELa~Q  167 (167)
                      ||++|.|
T Consensus        57 rR~aA~q   63 (812)
T PRK11664         57 RRLAARN   63 (812)
T ss_pred             hHHHHHH
Confidence            9999986

>COG4889 Predicted helicase [General function prediction only]

Probab=86.37  E-value=0.41  Score=43.84  Aligned_cols=45  Identities=24%  Similarity=0.206  Sum_probs=30.1

Q ss_pred             HHHHHHHHHCCCCCCchHHHhHHHHHHccCCc----EEEEeecCCCcccc
Q psy11948         11 ETIIRALYQKGFKTPTKIQSMVMPSALLARKD----IVGAAETGSGKTLA   56 (167)
Q Consensus        11 ~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d----~i~~a~tgsGKt~~   56 (167)
                      .++..+|.-+.=.+|.|+|+.+|.+.+.|..+    -++ ..-|+|||+.
T Consensus       148 ~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLI-MAcGTGKTfT  196 (1518)
T COG4889         148 TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLI-MACGTGKTFT  196 (1518)
T ss_pred             cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEE-EecCCCccch
Confidence            35566666666679999999999998876332    122 2236777764

>PRK09401 reverse gyrase; Reviewed

Probab=86.29  E-value=0.18  Score=47.53  Aligned_cols=55  Identities=27%  Similarity=0.278  Sum_probs=41.9

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+..|...    ..++|+++.||||+|||. |++++...+.                                      
T Consensus        80 ~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~--------------------------------------  120 (1176)
T PRK09401         80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLA--------------------------------------  120 (1176)
T ss_pred             CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHH--------------------------------------
Confidence            566666443    678999999999999995 6666554332                                      


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                         ....++|||+||||||.|
T Consensus       121 ---~~g~~alIL~PTreLa~Q  138 (1176)
T PRK09401        121 ---KKGKKSYIIFPTRLLVEQ  138 (1176)
T ss_pred             ---hcCCeEEEEeccHHHHHH
Confidence               124689999999999987

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=86.29  E-value=0.2  Score=44.57  Aligned_cols=43  Identities=33%  Similarity=0.387  Sum_probs=37.8

Q ss_pred             cceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEccch
Q psy11948         83 KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTR  162 (167)
Q Consensus        83 ~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTR  162 (167)
                      .+.+++++||||||++|++|++..+.                                          ...+++||+|||
T Consensus       283 ~~~Ll~~~TGSGKT~va~~~il~~~~------------------------------------------~g~q~lilaPT~  320 (681)
T PRK10917        283 MNRLLQGDVGSGKTVVAALAALAAIE------------------------------------------AGYQAALMAPTE  320 (681)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHHHH------------------------------------------cCCeEEEEeccH
Confidence            57899999999999999999987663                                          246799999999


Q ss_pred             hhhcC
Q psy11948        163 ELAIQ  167 (167)
Q Consensus       163 ELa~Q  167 (167)
                      +||.|
T Consensus       321 ~LA~Q  325 (681)
T PRK10917        321 ILAEQ  325 (681)
T ss_pred             HHHHH
Confidence            99987

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=86.14  E-value=0.65  Score=38.03  Aligned_cols=26  Identities=27%  Similarity=0.404  Sum_probs=20.1

Q ss_pred             hHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         31 MVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        31 ~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ..+..+..++.+++++++||||||..
T Consensus       153 ~~l~~~v~~~~nilI~G~tGSGKTTl  178 (344)
T PRK13851        153 AFLHACVVGRLTMLLCGPTGSGKTTM  178 (344)
T ss_pred             HHHHHHHHcCCeEEEECCCCccHHHH
Confidence            34444555568999999999999974

>KOG0352|consensus

Probab=86.01  E-value=0.44  Score=40.19  Aligned_cols=25  Identities=32%  Similarity=0.619  Sum_probs=23.0

Q ss_pred             ccccceeeeecccCccceeeecchh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ....|+.++.|||+||.+.|-+|.+
T Consensus        34 K~k~DVyVsMPTGaGKSLCyQLPaL   58 (641)
T KOG0352|consen   34 KRKCDVYVSMPTGAGKSLCYQLPAL   58 (641)
T ss_pred             hccCcEEEeccCCCchhhhhhchHH
Confidence            4679999999999999999999987

>KOG0329|consensus

Probab=86.00  E-value=0.47  Score=37.46  Aligned_cols=69  Identities=32%  Similarity=0.486  Sum_probs=56.7

Q ss_pred             chhhhhhc-ccCCCCcccc----ccccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDE----NDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~----~~~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      -++..+.. +++.|.+.|.    ++-.|.|+++.|.+|-|||.+|.+..++.+-                          
T Consensus        52 ellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqie--------------------------  105 (387)
T KOG0329|consen   52 ELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIE--------------------------  105 (387)
T ss_pred             HHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcC--------------------------
Confidence            34555544 8999988874    3467899999999999999999999998884                          


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   +..+.+.+|++|.|||||.|
T Consensus       106 -------------pv~g~vsvlvmchtrelafq  125 (387)
T KOG0329|consen  106 -------------PVDGQVSVLVMCHTRELAFQ  125 (387)
T ss_pred             -------------CCCCeEEEEEEeccHHHHHH
Confidence                         33456889999999999987

>KOG0925|consensus

Probab=85.94  E-value=1.9  Score=37.18  Aligned_cols=55  Identities=25%  Similarity=0.201  Sum_probs=41.0

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      |.-|.+++.++.-.+.|++. -.-|-=-|+..+-.++..++-+++.+.||||||.-
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R-~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQ   78 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKR-RELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQ   78 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHH-hcCchHHhHHHHHHHHhcCceEEEEecCCCCcccc
Confidence            35688888998888877764 33454456666666666658899999999999975

>PHA02653 RNA helicase NPH-II; Provisional

Probab=85.87  E-value=0.34  Score=43.18  Aligned_cols=52  Identities=19%  Similarity=0.101  Sum_probs=38.3

Q ss_pred             ccccceeeeecccCcccee---------eecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccc
Q psy11948         80 SARKDIVGAAETGSGKTLA---------FGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTR  150 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~---------~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~  150 (167)
                      ..++|+++.|+||+|||.+         |++|.+..+.+-.                                    ...
T Consensus       177 ~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~------------------------------------~~~  220 (675)
T PHA02653        177 ISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID------------------------------------PNF  220 (675)
T ss_pred             HhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc------------------------------------ccc
Confidence            6789999999999999987         6666655442100                                    012


Q ss_pred             cccceEEEccchhhhcC
Q psy11948        151 NKLYALILAPTRELAIQ  167 (167)
Q Consensus       151 ~~~~aLIl~PTRELa~Q  167 (167)
                      ...+++|++||||||.|
T Consensus       221 ~~~~ilvt~PrreLa~q  237 (675)
T PHA02653        221 IERPIVLSLPRVALVRL  237 (675)
T ss_pred             CCcEEEEECcHHHHHHH
Confidence            34589999999999986

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=85.87  E-value=0.2  Score=41.04  Aligned_cols=22  Identities=50%  Similarity=0.679  Sum_probs=18.7

Q ss_pred             ceeeeecccCccceeeecchhh
Q psy11948         84 DIVGAAETGSGKTLAFGIPILT  105 (167)
Q Consensus        84 d~~~~a~tgsgkt~~~~~p~i~  105 (167)
                      .+++.+|||+|||.+|++|++.
T Consensus        16 ~~~i~apTGsGKT~~~~~~~l~   37 (357)
T TIGR03158        16 IIFNTAPTGAGKTLAWLTPLLH   37 (357)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3688999999999998887764

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.

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=85.65  E-value=0.43  Score=39.32  Aligned_cols=23  Identities=39%  Similarity=0.442  Sum_probs=19.7

Q ss_pred             cEEEEeecCCCcccccccchhhh
Q psy11948         42 DIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        42 d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ++++.++||||||.++.+|-+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~   23 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT   23 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc
Confidence            46899999999999999887654

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=85.17  E-value=0.88  Score=40.47  Aligned_cols=33  Identities=27%  Similarity=0.280  Sum_probs=25.7

Q ss_pred             CCchHHHhHHHHHHcc----CCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSALLA----RKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~----~~d~i~~a~tgsGKt~~   56 (167)
                      .|+..|..+|..+..+    .+..++.+-||||||+.
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~   45 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFT   45 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHH
Confidence            7999999999887543    23566888899999874

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=84.87  E-value=0.27  Score=44.44  Aligned_cols=47  Identities=28%  Similarity=0.383  Sum_probs=40.5

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..+.|+++++|||+|||+..++.+++.+.+                                         ..-++++||
T Consensus        45 ~~~~N~li~aPTgsGKTlIA~lai~~~l~~-----------------------------------------~~~k~vYiv   83 (766)
T COG1204          45 LSDENVLISAPTGSGKTLIALLAILSTLLE-----------------------------------------GGGKVVYIV   83 (766)
T ss_pred             cCCCcEEEEcCCCCchHHHHHHHHHHHHHh-----------------------------------------cCCcEEEEe
Confidence            347999999999999999999999988863                                         145799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |+|+||.|
T Consensus        84 PlkALa~E   91 (766)
T COG1204          84 PLKALAEE   91 (766)
T ss_pred             ChHHHHHH
Confidence            99999964

>PRK13764 ATPase; Provisional

Probab=84.82  E-value=0.73  Score=40.53  Aligned_cols=17  Identities=29%  Similarity=0.401  Sum_probs=14.9

Q ss_pred             CCcEEEEeecCCCcccc
Q psy11948         40 RKDIVGAAETGSGKTLA   56 (167)
Q Consensus        40 ~~d~i~~a~tgsGKt~~   56 (167)
                      +..++++++||||||..
T Consensus       257 ~~~ILIsG~TGSGKTTl  273 (602)
T PRK13764        257 AEGILIAGAPGAGKSTF  273 (602)
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            37899999999999973

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=84.71  E-value=0.85  Score=37.55  Aligned_cols=17  Identities=29%  Similarity=0.335  Sum_probs=14.7

Q ss_pred             CcEEEEeecCCCccccc
Q psy11948         41 KDIVGAAETGSGKTLAF   57 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~~   57 (167)
                      .-++++++||||||...
T Consensus       135 glilI~GpTGSGKTTtL  151 (358)
T TIGR02524       135 GIVFITGATGSGKSTLL  151 (358)
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            67999999999999743

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>KOG1802|consensus

Probab=84.59  E-value=0.97  Score=40.18  Aligned_cols=46  Identities=15%  Similarity=0.089  Sum_probs=36.4

Q ss_pred             HHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         16 ALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        16 ~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .+...++.++..-|..|+..++.. -=.++++|.|+|||..-.--+.
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~r-plsLIQGPPGTGKTvtsa~IVy  447 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQR-PLSLIQGPPGTGKTVTSATIVY  447 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcC-CceeeecCCCCCceehhHHHHH
Confidence            455567888889999999999987 5667899999999986544333

>KOG2340|consensus

Probab=84.26  E-value=1  Score=39.02  Aligned_cols=45  Identities=13%  Similarity=0.206  Sum_probs=32.3

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeec-CCCc--ccccccchhhhhhc
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAET-GSGK--TLAFGIPILTGIVN   67 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~t-gsGK--t~~~~lp~l~~~~~   67 (167)
                      -...|+.|.+-+-.+... +|++.-..| +.|+  +..|++.+|.++++
T Consensus       214 s~pltalQ~~L~~~m~~Y-rDl~y~~~s~kn~~e~R~lYclH~lNHi~K  261 (698)
T KOG2340|consen  214 SEPLTALQKELFKIMFNY-RDLLYPTRSQKNGEEYRSLYCLHALNHILK  261 (698)
T ss_pred             cCcchHHHHHHHHHHHhh-hhhccccccccccchhhhhHHHHHHHHHHH
Confidence            357889999999888877 898854443 3444  44577888888874

>PRK10536 hypothetical protein; Provisional

Probab=84.13  E-value=1.2  Score=35.04  Aligned_cols=45  Identities=16%  Similarity=0.143  Sum_probs=32.8

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      .++..-+..|...+-.+... .-+++.++.|+|||+...--.+..+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~-~lV~i~G~aGTGKT~La~a~a~~~l   99 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESK-QLIFATGEAGCGKTWISAAKAAEAL   99 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcC-CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            35566777899988877766 6888999999999986544444333

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=83.98  E-value=0.3  Score=45.03  Aligned_cols=44  Identities=25%  Similarity=0.245  Sum_probs=38.5

Q ss_pred             ccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEccc
Q psy11948         82 RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPT  161 (167)
Q Consensus        82 ~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PT  161 (167)
                      ++|.+++++||+|||.+|+.|++..+.                                          ...+++||+||
T Consensus       472 ~~d~Ll~adTGsGKT~val~a~l~al~------------------------------------------~g~qvlvLvPT  509 (926)
T TIGR00580       472 PMDRLVCGDVGFGKTEVAMRAAFKAVL------------------------------------------DGKQVAVLVPT  509 (926)
T ss_pred             cCCEEEECCCCccHHHHHHHHHHHHHH------------------------------------------hCCeEEEEeCc
Confidence            479999999999999999999987663                                          12589999999


Q ss_pred             hhhhcC
Q psy11948        162 RELAIQ  167 (167)
Q Consensus       162 RELa~Q  167 (167)
                      ++||.|
T Consensus       510 ~~LA~Q  515 (926)
T TIGR00580       510 TLLAQQ  515 (926)
T ss_pred             HHHHHH
Confidence            999988

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=83.97  E-value=1.3  Score=38.09  Aligned_cols=38  Identities=24%  Similarity=0.230  Sum_probs=25.6

Q ss_pred             HHHCCCCCCchHHHhHHHHHHccCCc-EEEEeecCCCccccc
Q psy11948         17 LYQKGFKTPTKIQSMVMPSALLARKD-IVGAAETGSGKTLAF   57 (167)
Q Consensus        17 l~~~g~~~pt~iQ~~~ip~~l~~~~d-~i~~a~tgsGKt~~~   57 (167)
                      |.+.||   ++-|...+-.++...+. ++++++||||||...
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL  259 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL  259 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            455565   45566666555554344 679999999999864

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>TIGR00595 priA primosomal protein N'

Probab=83.59  E-value=0.39  Score=41.30  Aligned_cols=18  Identities=39%  Similarity=0.329  Sum_probs=14.2

Q ss_pred             EEEeecCCCcccccccch
Q psy11948         44 VGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        44 i~~a~tgsGKt~~~~lp~   61 (167)
                      ++.++||||||..|+..+
T Consensus         1 LL~g~TGsGKT~v~l~~i   18 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAI   18 (505)
T ss_pred             CccCCCCCCHHHHHHHHH
Confidence            357899999999986543

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).

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=83.43  E-value=0.62  Score=39.36  Aligned_cols=23  Identities=43%  Similarity=0.583  Sum_probs=20.3

Q ss_pred             cEEEEeecCCCcccccccchhhh
Q psy11948         42 DIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        42 d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ++++.++||||||..+.+|.+..
T Consensus        46 h~lvig~tgSGKt~~~viP~ll~   68 (469)
T PF02534_consen   46 HVLVIGPTGSGKTTSFVIPNLLN   68 (469)
T ss_pred             EEEEEeCCCCCccceeeHhHHHh
Confidence            59999999999999999987643

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>KOG0950|consensus

Probab=83.42  E-value=0.68  Score=42.39  Aligned_cols=57  Identities=25%  Similarity=0.346  Sum_probs=42.8

Q ss_pred             CCHHHHH-HHHHCCCCCCchHHHhHH--HHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          9 IPETIIR-ALYQKGFKTPTKIQSMVM--PSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         9 l~~~l~~-~l~~~g~~~pt~iQ~~~i--p~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +++.+.. ..+..|+..++..|..|+  |.++.+ .++|...||+.|||++--+=++..++
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~-~nliys~Pts~gktlvaeilml~~~l  266 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLER-KNLIYSLPTSAGKTLVAEILMLREVL  266 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcc-cceEEeCCCccchHHHHHHHHHHHHH
Confidence            3444444 344679999999999998  778855 99999999999999985554444444

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=83.41  E-value=0.33  Score=42.87  Aligned_cols=55  Identities=27%  Similarity=0.326  Sum_probs=43.0

Q ss_pred             CCCcccccc----------ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhh
Q psy11948         71 NPTEEDEND----------SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESA  140 (167)
Q Consensus        71 ~~~~~~~~~----------~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~  140 (167)
                      .+|..|..+          ....+.+++++||+|||.+|++|++..+.                                
T Consensus       235 ~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~--------------------------------  282 (630)
T TIGR00643       235 KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE--------------------------------  282 (630)
T ss_pred             CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH--------------------------------
Confidence            467777544          11246799999999999999999987653                                


Q ss_pred             cchhhhhccccccceEEEccchhhhcC
Q psy11948        141 NTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       141 ~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                ...+++||+||++||.|
T Consensus       283 ----------~g~qvlilaPT~~LA~Q  299 (630)
T TIGR00643       283 ----------AGYQVALMAPTEILAEQ  299 (630)
T ss_pred             ----------cCCcEEEECCHHHHHHH
Confidence                      23579999999999987

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=83.03  E-value=1.6  Score=34.31  Aligned_cols=39  Identities=26%  Similarity=0.261  Sum_probs=25.4

Q ss_pred             HHHHCCCCCCchHHHhHHHHHHc-cCCcEEEEeecCCCccccc
Q psy11948         16 ALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        16 ~l~~~g~~~pt~iQ~~~ip~~l~-~~~d~i~~a~tgsGKt~~~   57 (167)
                      .|.+.|+   ++-|...|-.++. ...-++++++||||||...
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l   97 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL   97 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH
Confidence            3556664   4445555655443 3245889999999999854

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=82.89  E-value=0.34  Score=43.84  Aligned_cols=53  Identities=19%  Similarity=0.265  Sum_probs=41.4

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+..|-.+    +.|+  ++.++||+|||++|.+|++...+                                      
T Consensus        78 ~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al--------------------------------------  117 (790)
T PRK09200         78 RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL--------------------------------------  117 (790)
T ss_pred             CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHH--------------------------------------
Confidence            566666444    3333  99999999999999999985443                                      


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .+.+++|++||++||.|
T Consensus       118 ----~G~~v~VvTpt~~LA~q  134 (790)
T PRK09200        118 ----EGKGVHLITVNDYLAKR  134 (790)
T ss_pred             ----cCCCeEEEeCCHHHHHH
Confidence                24579999999999987

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=82.33  E-value=0.4  Score=43.68  Aligned_cols=45  Identities=27%  Similarity=0.275  Sum_probs=37.7

Q ss_pred             cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEcc
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP  160 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~P  160 (167)
                      .+.++++.++||+|||..|.+++++...                                          ...+++|+.|
T Consensus        16 ~~~~vIi~a~TGSGKTT~vpl~lL~~~~------------------------------------------~~~~ilvlqP   53 (819)
T TIGR01970        16 AHPQVVLEAPPGAGKSTAVPLALLDAPG------------------------------------------IGGKIIMLEP   53 (819)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHhhc------------------------------------------cCCeEEEEeC
Confidence            4678999999999999999999986541                                          1247999999


Q ss_pred             chhhhcC
Q psy11948        161 TRELAIQ  167 (167)
Q Consensus       161 TRELa~Q  167 (167)
                      ||++|.|
T Consensus        54 rR~aA~q   60 (819)
T TIGR01970        54 RRLAARS   60 (819)
T ss_pred             cHHHHHH
Confidence            9999976

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=82.25  E-value=0.61  Score=38.00  Aligned_cols=16  Identities=50%  Similarity=0.611  Sum_probs=14.3

Q ss_pred             CcEEEEeecCCCcccc
Q psy11948         41 KDIVGAAETGSGKTLA   56 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~   56 (167)
                      .++++.+|||||||+-
T Consensus        98 SNILLiGPTGsGKTlL  113 (408)
T COG1219          98 SNILLIGPTGSGKTLL  113 (408)
T ss_pred             ccEEEECCCCCcHHHH
Confidence            6899999999999973

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=82.24  E-value=0.86  Score=40.41  Aligned_cols=25  Identities=28%  Similarity=0.412  Sum_probs=21.8

Q ss_pred             CCcEEEEeecCCCcccccccchhhh
Q psy11948         40 RKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        40 ~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ..++++.|+||||||..+.+|-+..
T Consensus       175 ~~HvlviapTgSGKgvg~ViPnLL~  199 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPTLLS  199 (636)
T ss_pred             CceEEEEecCCCCCceEEEccchhh
Confidence            3579999999999999999987754

>KOG1133|consensus

Probab=82.16  E-value=1.2  Score=39.56  Aligned_cols=43  Identities=33%  Similarity=0.285  Sum_probs=31.5

Q ss_pred             CCchHHHhHHHHH---HccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         24 TPTKIQSMVMPSA---LLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        24 ~pt~iQ~~~ip~~---l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|+.||...+..+   +..++=-|.-+|||+|||++.+-..+..+-
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~   60 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLR   60 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHH
Confidence            6888999877654   344366678999999999987765555443

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=82.00  E-value=1.4  Score=42.05  Aligned_cols=41  Identities=24%  Similarity=0.370  Sum_probs=29.1

Q ss_pred             CCCCCCchHHH--hHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         20 KGFKTPTKIQS--MVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        20 ~g~~~pt~iQ~--~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      ..|...-||..  ..|...+.++..++++++||||||.-  +|.+
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~  102 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQ--LPKI  102 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHH--HHHH
Confidence            45666677766  45555666657788999999999993  4543

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.

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

Probab=81.69  E-value=2.5  Score=34.83  Aligned_cols=43  Identities=23%  Similarity=0.118  Sum_probs=31.3

Q ss_pred             CCchHHHhHHHHHH---ccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         24 TPTKIQSMVMPSAL---LARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l---~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .+|+-|+++-..++   ....|.++.|-||+|||.. +.+.+...++
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~  142 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALN  142 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHh
Confidence            68899987765544   3348999999999999984 3455555554

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=81.63  E-value=1.9  Score=35.44  Aligned_cols=54  Identities=20%  Similarity=0.227  Sum_probs=35.9

Q ss_pred             CchHHHhHHHHH------HccCCcEEEEeecCCCcccccccchhhhhhcccCCCCccccccccccceeeeecccC
Q psy11948         25 PTKIQSMVMPSA------LLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETGS   93 (167)
Q Consensus        25 pt~iQ~~~ip~~------l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~~~a~tgs   93 (167)
                      +++=|+.++..+      ..+ ..+.+.++-|+|||+  ++-.+...++            ..+..+++.|+||.
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~-~~~fv~G~~GtGKs~--l~~~i~~~~~------------~~~~~~~~~a~tg~   61 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEG-LNFFVTGPAGTGKSF--LIKAIIDYLR------------SRGKKVLVTAPTGI   61 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCC-cEEEEEcCCCCChhH--HHHHHHHHhc------------cccceEEEecchHH
Confidence            456688887766      455 789999999999996  3322222221            13456778888873

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=81.62  E-value=0.9  Score=35.42  Aligned_cols=27  Identities=37%  Similarity=0.446  Sum_probs=19.4

Q ss_pred             hHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         31 MVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        31 ~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ..+.....++..++++++||||||...
T Consensus       118 ~~l~~~v~~~~~ili~G~tGSGKTT~l  144 (270)
T PF00437_consen  118 EFLRSAVRGRGNILISGPTGSGKTTLL  144 (270)
T ss_dssp             HHHHHCHHTTEEEEEEESTTSSHHHHH
T ss_pred             HHHhhccccceEEEEECCCccccchHH
Confidence            334333344589999999999999754

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=81.52  E-value=1  Score=35.60  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=19.8

Q ss_pred             HHHHHHccCCcEEEEeecCCCcccc
Q psy11948         32 VMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        32 ~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .+..++..++.+++++++|+|||..
T Consensus        25 ll~~l~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   25 LLDLLLSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HHHHHHHCTEEEEEESSTTSSHHHH
T ss_pred             HHHHHHHcCCcEEEECCCCCchhHH
Confidence            3345556669999999999999974

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=81.15  E-value=1.4  Score=37.73  Aligned_cols=31  Identities=29%  Similarity=0.281  Sum_probs=22.7

Q ss_pred             chHHHhHHHHHHccCCc-EEEEeecCCCcccc
Q psy11948         26 TKIQSMVMPSALLARKD-IVGAAETGSGKTLA   56 (167)
Q Consensus        26 t~iQ~~~ip~~l~~~~d-~i~~a~tgsGKt~~   56 (167)
                      ++.|...+-.++...+- +++.+|||||||..
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT  274 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT  274 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH
Confidence            56677777666655444 56899999999985

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=81.06  E-value=0.97  Score=40.32  Aligned_cols=25  Identities=28%  Similarity=0.308  Sum_probs=21.6

Q ss_pred             CCcEEEEeecCCCcccccccchhhh
Q psy11948         40 RKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        40 ~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ..++++.|+||||||..|.+|-+-.
T Consensus       139 ~~hvlviApTgSGKgvg~VIPnLL~  163 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPTLLT  163 (670)
T ss_pred             CceEEEEecCCCCceeeehHhHHhc
Confidence            3589999999999999999987654

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=81.05  E-value=1.7  Score=38.01  Aligned_cols=38  Identities=26%  Similarity=0.378  Sum_probs=24.9

Q ss_pred             HHHCCCCCCchHHHhHHHHHHcc-CCcEEEEeecCCCccccc
Q psy11948         17 LYQKGFKTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        17 l~~~g~~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~   57 (167)
                      |.+.||   .+-|...|..++.. .--++++++||||||...
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl  333 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL  333 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH
Confidence            556665   34455555554443 235779999999999864

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>KOG1132|consensus

Probab=81.01  E-value=0.81  Score=41.59  Aligned_cols=44  Identities=23%  Similarity=0.250  Sum_probs=33.4

Q ss_pred             CCchHHHhHHHHHHcc---CCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         24 TPTKIQSMVMPSALLA---RKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~---~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      .|++.|...+-.+++.   ..+.++-+|||+|||++.+=..+....+
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~   67 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQH   67 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHH
Confidence            7899999888766542   3678999999999999887655544443

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=80.58  E-value=3.5  Score=36.50  Aligned_cols=30  Identities=27%  Similarity=0.256  Sum_probs=26.4

Q ss_pred             chHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         26 TKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        26 t~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      ++.|+.++-..+.. +-+++.+..|+|||..
T Consensus       154 ~d~Qk~Av~~a~~~-~~~vItGgpGTGKTt~  183 (615)
T PRK10875        154 VDWQKVAAAVALTR-RISVISGGPGTGKTTT  183 (615)
T ss_pred             CHHHHHHHHHHhcC-CeEEEEeCCCCCHHHH
Confidence            57999999888877 8899999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	167
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		9e-09
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		3e-08
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-08
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		6e-08
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		2e-05
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-06
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-06
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		4e-06
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		8e-05
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		5e-06
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-05
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		1e-05
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-05
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		8e-04
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-05
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-05
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-05
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		8e-05
3ly5_A	262	Ddx18 Dead-Domain Length = 262		8e-05
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		9e-05
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		2e-04
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		3e-04
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-04
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		3e-04
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		3e-04
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		5e-04
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		5e-04
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		7e-04
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		8e-04
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		8e-04

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 3  EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
          E+  F +   I+ AL+ +G  TPT IQ+  +P AL   KD++G A TG+GKTLAF +PI
Sbjct: 2  EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEG-KDLIGQARTGTGKTLAFALPI 59

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 54.7 bits (130), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 3  EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
          E+  F +   I+ AL+ +G  TPT I++  +P AL   KD++G A TG+GKTLAF +PI
Sbjct: 2  EFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEG-KDLIGQARTGTGKTLAFALPI 59

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 3/63 (4%)
Query: 3  EWVKFN---IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI 59
          E+  FN   + + I+ A+  KGF+ PT IQ  V+P  L    +IV  A TGSGKT +F I
Sbjct: 4  EYXNFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAI 63
Query: 60 PIL 62
          P++
Sbjct: 64 PLI 66

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
             + + +  A  Q G+  PTKIQ   +P AL  R DI+G AETGSGKT AF +PIL  + 
Sbjct: 48  LGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGR-DIIGLAETGSGKTGAFALPILNAL- 105
Query: 67  NKLENP 72
             LE P
Sbjct: 106 --LETP 109

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 37/85 (43%), Gaps = 39/85 (45%)
Query: 83  KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSANT 142
           +DI+G AETGSGKT AF +PIL  +   LE P                            
Sbjct: 81  RDIIGLAETGSGKTGAFALPILNAL---LETP---------------------------- 109
Query: 143 TEFVKKTRNKLYALILAPTRELAIQ 167
                    +L+AL+L PTRELA Q
Sbjct: 110 --------QRLFALVLTPTRELAFQ 126

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           +  +   ++ + II  + + G+K PT IQ   +P  + + +D++  A+TGSGKT AF +P
Sbjct: 55  IQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIP-VISSGRDLMACAQTGSGKTAAFLLP 113
Query: 61  ILTGIVNKLENPTE 74
           IL+ +   LE+P E
Sbjct: 114 ILSKL---LEDPHE 124

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 6  KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          ++ I   +++ +   GF+ PT IQ   +P  L  R +++ +A TGSGKTLAF IPIL
Sbjct: 33 EYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGR-ELLASAPTGSGKTLAFSIPIL 88

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 37/60 (61%), Gaps = 5/60 (8%)
Query: 9  IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNK 68
          I   I+ A YQ+    PT IQ   +P A+L  +DI+  A+TGSGKT AF IPI+  +V +
Sbjct: 34 IRNNILLASYQR----PTPIQKNAIP-AILEHRDIMACAQTGSGKTAAFLIPIINHLVCQ 88

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 37/86 (43%), Gaps = 30/86 (34%)
Query: 82  RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSAN 141
            +DI+  A+TGSGKT AF IPI+  +V +                              N
Sbjct: 60  HRDIMACAQTGSGKTAAFLIPIINHLVCQ----------------------------DLN 91
Query: 142 TTEFVKKTRNKLYALILAPTRELAIQ 167
              + K    K   LILAPTRELAIQ
Sbjct: 92  QQRYSKTAYPK--CLILAPTRELAIQ 115

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/66 (43%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 11 ETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT-GIVNKL 69
          E I +A+ + GFK  T++QS  +P  +L  K++V  A+TGSGKT A+ IPIL  G+ + +
Sbjct: 3  EKIEQAIREMGFKNFTEVQSKTIP-LMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLV 61
Query: 70 ENPTEE 75
            PT E
Sbjct: 62 VTPTRE 67

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 8   NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
           N P  ++  + ++ F  PT IQ+   P AL +  D+VG A+TGSGKTL++ +P +  I +
Sbjct: 49  NFPANVMDVIARQNFTEPTAIQAQGWPVAL-SGLDMVGVAQTGSGKTLSYLLPAIVHINH 107
Query: 68  K 68
           +
Sbjct: 108 Q 108

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 8  NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN 67
          N P  ++  + ++ F  PT IQ+   P AL +  D+VG A+TGSGKTL++ +P +  I +
Sbjct: 35 NFPANVMDVIARQNFTEPTAIQAQGWPVAL-SGLDMVGVAQTGSGKTLSYLLPAIVHINH 93
Query: 68 K 68
          +
Sbjct: 94 Q 94

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          F + +  ++ L +  ++  T+IQ   +  AL   KD++GAA+TGSGKTLAF +P+L  +
Sbjct: 30 FPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQG-KDVLGAAKTGSGKTLAFLVPVLEAL 87

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 16/25 (64%), Positives = 22/25 (88%)
Query: 83  KDIVGAAETGSGKTLAFGIPILTGI 107
           KD++GAA+TGSGKTLAF +P+L  +
Sbjct: 63  KDVLGAAKTGSGKTLAFLVPVLEAL 87

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 7  FNIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
           N+ E+++R +Y  GF+ P+ IQ   ++P   +   D++  A++G+GKT  F I IL  I
Sbjct: 19 MNLSESLLRGIYAYGFEKPSAIQQRAILPC--IKGYDVIAQAQSGTGKTATFAISILQQI 76

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 7   FNIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
            N+ E+++R +Y  GF+ P+ IQ   ++P   +   D++  A++G+GKT  F I IL  I
Sbjct: 45  MNLSESLLRGIYAYGFEKPSAIQQRAILPC--IKGYDVIAQAQSGTGKTATFAISILQQI 102

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F +   ++  +++ GF+ P+ IQ   +P A+  R DI+  A+ G+GKT AF IP L  + 
Sbjct: 26 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGR-DILARAKNGTGKTAAFVIPTLEKVK 84
Query: 67 NKL 69
           KL
Sbjct: 85 PKL 87

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 6  KFNIPETIIRALYQKGFKTPTKIQS-MVMPSALLARKDIVGAAETGSGKTLAFGIPILTG 64
            N+ E+++R +Y  GF+ P+ IQ   ++P   +   D++  A++G+G T  F I IL  
Sbjct: 19 DMNLSESLLRGIYAYGFEXPSAIQQRAILPC--IXGYDVIAQAQSGTGXTATFAISILQQ 76
Query: 65 I 65
          I
Sbjct: 77 I 77

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 9   IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
           + E  ++A+ + GF   T+IQ   +   LL  +D++ AA+TGSGKTLAF IP +  IV
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSI-RPLLEGRDLLAAAKTGSGKTLAFLIPAVELIV 117

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 8  NIPETIIRALYQKGFKTPTKIQSM-VMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          N+ E+++R +Y  GF+ P+ IQ   ++P   +   D++  A++G+GKT  F I IL
Sbjct: 36 NLKESLLRGIYAYGFEKPSAIQQRAIIPC--IKGYDVIAQAQSGTGKTATFAISIL 89

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 3  EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          ++ +F     II A+    F  PT+IQ  ++P AL   +  VG ++TG+GKT A+ +PI 
Sbjct: 5  QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG-ESXVGQSQTGTGKTHAYLLPIX 63
Query: 63 TGI 65
            I
Sbjct: 64 EKI 66

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9   IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
           + E ++R +Y  GF+ P+ IQ   +   +  R D++  +++G+GKT  F I +L  +
Sbjct: 45  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 100

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9   IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
           + E ++R +Y  GF+ P+ IQ   +   +  R D++  +++G+GKT  F I +L  +
Sbjct: 45  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 100

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9  IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          + E ++R +Y  GF+ P+ IQ   +   +  R D++  +++G+GKT  F I +L  +
Sbjct: 23 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 78

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9  IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          + E ++R +Y  GF+ P+ IQ   +   +  R D++  +++G+GKT  F I +L  +
Sbjct: 44 LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSISVLQCL 99

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9  IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          + E ++R +Y  GF+ P+ IQ   +   +  R D++  +++G+GKT  F + +L  +
Sbjct: 8  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSVSVLQCL 63

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 9  IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          + E ++R +Y  GF+ P+ IQ   +   +  R D++  +++G+GKT  F + +L  +
Sbjct: 8  LREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSVSVLQCL 63

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 1  MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
          M+ +  F +   ++RA+   GF+ P+++Q   +P A+L   D++  A++G GKT  F + 
Sbjct: 6  MSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLA 64
Query: 61 ILTGI 65
           L  +
Sbjct: 65 TLQQL 69

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 42/88 (47%), Gaps = 25/88 (28%)
Query: 82  RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTXXXXXXXXXXXXXXXXXXXXXXXSAN 141
           ++D++  A+TGSGKT AF +PIL+ I +  + P                           
Sbjct: 52  KRDLMACAQTGSGKTAAFLLPILSQIYS--DGPGEALRA--------------------- 88
Query: 142 TTEFVKKTRNKLY--ALILAPTRELAIQ 167
             E  +  R K Y  +L+LAPTRELA+Q
Sbjct: 89  MKENGRYGRRKQYPISLVLAPTRELAVQ 116

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 52/103 (50%), Gaps = 8/103 (7%)
Query: 3   EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
           E+  + +   ++  +++ G++ P+ IQ   +P AL  R DI+  A+ G+GK+ A+ IP+L
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGR-DILARAKNGTGKSGAYLIPLL 62
Query: 63  TGIVNKLEN-------PTEEDENDSARKDIVGAAETGSGKTLA 98
             +  K +N       PT E     ++  I  +   G  K +A
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMA 105

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	167
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	1e-18
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-18
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	4e-18
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	4e-18
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	9e-18
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-17
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	9e-17
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	1e-16
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-16
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	3e-16
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	4e-16
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	4e-16
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-16
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-15
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-15
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	3e-15
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	5e-15
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	5e-15
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	5e-15
3bor_A	237	Human initiation factor 4A-II; translation initiat	5e-15
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	6e-15
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-14
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-14
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-14
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-14
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-14
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	5e-14
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-13
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-13
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-13
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	8e-12
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	4e-09
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	1e-07
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	3e-06

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score = 78.4 bits (194), Expect = 1e-18
 Identities = 23/56 (41%), Positives = 37/56 (66%), Gaps = 1/56 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          F + +  ++ L +  ++  T+IQ   +  AL   KD++GAA+TGSGKTLAF +P+L
Sbjct: 30 FPLSKKTLKGLQEAQYRLVTEIQKQTIGLAL-QGKDVLGAAKTGSGKTLAFLVPVL 84

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 78.0 bits (193), Expect = 2e-18
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F     II A+    F  PT+IQ  ++P   L  + +VG ++TG+GKT A+ +PI+  I 
Sbjct: 9  FPFQPFIIEAIKTLRFYKPTEIQERIIP-GALRGESMVGQSQTGTGKTHAYLLPIMEKIK 67

Query: 67 NKLENP 72
           +    
Sbjct: 68 PERAEV 73

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score = 79.5 bits (196), Expect = 4e-18
 Identities = 30/161 (18%), Positives = 51/161 (31%), Gaps = 76/161 (47%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
             + + I +A+ +  F   T +Q   +                          PIL+   
Sbjct: 26  GVLDKEIHKAITRMEFPGLTPVQQKTIK-------------------------PILSS-- 58

Query: 67  NKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEE 126
                            D++  A+TG+GKT AF IPI   ++N   +             
Sbjct: 59  --------------EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS------------ 92

Query: 127 EAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
                                  +  + A+I+APTR+LA+Q
Sbjct: 93  -----------------------QYMVKAVIVAPTRDLALQ 110

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score = 78.7 bits (195), Expect = 4e-18
 Identities = 25/59 (42%), Positives = 36/59 (61%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
           N+ + I+ A+  KGF+ PT IQ  V+P  L    +IV  A TGSGKT +F IP++  +
Sbjct: 11 LNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELV 69

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score = 78.7 bits (194), Expect = 9e-18
 Identities = 29/161 (18%), Positives = 50/161 (31%), Gaps = 76/161 (47%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
             + + I +A+ +  F   T +Q   +   L             S +             
Sbjct: 77  GVLDKEIHKAITRMEFPGLTPVQQKTIKPIL-------------SSE------------- 110

Query: 67  NKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEE 126
                            D++  A+TG+GKT AF IPI   ++N   +             
Sbjct: 111 ---------------DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS------------ 143

Query: 127 EAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
                                  +  + A+I+APTR+LA+Q
Sbjct: 144 -----------------------QYMVKAVIVAPTRDLALQ 161

>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} Length = 249

 Score = 75.0 bits (185), Expect = 3e-17
 Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 1/56 (1%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
             + + +  A  Q G+  PTKIQ   +P AL   +DI+G AETGSGKT AF +PIL
Sbjct: 48  LGVTDVLCEACDQLGWTKPTKIQIEAIPLAL-QGRDIIGLAETGSGKTGAFALPIL 102

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score = 72.9 bits (180), Expect = 9e-17
 Identities = 18/66 (27%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          + +   ++  +++ G++ P+ IQ   +P   L+ +DI+  A+ G+GK+ A+ IP+L  + 
Sbjct: 8  YCLKRELLMGIFEMGWEKPSPIQEESIP-IALSGRDILARAKNGTGKSGAYLIPLLERLD 66

Query: 67 NKLENP 72
           K +N 
Sbjct: 67 LKKDNI 72

>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} Length = 262

 Score = 73.9 bits (182), Expect = 1e-16
 Identities = 23/55 (41%), Positives = 35/55 (63%), Gaps = 1/55 (1%)

Query: 8   NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
            + E  ++A+ + GF   T+IQ   +   LL  +D++ AA+TGSGKTLAF IP +
Sbjct: 60  LVNENTLKAIKEMGFTNMTEIQHKSIR-PLLEGRDLLAAAKTGSGKTLAFLIPAV 113

>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 Length = 207

 Score = 72.2 bits (178), Expect = 2e-16
 Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          F +   I+ AL+ +G  TPT IQ+  +P   L  KD++G A TG+GKTLAF +PI   +
Sbjct: 6  FPLKPEILEALHGRGLTTPTPIQAAALP-LALEGKDLIGQARTGTGKTLAFALPIAERL 63

>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} Length = 245

 Score = 72.6 bits (179), Expect = 3e-16
 Identities = 23/60 (38%), Positives = 38/60 (63%), Gaps = 1/60 (1%)

Query: 6  KFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          ++ I   +++ +   GF+ PT IQ   +P  +L  ++++ +A TGSGKTLAF IPIL  +
Sbjct: 33 EYKINSRLLQNILDAGFQMPTPIQMQAIP-VMLHGRELLASAPTGSGKTLAFSIPILMQL 91

>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} Length = 242

 Score = 71.8 bits (177), Expect = 4e-16
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 3  EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
           + + N P  ++  + ++ F  PT IQ+   P AL    D+VG A+TGSGKTL++ +P +
Sbjct: 30 NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGL-DMVGVAQTGSGKTLSYLLPAI 88

Query: 63 TGI 65
            I
Sbjct: 89 VHI 91

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score = 72.9 bits (180), Expect = 4e-16
 Identities = 25/54 (46%), Positives = 37/54 (68%), Gaps = 1/54 (1%)

Query: 9  IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          + E I +A+ + GFK  T++QS  +P  +L  K++V  A+TGSGKT A+ IPIL
Sbjct: 1  MNEKIEQAIREMGFKNFTEVQSKTIP-LMLQGKNVVVRAKTGSGKTAAYAIPIL 53

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 72.6 bits (179), Expect = 7e-16
 Identities = 35/168 (20%), Positives = 52/168 (30%), Gaps = 70/168 (41%)

Query: 3   EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI- 61
            +    + E I+  +    +  PT +Q                             IPI 
Sbjct: 16  SFSDVEMGEIIMGNIELTRYTRPTPVQ--------------------------KHAIPII 49

Query: 62  LTGIVNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVN--KLENPTEEDE 119
                                +D++  A+TGSGKT AF +PIL+ I +    E      E
Sbjct: 50  KEK------------------RDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKE 91

Query: 120 NDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
           N      +                           +L+LAPTRELA+Q
Sbjct: 92  NGRYGRRKQYP-----------------------ISLVLAPTRELAVQ 116

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score = 71.4 bits (176), Expect = 2e-15
 Identities = 17/67 (25%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGI 65
            +   +++ +Y   F+ P+KIQ   +P  L    ++++  +++G+GKT AF + +LT +
Sbjct: 10 LGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRV 69

Query: 66 VNKLENP 72
            +  +P
Sbjct: 70 NPEDASP 76

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score = 71.0 bits (175), Expect = 3e-15
 Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
            + E ++R ++  GF+ P+ IQ   +   ++   D++  A++G+GKT  F I  L  I 
Sbjct: 26 MELDENLLRGVFGYGFEEPSAIQQRAIM-PIIEGHDVLAQAQSGTGKTGTFSIAALQRID 84

Query: 67 NKLENP 72
            ++ P
Sbjct: 85 TSVKAP 90

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score = 70.7 bits (174), Expect = 3e-15
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
            N+ E+++R +Y  GF+ P+ IQ   +    +   D++  A++G+GKT  F I IL  I 
Sbjct: 45  MNLSESLLRGIYAYGFEKPSAIQQRAIL-PCIKGYDVIAQAQSGTGKTATFAISILQQIE 103

Query: 67  NKLENP 72
             L+  
Sbjct: 104 LDLKAT 109

>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} Length = 228

 Score = 68.7 bits (169), Expect = 5e-15
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          F     +++++ + G   PT IQS   P  L    D++  A+TG+GKTL++ +P    +
Sbjct: 25 FQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGI-DLIVVAQTGTGKTLSYLMPGFIHL 82

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score = 70.3 bits (173), Expect = 5e-15
 Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
             + E ++R +Y  GF+ P+ IQ   +   ++  +D++  +++G+GKT  F I +L  + 
Sbjct: 42  MGLREDLLRGIYAYGFEKPSAIQQRAIK-QIIKGRDVIAQSQSGTGKTATFSISVLQCLD 100

Query: 67  NKLENP 72
            ++   
Sbjct: 101 IQVRET 106

>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 Length = 224

 Score = 68.7 bits (169), Expect = 5e-15
 Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 1  MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
          + ++    + E ++R ++  GF+ P+ IQ   +   ++   D++  A++G+GKT  F I 
Sbjct: 13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIM-PIIEGHDVLAQAQSGTGKTGTFSIA 71

Query: 61 ILTGIVNKLENP 72
           L  I   ++ P
Sbjct: 72 ALQRIDTSVKAP 83

>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* Length = 237

 Score = 68.8 bits (169), Expect = 5e-15
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 1  MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
          +  +   N+ E+++R +Y  GF+ P+ IQ   +    +   D++  A++G+GKT  F I 
Sbjct: 29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAII-PCIKGYDVIAQAQSGTGKTATFAIS 87

Query: 61 ILTGIVNKLENP 72
          IL  +  + +  
Sbjct: 88 ILQQLEIEFKET 99

>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 Length = 253

 Score = 69.1 bits (170), Expect = 6e-15
 Identities = 37/162 (22%), Positives = 48/162 (29%), Gaps = 75/162 (46%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI-LTGI 65
             +  TI   +    ++ PT IQ                             IP  L   
Sbjct: 28  LKLDPTIRNNILLASYQRPTPIQ--------------------------KNAIPAILEH- 60

Query: 66  VNKLENPTEEDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLE 125
                            +DI+  A+TGSGKT AF IPI+  +V +  N     +      
Sbjct: 61  -----------------RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK- 102

Query: 126 EEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
                                         LILAPTRELAIQ
Sbjct: 103 -----------------------------CLILAPTRELAIQ 115

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score = 69.5 bits (171), Expect = 1e-14
 Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGI 65
            +   +++ +Y  GF  P+KIQ   +P  L    ++++  +++G+GKT AF + +L+ +
Sbjct: 30 LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 89

Query: 66 VNKLENP 72
              + P
Sbjct: 90 EPANKYP 96

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F +   ++  +++ GF+ P+ IQ   +P A+  R DI+  A+ G+GKT AF IP L  + 
Sbjct: 26 FYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGR-DILARAKNGTGKTAAFVIPTLEKVK 84

Query: 67 NKLENP 72
           KL   
Sbjct: 85 PKLNKI 90

>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* Length = 230

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
            +   ++  L   GF+ P+ +Q   +P       D++  A++G+GKT  F    L  +V
Sbjct: 29 LLLSRPVLEGLRAAGFERPSPVQLKAIP-LGRCGLDLIVQAKSGTGKTCVFSTIALDSLV 87

Query: 67 NKLENP 72
           +  + 
Sbjct: 88 LENLST 93

>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 Length = 220

 Score = 67.3 bits (165), Expect = 2e-14
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F +   ++RA+   GF+ P+++Q   +P A+L   D++  A++G GKT  F +  L  + 
Sbjct: 19 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGM-DVLCQAKSGMGKTAVFVLATLQQLE 77

Query: 67 NKLENP 72
                
Sbjct: 78 PVTGQV 83

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score = 67.7 bits (166), Expect = 4e-14
 Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 7   FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGIPILTGI 65
             +   +++ +Y  GF  P+KIQ   +P  L    ++++  +++G+GKT AF + +L+ +
Sbjct: 97  LRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV 156

Query: 66  VNKLENP 72
               + P
Sbjct: 157 EPANKYP 163

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 67.6 bits (166), Expect = 5e-14
 Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 3   EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
            +   ++ + II  + + G+K PT IQ   +P  + + +D++  A+TGSGKT AF +PIL
Sbjct: 57  HFTSADLRDIIIDNVNKSGYKIPTPIQKCSIP-VISSGRDLMACAQTGSGKTAAFLLPIL 115

Query: 63  TGIVNK 68
           + ++  
Sbjct: 116 SKLLED 121

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score = 65.7 bits (161), Expect = 2e-13
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F +   ++RA+   GF+ P+++Q   +P A+L   D++  A++G GKT  F +  L  + 
Sbjct: 13 FLLKPELLRAIVDCGFEHPSEVQHECIPQAILGM-DVLCQAKSGMGKTAVFVLATLQQLE 71

Query: 67 NKLENP 72
                
Sbjct: 72 PVTGQV 77

>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} Length = 300

 Score = 64.7 bits (158), Expect = 3e-13
 Identities = 17/73 (23%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALL-ARKDIVGAAETGSGKTLAFGI 59
           +  + +  +   +++ +Y  GF  P+KIQ   +P  L    ++++  +++G+GKT AF +
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150

Query: 60  PILTGIVNKLENP 72
            +L+ +    + P
Sbjct: 151 AMLSQVEPANKYP 163

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 64.7 bits (158), Expect = 5e-13
 Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 1/56 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          +N  E       +K  K  T  Q +     ++  K     A TG GKT    +  L
Sbjct: 4  WNEYEDFRSFFKKKFGKDLTGYQRLWAK-RIVQGKSFTMVAPTGVGKTTFGMMTAL 58

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 15/56 (26%), Positives = 27/56 (48%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
            +P  +I  + ++G K     Q+  +   LL    ++  + TGSGKTL   + I+
Sbjct: 13 LKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGII 68

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
            + E I   L ++G ++    Q+  + S +L  K+ + +  T SGKTL   I ++
Sbjct: 6  LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMV 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	167
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.85
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.81
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.81
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.8
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.8
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.79
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.79
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.79
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.78
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.78
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.78
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.78
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.78
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.77
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.77
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.77
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.74
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.74
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.74
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.73
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.72
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.7
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.69
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.68
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.67
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.66
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.66
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.64
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.53
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.53
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.51
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.5
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.48
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.46
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.44
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.39
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.33
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.31
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.29
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.27
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.26
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.26
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.25
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.24
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.21
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.2
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.18
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.16
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.15
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.15
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.1
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.1
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.07
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.07
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.06
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.03
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.98
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.98
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.92
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.9
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.89
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.88
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.87
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.86
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.78
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.69
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.67
3h1t_A	590	Type I site-specific restriction-modification syst	98.66
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.66
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.61
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.6
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.53
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.32
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.13
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.57
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.35
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	97.3
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	97.28
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	97.28
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	97.26
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	97.18
1yks_A	440	Genome polyprotein [contains: flavivirin protease	97.17
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	97.11
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	97.11
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	97.08
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	96.93
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	96.91
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	96.9
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	96.89
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	96.83
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	96.73
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	96.73
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.7
3bor_A	237	Human initiation factor 4A-II; translation initiat	96.66
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	96.65
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	96.62
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.61
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	96.56
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	96.52
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	96.51
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	96.3
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	96.12
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	95.96
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	95.92
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	95.73
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	95.69
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	95.68
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	95.65
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	95.43
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	95.37
1yks_A	440	Genome polyprotein [contains: flavivirin protease	95.24
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	95.09
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	94.86
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	94.85
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	94.73
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	94.51
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	94.5
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	94.48
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	94.41
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	94.35
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	94.02
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	93.96
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	93.84
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	93.49
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	93.41
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	93.4
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	93.22
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.96
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	92.96
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	92.81
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	92.67
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	92.59
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	92.42
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	92.12
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	92.1
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	92.07
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	91.63
3b6e_A	216	Interferon-induced helicase C domain-containing P;	91.5
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	91.47
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	90.9
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	90.71
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	90.63
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	90.46
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	90.24
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	90.11
4gl2_A	699	Interferon-induced helicase C domain-containing P;	89.94
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	89.64
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	89.13
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	88.38
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	87.95
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	87.93
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	87.56
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	85.62
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	85.58
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	85.14
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	84.62
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	82.79
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	82.39
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	80.96

>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=99.85  E-value=7.7e-22  Score=155.91  Aligned_cols=66  Identities=24%  Similarity=0.584  Sum_probs=60.8

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHcc-CCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++|+|++.++++|..+||..||++|.++||.++.| ++|++++++||||||++|++|++..+.
T Consensus        91 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~  157 (300)
T 3fmo_B           91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE  157 (300)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             cCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhh
Confidence            358999999999999999999999999999999999976 589999999999999999999987654

>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=99.81  E-value=1.9e-20  Score=154.36  Aligned_cols=66  Identities=33%  Similarity=0.615  Sum_probs=62.4

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +.+|++++|++.++++|.++||..|||+|+++||.++.| +|++++++||||||++|++|++..+..
T Consensus        55 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g-~d~i~~a~TGsGKT~a~~lpil~~l~~  120 (434)
T 2db3_A           55 IQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSG-RDLMACAQTGSGKTAAFLLPILSKLLE  120 (434)
T ss_dssp             CCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             cCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcC-CCEEEECCCCCCchHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999998 999999999999999999999988773

>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=99.81  E-value=4.4e-20  Score=141.04  Aligned_cols=65  Identities=35%  Similarity=0.601  Sum_probs=61.6

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|.+++|++.++++|.+.||..|+++|.++||.++.| +|++++++||+|||++|++|++..+.
T Consensus        28 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g-~~~l~~apTGsGKT~~~~l~~l~~l~   92 (242)
T 3fe2_A           28 VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSG-LDMVGVAQTGSGKTLSYLLPAIVHIN   92 (242)
T ss_dssp             CSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHT-CCEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCcCHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999998 99999999999999999999988765

>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=99.80  E-value=4.2e-20  Score=137.28  Aligned_cols=64  Identities=28%  Similarity=0.591  Sum_probs=60.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.+.||..|+++|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~lv~apTGsGKT~~~~~~~~~~~~   66 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSG-RDILARAKNGTGKSGAYLIPLLERLD   66 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTT-CCEEEECCSSSTTHHHHHHHHHHHCC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccC-CCEEEECCCCCchHHHHHHHHHHHhc
Confidence            58999999999999999999999999999999999988 99999999999999999999876654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.80  E-value=2.6e-20  Score=140.15  Aligned_cols=64  Identities=36%  Similarity=0.626  Sum_probs=60.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.+.||..|+++|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus         4 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~~~~~~l~~l~   67 (219)
T 1q0u_A            4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG-ESMVGQSQTGTGKTHAYLLPIMEKIK   67 (219)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHT-CCEEEECCSSHHHHHHHHHHHHHHCC
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999998 99999999999999999999887654

>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=99.79  E-value=6.3e-20  Score=139.17  Aligned_cols=64  Identities=25%  Similarity=0.480  Sum_probs=60.3

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|++.++++|.+.||..|+++|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus        24 ~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~l~~a~TGsGKT~~~~l~~l~~l~   87 (230)
T 2oxc_A           24 ADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCG-LDLIVQAKSGTGKTCVFSTIALDSLV   87 (230)
T ss_dssp             CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCCcHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999998 99999999999999999999987654

>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=99.79  E-value=6.7e-20  Score=140.99  Aligned_cols=64  Identities=42%  Similarity=0.677  Sum_probs=60.6

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|++.++++|...||..|+++|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus        43 ~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~-~~~lv~a~TGsGKT~~~~~~il~~l~  106 (249)
T 3ber_A           43 KTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQG-RDIIGLAETGSGKTGAFALPILNALL  106 (249)
T ss_dssp             CCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCC-CCEEEEcCCCCCchhHhHHHHHHHHh
Confidence            57999999999999999999999999999999999998 99999999999999999999987665

>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=99.79  E-value=5.1e-20  Score=140.35  Aligned_cols=65  Identities=29%  Similarity=0.618  Sum_probs=60.4

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++|+|++.++++|.+.||..|+++|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus        29 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~-~~~li~apTGsGKT~~~~l~~l~~l~   93 (237)
T 3bor_A           29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKG-YDVIAQAQSGTGKTATFAISILQQLE   93 (237)
T ss_dssp             CCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEECCCSSHHHHHHHHHHHHHHCC
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCCcHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999998 99999999999999999999887654

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.78  E-value=1.5e-19  Score=137.30  Aligned_cols=65  Identities=35%  Similarity=0.623  Sum_probs=61.5

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +++|++++|++.++++|.+.||..|+++|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus        24 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~li~a~TGsGKT~~~~~~~l~~l~   88 (236)
T 2pl3_A           24 ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQG-KDVLGAAKTGSGKTLAFLVPVLEALY   88 (236)
T ss_dssp             CSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEEeCCCCcHHHHHHHHHHHHHH
Confidence            467999999999999999999999999999999999988 99999999999999999999988776

>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=99.78  E-value=1.5e-19  Score=136.09  Aligned_cols=65  Identities=26%  Similarity=0.522  Sum_probs=60.7

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++++|++.++++|.+.||..|+++|.++++.++.| +|++++++||+|||++|.+|++..+.
T Consensus        13 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~lv~~pTGsGKT~~~~~~~l~~l~   77 (224)
T 1qde_A           13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG-HDVLAQAQSGTGKTGTFSIAALQRID   77 (224)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC-CCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999998 99999999999999999999987654

>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=99.78  E-value=2.3e-19  Score=134.83  Aligned_cols=64  Identities=28%  Similarity=0.555  Sum_probs=59.6

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++++|++.++++|.+.||..|+++|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus        14 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~li~~~TGsGKT~~~~~~~~~~~~   77 (220)
T 1t6n_A           14 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLATLQQLE   77 (220)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCCchhhhhhHHHHHhhh
Confidence            57999999999999999999999999999999999998 89999999999999999999876543

>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=99.78  E-value=9e-20  Score=137.83  Aligned_cols=65  Identities=28%  Similarity=0.461  Sum_probs=60.5

Q ss_pred             CCcccc-CCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVK-FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~-l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|.+ +++++.++++|.+.||..|+++|.++||.++.| +|++++++||+|||++|++|++..+.
T Consensus        18 ~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~l~~apTGsGKT~~~~l~~~~~l~   83 (228)
T 3iuy_A           18 TCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQG-IDLIVVAQTGTGKTLSYLMPGFIHLD   83 (228)
T ss_dssp             CCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHC
T ss_pred             hhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHHH
Confidence            357888 899999999999999999999999999999988 99999999999999999999987765

>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=99.78  E-value=1.4e-19  Score=138.23  Aligned_cols=65  Identities=37%  Similarity=0.686  Sum_probs=59.4

Q ss_pred             CCccccC----CCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKF----NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l----~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|+++    +|++.++++|.+.||..|+++|.++||.++.| +|++++++||+|||++|++|++..+.
T Consensus        24 ~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~l~~a~TGsGKT~~~~l~~l~~l~   92 (245)
T 3dkp_A           24 IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHG-RELLASAPTGSGKTLAFSIPILMQLK   92 (245)
T ss_dssp             CSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHC
T ss_pred             ccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            3567776    89999999999999999999999999999998 99999999999999999999987664

>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=99.77  E-value=2.9e-19  Score=132.66  Aligned_cols=64  Identities=44%  Similarity=0.735  Sum_probs=60.5

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.+.||..|+++|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus         1 ~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~li~~~TGsGKT~~~~~~~~~~l~   64 (207)
T 2gxq_A            1 MEFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEG-KDLIGQARTGTGKTLAFALPIAERLA   64 (207)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCC-CCEEEECCCCChHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999998 99999999999999999999987765

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

Probab=99.77  E-value=2.5e-19  Score=145.49  Aligned_cols=66  Identities=30%  Similarity=0.515  Sum_probs=62.4

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +.+|++|+|++.++++|...||..|||+|.++||.++.| +|++++++||+|||++|++|++..+..
T Consensus        14 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~-~~~lv~a~TGsGKT~~~~~~~l~~~~~   79 (417)
T 2i4i_A           14 IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEK-RDLMACAQTGSGKTAAFLLPILSQIYS   79 (417)
T ss_dssp             CSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             cCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccC-CCEEEEcCCCCHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999999999999988 999999999999999999999988763

>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=99.77  E-value=6.8e-20  Score=140.62  Aligned_cols=66  Identities=35%  Similarity=0.575  Sum_probs=62.1

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +++|++|+|++.++++|...||..|+++|.++|+.++.| +|++++++||+|||++|++|++..+..
T Consensus        22 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~-~~~l~~a~TGsGKT~~~~~~~l~~l~~   87 (253)
T 1wrb_A           22 IENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEH-RDIMACAQTGSGKTAAFLIPIINHLVC   87 (253)
T ss_dssp             CCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            467999999999999999999999999999999999998 999999999999999999999888763

>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=99.74  E-value=8.5e-19  Score=135.74  Aligned_cols=63  Identities=38%  Similarity=0.569  Sum_probs=56.0

Q ss_pred             ccccCC--CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          3 EWVKFN--IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         3 ~f~~l~--l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +|++++  |++.++++|.+.||..|+++|.++||.++.| +|++++++||+|||++|++|++..+.
T Consensus        53 ~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~~~l~~l~~l~  117 (262)
T 3ly5_A           53 SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEG-RDLLAAAKTGSGKTLAFLIPAVELIV  117 (262)
T ss_dssp             CC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHT-CCCEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             ChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCC-CcEEEEccCCCCchHHHHHHHHHHHH
Confidence            577777  9999999999999999999999999999999 99999999999999999999988766

>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=99.74  E-value=1.1e-18  Score=144.94  Aligned_cols=65  Identities=25%  Similarity=0.585  Sum_probs=59.6

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHcc-CCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|.+++|++.++++|.++||..|||+|.++||.++.+ ++|++++++||||||++|++|++..+.
T Consensus        92 ~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~  157 (479)
T 3fmp_B           92 KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE  157 (479)
T ss_dssp             CCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCC
T ss_pred             CCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999975 589999999999999999999876654

>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=99.74  E-value=2.1e-18  Score=139.52  Aligned_cols=66  Identities=24%  Similarity=0.584  Sum_probs=60.3

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHcc-CCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++++|++.++++|.+.||..|+|+|.++|+.++.+ +++++++++||+|||++|++|++..+.
T Consensus        24 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~   90 (412)
T 3fht_A           24 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVE   90 (412)
T ss_dssp             SSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             cCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhh
Confidence            468999999999999999999999999999999999976 589999999999999999999876654

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.73  E-value=2.7e-18  Score=139.41  Aligned_cols=63  Identities=25%  Similarity=0.618  Sum_probs=59.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      .+|++|+|++.++++|.+.||..|+|+|.++|+.++.| +|++++++||+|||++|++|++..+
T Consensus        37 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~-~~~lv~a~TGsGKT~~~~~~~~~~l   99 (410)
T 2j0s_A           37 PTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG-RDVIAQSQSGTGKTATFSISVLQCL   99 (410)
T ss_dssp             CSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHTC
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCC-CCEEEECCCCCCchHHHHHHHHHHH
Confidence            57999999999999999999999999999999999998 9999999999999999999987654

>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=99.72  E-value=7e-18  Score=135.48  Aligned_cols=66  Identities=24%  Similarity=0.570  Sum_probs=60.0

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccC-CcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLAR-KDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~-~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++++|++.++++|.+.||..|+|+|.++++.++.+. ++++++++||+|||++|++|++..+.
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~   70 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVN   70 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhc
Confidence            4689999999999999999999999999999999998763 79999999999999999998876543

>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=99.70  E-value=1.4e-17  Score=134.57  Aligned_cols=64  Identities=31%  Similarity=0.642  Sum_probs=59.8

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|++.++++|.+.||..|+|+|.++++.++.| ++++++++||+|||++|++|++..+.
T Consensus        21 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~-~~~li~a~TGsGKT~~~~~~~~~~~~   84 (400)
T 1s2m_A           21 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITG-RDILARAKNGTGKTAAFVIPTLEKVK   84 (400)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHT-CCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcC-CCEEEECCCCcHHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999998 89999999999999999999876543

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.69  E-value=1.3e-17  Score=134.21  Aligned_cols=64  Identities=28%  Similarity=0.555  Sum_probs=59.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|.+.||..|+|+|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~~~~~~~~~l~   71 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLATLQQLE   71 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTT-CCEEEECSSCSSHHHHHHHHHHHHCC
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcC-CcEEEECCCCCcHHHHHHHHHHHhhc
Confidence            57999999999999999999999999999999999998 99999999999999999999876543

>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=99.68  E-value=1.3e-17  Score=134.21  Aligned_cols=64  Identities=27%  Similarity=0.522  Sum_probs=59.9

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++++|++.++++|.+.||..|+|+|.++++.++.| +|++++++||+|||++|.+|++..+.
T Consensus        21 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~-~~~lv~~~TGsGKT~~~~~~~~~~l~   84 (394)
T 1fuu_A           21 YKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG-HDVLAQAQSGTGKTGTFSIAALQRID   84 (394)
T ss_dssp             CSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHT-CCEEECCCSSHHHHHHHHHHHHHHCC
T ss_pred             CChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCC-CCEEEECCCCChHHHHHHHHHHHHhh
Confidence            67999999999999999999999999999999999998 99999999999999999999876654

>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=99.67  E-value=4.1e-17  Score=132.17  Aligned_cols=64  Identities=31%  Similarity=0.629  Sum_probs=59.8

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|+++++++.++++|.+.||..|+++|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus        40 ~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~-~~~lv~a~TGsGKT~~~~~~~~~~~~  103 (414)
T 3eiq_A           40 DSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG-YDVIAQAQSGTGKTATFAISILQQIE  103 (414)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEECCCSCSSSHHHHHHHHHHHCC
T ss_pred             cCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCC-CCEEEECCCCCcccHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999998 89999999999999999999887654

>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=99.66  E-value=5.6e-17  Score=129.02  Aligned_cols=64  Identities=39%  Similarity=0.659  Sum_probs=59.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      ++|++++|++.++++|.+.||..|+|+|.++++.++.+++++++.++||+|||++|++|++..+
T Consensus         6 ~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~   69 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELV   69 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHS
T ss_pred             CchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999999998867999999999999999998887554

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

Probab=99.66  E-value=2.9e-17  Score=139.73  Aligned_cols=57  Identities=32%  Similarity=0.522  Sum_probs=53.6

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHH--ccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSAL--LARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l--~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |+++++++|...||..|+|+|.++|+.++  .| +|++++++||+|||++|++|++..+.
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~-~dvlv~apTGsGKTl~~~lpil~~l~   86 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSED-HDVIARAKTGTGKTFAFLIPIFQHLI   86 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSS-EEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCC-CeEEEEcCCCcHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999  45 89999999999999999999988776

>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=99.64  E-value=4.9e-17  Score=137.43  Aligned_cols=59  Identities=32%  Similarity=0.536  Sum_probs=54.2

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHcc-CCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      |+++++++|.+.||..|+|+|.++|+.++.+ ++|++++++||+|||++|++|++..+..
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~  138 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN  138 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHh
Confidence            9999999999999999999999999999942 3899999999999999999999887763

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.53  E-value=3.6e-15  Score=129.77  Aligned_cols=64  Identities=25%  Similarity=0.278  Sum_probs=58.7

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHH-HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPS-ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~-~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++++.+.+++.||..|+++|.++|+. +..+ ++++++++||||||+++.+|++..+.
T Consensus         1 ~~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~-~~~lv~apTGsGKT~~~~l~il~~~~   65 (720)
T 2zj8_A            1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEG-KNALISIPTASGKTLIAEIAMVHRIL   65 (720)
T ss_dssp             CBGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGT-CEEEEECCGGGCHHHHHHHHHHHHHH
T ss_pred             CcHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCC-CcEEEEcCCccHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999999998 6666 99999999999999999999886654

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

Probab=99.53  E-value=4.9e-15  Score=128.72  Aligned_cols=64  Identities=22%  Similarity=0.340  Sum_probs=58.4

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHH-HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPS-ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~-~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++++.+.+.+.||..|+|+|.++|+. +..+ ++++++++||||||+++.++++..+.
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~-~~~lv~apTGsGKT~~~~l~il~~~~   72 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEG-NRLLLTSPTGSGKTLIAEMGIISFLL   72 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTT-CCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCC-CcEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999999998 5555 99999999999999999999886654

>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=99.51  E-value=1.4e-14  Score=113.96  Aligned_cols=53  Identities=47%  Similarity=0.676  Sum_probs=49.8

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      |++++.++|.++||..|+|+|.++++.++.+ +++++.++||+|||++|++|++
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~-~~~lv~~~TGsGKT~~~~~~~~   53 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQG-KNVVVRAKTGSGKTAAYAIPIL   53 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcC-CCEEEEcCCCCcHHHHHHHHHH
Confidence            6899999999999999999999999999988 8999999999999999888875

>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=99.50  E-value=4.2e-15  Score=125.37  Aligned_cols=61  Identities=26%  Similarity=0.382  Sum_probs=58.0

Q ss_pred             CCccccCCCCHHHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          1 MAEWVKFNIPETIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      |.+|++|+|++.+.+.|++ .||..|+|+|.++|+.++.| +|+++.++||+|||++|.+|.+
T Consensus         1 ~~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g-~d~lv~apTGsGKTl~~~lp~l   62 (523)
T 1oyw_A            1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSG-RDCLVVMPTGGGKSLCYQIPAL   62 (523)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTT-CCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcC-CCEEEECCCCcHHHHHHHHHHH
Confidence            6789999999999999998 89999999999999999998 8999999999999999998875

>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=99.48  E-value=2.6e-14  Score=122.14  Aligned_cols=57  Identities=19%  Similarity=0.300  Sum_probs=53.3

Q ss_pred             ccCCCCHHHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          5 VKFNIPETIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         5 ~~l~l~~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .+|++++.+.+.|++ .||..|+|+|.++|+.++.| +|+++.++||+|||++|.+|.+
T Consensus        24 ~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g-~d~lv~~pTGsGKTl~~~lpal   81 (591)
T 2v1x_A           24 EDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAG-KEVFLVMPTGGGKSLCYQLPAL   81 (591)
T ss_dssp             SCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTT-CCEEEECCTTSCTTHHHHHHHH
T ss_pred             ccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcC-CCEEEEECCCChHHHHHHHHHH
Confidence            358899999999998 69999999999999999998 9999999999999999999885

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.46  E-value=2.8e-15  Score=130.11  Aligned_cols=64  Identities=17%  Similarity=0.225  Sum_probs=56.0

Q ss_pred             CccccCC--CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFN--IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~--l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+  |++++.+++++.||..|+|+|.++++.++.+ ++++++++||+|||+++.++++..+.
T Consensus         1 m~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~-~~~lv~apTGsGKT~~~~l~il~~~~   66 (702)
T 2p6r_A            1 MKVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSG-KNLLLAMPTAAGKTLLAEMAMVREAI   66 (702)
T ss_dssp             CCSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTC-SCEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             CchhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCC-CcEEEEcCCccHHHHHHHHHHHHHHH
Confidence            5899999  9999999999999999999999999998877 99999999999999999998876644

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

Probab=99.39  E-value=1e-13  Score=112.92  Aligned_cols=51  Identities=24%  Similarity=0.095  Sum_probs=42.6

Q ss_pred             HHHHHHHHH-CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         11 ETIIRALYQ-KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        11 ~~l~~~l~~-~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      +.+.+.+++ .|| .|+|+|.++||.++.| +|++++++||+|||++|++|++.
T Consensus         8 ~~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~-~~~lv~apTGsGKT~~~l~~~~~   59 (414)
T 3oiy_A            8 EDFRSFFKKKFGK-DLTGYQRLWAKRIVQG-KSFTMVAPTGVGKTTFGMMTALW   59 (414)
T ss_dssp             HHHHHHHHHHHSS-CCCHHHHHHHHHHTTT-CCEECCSCSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCC-CCCHHHHHHHHHHhcC-CCEEEEeCCCCCHHHHHHHHHHH
Confidence            345556665 466 8999999999999998 89999999999999988888754

>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=99.33  E-value=3.8e-13  Score=117.84  Aligned_cols=41  Identities=29%  Similarity=0.379  Sum_probs=37.3

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      ..|| .||+||..++|.++.| +  |+.++||+|||++|.+|++.
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G-~--Iaea~TGeGKTlaf~LP~~l  119 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDG-N--IAEMKTGEGKTLTSTLPVYL  119 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTT-S--EEECCTTSCHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCC-C--EEEccCCcHHHHHHHHHHHH
Confidence            5799 9999999999999998 5  89999999999999999863

>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=99.31  E-value=4.6e-14  Score=121.22  Aligned_cols=58  Identities=12%  Similarity=-0.010  Sum_probs=43.9

Q ss_pred             CCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         7 l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +++++.++++|... ...|+|+|+.++|.++.| +|++++++||||||++|++|++..+.
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g-~dvlv~a~TGSGKT~~~~lpil~~l~  212 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKK-RLTIMDLHPGAGKTKRILPSIVREAL  212 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTT-CEEEECCCTTSSTTTTHHHHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcC-CeEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            56777766666654 589999999999888888 99999999999999999999987765

>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=99.29  E-value=1.7e-12  Score=117.32  Aligned_cols=59  Identities=25%  Similarity=0.260  Sum_probs=46.0

Q ss_pred             cccCCCCHHHH-----HHHH-HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          4 WVKFNIPETII-----RALY-QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         4 f~~l~l~~~l~-----~~l~-~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |..+++++.+.     +.+. ..||. | ++|.++||.++.| +|++++++||||||+ |.+|++..+.
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~g~~-p-~iQ~~ai~~il~g-~dvlv~apTGSGKTl-~~lp~l~~~~   96 (1054)
T 1gku_B           32 ASLCLFPEDFLLKEFVEFFRKCVGEP-R-AIQKMWAKRILRK-ESFAATAPTGVGKTS-FGLAMSLFLA   96 (1054)
T ss_dssp             CCCSCCTTHHHHHHHHHHHHTTTCSC-C-HHHHHHHHHHHTT-CCEECCCCBTSCSHH-HHHHHHHHHH
T ss_pred             ccccccccccchHHHHHHHHHhcCCC-H-HHHHHHHHHHHhC-CCEEEEcCCCCCHHH-HHHHHHHHHh
Confidence            44455544332     4444 58999 9 9999999999988 999999999999998 8888876554

>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=99.27  E-value=4.2e-13  Score=121.68  Aligned_cols=62  Identities=16%  Similarity=0.061  Sum_probs=54.5

Q ss_pred             ccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948          3 EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         3 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      .|..+++++.+...+...++..|+++|.++|+.++.| +|++++++||||||++|.+|++..+
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g-~dvLV~ApTGSGKTlva~l~i~~~l  224 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRG-ESVLVSAHTSAGKTVVAEYAIAQSL  224 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTT-CCEEEECCSSSHHHHHHHHHHHHHH
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcC-CCEEEECCCCCChHHHHHHHHHHHH
Confidence            5777888888888888888889999999999999888 9999999999999999999887654

>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=99.26  E-value=1.5e-12  Score=122.03  Aligned_cols=58  Identities=28%  Similarity=0.403  Sum_probs=52.3

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |++...++|...+|..++|+|.++|+.++.++.+++++||||||||+++.+|++..+.
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~  968 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLL  968 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHH
Confidence            4567788899999999999999999999988789999999999999999999987765

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

Probab=99.26  E-value=2e-12  Score=111.60  Aligned_cols=52  Identities=19%  Similarity=0.107  Sum_probs=42.7

Q ss_pred             HHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         14 IRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        14 ~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ..+|..+||..|+++|.++++.++.| +|++++++||+|||++|.+|++..+.
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g-~~~iv~~~TGsGKTl~~~~~i~~~l~   54 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKG-KNTIICAPTGCGKTFVSLLICEHHLK   54 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcC-CCEEEEcCCCchHHHHHHHHHHHHHH
Confidence            45688899999999999999999988 99999999999999999999887654

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

Probab=99.25  E-value=3.3e-12  Score=115.80  Aligned_cols=44  Identities=25%  Similarity=0.080  Sum_probs=38.6

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ..|| .|||+|.++||.++.| +|++++++||||||++|+++++..
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g-~dvlv~ApTGSGKTl~~l~~il~~  117 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQG-KSFTMVAPTGVGKTTFGMMTALWL  117 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTT-CCEEECCSTTCCHHHHHHHHHHHH
T ss_pred             hcCC-CCCHHHHHHHHHHHcC-CCEEEEeCCCCcHHHHHHHHHHHH
Confidence            4688 6999999999999998 999999999999999777776543

>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=99.24  E-value=6e-13  Score=110.20  Aligned_cols=44  Identities=18%  Similarity=0.123  Sum_probs=38.0

Q ss_pred             CCCCCchHHHhHHHHHHccCCcE-EEEeecCCCcccccccchhhhhh
Q psy11948         21 GFKTPTKIQSMVMPSALLARKDI-VGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l~~~~d~-i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |+..|+|+|+ +||.++.+ +|+ +++++||||||++|++|++....
T Consensus         1 G~~q~~~iq~-~i~~~l~~-~~~~lv~a~TGsGKT~~~~~~~l~~~~   45 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRK-KRLTIMDLHPGAGKTKRILPSIVREAL   45 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGST-TCEEEECCCTTSSCCTTHHHHHHHHHH
T ss_pred             CCCCCCCcHH-HHHHHHhc-CCeEEEECCCCCCHhhHHHHHHHHHHH
Confidence            7889999985 79999999 555 99999999999999999886544

>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=99.21  E-value=5.7e-12  Score=105.46  Aligned_cols=46  Identities=24%  Similarity=0.133  Sum_probs=38.1

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++...|+|+|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~~-~~~l~~~~tGsGKT~~~~~~~~~~~~   48 (556)
T 4a2p_A            3 METKKARSYQIELAQPAING-KNALICAPTGSGKTFVSILICEHHFQ   48 (556)
T ss_dssp             -----CCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCChHHHHHHHHHHHHHH
Confidence            34568999999999999998 89999999999999999999877665

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

Probab=99.20  E-value=7.1e-12  Score=104.60  Aligned_cols=42  Identities=24%  Similarity=0.177  Sum_probs=39.0

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|+|+|.++++.++.| +|++++++||+|||++|++|++..+.
T Consensus         4 ~~~~~Q~~~i~~~~~~-~~~l~~~~tGsGKT~~~~~~~~~~~~   45 (555)
T 3tbk_A            4 KPRNYQLELALPAKKG-KNTIICAPTGCGKTFVSLLICEHHLK   45 (555)
T ss_dssp             CCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHhCC-CCEEEEeCCCChHHHHHHHHHHHHHH
Confidence            7999999999999988 89999999999999999999987765

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

Probab=99.18  E-value=2.4e-13  Score=117.69  Aligned_cols=50  Identities=24%  Similarity=0.250  Sum_probs=38.9

Q ss_pred             HHHHCCCC-----CCchHHH-----hHHHHHH------ccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         16 ALYQKGFK-----TPTKIQS-----MVMPSAL------LARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        16 ~l~~~g~~-----~pt~iQ~-----~~ip~~l------~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +|..+||.     .||++|+     ++||.++      .+ +|++++++||||||++|++|++..+.
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g-~dvlv~apTGSGKTl~~ll~il~~l~  267 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKR-QLTVLDLHPGAGKTRRILPQIIKDAI  267 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTT-CEEEECCCTTTTTTTTHHHHHHHHHH
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcC-CeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            45566777     9999999     9999877      66 89999999999999999888876544

>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=99.16  E-value=1.7e-11  Score=115.15  Aligned_cols=47  Identities=36%  Similarity=0.417  Sum_probs=43.7

Q ss_pred             CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ||+.++++|.+++|.++..+.+++++||||||||+++.++++..+.+
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~  122 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGK  122 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGG
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHh
Confidence            89999999999999999776999999999999999999999988874

>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=99.15  E-value=1.6e-11  Score=108.08  Aligned_cols=47  Identities=23%  Similarity=0.115  Sum_probs=39.3

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ..|+..|+|+|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~-~~~ll~~~TGsGKTl~~~~~i~~~l~  289 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAING-KNALICAPTGSGKTFVSILICEHHFQ  289 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhC-CCEEEEeCCCChHHHHHHHHHHHHHH
Confidence            457999999999999999988 99999999999999999999887665

>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=99.15  E-value=6.9e-12  Score=109.83  Aligned_cols=41  Identities=22%  Similarity=0.186  Sum_probs=35.6

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      .|. .||+||..++|.++.| +  |+.++||+|||++|.+|++..
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G-~--Iaem~TGsGKTlaf~LP~l~~  111 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNER-C--IAEMRTGEGKTLTATLPAYLN  111 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSS-E--EEECCTTSCHHHHHHHHHHHH
T ss_pred             cCC-CCChHHHhhcccccCC-e--eeeecCCchHHHHHHHHHHHH
Confidence            454 9999999999999988 4  899999999999999998743

>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=99.10  E-value=4.3e-11  Score=105.13  Aligned_cols=54  Identities=19%  Similarity=0.132  Sum_probs=42.6

Q ss_pred             HHHHHHHHHCCCCCCchHHHhHHHHHHcc-----CCcEEEEeecCCCcccccccchhhhh
Q psy11948         11 ETIIRALYQKGFKTPTKIQSMVMPSALLA-----RKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        11 ~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~-----~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      +.+.+.+...+| .||++|.++|+.++.+     .++++++++||||||++|++|++..+
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l  414 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNY  414 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHH
Confidence            445555678999 9999999999998865     14788888888888888888876543

>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=99.10  E-value=1.9e-11  Score=90.42  Aligned_cols=47  Identities=26%  Similarity=0.080  Sum_probs=40.7

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ......|+++|.++++.++.+ +++++.++||+|||++++++++..+.
T Consensus        28 ~~~~~~l~~~Q~~~i~~~~~~-~~~li~~~tGsGKT~~~~~~~~~~~~   74 (216)
T 3b6e_A           28 PEPELQLRPYQMEVAQPALEG-KNIIICLPTGSGKTRVAVYIAKDHLD   74 (216)
T ss_dssp             CSCCCCCCHHHHHHHHHHHTT-CCEEEECSCHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCchHHHHHHHHHHhcC-CCEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            445669999999999999988 89999999999999999888876544

>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=99.07  E-value=4.5e-11  Score=105.17  Aligned_cols=42  Identities=29%  Similarity=0.347  Sum_probs=37.0

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ..|+ .||+||..++|.++.| +  |+.++||+|||++|.+|++..
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G-~--Iaem~TGeGKTLa~~LP~~l~  148 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLG-N--VAEMKTGEGKTLTCVLPAYLN  148 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTT-E--EEECCTTSCHHHHTHHHHHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhcC-C--EEEecCCCccHHHHHHHHHHH
Confidence            4688 9999999999999988 4  899999999999999998643

>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=99.07  E-value=5.4e-11  Score=106.43  Aligned_cols=47  Identities=23%  Similarity=0.115  Sum_probs=38.9

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      -.|+..|+++|.++|+.++.| +|++++++||+|||++|++|++..+.
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g-~~~ll~a~TGsGKTl~~~~~i~~~l~  289 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAING-KNALICAPTGSGKTFVSILICEHHFQ  289 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHTTTT
T ss_pred             ccCCCCCCHHHHHHHHHHHcC-CCEEEEeCCCchHHHHHHHHHHHHHH
Confidence            457889999999999999998 99999999999999999999876654

>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=99.06  E-value=8.2e-11  Score=103.38  Aligned_cols=58  Identities=22%  Similarity=0.233  Sum_probs=52.2

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      ..|.++++++.+.+.+...+ ..|+++|+.+|+.++.++.+++++++||+|||+  .+|.+
T Consensus        72 ~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~l  129 (773)
T 2xau_A           72 NPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQF  129 (773)
T ss_dssp             CTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHH
T ss_pred             CCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHH
Confidence            57999999999999999888 799999999999999886889999999999998  45554

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.03  E-value=5.5e-11  Score=104.70  Aligned_cols=41  Identities=22%  Similarity=0.229  Sum_probs=36.3

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      -.|+ .||+||..++|.++.| +  |+.+.||+|||++|.+|++.
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG-~--IaeakTGeGKTLvf~Lp~~L  115 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEG-K--IAEMKTGEGKTLVATLAVAL  115 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTT-S--EEECCSTHHHHHHHHHHHHH
T ss_pred             HhCC-CCcHHHHhhcccccCC-c--eeeccCCCchHHHHHHHHHH
Confidence            3699 9999999999999988 4  88999999999999888854

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

Probab=98.98  E-value=1.8e-10  Score=103.65  Aligned_cols=47  Identities=17%  Similarity=0.183  Sum_probs=40.0

Q ss_pred             HHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhh
Q psy11948         17 LYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus        17 l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      ....+|. |+++|.++|+.+..| ++++++++||+|||++|.++++..+
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g-~~vLV~apTGSGKTlva~lai~~~l  126 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRG-ESVLVSAHTSAGKTVVAEYAIAQSL  126 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHT-CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcC-CCEEEECCCCCChHHHHHHHHHHHh
Confidence            3455775 999999999999988 9999999999999999988776543

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=98.98  E-value=2.1e-10  Score=86.89  Aligned_cols=45  Identities=20%  Similarity=0.217  Sum_probs=38.3

Q ss_pred             CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         21 GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ....++++|.++++.+..| ++++++++||||||..+.++++....
T Consensus        58 ~~~p~~~~q~~~i~~i~~g-~~~~i~g~TGsGKTt~~~~~~~~~~~  102 (235)
T 3llm_A           58 ELLPVKKFESEILEAISQN-SVVIIRGATGCGKTTQVPQFILDDFI  102 (235)
T ss_dssp             HTSGGGGGHHHHHHHHHHC-SEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             hcCChHHHHHHHHHHHhcC-CEEEEEeCCCCCcHHhHHHHHhcchh
Confidence            3446789999999999988 99999999999999988887766544

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

Probab=98.92  E-value=5.7e-10  Score=100.38  Aligned_cols=43  Identities=21%  Similarity=0.141  Sum_probs=37.7

Q ss_pred             HCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         19 QKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        19 ~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      ..+| .|+++|.++|+.++.| +|++++++||+|||++|.+++..
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g-~~vlv~apTGsGKTlv~~~~i~~   77 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQG-DSVFVAAHTSAGKTVVAEYAIAM   77 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTT-CEEEEECCTTSCSHHHHHHHHHH
T ss_pred             hCCC-CCCHHHHHHHHHHHcC-CCEEEEECCCCcHHHHHHHHHHH
Confidence            3466 5899999999999998 99999999999999988887754

>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=98.90  E-value=2.1e-10  Score=99.00  Aligned_cols=43  Identities=26%  Similarity=0.105  Sum_probs=38.9

Q ss_pred             CCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         23 KTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      -.|+|+|.++++.++.| +|++++++||+|||++|.+|++..+.
T Consensus         6 ~~l~~~Q~~~i~~il~g-~~~ll~~~TGsGKTl~~~~~i~~~l~   48 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALEG-KNIIICLPTGCGKTRVAVYIAKDHLD   48 (699)
T ss_dssp             -CCCHHHHHHHHHHHSS-CCEEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHhC-CCEEEEcCCCCcHHHHHHHHHHHHHH
Confidence            37999999999999998 89999999999999999999887665

>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=98.89  E-value=2.7e-10  Score=94.47  Aligned_cols=33  Identities=30%  Similarity=0.319  Sum_probs=24.0

Q ss_pred             HHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         34 PSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        34 p~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.++.++++++++++||||||++|++|++..+.
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~   47 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAI   47 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHH
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHH
Confidence            344454488888888888888888888876544

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=98.88  E-value=5.7e-10  Score=93.01  Aligned_cols=42  Identities=14%  Similarity=0.048  Sum_probs=37.0

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ...|++.|..+++.++.+ ++++++++||+|||++++.++...
T Consensus       111 ~~~l~~~Q~~ai~~~~~~-~~~ll~~~tGsGKT~~~~~~~~~~  152 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVN-RRRILNLPTSAGRSLIQALLARYY  152 (510)
T ss_dssp             EECCCHHHHHHHHHHHHH-SEEEEECCSTTTHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhc-CCcEEEeCCCCCHHHHHHHHHHHH
Confidence            348999999999999988 899999999999999998776544

>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=98.87  E-value=2.2e-09  Score=97.86  Aligned_cols=56  Identities=18%  Similarity=0.123  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHH-HCCCCCCchHHHhHHHHHHc----cC-CcEEEEeecCCCcccccccchhh
Q psy11948          7 FNIPETIIRALY-QKGFKTPTKIQSMVMPSALL----AR-KDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus         7 l~l~~~l~~~l~-~~g~~~pt~iQ~~~ip~~l~----~~-~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      ++++....+.+. ..+|. |||+|.++|+.++.    |. +|++++++||+|||++++++.+.
T Consensus       586 ~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~  647 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFL  647 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHH
Confidence            556777777765 56885 79999999999887    41 38999999999999888777654

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=98.86  E-value=7.2e-10  Score=85.98  Aligned_cols=39  Identities=15%  Similarity=0.131  Sum_probs=33.5

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      .|+++|.++++.++.+ .+.+++++||+|||++++.++..
T Consensus       113 ~l~~~Q~~ai~~~l~~-~~~ll~~~tGsGKT~~~~~~~~~  151 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVN-RRRILNLPTSAGRSLIQALLARY  151 (282)
T ss_dssp             CCCHHHHHHHHHHHHH-SEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHhc-CCeEEEcCCCCCcHHHHHHHHHH
Confidence            8999999999999988 77888999999999988665543

>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=98.78  E-value=3.5e-09  Score=87.42  Aligned_cols=38  Identities=26%  Similarity=0.118  Sum_probs=33.8

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .|+|.|.++++.++.+ .+++++++||+|||+.++.++.
T Consensus        93 ~l~~~Q~~ai~~i~~~-~~~ll~~~TGsGKT~~~l~~i~  130 (472)
T 2fwr_A           93 SLRDYQEKALERWLVD-KRGCIVLPTGSGKTHVAMAAIN  130 (472)
T ss_dssp             CBCHHHHHHHHHHTTT-TEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhc-CCEEEEeCCCCCHHHHHHHHHH
Confidence            6899999999999888 7899999999999998877663

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.69  E-value=6.7e-09  Score=87.91  Aligned_cols=41  Identities=24%  Similarity=0.028  Sum_probs=32.8

Q ss_pred             CCCCCchHHHhHHHHH----HccCCcEEEEeecCCCcccccccchhh
Q psy11948         21 GFKTPTKIQSMVMPSA----LLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        21 g~~~pt~iQ~~~ip~~----l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      || .|.|.|.+.+..+    ..| +|+++.++||+|||++|++|.+.
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~-~~~~~~a~TGtGKT~~~l~p~l~   45 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNN-FLVALNAPTGSGKTLFSLLVSLE   45 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTT-CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcC-CcEEEECCCCccHHHHHHHHHHh
Confidence            44 6899999977644    345 89999999999999999888864

>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=98.67  E-value=8.8e-09  Score=83.73  Aligned_cols=39  Identities=21%  Similarity=0.135  Sum_probs=34.5

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      .|+|+|.++++.++.+  ++++.++||+|||+.++.+++..
T Consensus         9 ~l~~~Q~~~i~~~~~~--~~ll~~~tG~GKT~~~~~~~~~~   47 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET--NCLIVLPTGLGKTLIAMMIAEYR   47 (494)
T ss_dssp             CCCHHHHHHHHHGGGS--CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHhhC--CEEEEcCCCCCHHHHHHHHHHHH
Confidence            6899999999998877  99999999999999888887654

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.66  E-value=1.3e-08  Score=86.54  Aligned_cols=43  Identities=23%  Similarity=0.279  Sum_probs=32.2

Q ss_pred             CCCchHHHhHHHHHHc----cCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         23 KTPTKIQSMVMPSALL----ARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~----~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ..|+++|..+|+.++.    |.++++++++||+|||+++ ++++..+.
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~  223 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLW  223 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHH
Confidence            3799999999998876    5467899999999999984 34444433

>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=98.66  E-value=2.1e-08  Score=76.13  Aligned_cols=37  Identities=27%  Similarity=0.148  Sum_probs=32.4

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccch
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      .|+++|.+++..++.+ .+++++++||+|||..++.++
T Consensus        93 ~l~~~Q~~ai~~~~~~-~~~ll~~~tG~GKT~~a~~~~  129 (237)
T 2fz4_A           93 SLRDYQEKALERWLVD-KRGCIVLPTGSGKTHVAMAAI  129 (237)
T ss_dssp             CCCHHHHHHHHHHTTT-SEEEEEESSSTTHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhC-CCEEEEeCCCCCHHHHHHHHH
Confidence            7899999999998888 789999999999998776554

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.61  E-value=1.1e-08  Score=86.43  Aligned_cols=41  Identities=20%  Similarity=0.148  Sum_probs=29.9

Q ss_pred             CCCCCCchHHHhHHHHH----HccCCcEEEEeecCCCcccccccchh
Q psy11948         20 KGFKTPTKIQSMVMPSA----LLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~----l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      .|| .|+|+|.+++..+    ..| +++++.++||+|||++|++|.+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~-~~~~~~a~TGtGKT~~~l~~~~   48 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHG-KTLLLNAKPGLGKTVFVEVLGM   48 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTT-CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcC-CCEEEEcCCCCcHHHHHHHHHH
Confidence            467 8999999987543    455 8999999999999999988874

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.60  E-value=1.2e-08  Score=87.54  Aligned_cols=42  Identities=19%  Similarity=0.048  Sum_probs=32.4

Q ss_pred             CCchHHHhHHHH----HHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         24 TPTKIQSMVMPS----ALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        24 ~pt~iQ~~~ip~----~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .|.|.|.+.+..    +..| +++++.|+||+|||++|++|.+..+.
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~-~~~~~~apTGtGKT~a~l~p~l~~~~   48 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKS-YGVALESPTGSGKTIMALKSALQYSS   48 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHS-SEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcC-CCEEEECCCCCCHHHHHHHHHHHhhh
Confidence            678899888753    3455 89999999999999999999887654

>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=98.53  E-value=3.5e-09  Score=91.44  Aligned_cols=38  Identities=21%  Similarity=0.116  Sum_probs=25.8

Q ss_pred             CchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948         25 PTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus        25 pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      |...|++.|+..+.+++|++++++||||||.+|.+|++
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll  254 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYA  254 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHH
Confidence            44455555655555547888888888888877776664

>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=98.32  E-value=2.5e-07  Score=83.55  Aligned_cols=35  Identities=26%  Similarity=0.064  Sum_probs=25.2

Q ss_pred             CCCchHHHhHHHHHHcc-------------CCcEEEEeecCCCccccc
Q psy11948         23 KTPTKIQSMVMPSALLA-------------RKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~-------------~~d~i~~a~tgsGKt~~~   57 (167)
                      ..|+|+|..+++.++.+             +++.++.++||||||+++
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~  317 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS  317 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH
Confidence            36999999999998752             245666666666666654

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

Probab=98.13  E-value=6.1e-07  Score=77.77  Aligned_cols=14  Identities=21%  Similarity=0.259  Sum_probs=12.0

Q ss_pred             ceEEEccchhhhcC
Q psy11948        154 YALILAPTRELAIQ  167 (167)
Q Consensus       154 ~aLIl~PTRELa~Q  167 (167)
                      +++|++||||||.|
T Consensus       181 ~gl~l~PtR~LA~Q  194 (677)
T 3rc3_A          181 SGVYCGPLKLLAHE  194 (677)
T ss_dssp             SEEEEESSHHHHHH
T ss_pred             CeEEEeCHHHHHHH
Confidence            35999999999986

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.57  E-value=8.7e-05  Score=63.53  Aligned_cols=38  Identities=26%  Similarity=0.217  Sum_probs=32.1

Q ss_pred             chHHHhHHHHHHccCCcEEEEeecCCCcc--cccccchhhh
Q psy11948         26 TKIQSMVMPSALLARKDIVGAAETGSGKT--LAFGIPILTG   64 (167)
Q Consensus        26 t~iQ~~~ip~~l~~~~d~i~~a~tgsGKt--~~~~lp~l~~   64 (167)
                      ++.|+.+++.++.+ +++++.+++|+|||  .+++++.+..
T Consensus       151 ~~~Q~~Ai~~~l~~-~~~vi~G~pGTGKTt~l~~ll~~l~~  190 (608)
T 1w36_D          151 INWQKVAAAVALTR-RISVISGGPGTGKTTTVAKLLAALIQ  190 (608)
T ss_dssp             CCHHHHHHHHHHTB-SEEEEECCTTSTHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhcC-CCEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            78999999999987 89999999999999  5565666543

>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=97.35  E-value=0.0001  Score=64.25  Aligned_cols=41  Identities=37%  Similarity=0.429  Sum_probs=32.5

Q ss_pred             CCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948         20 KGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      .|. .|+++|...--.+..| +  |+...||+|||+++.+|++-.
T Consensus        72 lg~-r~~dvQligg~~L~~G-~--iaEM~TGEGKTLva~lp~~ln  112 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEG-K--VAEMKTGEGKTLAATMPIYLN  112 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTT-C--EEECCTTSCHHHHTHHHHHHH
T ss_pred             hCC-CCcHHHHHHHHHHhCC-C--hhhccCCCCccHHHHHHHHHH
Confidence            465 7999999998777766 3  788889999998888887543

>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=97.30  E-value=3.3e-05  Score=60.33  Aligned_cols=69  Identities=30%  Similarity=0.537  Sum_probs=55.6

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccc--cceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SAR--KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~--~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      .++..+.. ++..|+..|...    ..+  +|+++.++||+|||++|++|+++.+..                       
T Consensus       102 ~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~-----------------------  158 (300)
T 3fmo_B          102 QLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP-----------------------  158 (300)
T ss_dssp             HHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCT-----------------------
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhc-----------------------
Confidence            34444444 888999999665    344  999999999999999999999987742                       


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                      ....+++|||+||||||.|
T Consensus       159 ----------------~~~~~~~lil~PtreLa~Q  177 (300)
T 3fmo_B          159 ----------------ANKYPQCLCLSPTYELALQ  177 (300)
T ss_dssp             ----------------TSCSCCEEEECSSHHHHHH
T ss_pred             ----------------cCCCceEEEEcCcHHHHHH
Confidence                            2346789999999999987

>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=97.28  E-value=3.6e-05  Score=57.92  Aligned_cols=73  Identities=36%  Similarity=0.505  Sum_probs=56.4

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+..|...    ..++|+++.++||+|||++|++|++..+......                      
T Consensus        40 l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~----------------------   97 (242)
T 3fe2_A           40 VMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFL----------------------   97 (242)
T ss_dssp             HHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCC----------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhcccc----------------------
Confidence            4444444 778899888665    5779999999999999999999999887632211                      


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....+++|||+||||||.|
T Consensus        98 ------------~~~~~~~~lil~Pt~~L~~Q  117 (242)
T 3fe2_A           98 ------------ERGDGPICLVLAPTRELAQQ  117 (242)
T ss_dssp             ------------CTTCCCSEEEECSSHHHHHH
T ss_pred             ------------ccCCCCEEEEEeCcHHHHHH
Confidence                        12346789999999999986

>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=97.28  E-value=3.6e-05  Score=57.21  Aligned_cols=74  Identities=31%  Similarity=0.479  Sum_probs=53.9

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+..|...    ..++|+++.++||+|||++|++|++..+......                      
T Consensus        31 l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~----------------------   88 (228)
T 3iuy_A           31 LLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPIS----------------------   88 (228)
T ss_dssp             HHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccch----------------------
Confidence            3344444 777888888665    5789999999999999999999999877532111                      


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 ......+++|||+||||||.|
T Consensus        89 -----------~~~~~~~~~lil~Pt~~L~~q  109 (228)
T 3iuy_A           89 -----------REQRNGPGMLVLTPTRELALH  109 (228)
T ss_dssp             ---------------CCCSEEEECSSHHHHHH
T ss_pred             -----------hhccCCCcEEEEeCCHHHHHH
Confidence                       012356789999999999976

>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=97.26  E-value=0.00015  Score=59.94  Aligned_cols=35  Identities=23%  Similarity=0.031  Sum_probs=27.9

Q ss_pred             CCCchHHHhHHHHHH---ccCCcEEEEeecCCCccccc
Q psy11948         23 KTPTKIQSMVMPSAL---LARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l---~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ..|.|+|.+++..+.   ..+.++++..+||+|||+..
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~a   73 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT   73 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHH
Confidence            368999999997663   23378899999999999874

>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=97.18  E-value=5.1e-05  Score=62.07  Aligned_cols=73  Identities=36%  Similarity=0.545  Sum_probs=57.8

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+..|..+    ..++|++++++||+|||++|++|++..++.....                      
T Consensus        67 l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~----------------------  124 (434)
T 2db3_A           67 IIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE----------------------  124 (434)
T ss_dssp             HHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC----------------------
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc----------------------
Confidence            3334433 888999999765    6789999999999999999999999988743211                      


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....+++|||+||||||.|
T Consensus       125 ------------~~~~~~~~lil~PtreLa~Q  144 (434)
T 2db3_A          125 ------------LELGRPQVVIVSPTRELAIQ  144 (434)
T ss_dssp             ------------CCTTCCSEEEECSSHHHHHH
T ss_pred             ------------cccCCccEEEEecCHHHHHH
Confidence                        12346899999999999987

>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=97.17  E-value=0.0001  Score=60.54  Aligned_cols=31  Identities=26%  Similarity=0.154  Sum_probs=26.7

Q ss_pred             HHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948         36 ALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        36 ~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ++.| +|++++++||||||++|++|++..+..
T Consensus         5 l~~g-~~vlv~a~TGSGKT~~~l~~~l~~~~~   35 (440)
T 1yks_A            5 LKKG-MTTVLDFHPGAGKTRRFLPQILAECAR   35 (440)
T ss_dssp             TSTT-CEEEECCCTTSSTTTTHHHHHHHHHHH
T ss_pred             hhCC-CCEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            3455 999999999999999999999987654

>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=97.11  E-value=0.00023  Score=64.00  Aligned_cols=39  Identities=21%  Similarity=0.175  Sum_probs=29.8

Q ss_pred             CCCchHHHhHHHHHHcc-CCcEEEEeecCCCcccccccch
Q psy11948         23 KTPTKIQSMVMPSALLA-RKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~-~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      ..|+|.|..++..++.. ...++++.+||+|||+.++..+
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i  191 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMIL  191 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHH
Confidence            47899999999887754 2478888888888888765444

>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=97.11  E-value=5.1e-05  Score=58.00  Aligned_cols=72  Identities=46%  Similarity=0.535  Sum_probs=55.1

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|++++++||+|||++|++|++..+.....                       
T Consensus        65 l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~-----------------------  121 (262)
T 3ly5_A           65 TLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRF-----------------------  121 (262)
T ss_dssp             HHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTC-----------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccc-----------------------
Confidence            3334433 777888888665    567999999999999999999999988763211                       


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  ......++|||+||||||.|
T Consensus       122 ------------~~~~~~~~lil~Pt~~La~q  141 (262)
T 3ly5_A          122 ------------MPRNGTGVLILSPTRELAMQ  141 (262)
T ss_dssp             ------------CGGGCCCEEEECSSHHHHHH
T ss_pred             ------------cccCCceEEEEeCCHHHHHH
Confidence                        11245789999999999986

>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=97.08  E-value=7.3e-05  Score=56.12  Aligned_cols=69  Identities=41%  Similarity=0.623  Sum_probs=54.4

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..|+..|...    ..++|+++.++||+|||++|++|++..+..                          
T Consensus        40 l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~--------------------------   93 (245)
T 3dkp_A           40 LLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQ--------------------------   93 (245)
T ss_dssp             HHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCS--------------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhh--------------------------
Confidence            3344444 777888888665    568999999999999999999999987742                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....+++|||+||||||.|
T Consensus        94 ------------~~~~~~~~lil~Pt~~L~~q  113 (245)
T 3dkp_A           94 ------------PANKGFRALIISPTRELASQ  113 (245)
T ss_dssp             ------------CCSSSCCEEEECSSHHHHHH
T ss_pred             ------------cccCCceEEEEeCCHHHHHH
Confidence                        11345789999999999986

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=96.93  E-value=0.00011  Score=54.74  Aligned_cols=65  Identities=43%  Similarity=0.572  Sum_probs=52.1

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++|+++.++||+|||++|++|+++.+.....                               
T Consensus        44 ~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~-------------------------------   92 (236)
T 2pl3_A           44 QYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW-------------------------------   92 (236)
T ss_dssp             TCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC-------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc-------------------------------
Confidence            677888888654    567999999999999999999999988763211                               


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .....+++|||+|||+||.|
T Consensus        93 ----~~~~~~~~lil~Pt~~L~~q  112 (236)
T 2pl3_A           93 ----TSTDGLGVLIISPTRELAYQ  112 (236)
T ss_dssp             ----CGGGCCCEEEECSSHHHHHH
T ss_pred             ----cccCCceEEEEeCCHHHHHH
Confidence                12345789999999999986

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

Probab=96.91  E-value=0.00037  Score=57.08  Aligned_cols=27  Identities=22%  Similarity=0.147  Sum_probs=24.1

Q ss_pred             CcEEEEeecCCCcccccccchhhhhhc
Q psy11948         41 KDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ++++++++||||||++|++|++..+..
T Consensus         3 ~~~lv~a~TGsGKT~~~l~~~l~~~~~   29 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRVLPQLVREAVK   29 (431)
T ss_dssp             CEEEEECCTTSCTTTTHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            899999999999999999999866553

>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=96.90  E-value=0.00013  Score=54.99  Aligned_cols=77  Identities=43%  Similarity=0.519  Sum_probs=55.5

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|+++.++||+|||++|++|++..+........                    
T Consensus        34 l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~--------------------   93 (253)
T 1wrb_A           34 IRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQ--------------------   93 (253)
T ss_dssp             TTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC-----------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccc--------------------
Confidence            3333433 677888888655    567999999999999999999999988764321100                    


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                .......+++|||+||||||.|
T Consensus        94 ----------~~~~~~~~~~lil~Pt~~L~~q  115 (253)
T 1wrb_A           94 ----------RYSKTAYPKCLILAPTRELAIQ  115 (253)
T ss_dssp             -------------CCBCCSEEEECSSHHHHHH
T ss_pred             ----------cccccCCceEEEEECCHHHHHH
Confidence                      0012345799999999999987

>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=96.89  E-value=0.00016  Score=52.62  Aligned_cols=61  Identities=34%  Similarity=0.603  Sum_probs=50.0

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++|+++.++||+|||++|++|++..+..                                  
T Consensus        22 g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~----------------------------------   67 (206)
T 1vec_A           22 GWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDL----------------------------------   67 (206)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCT----------------------------------
T ss_pred             CCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcc----------------------------------
Confidence            667788887654    567899999999999999999999877642                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ....+++|||+|||+|+.|
T Consensus        68 -----~~~~~~~lil~Pt~~L~~q   86 (206)
T 1vec_A           68 -----KKDNIQAMVIVPTRELALQ   86 (206)
T ss_dssp             -----TSCSCCEEEECSCHHHHHH
T ss_pred             -----cCCCeeEEEEeCcHHHHHH
Confidence                 2345789999999999976

>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=96.83  E-value=0.00015  Score=53.97  Aligned_cols=68  Identities=34%  Similarity=0.495  Sum_probs=53.6

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|+++.++||+|||++|++|++..+..                          
T Consensus        35 l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~--------------------------   88 (230)
T 2oxc_A           35 VLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVL--------------------------   88 (230)
T ss_dssp             HHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCT--------------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHh--------------------------
Confidence            3344433 777788888655    567999999999999999999999987752                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....++|||+||||||.|
T Consensus        89 -------------~~~~~~~lil~Pt~~L~~q  107 (230)
T 2oxc_A           89 -------------ENLSTQILILAPTREIAVQ  107 (230)
T ss_dssp             -------------TSCSCCEEEECSSHHHHHH
T ss_pred             -------------cCCCceEEEEeCCHHHHHH
Confidence                         1234689999999999986

>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=96.73  E-value=0.00021  Score=54.12  Aligned_cols=61  Identities=49%  Similarity=0.763  Sum_probs=51.4

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++|+++.++||+|||++|++|++..+..                                  
T Consensus        62 g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~----------------------------------  107 (249)
T 3ber_A           62 GWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLE----------------------------------  107 (249)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHH----------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhc----------------------------------
Confidence            777888888665    567999999999999999999999987752                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ....+++|||+||||||.|
T Consensus       108 -----~~~~~~~lil~Ptr~L~~q  126 (249)
T 3ber_A          108 -----TPQRLFALVLTPTRELAFQ  126 (249)
T ss_dssp             -----SCCSSCEEEECSSHHHHHH
T ss_pred             -----CCCCceEEEEeCCHHHHHH
Confidence                 2345789999999999976

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

Probab=96.73  E-value=0.00022  Score=57.22  Aligned_cols=79  Identities=35%  Similarity=0.558  Sum_probs=54.4

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..|+..|...    ..++|+++.++||+|||++|++|++..+........                .......     
T Consensus        34 ~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~----------------~~~~~~~-----   92 (417)
T 2i4i_A           34 RYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEA----------------LRAMKEN-----   92 (417)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHH----------------HHHHHHC-----
T ss_pred             CCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccch----------------hhccccc-----
Confidence            788899988665    568999999999999999999999988764321100                0000000     


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                      .........+++|||+||||||.|
T Consensus        93 ~~~~~~~~~~~~lil~Pt~~L~~q  116 (417)
T 2i4i_A           93 GRYGRRKQYPISLVLAPTRELAVQ  116 (417)
T ss_dssp             BTTBSCSBCCSEEEECSSHHHHHH
T ss_pred             cccccccCCccEEEECCcHHHHHH
Confidence            000122345789999999999986

>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=96.70  E-value=0.00023  Score=51.77  Aligned_cols=64  Identities=44%  Similarity=0.644  Sum_probs=50.7

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++|+++.++||+|||.+|++|++..+....                                
T Consensus        20 ~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~--------------------------------   67 (207)
T 2gxq_A           20 GLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ--------------------------------   67 (207)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC--------------------------------
T ss_pred             CCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc--------------------------------
Confidence            666777777554    56789999999999999999999998775311                                


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .....+++||++|||+|+.|
T Consensus        68 ----~~~~~~~~lil~P~~~L~~q   87 (207)
T 2gxq_A           68 ----ERGRKPRALVLTPTRELALQ   87 (207)
T ss_dssp             ----CTTCCCSEEEECSSHHHHHH
T ss_pred             ----ccCCCCcEEEEECCHHHHHH
Confidence                11345789999999999976

>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=96.66  E-value=0.00016  Score=54.12  Aligned_cols=68  Identities=38%  Similarity=0.567  Sum_probs=53.7

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|+++.++||+|||++|++|++..+..                          
T Consensus        41 l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~--------------------------   94 (237)
T 3bor_A           41 LLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI--------------------------   94 (237)
T ss_dssp             HHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCT--------------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHh--------------------------
Confidence            3444434 777888888655    567899999999999999999999987642                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....++|||+||||||.|
T Consensus        95 -------------~~~~~~~lil~Pt~~L~~q  113 (237)
T 3bor_A           95 -------------EFKETQALVLAPTRELAQQ  113 (237)
T ss_dssp             -------------TSCSCCEEEECSSHHHHHH
T ss_pred             -------------cCCCceEEEEECcHHHHHH
Confidence                         1234689999999999976

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=96.65  E-value=0.00017  Score=53.25  Aligned_cols=61  Identities=43%  Similarity=0.608  Sum_probs=50.2

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++|+++.++||+|||.+|++|++..+..                                  
T Consensus        23 g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~----------------------------------   68 (219)
T 1q0u_A           23 RFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKP----------------------------------   68 (219)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCT----------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHh----------------------------------
Confidence            667788887654    567999999999999999999999987742                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ....+++|||+||||||.|
T Consensus        69 -----~~~~~~~lil~Pt~~L~~q   87 (219)
T 1q0u_A           69 -----ERAEVQAVITAPTRELATQ   87 (219)
T ss_dssp             -----TSCSCCEEEECSSHHHHHH
T ss_pred             -----CcCCceEEEEcCcHHHHHH
Confidence                 1235789999999999976

>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=96.62  E-value=0.00029  Score=59.10  Aligned_cols=71  Identities=34%  Similarity=0.527  Sum_probs=55.1

Q ss_pred             hhhhhc-ccCCCCcccccc----c--cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         62 LTGIVN-KLENPTEEDEND----S--ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        62 l~~~~~-~~~~~~~~~~~~----~--~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      +..+.. ++..++..|...    .  .++|+++.++||+|||++|++|+++.+.....                      
T Consensus        84 ~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~----------------------  141 (563)
T 3i5x_A           84 HKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF----------------------  141 (563)
T ss_dssp             HHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT----------------------
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccc----------------------
Confidence            333333 778899988665    2  57899999999999999999999988864321                      


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....+++|||+||||||.|
T Consensus       142 -------------~~~~~~~~lil~Ptr~La~Q  161 (563)
T 3i5x_A          142 -------------DSQYMVKAVIVAPTRDLALQ  161 (563)
T ss_dssp             -------------SSTTSCCEEEECSSHHHHHH
T ss_pred             -------------cccCCeeEEEEcCcHHHHHH
Confidence                         11245789999999999987

>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=96.61  E-value=0.00029  Score=51.96  Aligned_cols=61  Identities=38%  Similarity=0.554  Sum_probs=50.3

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++|+++.++||+|||.+|++|++..+..                                  
T Consensus        33 g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~----------------------------------   78 (224)
T 1qde_A           33 GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT----------------------------------   78 (224)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCT----------------------------------
T ss_pred             CCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhc----------------------------------
Confidence            677788888654    567899999999999999999999987742                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ....+++|||+|||+||.|
T Consensus        79 -----~~~~~~~lil~Pt~~L~~q   97 (224)
T 1qde_A           79 -----SVKAPQALMLAPTRELALQ   97 (224)
T ss_dssp             -----TCCSCCEEEECSSHHHHHH
T ss_pred             -----cCCCceEEEEECCHHHHHH
Confidence                 1345789999999999976

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

Probab=96.56  E-value=0.00033  Score=59.23  Aligned_cols=65  Identities=35%  Similarity=0.560  Sum_probs=52.6

Q ss_pred             ccCCCCcccccc----c--cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhc
Q psy11948         68 KLENPTEEDEND----S--ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESAN  141 (167)
Q Consensus        68 ~~~~~~~~~~~~----~--~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~  141 (167)
                      ++..++..|...    .  .++|+++.++||+|||++|++|+++.+.....                             
T Consensus        40 g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~-----------------------------   90 (579)
T 3sqw_A           40 EFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-----------------------------   90 (579)
T ss_dssp             TCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-----------------------------
T ss_pred             CCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc-----------------------------
Confidence            777888888665    2  68999999999999999999999988864211                             


Q ss_pred             chhhhhccccccceEEEccchhhhcC
Q psy11948        142 TTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       142 ~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                            .....+++|||+||||||.|
T Consensus        91 ------~~~~~~~~lvl~Ptr~La~Q  110 (579)
T 3sqw_A           91 ------DSQYMVKAVIVAPTRDLALQ  110 (579)
T ss_dssp             ------SSTTSCCEEEECSSHHHHHH
T ss_pred             ------cccCCCeEEEEcchHHHHHH
Confidence                  11345789999999999987

>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=96.52  E-value=0.00035  Score=51.39  Aligned_cols=68  Identities=31%  Similarity=0.475  Sum_probs=52.5

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|+++.++||+|||.+|++|++..+..                          
T Consensus        25 l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~--------------------------   78 (220)
T 1t6n_A           25 LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP--------------------------   78 (220)
T ss_dssp             HHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCC--------------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhc--------------------------
Confidence            3444443 677788888654    467899999999999999999999877631                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   ....+++|||+|||+|+.|
T Consensus        79 -------------~~~~~~~lil~Pt~~L~~q   97 (220)
T 1t6n_A           79 -------------VTGQVSVLVMCHTRELAFQ   97 (220)
T ss_dssp             -------------CTTCCCEEEECSCHHHHHH
T ss_pred             -------------cCCCEEEEEEeCCHHHHHH
Confidence                         1234689999999999976

>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=96.51  E-value=0.00039  Score=57.19  Aligned_cols=69  Identities=30%  Similarity=0.531  Sum_probs=54.9

Q ss_pred             chhhhhhc-ccCCCCcccccc----cc--ccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SA--RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~--~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      .++..+.. ++..|+..|...    ..  ++|+++.++||+|||++|++|++..+..                       
T Consensus       102 ~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~-----------------------  158 (479)
T 3fmp_B          102 QLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP-----------------------  158 (479)
T ss_dssp             HHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCT-----------------------
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhh-----------------------
Confidence            34455555 888999998665    33  4899999999999999999999987742                       


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                      ....+++|||+||||||.|
T Consensus       159 ----------------~~~~~~~lil~Pt~~La~Q  177 (479)
T 3fmp_B          159 ----------------ANKYPQCLCLSPTYELALQ  177 (479)
T ss_dssp             ----------------TSCSCCEEEECSSHHHHHH
T ss_pred             ----------------cCCCCcEEEEeChHHHHHH
Confidence                            2345689999999999987

>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=96.30  E-value=0.00063  Score=54.49  Aligned_cols=69  Identities=36%  Similarity=0.590  Sum_probs=54.7

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.. ++..|+..|...    ..++|+++.++||+|||++|++|+++.+..                         
T Consensus        47 ~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~-------------------------  101 (410)
T 2j0s_A           47 DLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI-------------------------  101 (410)
T ss_dssp             HHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCT-------------------------
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhh-------------------------
Confidence            34444544 788899988665    567999999999999999999999977631                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    .....++|||+|||+||.|
T Consensus       102 --------------~~~~~~~lil~Pt~~L~~q  120 (410)
T 2j0s_A          102 --------------QVRETQALILAPTRELAVQ  120 (410)
T ss_dssp             --------------TSCSCCEEEECSSHHHHHH
T ss_pred             --------------ccCCceEEEEcCcHHHHHH
Confidence                          1234689999999999986

>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=96.12  E-value=0.00088  Score=53.39  Aligned_cols=69  Identities=30%  Similarity=0.531  Sum_probs=54.0

Q ss_pred             chhhhhhc-ccCCCCcccccc----cc--ccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SA--RKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~--~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      .++..+.. ++..|+..|...    ..  ++++++.++||+|||++|++|+++.+..                       
T Consensus        35 ~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~-----------------------   91 (412)
T 3fht_A           35 QLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP-----------------------   91 (412)
T ss_dssp             HHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCT-----------------------
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhh-----------------------
Confidence            34444444 788888888655    33  4899999999999999999999987742                       


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                      ....+++|||+|||+||.|
T Consensus        92 ----------------~~~~~~~lil~P~~~L~~q  110 (412)
T 3fht_A           92 ----------------ANKYPQCLCLSPTYELALQ  110 (412)
T ss_dssp             ----------------TSCSCCEEEECSSHHHHHH
T ss_pred             ----------------cCCCCCEEEECCCHHHHHH
Confidence                            2345689999999999976

>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=95.96  E-value=0.0012  Score=52.80  Aligned_cols=68  Identities=40%  Similarity=0.570  Sum_probs=53.6

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|+++.++||+|||++|++|+++.+..                          
T Consensus        51 ~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~--------------------------  104 (414)
T 3eiq_A           51 LLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL--------------------------  104 (414)
T ss_dssp             HHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCT--------------------------
T ss_pred             HHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhh--------------------------
Confidence            3444433 777888888655    568899999999999999999999987642                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....++|||+|||+||.|
T Consensus       105 -------------~~~~~~~lil~P~~~L~~q  123 (414)
T 3eiq_A          105 -------------DLKATQALVLAPTRELAQQ  123 (414)
T ss_dssp             -------------TSCSCCEEEECSSHHHHHH
T ss_pred             -------------cCCceeEEEEeChHHHHHH
Confidence                         1234679999999999976

>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=95.92  E-value=0.0011  Score=52.33  Aligned_cols=69  Identities=33%  Similarity=0.570  Sum_probs=53.1

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccc--cceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SAR--KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVL  132 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~--~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~  132 (167)
                      .++..+.. ++..|+..|...    ..+  +++++.++||+|||++|++|++..+..                       
T Consensus        15 ~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~-----------------------   71 (395)
T 3pey_A           15 ELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNP-----------------------   71 (395)
T ss_dssp             HHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCT-----------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhcc-----------------------
Confidence            34444444 677888888654    233  899999999999999999999877642                       


Q ss_pred             HHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        133 EELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       133 e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                      .....++|||+|||+|+.|
T Consensus        72 ----------------~~~~~~~lil~P~~~L~~q   90 (395)
T 3pey_A           72 ----------------EDASPQAICLAPSRELARQ   90 (395)
T ss_dssp             ----------------TCCSCCEEEECSSHHHHHH
T ss_pred             ----------------CCCCccEEEECCCHHHHHH
Confidence                            1245689999999999976

>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=95.73  E-value=0.0015  Score=51.95  Aligned_cols=69  Identities=43%  Similarity=0.666  Sum_probs=54.3

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.. ++..++..|...    ..++++++.++||+|||++|++|++..+..                         
T Consensus        31 ~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~-------------------------   85 (400)
T 1s2m_A           31 ELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKP-------------------------   85 (400)
T ss_dssp             HHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCT-------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhh-------------------------
Confidence            34455554 777888888665    467899999999999999999999877642                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    .....++|||+|||+|+.|
T Consensus        86 --------------~~~~~~~lil~P~~~L~~q  104 (400)
T 1s2m_A           86 --------------KLNKIQALIMVPTRELALQ  104 (400)
T ss_dssp             --------------TSCSCCEEEECSSHHHHHH
T ss_pred             --------------ccCCccEEEEcCCHHHHHH
Confidence                          1234689999999999976

>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=95.69  E-value=0.0018  Score=51.32  Aligned_cols=61  Identities=30%  Similarity=0.439  Sum_probs=49.8

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..+++.|...    ..++|+++.++||+|||++|++|++..+..                                  
T Consensus        27 g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~----------------------------------   72 (391)
T 1xti_A           27 GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEP----------------------------------   72 (391)
T ss_dssp             SCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCC----------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcc----------------------------------
Confidence            677788888654    567899999999999999999999877641                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           .....++|||+|||+|+.|
T Consensus        73 -----~~~~~~~lil~P~~~L~~q   91 (391)
T 1xti_A           73 -----VTGQVSVLVMCHTRELAFQ   91 (391)
T ss_dssp             -----CTTCCCEEEECSCHHHHHH
T ss_pred             -----cCCCeeEEEECCCHHHHHH
Confidence                 1234689999999999976

>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=95.68  E-value=0.0017  Score=50.25  Aligned_cols=38  Identities=45%  Similarity=0.583  Sum_probs=31.0

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILT  105 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~  105 (167)
                      ++..+++.|...    ..++++++.++||+|||++|++|+++
T Consensus        13 g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           13 GFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             TCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            566677777554    45789999999999999999999875

>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=95.65  E-value=0.0032  Score=51.73  Aligned_cols=57  Identities=28%  Similarity=0.316  Sum_probs=43.5

Q ss_pred             CCCCcccc---ccccccce-eeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhh
Q psy11948         70 ENPTEEDE---NDSARKDI-VGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEF  145 (167)
Q Consensus        70 ~~~~~~~~---~~~~~~d~-~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~  145 (167)
                      .+|+++|+   ....++|+ ++.++||+|||++|++|++.....                                    
T Consensus         3 ~q~~~iq~~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~------------------------------------   46 (451)
T 2jlq_A            3 AMGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL------------------------------------   46 (451)
T ss_dssp             CCCSCCCCCCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH------------------------------------
T ss_pred             CCCCCcHHHHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh------------------------------------
Confidence            34555543   22456676 999999999999999999876541                                    


Q ss_pred             hhccccccceEEEccchhhhcC
Q psy11948        146 VKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       146 ~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ...++|||+||||||.|
T Consensus        47 -----~~~~~lvl~Ptr~La~Q   63 (451)
T 2jlq_A           47 -----RRLRTLILAPTRVVAAE   63 (451)
T ss_dssp             -----TTCCEEEEESSHHHHHH
T ss_pred             -----cCCcEEEECCCHHHHHH
Confidence                 23689999999999987

>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=95.43  E-value=0.0014  Score=51.89  Aligned_cols=68  Identities=37%  Similarity=0.580  Sum_probs=52.9

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.. ++..++..|...    ..++|+++.++||+|||++|++|++..+..                          
T Consensus        32 l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~--------------------------   85 (394)
T 1fuu_A           32 LLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT--------------------------   85 (394)
T ss_dssp             HHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCT--------------------------
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhc--------------------------
Confidence            3333333 677888888655    467899999999999999999999877642                          


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   ....+++|||+|||+|+.|
T Consensus        86 -------------~~~~~~~lil~P~~~L~~q  104 (394)
T 1fuu_A           86 -------------SVKAPQALMLAPTRELALQ  104 (394)
T ss_dssp             -------------TCCSCCEEEECSSHHHHHH
T ss_pred             -------------cCCCCCEEEEcCCHHHHHH
Confidence                         1345689999999999976

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=95.37  E-value=0.01  Score=52.23  Aligned_cols=34  Identities=21%  Similarity=0.054  Sum_probs=26.7

Q ss_pred             CCchHHHhHHHHHH----ccCCcEEEEeecCCCcccccc
Q psy11948         24 TPTKIQSMVMPSAL----LARKDIVGAAETGSGKTLAFG   58 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l----~~~~d~i~~a~tgsGKt~~~~   58 (167)
                      .+.|.|..++..++    .+ .+.|+..++|.|||+..+
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~-~~~ILademGlGKT~~ai  273 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKG-DNGILADEMGLGKTVQTV  273 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTT-CCEEECCCTTSSTTHHHH
T ss_pred             CcCHHHHHHHHHHHHHhhcC-CCEEEEeCCCcchHHHHH
Confidence            56789999997554    44 788999999999997543

>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=95.24  E-value=0.0037  Score=51.21  Aligned_cols=30  Identities=27%  Similarity=0.199  Sum_probs=26.5

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ..++|+++.++||+|||++|++|+++.+..
T Consensus         6 ~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~   35 (440)
T 1yks_A            6 KKGMTTVLDFHPGAGKTRRFLPQILAECAR   35 (440)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHH
T ss_pred             hCCCCEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            468999999999999999999999986653

>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=95.09  E-value=0.0057  Score=52.43  Aligned_cols=57  Identities=28%  Similarity=0.333  Sum_probs=46.3

Q ss_pred             CCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhh
Q psy11948         70 ENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEF  145 (167)
Q Consensus        70 ~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~  145 (167)
                      ..++++|...    ..++|+++.++||+|||++|++|+++.+..                                    
T Consensus       170 ~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~------------------------------------  213 (618)
T 2whx_A          170 RIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK------------------------------------  213 (618)
T ss_dssp             CCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH------------------------------------
T ss_pred             ccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh------------------------------------
Confidence            4555554332    678999999999999999999999987752                                    


Q ss_pred             hhccccccceEEEccchhhhcC
Q psy11948        146 VKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       146 ~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                           ..+++|||+||||||.|
T Consensus       214 -----~~~~vLvl~PtreLa~Q  230 (618)
T 2whx_A          214 -----RRLRTLILAPTRVVAAE  230 (618)
T ss_dssp             -----TTCCEEEEESSHHHHHH
T ss_pred             -----CCCeEEEEcChHHHHHH
Confidence                 24689999999999987

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

Probab=94.86  E-value=0.0034  Score=50.46  Aligned_cols=55  Identities=25%  Similarity=0.083  Sum_probs=43.6

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+..|...    ..++|+++.++||+|||++|++|++...                                       
T Consensus        21 ~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~---------------------------------------   61 (414)
T 3oiy_A           21 DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---------------------------------------   61 (414)
T ss_dssp             CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH---------------------------------------
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh---------------------------------------
Confidence            456666443    5678999999999999999888877544                                       


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                         ...+++|||+||||||.|
T Consensus        62 ---~~~~~~lil~Pt~~L~~q   79 (414)
T 3oiy_A           62 ---RKGKKSALVFPTVTLVKQ   79 (414)
T ss_dssp             ---TTTCCEEEEESSHHHHHH
T ss_pred             ---cCCCEEEEEECCHHHHHH
Confidence               134689999999999987

>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=94.85  E-value=0.0041  Score=48.53  Aligned_cols=60  Identities=45%  Similarity=0.634  Sum_probs=47.9

Q ss_pred             ccCCCCcccccc----ccc-cceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcc
Q psy11948         68 KLENPTEEDEND----SAR-KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT  142 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~-~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~  142 (167)
                      ++..++..|...    ..+ +++++.++||+|||++|++|++..+..                                 
T Consensus        25 g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~---------------------------------   71 (367)
T 1hv8_A           25 GFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE---------------------------------   71 (367)
T ss_dssp             TCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS---------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcc---------------------------------
Confidence            677788888655    234 799999999999999999999876531                                 


Q ss_pred             hhhhhccccccceEEEccchhhhcC
Q psy11948        143 TEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       143 ~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                             ....++|||+|||+|+.|
T Consensus        72 -------~~~~~~lil~P~~~L~~q   89 (367)
T 1hv8_A           72 -------NNGIEAIILTPTRELAIQ   89 (367)
T ss_dssp             -------SSSCCEEEECSCHHHHHH
T ss_pred             -------cCCCcEEEEcCCHHHHHH
Confidence                   234689999999999976

>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=94.73  E-value=0.0058  Score=50.31  Aligned_cols=47  Identities=32%  Similarity=0.390  Sum_probs=40.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++++++.++||+|||++|++|+++.+..                                         ...++|||+
T Consensus        19 ~~~~~vlv~a~TGsGKT~~~~l~il~~~~~-----------------------------------------~~~~~lvl~   57 (459)
T 2z83_A           19 RKRQMTVLDLHPGSGKTRKILPQIIKDAIQ-----------------------------------------QRLRTAVLA   57 (459)
T ss_dssp             STTCEEEECCCTTSCTTTTHHHHHHHHHHH-----------------------------------------TTCCEEEEE
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHHHHHHHh-----------------------------------------CCCcEEEEC
Confidence            457899999999999999999999977641                                         236899999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      ||||||.|
T Consensus        58 Ptr~La~Q   65 (459)
T 2z83_A           58 PTRVVAAE   65 (459)
T ss_dssp             CSHHHHHH
T ss_pred             chHHHHHH
Confidence            99999987

>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=94.51  E-value=0.0043  Score=54.83  Aligned_cols=55  Identities=18%  Similarity=0.233  Sum_probs=44.7

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++ .|+++|..+    +.|+  ++.++||+|||++|.+|++...+                                   
T Consensus        81 G~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL-----------------------------------  122 (844)
T 1tf5_A           81 GM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL-----------------------------------  122 (844)
T ss_dssp             SC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT-----------------------------------
T ss_pred             CC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHH-----------------------------------
Confidence            66 899999665    5555  99999999999999999984322                                   


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                             ...+++||+||||||.|
T Consensus       123 -------~g~~vlVltptreLA~q  139 (844)
T 1tf5_A          123 -------TGKGVHVVTVNEYLASR  139 (844)
T ss_dssp             -------TSSCEEEEESSHHHHHH
T ss_pred             -------cCCCEEEEeCCHHHHHH
Confidence                   12479999999999986

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=94.50  E-value=0.0055  Score=52.52  Aligned_cols=47  Identities=28%  Similarity=0.179  Sum_probs=40.1

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++++++.||||+|||++|++|++..+..                                         ...+++|++
T Consensus        20 ~~~~~~~~~apTGtGKT~a~l~p~l~~~~~-----------------------------------------~~~kvli~t   58 (620)
T 4a15_A           20 QKSYGVALESPTGSGKTIMALKSALQYSSE-----------------------------------------RKLKVLYLV   58 (620)
T ss_dssp             HHSSEEEEECCTTSCHHHHHHHHHHHHHHH-----------------------------------------HTCEEEEEE
T ss_pred             HcCCCEEEECCCCCCHHHHHHHHHHHhhhh-----------------------------------------cCCeEEEEC
Confidence            367999999999999999999999987641                                         125799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||+|+.|
T Consensus        59 ~T~~l~~Q   66 (620)
T 4a15_A           59 RTNSQEEQ   66 (620)
T ss_dssp             SSHHHHHH
T ss_pred             CCHHHHHH
Confidence            99999876

>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=94.48  E-value=0.023  Score=48.73  Aligned_cols=38  Identities=24%  Similarity=0.028  Sum_probs=28.3

Q ss_pred             CCchHHHhHHHHHH--------ccCCcEEEEeecCCCcccccccch
Q psy11948         24 TPTKIQSMVMPSAL--------LARKDIVGAAETGSGKTLAFGIPI   61 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l--------~~~~d~i~~a~tgsGKt~~~~lp~   61 (167)
                      .+.|.|.+++..+.        .++...|+...+|.|||+..+..+
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i  100 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLI  100 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHH
Confidence            67899999998764        233678888889999987654433

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

Probab=94.41  E-value=0.0084  Score=48.94  Aligned_cols=27  Identities=26%  Similarity=0.195  Sum_probs=23.9

Q ss_pred             ccceeeeecccCccceeeecchhhhhh
Q psy11948         82 RKDIVGAAETGSGKTLAFGIPILTGIV  108 (167)
Q Consensus        82 ~~d~~~~a~tgsgkt~~~~~p~i~~~~  108 (167)
                      ++++++.++||+|||.+|++|+++...
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~   28 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAV   28 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            578999999999999999999986554

>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=94.02  E-value=0.0054  Score=52.98  Aligned_cols=58  Identities=22%  Similarity=0.260  Sum_probs=45.4

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..++..|...    ..++++++++|||+|||+++.+|+++.+..                                  
T Consensus        22 g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~----------------------------------   67 (702)
T 2p6r_A           22 GIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK----------------------------------   67 (702)
T ss_dssp             ---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT----------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh----------------------------------
Confidence            455677777544    567999999999999999999999876641                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                              ..++||++|||+||.|
T Consensus        68 --------~~~~l~i~P~r~La~q   83 (702)
T 2p6r_A           68 --------GGKSLYVVPLRALAGE   83 (702)
T ss_dssp             --------TCCEEEEESSHHHHHH
T ss_pred             --------CCcEEEEeCcHHHHHH
Confidence                    3579999999999976

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

Probab=93.96  E-value=0.0074  Score=49.81  Aligned_cols=51  Identities=20%  Similarity=0.073  Sum_probs=41.9

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++|+++.++||+|||++|++|+++.+....                                     .....++|||+
T Consensus        17 ~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~-------------------------------------~~~~~~~lil~   59 (555)
T 3tbk_A           17 KKGKNTIICAPTGCGKTFVSLLICEHHLKKFP-------------------------------------CGQKGKVVFFA   59 (555)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC-------------------------------------SSCCCCEEEEC
T ss_pred             hCCCCEEEEeCCCChHHHHHHHHHHHHHHhcc-------------------------------------cCCCCEEEEEe
Confidence            45789999999999999999999998775321                                     12256899999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||+|+.|
T Consensus        60 P~~~L~~q   67 (555)
T 3tbk_A           60 NQIPVYEQ   67 (555)
T ss_dssp             SSHHHHHH
T ss_pred             CCHHHHHH
Confidence            99999976

>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=93.84  E-value=0.0076  Score=49.88  Aligned_cols=51  Identities=25%  Similarity=0.134  Sum_probs=41.7

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++|+++.++||+|||++|++|+++.+....                                     .....++|||+
T Consensus        20 ~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~-------------------------------------~~~~~~~lil~   62 (556)
T 4a2p_A           20 INGKNALICAPTGSGKTFVSILICEHHFQNMP-------------------------------------AGRKAKVVFLA   62 (556)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC-------------------------------------SSCCCCEEEEC
T ss_pred             HcCCCEEEEcCCCChHHHHHHHHHHHHHHhCc-------------------------------------ccCCCeEEEEe
Confidence            45789999999999999999999988775321                                     12256899999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||+|+.|
T Consensus        63 P~~~L~~q   70 (556)
T 4a2p_A           63 TKVPVYEQ   70 (556)
T ss_dssp             SSHHHHHH
T ss_pred             CCHHHHHH
Confidence            99999976

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

Probab=93.49  E-value=0.01  Score=50.84  Aligned_cols=62  Identities=18%  Similarity=0.029  Sum_probs=45.4

Q ss_pred             cCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchh
Q psy11948         69 LENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTE  144 (167)
Q Consensus        69 ~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  144 (167)
                      +..++..|...    ..++|++++++||+|||++|++|+++.+....                                 
T Consensus        11 ~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~---------------------------------   57 (696)
T 2ykg_A           11 PFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFP---------------------------------   57 (696)
T ss_dssp             --CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC---------------------------------
T ss_pred             CCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCc---------------------------------
Confidence            34455555433    46789999999999999999999987764211                                 


Q ss_pred             hhhccccccceEEEccchhhhcC
Q psy11948        145 FVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       145 ~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .....++|||+|||+|+.|
T Consensus        58 ----~~~~~~~lvl~Pt~~L~~Q   76 (696)
T 2ykg_A           58 ----QGQKGKVVFFANQIPVYEQ   76 (696)
T ss_dssp             ----TTCCCCEEEECSSHHHHHH
T ss_pred             ----cCCCCeEEEEECCHHHHHH
Confidence                1123579999999999976

>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=93.41  E-value=0.037  Score=47.77  Aligned_cols=37  Identities=22%  Similarity=0.331  Sum_probs=27.3

Q ss_pred             CCCCCCchHHHhHHHHHHc----cCCcEEEEeecCCCccccc
Q psy11948         20 KGFKTPTKIQSMVMPSALL----ARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        20 ~g~~~pt~iQ~~~ip~~l~----~~~d~i~~a~tgsGKt~~~   57 (167)
                      .+| .|++.|..+|..+..    |.+..++.+.||||||+.+
T Consensus         5 ~~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~   45 (664)
T 1c4o_A            5 RGP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTM   45 (664)
T ss_dssp             CSC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH
T ss_pred             CCC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHH
Confidence            367 999999999976653    3234677888999998744

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

Probab=93.40  E-value=0.013  Score=50.63  Aligned_cols=59  Identities=22%  Similarity=0.294  Sum_probs=47.0

Q ss_pred             ccCCCCcccccc-----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcc
Q psy11948         68 KLENPTEEDEND-----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT  142 (167)
Q Consensus        68 ~~~~~~~~~~~~-----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~  142 (167)
                      ++..++..|...     ..++++++++|||+|||+++.+++++.+..                                 
T Consensus        27 g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~---------------------------------   73 (715)
T 2va8_A           27 GIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK---------------------------------   73 (715)
T ss_dssp             SCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH---------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH---------------------------------
Confidence            455667766443     457899999999999999999999877641                                 


Q ss_pred             hhhhhccccccceEEEccchhhhcC
Q psy11948        143 TEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       143 ~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                              ...++||++|||+||.|
T Consensus        74 --------~~~~il~i~P~r~La~q   90 (715)
T 2va8_A           74 --------NGGKAIYVTPLRALTNE   90 (715)
T ss_dssp             --------SCSEEEEECSCHHHHHH
T ss_pred             --------CCCeEEEEeCcHHHHHH
Confidence                    13579999999999976

>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=93.22  E-value=0.013  Score=50.65  Aligned_cols=59  Identities=24%  Similarity=0.254  Sum_probs=46.5

Q ss_pred             ccCCCCcccccc-----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcc
Q psy11948         68 KLENPTEEDEND-----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANT  142 (167)
Q Consensus        68 ~~~~~~~~~~~~-----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~  142 (167)
                      ++..++..|...     ..++++++++|||+|||+++.+|+++.+..                                 
T Consensus        20 g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~---------------------------------   66 (720)
T 2zj8_A           20 GIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILT---------------------------------   66 (720)
T ss_dssp             TCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHH---------------------------------
T ss_pred             CCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHh---------------------------------
Confidence            455666666332     457899999999999999999999977642                                 


Q ss_pred             hhhhhccccccceEEEccchhhhcC
Q psy11948        143 TEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       143 ~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                              ...++||++|||+||.|
T Consensus        67 --------~~~~~l~i~P~raLa~q   83 (720)
T 2zj8_A           67 --------QGGKAVYIVPLKALAEE   83 (720)
T ss_dssp             --------HCSEEEEECSSGGGHHH
T ss_pred             --------CCCEEEEEcCcHHHHHH
Confidence                    13579999999999976

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=92.96  E-value=0.08  Score=43.39  Aligned_cols=39  Identities=18%  Similarity=0.153  Sum_probs=30.5

Q ss_pred             HHHCCCCCCchHHHhHHHHHHcc----CCcEEEEeecCCCccc
Q psy11948         17 LYQKGFKTPTKIQSMVMPSALLA----RKDIVGAAETGSGKTL   55 (167)
Q Consensus        17 l~~~g~~~pt~iQ~~~ip~~l~~----~~d~i~~a~tgsGKt~   55 (167)
                      ..-+.|..+++-|+.++..++..    ...+++.++.|+|||.
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~   60 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATT   60 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHH
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHH
Confidence            44567999999999999876532    3489999999999995

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=92.96  E-value=0.079  Score=45.37  Aligned_cols=55  Identities=18%  Similarity=0.124  Sum_probs=37.2

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhcccCCCCccccccccccceeeeeccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIVGAAETG   92 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~~~a~tg   92 (167)
                      .+.+-|.+|+-.++....-.++++|.|+|||....- ++..+..             .+..++++++|.
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~-~I~~l~~-------------~~~~ILv~a~TN  243 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVE-IILQAVK-------------QGLKVLCCAPSN  243 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHH-HHHHHHH-------------TTCCEEEEESSH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHH-HHHHHHh-------------CCCeEEEEcCch
Confidence            467899999988887623468999999999986432 2333331             234577777763

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

Probab=92.81  E-value=0.021  Score=49.46  Aligned_cols=46  Identities=30%  Similarity=0.384  Sum_probs=40.6

Q ss_pred             cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEcc
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP  160 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~P  160 (167)
                      .++|+++.++||+|||++|++|++..+..                                         ...++|||+|
T Consensus       240 ~g~dvlv~apTGSGKTl~~ll~il~~l~~-----------------------------------------~~~~~lilaP  278 (673)
T 2wv9_A          240 KRQLTVLDLHPGAGKTRRILPQIIKDAIQ-----------------------------------------KRLRTAVLAP  278 (673)
T ss_dssp             TTCEEEECCCTTTTTTTTHHHHHHHHHHH-----------------------------------------TTCCEEEEES
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHHHHh-----------------------------------------CCCcEEEEcc
Confidence            78999999999999999999999977641                                         2478999999


Q ss_pred             chhhhcC
Q psy11948        161 TRELAIQ  167 (167)
Q Consensus       161 TRELa~Q  167 (167)
                      |||||.|
T Consensus       279 Tr~La~Q  285 (673)
T 2wv9_A          279 TRVVAAE  285 (673)
T ss_dssp             SHHHHHH
T ss_pred             HHHHHHH
Confidence            9999987

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=92.67  E-value=0.019  Score=48.25  Aligned_cols=26  Identities=23%  Similarity=0.256  Sum_probs=23.0

Q ss_pred             ccccceeeeecccCccceeeecchhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILT  105 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~  105 (167)
                      ..++++++.++||+|||++|++|.+.
T Consensus        24 ~~~~~~~~~a~TGtGKT~~~l~~~~~   49 (540)
T 2vl7_A           24 KHGKTLLLNAKPGLGKTVFVEVLGMQ   49 (540)
T ss_dssp             HTTCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             HcCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            35689999999999999999999864

>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=92.59  E-value=0.025  Score=48.18  Aligned_cols=38  Identities=32%  Similarity=0.434  Sum_probs=32.0

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILT  105 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~  105 (167)
                      ++..++..|...    ..++|+++.+|||+|||++|.+|++.
T Consensus        41 g~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           41 KLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             CCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH
Confidence            566777777554    67899999999999999999999973

>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=92.42  E-value=0.018  Score=50.53  Aligned_cols=62  Identities=21%  Similarity=0.075  Sum_probs=47.0

Q ss_pred             cCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchh
Q psy11948         69 LENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTE  144 (167)
Q Consensus        69 ~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  144 (167)
                      +..++..|...    ..++|++++++||+|||++|++|++..+....                                 
T Consensus       246 ~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~---------------------------------  292 (797)
T 4a2q_A          246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---------------------------------  292 (797)
T ss_dssp             --CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC---------------------------------
T ss_pred             CCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhcc---------------------------------
Confidence            44566666443    46799999999999999999999988775321                                 


Q ss_pred             hhhccccccceEEEccchhhhcC
Q psy11948        145 FVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       145 ~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .....++|||+||++|+.|
T Consensus       293 ----~~~~~~~Lvl~Pt~~L~~Q  311 (797)
T 4a2q_A          293 ----AGRKAKVVFLATKVPVYEQ  311 (797)
T ss_dssp             ----SSCCCCEEEECSSHHHHHH
T ss_pred             ----ccCCCeEEEEeCCHHHHHH
Confidence                1225689999999999976

>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=92.12  E-value=0.012  Score=52.07  Aligned_cols=53  Identities=19%  Similarity=0.192  Sum_probs=42.9

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+++|..+    +.|+  ++.++||+|||++|.+|++...+                                      
T Consensus        74 ~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l--------------------------------------  113 (853)
T 2fsf_A           74 RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNAL--------------------------------------  113 (853)
T ss_dssp             CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHT--------------------------------------
T ss_pred             CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHH--------------------------------------
Confidence            788888655    4455  89999999999999999985432                                      


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          ...+++||+||||||.|
T Consensus       114 ----~g~~vlVltPTreLA~Q  130 (853)
T 2fsf_A          114 ----TGKGVHVVTVNDYLAQR  130 (853)
T ss_dssp             ----TSSCCEEEESSHHHHHH
T ss_pred             ----cCCcEEEEcCCHHHHHH
Confidence                12579999999999986

>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=92.10  E-value=0.018  Score=51.20  Aligned_cols=71  Identities=21%  Similarity=0.189  Sum_probs=50.9

Q ss_pred             Ccccccccchhhhhhc-------ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCC
Q psy11948         52 GKTLAFGIPILTGIVN-------KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDEN  120 (167)
Q Consensus        52 GKt~~~~lp~l~~~~~-------~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~  120 (167)
                      |.++--++|-.-.+.+       ++ .|+++|..+    +.|+  ++.++||+|||++|.+|++...+            
T Consensus        86 ge~ld~~lpeafA~vrEa~~R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL------------  150 (922)
T 1nkt_A           86 PETLDDLLPEAFAVAREAAWRVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNAL------------  150 (922)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHT------------
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHH------------
Confidence            5666655553322222       44 888888665    4455  99999999999999999974332            


Q ss_pred             CCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        121 DSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       121 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                                    ...+++||+||||||.|
T Consensus       151 ------------------------------~g~~v~VvTpTreLA~Q  167 (922)
T 1nkt_A          151 ------------------------------AGNGVHIVTVNDYLAKR  167 (922)
T ss_dssp             ------------------------------TTSCEEEEESSHHHHHH
T ss_pred             ------------------------------hCCCeEEEeCCHHHHHH
Confidence                                          12379999999999976

>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=92.07  E-value=0.02  Score=52.29  Aligned_cols=55  Identities=20%  Similarity=0.262  Sum_probs=45.4

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .++..|..+    ..++|++++++||+|||++|.+|++..+.                                      
T Consensus       184 ~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~--------------------------------------  225 (1108)
T 3l9o_A          184 TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK--------------------------------------  225 (1108)
T ss_dssp             CCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH--------------------------------------
T ss_pred             CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh--------------------------------------
Confidence            456666444    56799999999999999999999987763                                      


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          ...++||++|||+||.|
T Consensus       226 ----~g~rvlvl~PtraLa~Q  242 (1108)
T 3l9o_A          226 ----NKQRVIYTSPIKALSNQ  242 (1108)
T ss_dssp             ----TTCEEEEEESSHHHHHH
T ss_pred             ----cCCeEEEEcCcHHHHHH
Confidence                23579999999999987

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

Probab=91.63  E-value=0.025  Score=51.57  Aligned_cols=55  Identities=25%  Similarity=0.083  Sum_probs=44.0

Q ss_pred             CCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhh
Q psy11948         71 NPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFV  146 (167)
Q Consensus        71 ~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~  146 (167)
                      .|+..|...    ..++|+++.++||+|||++|+.+++..+                                       
T Consensus        78 ~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~---------------------------------------  118 (1104)
T 4ddu_A           78 DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---------------------------------------  118 (1104)
T ss_dssp             CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH---------------------------------------
T ss_pred             CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH---------------------------------------
Confidence            477777554    5679999999999999997777766544                                       


Q ss_pred             hccccccceEEEccchhhhcC
Q psy11948        147 KKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       147 ~~~~~~~~aLIl~PTRELa~Q  167 (167)
                         ...+++|||+||||||.|
T Consensus       119 ---~~~~~~Lil~PtreLa~Q  136 (1104)
T 4ddu_A          119 ---RKGKKSALVFPTVTLVKQ  136 (1104)
T ss_dssp             ---TTTCCEEEEESSHHHHHH
T ss_pred             ---hcCCeEEEEechHHHHHH
Confidence               134689999999999987

>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=91.50  E-value=0.02  Score=41.28  Aligned_cols=52  Identities=25%  Similarity=0.129  Sum_probs=40.3

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++++++.++||+|||.+++.++...+....                                    ......++||++
T Consensus        46 ~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~------------------------------------~~~~~~~~lil~   89 (216)
T 3b6e_A           46 LEGKNIIICLPTGSGKTRVAVYIAKDHLDKKK------------------------------------KASEPGKVIVLV   89 (216)
T ss_dssp             HTTCCEEEECSCHHHHHHHHHHHHHHHHHHHH------------------------------------HTTCCCCEEEEE
T ss_pred             hcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcc------------------------------------cccCCCcEEEEE
Confidence            34689999999999999999999886654211                                    112346899999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      ||++|+.|
T Consensus        90 p~~~L~~q   97 (216)
T 3b6e_A           90 NKVLLVEQ   97 (216)
T ss_dssp             SSHHHHHH
T ss_pred             CHHHHHHH
Confidence            99999876

>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=91.47  E-value=0.03  Score=50.84  Aligned_cols=56  Identities=23%  Similarity=0.235  Sum_probs=45.8

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++. | ..|...    ..++|+++.++||+|||+ |.+|++..+..                                  
T Consensus        55 g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~----------------------------------   97 (1054)
T 1gku_B           55 GEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL----------------------------------   97 (1054)
T ss_dssp             CSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT----------------------------------
T ss_pred             CCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh----------------------------------
Confidence            555 6 666544    668999999999999998 99999877641                                  


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                             ..+++|||+||||||.|
T Consensus        98 -------~~~~~lil~PtreLa~Q  114 (1054)
T 1gku_B           98 -------KGKRCYVIFPTSLLVIQ  114 (1054)
T ss_dssp             -------TSCCEEEEESCHHHHHH
T ss_pred             -------cCCeEEEEeccHHHHHH
Confidence                   24689999999999987

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=90.90  E-value=0.16  Score=43.06  Aligned_cols=33  Identities=24%  Similarity=0.276  Sum_probs=25.9

Q ss_pred             CCCchHHHhHHHHHHccCCcEEEEeecCCCcccccc
Q psy11948         23 KTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFG   58 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~   58 (167)
                      ..+++-|.+++.   .....+++.|..|||||....
T Consensus         8 ~~Ln~~Q~~av~---~~~~~~lV~a~aGsGKT~~l~   40 (647)
T 3lfu_A            8 DSLNDKQREAVA---APRSNLLVLAGAGSGKTRVLV   40 (647)
T ss_dssp             TTCCHHHHHHHT---CCSSCEEEEECTTSCHHHHHH
T ss_pred             hcCCHHHHHHHh---CCCCCEEEEECCCCCHHHHHH
Confidence            468999999885   223679999999999997543

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=90.71  E-value=0.16  Score=43.08  Aligned_cols=32  Identities=19%  Similarity=0.179  Sum_probs=28.3

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .+++-|..++..++.+ ..+++.++.|+|||..
T Consensus       189 ~L~~~Q~~Av~~~~~~-~~~~I~G~pGTGKTt~  220 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGH-RLVVLTGGPGTGKSTT  220 (574)
T ss_dssp             TCCHHHHHHHHHHTTC-SEEEEECCTTSCHHHH
T ss_pred             CCCHHHHHHHHHHHhC-CEEEEEcCCCCCHHHH
Confidence            5789999999888877 8899999999999964

>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=90.63  E-value=0.028  Score=46.99  Aligned_cols=37  Identities=27%  Similarity=0.393  Sum_probs=30.0

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPIL  104 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i  104 (167)
                      ++..++..|...    ..++|+++.+|||+|||++|.+|++
T Consensus        22 g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l   62 (523)
T 1oyw_A           22 GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL   62 (523)
T ss_dssp             CCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHH
Confidence            455666666544    5678999999999999999999987

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=90.46  E-value=0.22  Score=42.49  Aligned_cols=34  Identities=18%  Similarity=0.132  Sum_probs=28.5

Q ss_pred             CCCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         23 KTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ..+++-|..++-.++.+ .-+++.++.|+|||...
T Consensus       179 ~~ln~~Q~~av~~~l~~-~~~li~GppGTGKT~~~  212 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQR-PLSLIQGPPGTGKTVTS  212 (624)
T ss_dssp             CCCCHHHHHHHHHHHTC-SEEEEECCTTSCHHHHH
T ss_pred             CCCCHHHHHHHHHHhcC-CCeEEECCCCCCHHHHH
Confidence            45788999999888866 67889999999999753

>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=90.24  E-value=0.041  Score=49.30  Aligned_cols=62  Identities=21%  Similarity=0.075  Sum_probs=46.6

Q ss_pred             cCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchh
Q psy11948         69 LENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTE  144 (167)
Q Consensus        69 ~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~  144 (167)
                      ...|+..|...    ..++|++++++||+|||++|++|++..+....                                 
T Consensus       246 ~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~---------------------------------  292 (936)
T 4a2w_A          246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---------------------------------  292 (936)
T ss_dssp             --CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC---------------------------------
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc---------------------------------
Confidence            44566666443    56799999999999999999999987775321                                 


Q ss_pred             hhhccccccceEEEccchhhhcC
Q psy11948        145 FVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       145 ~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                          .....++|||+||++|+.|
T Consensus       293 ----~~~~~~vLvl~Pt~~L~~Q  311 (936)
T 4a2w_A          293 ----AGRKAKVVFLATKVPVYEQ  311 (936)
T ss_dssp             ----SSCCCCEEEECSSHHHHHH
T ss_pred             ----ccCCCeEEEEeCCHHHHHH
Confidence                1124679999999999976

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=90.11  E-value=0.046  Score=40.52  Aligned_cols=51  Identities=22%  Similarity=0.269  Sum_probs=40.2

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++++++.++||+|||..|.+++++.....                                     .....+++++++
T Consensus        74 ~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~-------------------------------------~~~~~~~~l~~~  116 (235)
T 3llm_A           74 SQNSVVIIRGATGCGKTTQVPQFILDDFIQN-------------------------------------DRAAECNIVVTQ  116 (235)
T ss_dssp             HHCSEEEEECCTTSSHHHHHHHHHHHHHHHT-------------------------------------TCGGGCEEEEEE
T ss_pred             hcCCEEEEEeCCCCCcHHhHHHHHhcchhhc-------------------------------------CCCCceEEEEec
Confidence            4678999999999999999888887665421                                     112457899999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||+||.|
T Consensus       117 p~~~la~q  124 (235)
T 3llm_A          117 PRRISAVS  124 (235)
T ss_dssp             SSHHHHHH
T ss_pred             cchHHHHH
Confidence            99999875

>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=89.94  E-value=0.052  Score=46.49  Aligned_cols=52  Identities=23%  Similarity=0.116  Sum_probs=41.1

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++|+++.++||+|||++|++|+++.+....                                    ......++|||+
T Consensus        20 l~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~------------------------------------~~~~~~~vlvl~   63 (699)
T 4gl2_A           20 LEGKNIIICLPTGCGKTRVAVYIAKDHLDKKK------------------------------------KASEPGKVIVLV   63 (699)
T ss_dssp             HSSCCEEECCCTTSCHHHHHHHHHHHHHHHHH------------------------------------HHTCCCCBCCEE
T ss_pred             HhCCCEEEEcCCCCcHHHHHHHHHHHHHHhcc------------------------------------ccCCCCeEEEEE
Confidence            35789999999999999999999988775310                                    112236799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      ||++|+.|
T Consensus        64 P~~~L~~Q   71 (699)
T 4gl2_A           64 NKVLLVEQ   71 (699)
T ss_dssp             SCSHHHHH
T ss_pred             CCHHHHHH
Confidence            99999976

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=89.64  E-value=0.031  Score=49.95  Aligned_cols=55  Identities=16%  Similarity=0.163  Sum_probs=42.9

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++ .|+.+|..+    +.|+  ++.++||+|||++|.+|++...+                                   
T Consensus        77 G~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL-----------------------------------  118 (997)
T 2ipc_A           77 GM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNAL-----------------------------------  118 (997)
T ss_dssp             CC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHT-----------------------------------
T ss_pred             CC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHH-----------------------------------
Confidence            45 788888655    4444  89999999999999999964332                                   


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                             ...+++||+||||||.|
T Consensus       119 -------~G~qv~VvTPTreLA~Q  135 (997)
T 2ipc_A          119 -------TGKGVHVVTVNDYLARR  135 (997)
T ss_dssp             -------TCSCCEEEESSHHHHHH
T ss_pred             -------hCCCEEEEeCCHHHHHH
Confidence                   12369999999999986

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=89.13  E-value=0.068  Score=44.91  Aligned_cols=43  Identities=28%  Similarity=0.117  Sum_probs=37.6

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++|+++.++||+|||++|++|++.                                             ...+++|++
T Consensus        20 ~~~~~~~~~a~TGtGKT~~~l~p~l~---------------------------------------------~~~~v~i~~   54 (551)
T 3crv_A           20 RNNFLVALNAPTGSGKTLFSLLVSLE---------------------------------------------VKPKVLFVV   54 (551)
T ss_dssp             HTTCEEEEECCTTSSHHHHHHHHHHH---------------------------------------------HCSEEEEEE
T ss_pred             HcCCcEEEECCCCccHHHHHHHHHHh---------------------------------------------CCCeEEEEc
Confidence            35789999999999999999999984                                             135799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||+|+.|
T Consensus        55 pt~~l~~q   62 (551)
T 3crv_A           55 RTHNEFYP   62 (551)
T ss_dssp             SSGGGHHH
T ss_pred             CCHHHHHH
Confidence            99999976

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=88.38  E-value=0.38  Score=42.42  Aligned_cols=34  Identities=18%  Similarity=0.132  Sum_probs=28.3

Q ss_pred             CCCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         23 KTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ..+++-|..++-.++.+ .-.++.++.|+|||...
T Consensus       355 ~~Ln~~Q~~Av~~~l~~-~~~lI~GppGTGKT~ti  388 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQR-PLSLIQGPPGTGKTVTS  388 (800)
T ss_dssp             CCCCHHHHHHHHHHHTS-SEEEEECCTTSCHHHHH
T ss_pred             cCCCHHHHHHHHHhccC-CeEEEEcCCCCCHHHHH
Confidence            35688999999888876 67889999999999753

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=87.95  E-value=0.34  Score=42.78  Aligned_cols=34  Identities=21%  Similarity=0.134  Sum_probs=28.3

Q ss_pred             CCCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         23 KTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      ..+++-|..++-.++.+ .-+++.++.|+|||...
T Consensus       359 ~~Ln~~Q~~Av~~~l~~-~~~lI~GppGTGKT~~i  392 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQR-PLSLIQGPPGTGKTVTS  392 (802)
T ss_dssp             CCCCHHHHHHHHHHTTC-SEEEEECSTTSSHHHHH
T ss_pred             ccCCHHHHHHHHHHhcC-CCEEEECCCCCCHHHHH
Confidence            45679999999888765 56889999999999753

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

Probab=87.93  E-value=0.067  Score=48.37  Aligned_cols=54  Identities=20%  Similarity=0.264  Sum_probs=43.3

Q ss_pred             CCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhh
Q psy11948         72 PTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVK  147 (167)
Q Consensus        72 ~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~  147 (167)
                      ++..|..+    ..+++++++++||+|||++|.+++...+.                                       
T Consensus        87 L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~---------------------------------------  127 (1010)
T 2xgj_A           87 LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK---------------------------------------  127 (1010)
T ss_dssp             CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH---------------------------------------
T ss_pred             CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc---------------------------------------
Confidence            55555443    45789999999999999999998886652                                       


Q ss_pred             ccccccceEEEccchhhhcC
Q psy11948        148 KTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       148 ~~~~~~~aLIl~PTRELa~Q  167 (167)
                         ...++||++|||+||.|
T Consensus       128 ---~g~rvL~l~PtkaLa~Q  144 (1010)
T 2xgj_A          128 ---NKQRVIYTSPIKALSNQ  144 (1010)
T ss_dssp             ---TTCEEEEEESSHHHHHH
T ss_pred             ---cCCeEEEECChHHHHHH
Confidence               23589999999999987

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=87.56  E-value=0.39  Score=44.30  Aligned_cols=37  Identities=35%  Similarity=0.293  Sum_probs=27.9

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      .+|+-|.++|-..  + .++++.|.-|||||....-=++.
T Consensus        10 ~~t~eQ~~~i~~~--~-~~~~v~a~AGSGKT~vl~~ri~~   46 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--G-QDILVAAAAGSGKTAVLVERMIR   46 (1232)
T ss_dssp             CCCHHHHHHHHCC--S-SCEEEEECTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--C-CCEEEEecCCCcHHHHHHHHHHH
Confidence            6799999988532  4 79999999999999855433333

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=85.62  E-value=0.097  Score=43.05  Aligned_cols=47  Identities=21%  Similarity=0.195  Sum_probs=38.4

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..+++.+++++||+|||.+++.++...+..                                         ...++|||+
T Consensus       126 ~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~-----------------------------------------~~~~vlvl~  164 (510)
T 2oca_A          126 LVNRRRILNLPTSAGRSLIQALLARYYLEN-----------------------------------------YEGKILIIV  164 (510)
T ss_dssp             HHHSEEEEECCSTTTHHHHHHHHHHHHHHH-----------------------------------------CSSEEEEEE
T ss_pred             HhcCCcEEEeCCCCCHHHHHHHHHHHHHhC-----------------------------------------CCCeEEEEE
Confidence            346899999999999999999888765531                                         224899999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      ||++|+.|
T Consensus       165 P~~~L~~Q  172 (510)
T 2oca_A          165 PTTALTTQ  172 (510)
T ss_dssp             SSHHHHHH
T ss_pred             CcHHHHHH
Confidence            99999976

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

Probab=85.58  E-value=0.16  Score=45.90  Aligned_cols=46  Identities=24%  Similarity=0.252  Sum_probs=38.8

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++|+++.++||+|||++|.+++...+.                                          ...++||++
T Consensus        52 l~g~~vlv~apTGsGKTlv~~~~i~~~~~------------------------------------------~g~~vlvl~   89 (997)
T 4a4z_A           52 EQGDSVFVAAHTSAGKTVVAEYAIAMAHR------------------------------------------NMTKTIYTS   89 (997)
T ss_dssp             HTTCEEEEECCTTSCSHHHHHHHHHHHHH------------------------------------------TTCEEEEEE
T ss_pred             HcCCCEEEEECCCCcHHHHHHHHHHHHHh------------------------------------------cCCeEEEEe
Confidence            46799999999999999999988875442                                          236799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      |||+|+.|
T Consensus        90 PtraLa~Q   97 (997)
T 4a4z_A           90 PIKALSNQ   97 (997)
T ss_dssp             SCGGGHHH
T ss_pred             CCHHHHHH
Confidence            99999986

>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=85.14  E-value=0.15  Score=44.87  Aligned_cols=64  Identities=22%  Similarity=0.311  Sum_probs=48.3

Q ss_pred             hhhhhhc--ccCCCCcccccc----c------cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHH
Q psy11948         61 ILTGIVN--KLENPTEEDEND----S------ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEA  128 (167)
Q Consensus        61 ~l~~~~~--~~~~~~~~~~~~----~------~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~  128 (167)
                      .+..+..  .+ .++..|...    .      ..++.+++++||+|||++|++|++..+.                    
T Consensus       357 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~--------------------  415 (780)
T 1gm5_A          357 LAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYE--------------------  415 (780)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHH--------------------
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHH--------------------
Confidence            4455544  44 677777543    1      1258999999999999999999987663                    


Q ss_pred             HHHHHHHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        129 EEVLEELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       129 ~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                            ...+++||+|||+||.|
T Consensus       416 ----------------------~g~qvlvlaPtr~La~Q  432 (780)
T 1gm5_A          416 ----------------------AGFQTAFMVPTSILAIQ  432 (780)
T ss_dssp             ----------------------HTSCEEEECSCHHHHHH
T ss_pred             ----------------------cCCeEEEEeCcHHHHHH
Confidence                                  13589999999999987

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=84.62  E-value=0.51  Score=40.43  Aligned_cols=32  Identities=22%  Similarity=0.118  Sum_probs=24.8

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFG   58 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~   58 (167)
                      .+++-|.+++-.  .+ ..+++.|..|||||....
T Consensus         2 ~L~~~Q~~av~~--~~-~~~lV~AgaGSGKT~~l~   33 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VT-GPCLVLAGAGSGKTRVIT   33 (673)
T ss_dssp             CCCHHHHHHHHC--CS-SEEEECCCTTSCHHHHHH
T ss_pred             CCCHHHHHHHhC--CC-CCEEEEeCCCCChHHHHH
Confidence            478899998853  23 688999999999997543

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=82.79  E-value=1.1  Score=38.87  Aligned_cols=33  Identities=24%  Similarity=0.200  Sum_probs=26.2

Q ss_pred             CCCchHHHhHHHHHHccCCcEEEEeecCCCcccccc
Q psy11948         23 KTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFG   58 (167)
Q Consensus        23 ~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~   58 (167)
                      ..+++-|.+++-.  .+ ..+++.|.-|||||....
T Consensus        10 ~~Ln~~Q~~av~~--~~-g~~lV~AgAGSGKT~vL~   42 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TE-GPLLIMAGAGSGKTRVLT   42 (724)
T ss_dssp             TTSCHHHHHHHHC--CS-SCEEEEECTTSCHHHHHH
T ss_pred             hhCCHHHHHHHhC--CC-CCEEEEEcCCCCHHHHHH
Confidence            4689999998853  23 689999999999998543

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=82.39  E-value=1.1  Score=31.31  Aligned_cols=31  Identities=19%  Similarity=0.118  Sum_probs=21.6

Q ss_pred             chHHHhHHHHHH--------ccCCcEEEEeecCCCcccc
Q psy11948         26 TKIQSMVMPSAL--------LARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        26 t~iQ~~~ip~~l--------~~~~d~i~~a~tgsGKt~~   56 (167)
                      ++-|..++..+.        ..+..+++.+++|+|||..
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHH
Confidence            455666664443        1237899999999999964

>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=80.96  E-value=0.5  Score=40.83  Aligned_cols=43  Identities=21%  Similarity=0.182  Sum_probs=36.8

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEc
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILA  159 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~  159 (167)
                      ..++|+++.++||+|||.+|.+|+++.                                             ..++||++
T Consensus       230 ~~~~~vlv~ApTGSGKT~a~~l~ll~~---------------------------------------------g~~vLVl~  264 (666)
T 3o8b_A          230 QSFQVAHLHAPTGSGKSTKVPAAYAAQ---------------------------------------------GYKVLVLN  264 (666)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHHT---------------------------------------------TCCEEEEE
T ss_pred             HcCCeEEEEeCCchhHHHHHHHHHHHC---------------------------------------------CCeEEEEc
Confidence            467899999999999999999888631                                             24799999


Q ss_pred             cchhhhcC
Q psy11948        160 PTRELAIQ  167 (167)
Q Consensus       160 PTRELa~Q  167 (167)
                      ||||||.|
T Consensus       265 PTReLA~Q  272 (666)
T 3o8b_A          265 PSVAATLG  272 (666)
T ss_dssp             SCHHHHHH
T ss_pred             chHHHHHH
Confidence            99999987

---

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	167
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	6e-12
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-11
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-11
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	7e-11
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	7e-11
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	8e-11
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	2e-10
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	4e-10
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	5e-10
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	8e-10
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-08
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-08
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-07
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-05
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	1e-04

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

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]

 Score = 59.5 bits (143), Expect = 6e-12
 Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 1/86 (1%)

Query: 1   MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
           +  + +  +  TI   +    ++ PT IQ   +P A+L  +DI+  A+TGSGKT AF IP
Sbjct: 20  IENFDELKLDPTIRNNILLASYQRPTPIQKNAIP-AILEHRDIMACAQTGSGKTAAFLIP 78

Query: 61  ILTGIVNKLENPTEEDENDSARKDIV 86
           I+  +V +  N     +    +  I+
Sbjct: 79  IINHLVCQDLNQQRYSKTAYPKCLIL 104

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

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 DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 57.0 bits (136), Expect = 3e-11
 Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 3  EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
          ++ +F     II A+    F  PT+IQ  ++P   L  + +VG ++TG+GKT A+ +P
Sbjct: 2  QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIP-GALRGESMVGQSQTGTGKTHAYLLP 58

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (136), Expect = 3e-11
 Identities = 17/60 (28%), Positives = 37/60 (61%), Gaps = 1/60 (1%)

Query: 3  EWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          E+  + +   ++  +++ G++ P+ IQ   +P   L+ +DI+  A+ G+GK+ A+ IP+L
Sbjct: 4  EFEDYCLKRELLMGIFEMGWEKPSPIQEESIP-IALSGRDILARAKNGTGKSGAYLIPLL 62

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

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]

 Score = 56.4 bits (135), Expect = 7e-11
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 1  MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIP 60
          +  +   N+ E+++R +Y  GF+ P+ IQ   +    +   D++  A++G+GKT  F I 
Sbjct: 11 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAIL-PCIKGYDVIAQAQSGTGKTATFAIS 69

Query: 61 ILTGIVNKLENP 72
          IL  I   L+  
Sbjct: 70 ILQQIELDLKAT 81

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.4 bits (135), Expect = 7e-11
 Identities = 15/58 (25%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 4  WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
          +    + E ++R +Y  GF+ P+ IQ   +   ++  +D++  +++G+GKT  F I +
Sbjct: 19 FDTMGLREDLLRGIYAYGFEKPSAIQQRAIK-QIIKGRDVIAQSQSGTGKTATFSISV 75

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 56.1 bits (134), Expect = 8e-11
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPI 61
          F +   ++  +++ GF+ P+ IQ   +P   +  +DI+  A+ G+GKT AF IP 
Sbjct: 6  FYLKRELLMGIFEAGFEKPSPIQEEAIP-VAITGRDILARAKNGTGKTAAFVIPT 59

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.2 bits (132), Expect = 2e-10
 Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 4  WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT 63
          +    + E ++R ++  GF+ P+ IQ   +   ++   D++  A++G+GKT  F I  L 
Sbjct: 12 FDDMELDENLLRGVFGYGFEEPSAIQQRAIM-PIIEGHDVLAQAQSGTGKTGTFSIAALQ 70

Query: 64 GIVNKLENP 72
           I   ++ P
Sbjct: 71 RIDTSVKAP 79

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.1 bits (129), Expect = 4e-10
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 7  FNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV 66
          F +   ++RA+   GF+ P+++Q   +P   +   D++  A++G GKT  F +  L  + 
Sbjct: 6  FLLKPELLRAIVDCGFEHPSEVQHECIP-QAILGMDVLCQAKSGMGKTAVFVLATLQQLE 64

Query: 67 NKLENP 72
                
Sbjct: 65 PVTGQV 70

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 53.8 bits (128), Expect = 5e-10
 Identities = 11/58 (18%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 8  NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGI 65
          +I    +  L ++G +     Q+  +   + + K+++ A  T +GKTL   + ++   
Sbjct: 9  SISSYAVGILKEEGIEELFPPQAEAVE-KVFSGKNLLLAMPTAAGKTLLAEMAMVREA 65

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 53.1 bits (127), Expect = 8e-10
 Identities = 27/61 (44%), Positives = 37/61 (60%), Gaps = 3/61 (4%)

Query: 3  EWVKF---NIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI 59
          E++ F   N+ + I+ A+  KGF+ PT IQ  V+P  L    +IV  A TGSGKT +F I
Sbjct: 2  EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAI 61

Query: 60 P 60
          P
Sbjct: 62 P 62

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

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 = 49.5 bits (117), Expect = 2e-08
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 14 IRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
              ++K    P  IQ M     +L ++     A TG GKT       L
Sbjct: 33 FVEFFRKCVGEPRAIQKMWAK-RILRKESFAATAPTGVGKTSFGLAMSL 80

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 48.5 bits (114), Expect = 4e-08
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 1  MAEWVKFNIPETIIRALYQK-GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI 59
          MA+    N+     + L +  G++     Q  ++   +L+ +D +    TG GK+L + I
Sbjct: 1  MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIID-TVLSGRDCLVVMPTGGGKSLCYQI 59

Query: 60 PI 61
          P 
Sbjct: 60 PA 61

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 46.5 bits (109), Expect = 3e-07
 Identities = 16/93 (17%), Positives = 27/93 (29%), Gaps = 41/93 (44%)

Query: 75  EDENDSARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE 134
           ED+    ++  +     G+GKT  +   I+   + +                        
Sbjct: 2   EDDIFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR------------------------ 37

Query: 135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ 167
                             L  LILAPTR +A +
Sbjct: 38  -----------------GLRTLILAPTRVVAAE 53

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 41.4 bits (96), Expect = 2e-05
 Identities = 5/33 (15%), Positives = 13/33 (39%)

Query: 36 ALLARKDIVGAAETGSGKTLAFGIPILTGIVNK 68
              ++  +     G+GKT  +   I+   + +
Sbjct: 5  IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR 37

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} 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: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 38.6 bits (88), Expect = 1e-04
 Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 2/46 (4%)

Query: 17 LYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL 62
          + ++    P   Q ++         + +    TG GKTL   +   
Sbjct: 2  VLRRDLIQPRIYQEVIYAKCK--ETNCLIVLPTGLGKTLIAMMIAE 45

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	167
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.92
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.92
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.92
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.92
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.91
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.89
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.87
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.84
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.83
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.59
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.57
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.55
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.87
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.2
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.19
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.18
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.17
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.17
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.15
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.05
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.05
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	97.97
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.94
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	97.91
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	97.91
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.62
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	97.25
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	97.13
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	97.12
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	96.91
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.11
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.59
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	94.91
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	93.12
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.09
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	93.05
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	92.85
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	92.48
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	92.24
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	88.33
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	85.71
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	85.29
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	84.15
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	83.01
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	80.71

>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=99.92  E-value=3e-26  Score=170.75  Aligned_cols=64  Identities=28%  Similarity=0.555  Sum_probs=60.7

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ++|++|+|++.++++|+++||+.|||+|+++||.++.| +|++++|+||||||++|++|+++.+.
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g-~dvl~~A~TGsGKTla~~lp~l~~~~   64 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILG-MDVLCQAKSGMGKTAVFVLATLQQLE   64 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTT-CCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCeEEEeccccccccccccceeeeec
Confidence            58999999999999999999999999999999999999 99999999999999999999987654

>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=99.92  E-value=2.1e-26  Score=173.32  Aligned_cols=64  Identities=25%  Similarity=0.593  Sum_probs=61.1

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|++.++++|+++||..|||||+++||.++.| +|++++|+||||||++|++|+++.+.
T Consensus        17 ~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g-~dvi~~a~TGSGKTlayllPil~~l~   80 (222)
T d2j0sa1          17 PTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKG-RDVIAQSQSGTGKTATFSISVLQCLD   80 (222)
T ss_dssp             CSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHTCC
T ss_pred             CCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCC-CCeEEEcCcchhhhhhhccccccccc
Confidence            58999999999999999999999999999999999998 99999999999999999999987765

>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=99.92  E-value=5e-26  Score=169.37  Aligned_cols=64  Identities=28%  Similarity=0.591  Sum_probs=61.0

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|++.++++|.++||+.|||||+++||.++.| +|++++|+||||||++|++|++.++.
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g-~dvl~~a~TGsGKTlayllP~l~~~~   66 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSG-RDILARAKNGTGKSGAYLIPLLERLD   66 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTT-CCEEEECCSSSTTHHHHHHHHHHHCC
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCEEeeccCccccccccccchhhccc
Confidence            58999999999999999999999999999999999999 99999999999999999999987654

>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=99.92  E-value=6.8e-26  Score=170.11  Aligned_cols=65  Identities=31%  Similarity=0.627  Sum_probs=61.8

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      |.+|++|+|++.++++|.++||.+|||||+++||.++.| +|++++|+||||||++|++|+++++.
T Consensus        11 i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g-~dvl~~a~TGsGKTlayllp~l~~i~   75 (218)
T d2g9na1          11 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKG-YDVIAQAQSGTGKTATFAISILQQIE   75 (218)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHT-CCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             cCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCEEEEcccchhhhhhhhhhhhheec
Confidence            468999999999999999999999999999999999999 99999999999999999999988764

>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=99.91  E-value=2.1e-25  Score=166.71  Aligned_cols=65  Identities=26%  Similarity=0.522  Sum_probs=61.8

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +.+|++|+|+++++++|.++||+.|||+|+++||.++.| +|++++++||||||++|++|+++++.
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g-~dvl~~a~TGsGKT~a~~lp~i~~l~   73 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEG-HDVLAQAQSGTGKTGTFSIAALQRID   73 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHCC
T ss_pred             ccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCEEeecccccchhhhhHhhhHhhhh
Confidence            579999999999999999999999999999999999999 99999999999999999999988764

>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=99.89  E-value=4e-25  Score=167.84  Aligned_cols=66  Identities=35%  Similarity=0.575  Sum_probs=63.2

Q ss_pred             CCccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          1 MAEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      +.+|++|+|+++++++|.++||..|||+|+++||.++.| +|++++|+||||||++|++|+++++..
T Consensus        20 ~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g-~dvvi~a~TGsGKTlayllp~l~~l~~   85 (238)
T d1wrba1          20 IENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEH-RDIMACAQTGSGKTAAFLIPIINHLVC   85 (238)
T ss_dssp             CCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTT-CCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             cCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCC-CCEEEECCCCCCcceeeHHHHHHHHHh
Confidence            468999999999999999999999999999999999999 999999999999999999999998874

>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=99.87  E-value=2.5e-23  Score=154.73  Aligned_cols=63  Identities=40%  Similarity=0.653  Sum_probs=59.5

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      ++|++|+|+++++++|.++||..|||+|+++||.++.|+.|++++++||+|||++|.+|++..
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~   66 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIEL   66 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccc
Confidence            699999999999999999999999999999999999986799999999999999999998764

>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=99.84  E-value=8.2e-22  Score=146.15  Aligned_cols=64  Identities=31%  Similarity=0.642  Sum_probs=60.9

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .+|++|+|++.++++|+++||..|||+|+++||.++.| +|+++.|+||||||++|++|++..+.
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g-~dvi~~a~tGsGKTlay~lp~i~~~~   64 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITG-RDILARAKNGTGKTAAFVIPTLEKVK   64 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHT-CCEEEECCTTSCHHHHHHHHHHHHCC
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcC-CCEEEecCCcchhhhhhccccccccc
Confidence            38999999999999999999999999999999999999 99999999999999999999987655

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

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 DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.83  E-value=1.2e-21  Score=145.06  Aligned_cols=65  Identities=35%  Similarity=0.612  Sum_probs=62.0

Q ss_pred             CccccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhc
Q psy11948          2 AEWVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVN   67 (167)
Q Consensus         2 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~   67 (167)
                      ++|++|+|+++++++|++.||.+|||+|++|||.++.| +|++++|+||||||++|++|+++.+..
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G-~dvii~a~TGSGKTlayllp~l~~~~~   65 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRG-ESMVGQSQTGTGKTHAYLLPIMEKIKP   65 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHT-CCEEEECCSSHHHHHHHHHHHHHHCCT
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCC-CCeEeecccccccceeeeeeecccccc
Confidence            58999999999999999999999999999999999999 999999999999999999999887663

>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=99.59  E-value=1.4e-16  Score=117.11  Aligned_cols=61  Identities=26%  Similarity=0.400  Sum_probs=56.5

Q ss_pred             CCccccCCCCHHHHHHHHHC-CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchh
Q psy11948          1 MAEWVKFNIPETIIRALYQK-GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPIL   62 (167)
Q Consensus         1 ~~~f~~l~l~~~l~~~l~~~-g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l   62 (167)
                      |..++.|+|++.+.+.|++. ||+.++|+|.++|+.++.| +|++++++||+|||++|.+|++
T Consensus         1 ~~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g-~~vlv~apTGsGKT~~~~~~~~   62 (206)
T d1oywa2           1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSG-RDCLVVMPTGGGKSLCYQIPAL   62 (206)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTT-CCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCCCCcchhhhhhh
Confidence            56788899999999999987 9999999999999999998 8999999999999999988875

>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=99.57  E-value=2.5e-16  Score=118.19  Aligned_cols=59  Identities=22%  Similarity=0.137  Sum_probs=46.6

Q ss_pred             cccCCCCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhh
Q psy11948          4 WVKFNIPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTG   64 (167)
Q Consensus         4 f~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~   64 (167)
                      |.+..+.+.+ .++.+.++.+|+++|+.+||.++.| +|++++++||+|||++++++.+..
T Consensus        24 ~~~~~~~~~~-~~~~~~~~~~p~~~Q~~~i~~~l~g-~~~~i~apTGsGKT~~~~~~~~~~   82 (237)
T d1gkub1          24 FPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILRK-ESFAATAPTGVGKTSFGLAMSLFL   82 (237)
T ss_dssp             CTTHHHHHHH-HHHHHTTTCSCCHHHHHHHHHHHTT-CCEECCCCBTSCSHHHHHHHHHHH
T ss_pred             CccchhHHHH-HHHHHhccCCCCHHHHHHHHHHHCC-CCEEEEecCCChHHHHHHHHHHHH
Confidence            3333333443 4466778999999999999999999 999999999999999888877543

>d2p6ra3 c.37.1.19 (A:1-202) 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=99.55  E-value=9.5e-17  Score=117.78  Aligned_cols=57  Identities=19%  Similarity=0.258  Sum_probs=48.3

Q ss_pred             CCHHHHHHHHHCCCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhh
Q psy11948          9 IPETIIRALYQKGFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         9 l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      +++.+++.|++.||.+|+|+|.++++.++.| +|++++++||+|||+++.++++..+.
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~-~~~il~apTGsGKT~~a~l~i~~~~~   66 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSG-KNLLLAMPTAAGKTLLAEMAMVREAI   66 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTC-SCEEEECSSHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcC-CCEEEEcCCCCchhHHHHHHHHHHhh
Confidence            6889999999999999999999999999998 89999999999999988777765443

>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=98.87  E-value=4.6e-10  Score=80.80  Aligned_cols=40  Identities=20%  Similarity=0.158  Sum_probs=32.2

Q ss_pred             CCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhh
Q psy11948         22 FKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILT   63 (167)
Q Consensus        22 ~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~   63 (167)
                      +-+|.+.|..++..+. + ++++++++||+|||+++++++..
T Consensus         7 ~~~pr~~Q~~~~~~~~-~-~n~lv~~pTGsGKT~i~~~~~~~   46 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCK-E-TNCLIVLPTGLGKTLIAMMIAEY   46 (200)
T ss_dssp             HHCCCHHHHHHHHHGG-G-SCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHh-c-CCeEEEeCCCCcHHHHHHHHHHH
Confidence            3479999999998765 4 67999999999999877765543

>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=98.20  E-value=9.2e-08  Score=69.44  Aligned_cols=69  Identities=35%  Similarity=0.621  Sum_probs=58.6

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .+++.+.. ++..|+.+|..+    ..|+|+++.|+||+|||++|++|+++.+.                          
T Consensus        13 ~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~--------------------------   66 (206)
T d1veca_          13 ELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLD--------------------------   66 (206)
T ss_dssp             HHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCC--------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccc--------------------------
Confidence            45555655 899999999766    78999999999999999999999998764                          


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....+++|||+||||||.|
T Consensus        67 -------------~~~~~~~~lil~pt~el~~q   86 (206)
T d1veca_          67 -------------LKKDNIQAMVIVPTRELALQ   86 (206)
T ss_dssp             -------------TTSCSCCEEEECSCHHHHHH
T ss_pred             -------------ccccCcceEEEeecchhhHH
Confidence                         23456899999999999987

>d2fz4a1 c.37.1.19 (A:24-229) 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=98.19  E-value=3e-07  Score=66.49  Aligned_cols=33  Identities=27%  Similarity=0.166  Sum_probs=28.0

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCccccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~   57 (167)
                      .+.+.|.+++..++.+ ...++.++||+|||+..
T Consensus        70 ~Lr~yQ~eav~~~~~~-~~~ll~~~tG~GKT~~a  102 (206)
T d2fz4a1          70 SLRDYQEKALERWLVD-KRGCIVLPTGSGKTHVA  102 (206)
T ss_dssp             CCCHHHHHHHHHHTTT-SEEEEEESSSTTHHHHH
T ss_pred             CcCHHHHHHHHHHHhC-CCcEEEeCCCCCceehH
Confidence            5788999999988877 67788899999999743

>d1yksa1 c.37.1.14 (A:185-324) 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=98.18  E-value=1.9e-07  Score=62.30  Aligned_cols=16  Identities=44%  Similarity=0.675  Sum_probs=12.2

Q ss_pred             ccceEEEccchhhhcC
Q psy11948        152 KLYALILAPTRELAIQ  167 (167)
Q Consensus       152 ~~~aLIl~PTRELa~Q  167 (167)
                      ..+++|++|+|+|+.|
T Consensus        36 ~~~vli~~p~~~l~~q   51 (140)
T d1yksa1          36 RLRTLVLAPTRVVLSE   51 (140)
T ss_dssp             TCCEEEEESSHHHHHH
T ss_pred             CceeeeeecchhHHHH
Confidence            3568888888888765

>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=98.17  E-value=1.2e-07  Score=69.78  Aligned_cols=69  Identities=36%  Similarity=0.590  Sum_probs=58.8

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.+ ++..|+.+|..+    ..|+|+++.|+||||||++|++|+++.+..                         
T Consensus        27 ~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~-------------------------   81 (222)
T d2j0sa1          27 DLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI-------------------------   81 (222)
T ss_dssp             HHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCT-------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccc-------------------------
Confidence            45555555 899999999765    679999999999999999999999988752                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    ....+++||++||||||.|
T Consensus        82 --------------~~~~~~~lil~PtreLa~Q  100 (222)
T d2j0sa1          82 --------------QVRETQALILAPTRELAVQ  100 (222)
T ss_dssp             --------------TSCSCCEEEECSSHHHHHH
T ss_pred             --------------cccCceeEEecchHHHHHH
Confidence                          2456899999999999987

>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=98.17  E-value=1e-07  Score=69.27  Aligned_cols=68  Identities=31%  Similarity=0.477  Sum_probs=57.7

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHH
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEEL  135 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (167)
                      ++..+.+ ++..|+.+|..+    ..|+|+++.|+||+|||++|++|+++.+.                           
T Consensus        12 l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~---------------------------   64 (207)
T d1t6na_          12 LLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLE---------------------------   64 (207)
T ss_dssp             HHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCC---------------------------
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeec---------------------------
Confidence            4455555 899999999765    78999999999999999999999998764                           


Q ss_pred             HHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        136 EEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                  .....++++|++||||||.|
T Consensus        65 ------------~~~~~~~~lil~PtreL~~q   84 (207)
T d1t6na_          65 ------------PVTGQVSVLVMCHTRELAFQ   84 (207)
T ss_dssp             ------------CCTTCCCEEEECSCHHHHHH
T ss_pred             ------------ccCCCceEEEEeccchhhHH
Confidence                        23466899999999999986

>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=98.15  E-value=1.3e-07  Score=70.07  Aligned_cols=78  Identities=42%  Similarity=0.513  Sum_probs=60.6

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.+ ++..|+.+|..+    ..|+|+++.|+||+|||++|++|+++.+........                   
T Consensus        31 ~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~-------------------   91 (238)
T d1wrba1          31 TIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQ-------------------   91 (238)
T ss_dssp             STTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccc-------------------
Confidence            34455555 999999999765    688999999999999999999999999875432211                   


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                 .......+++|||+||||||.|
T Consensus        92 -----------~~~~~~~~~alil~pt~el~~q  113 (238)
T d1wrba1          92 -----------RYSKTAYPKCLILAPTRELAIQ  113 (238)
T ss_dssp             --------------CCBCCSEEEECSSHHHHHH
T ss_pred             -----------cccCCCCceEEEeccchhhhcc
Confidence                       0123567999999999999987

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

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 DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.05  E-value=1.5e-07  Score=68.02  Aligned_cols=49  Identities=35%  Similarity=0.541  Sum_probs=40.9

Q ss_pred             hhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         61 ILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        61 ~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ++..+.+ ++..|+.+|..+    ..|+|+++.|+||||||++|++|+++....
T Consensus        12 l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~   65 (209)
T d1q0ua_          12 IIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKP   65 (209)
T ss_dssp             HHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeecccccc
Confidence            3444444 888999999766    678999999999999999999999988764

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=98.05  E-value=7.8e-07  Score=67.47  Aligned_cols=32  Identities=19%  Similarity=0.227  Sum_probs=27.4

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      .|.+.|..++..++.. +..++.++||+|||+.
T Consensus       113 ~~rdyQ~~av~~~l~~-~~~il~~pTGsGKT~i  144 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVN-RRRILNLPTSAGRSLI  144 (282)
T ss_dssp             CCCHHHHHHHHHHHHH-SEEEECCCTTSCHHHH
T ss_pred             ccchHHHHHHHHHHhc-CCceeEEEcccCccHH
Confidence            6889999999888887 6778888999999974

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.00  E-value=2.6e-06  Score=63.96  Aligned_cols=57  Identities=19%  Similarity=0.163  Sum_probs=39.9

Q ss_pred             CCHHHHH-HHHHCCCCCCchHHHhHHHHHHcc-----CCcEEEEeecCCCcccccccchhhhhh
Q psy11948          9 IPETIIR-ALYQKGFKTPTKIQSMVMPSALLA-----RKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus         9 l~~~l~~-~l~~~g~~~pt~iQ~~~ip~~l~~-----~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      ....+.+ .+....| .+|.-|.+++..+..+     ..+-++++.+|||||..|+..+...+.
T Consensus        68 ~~~~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~  130 (264)
T d1gm5a3          68 IEGKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYE  130 (264)
T ss_dssp             CCTHHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHh
Confidence            3334444 4456677 8999999999887642     246688888888888877776655443

>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=97.97  E-value=3.7e-07  Score=66.78  Aligned_cols=69  Identities=39%  Similarity=0.563  Sum_probs=57.8

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.+ ++..|+.+|..+    ..|+|+++.|+||+|||++|++|+++.+..                         
T Consensus        22 ~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~-------------------------   76 (218)
T d2g9na1          22 SLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL-------------------------   76 (218)
T ss_dssp             HHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCT-------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecc-------------------------
Confidence            34444444 889999999765    788999999999999999999999988842                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    ....+++||++||||||.|
T Consensus        77 --------------~~~~~~alil~Pt~eL~~Q   95 (218)
T d2g9na1          77 --------------DLKATQALVLAPTRELAQQ   95 (218)
T ss_dssp             --------------TCCSCCEEEECSSHHHHHH
T ss_pred             --------------cccCccEEEEcccchhhhh
Confidence                          2456899999999999987

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.94  E-value=7.9e-06  Score=60.19  Aligned_cols=59  Identities=15%  Similarity=0.054  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHHHCCCCCCchHHHhHHHHHHc-----cCCcEEEEeecCCCcccccccchhhhh
Q psy11948          7 FNIPETIIRALYQKGFKTPTKIQSMVMPSALL-----ARKDIVGAAETGSGKTLAFGIPILTGI   65 (167)
Q Consensus         7 l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~-----~~~d~i~~a~tgsGKt~~~~lp~l~~~   65 (167)
                      +..+.+..+.+.+.=-..+|+-|..++..+..     ...+.++++.||||||..|+..+...+
T Consensus        38 ~~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~  101 (233)
T d2eyqa3          38 FKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAV  101 (233)
T ss_dssp             CCCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHH
T ss_pred             CCCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHH
Confidence            34456677766654445899999999977753     234678899999999988877765544

>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=97.91  E-value=5.9e-07  Score=65.36  Aligned_cols=69  Identities=36%  Similarity=0.565  Sum_probs=58.6

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .++..+.+ ++..|+.+|..+    ..|+|+++.++||+|||++|++|+++.+.                          
T Consensus        20 ~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~--------------------------   73 (212)
T d1qdea_          20 NLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRID--------------------------   73 (212)
T ss_dssp             HHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCC--------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhh--------------------------
Confidence            34555554 899999999776    68999999999999999999999998874                          


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                   .....++++||+||||||.|
T Consensus        74 -------------~~~~~~~~lil~pt~el~~q   93 (212)
T d1qdea_          74 -------------TSVKAPQALMLAPTRELALQ   93 (212)
T ss_dssp             -------------TTCCSCCEEEECSSHHHHHH
T ss_pred             -------------ccCCCcceEEEcccHHHhhh
Confidence                         23467899999999999986

>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=97.91  E-value=6.4e-07  Score=64.66  Aligned_cols=69  Identities=43%  Similarity=0.666  Sum_probs=56.6

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEE  134 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~  134 (167)
                      .+++.+.. ++..|+.+|..+    ..|+|+++.|+||+|||++|++|+++.+..                         
T Consensus        11 ~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~-------------------------   65 (206)
T d1s2ma1          11 ELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKP-------------------------   65 (206)
T ss_dssp             HHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCT-------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhcccccccccc-------------------------
Confidence            45556655 899999999766    688999999999999999999999987752                         


Q ss_pred             HHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        135 LEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                    ....+++++++|+++++.|
T Consensus        66 --------------~~~~~~~~~~~~~~~~~~~   84 (206)
T d1s2ma1          66 --------------KLNKIQALIMVPTRELALQ   84 (206)
T ss_dssp             --------------TSCSCCEEEECSSHHHHHH
T ss_pred             --------------ccccccceeeccchhhhhh
Confidence                          2455778899999988764

>d1a1va1 c.37.1.14 (A:190-325) 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=97.62  E-value=5.7e-06  Score=55.31  Aligned_cols=19  Identities=32%  Similarity=0.202  Sum_probs=15.0

Q ss_pred             cccceeeeecccCccceee
Q psy11948         81 ARKDIVGAAETGSGKTLAF   99 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~   99 (167)
                      ..+..++.++||+|||..+
T Consensus         7 ~~~~~ll~apTGsGKT~~~   25 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKV   25 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            3466788999999999643

>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=97.25  E-value=3.5e-05  Score=57.54  Aligned_cols=28  Identities=18%  Similarity=0.261  Sum_probs=23.6

Q ss_pred             cCCcEEEEeecCCCcccccccchhhhhh
Q psy11948         39 ARKDIVGAAETGSGKTLAFGIPILTGIV   66 (167)
Q Consensus        39 ~~~d~i~~a~tgsGKt~~~~lp~l~~~~   66 (167)
                      .++++++.++||||||++|+++++....
T Consensus         8 ~~~~~lv~~~TGsGKT~~~l~~~~~~~~   35 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKTKRYLPAIVREAI   35 (305)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCHHHHHHHHHHHHHH
Confidence            3499999999999999999878776554

>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=97.13  E-value=2.7e-05  Score=55.93  Aligned_cols=68  Identities=46%  Similarity=0.623  Sum_probs=54.8

Q ss_pred             chhhhhhc-ccCCCCcccccc----ccc-cceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHH
Q psy11948         60 PILTGIVN-KLENPTEEDEND----SAR-KDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLE  133 (167)
Q Consensus        60 p~l~~~~~-~~~~~~~~~~~~----~~~-~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e  133 (167)
                      .++..+.+ ++..|+..|...    ..+ .|+++.++||+|||.+|++|+++...                         
T Consensus        14 ~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~-------------------------   68 (208)
T d1hv8a1          14 NILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVN-------------------------   68 (208)
T ss_dssp             HHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSC-------------------------
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccc-------------------------
Confidence            45555555 889999999665    344 59999999999999999999987553                         


Q ss_pred             HHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        134 ELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                     ....+++|||+||||||.|
T Consensus        69 ---------------~~~~~~~lil~pt~~l~~q   87 (208)
T d1hv8a1          69 ---------------ENNGIEAIILTPTRELAIQ   87 (208)
T ss_dssp             ---------------SSSSCCEEEECSCHHHHHH
T ss_pred             ---------------cccCcceEEEeeccccchh
Confidence                           2456899999999999986

>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=97.12  E-value=2.4e-05  Score=56.99  Aligned_cols=67  Identities=19%  Similarity=0.122  Sum_probs=52.9

Q ss_pred             cchhhhhhc-ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHH
Q psy11948         59 IPILTGIVN-KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLE  133 (167)
Q Consensus        59 lp~l~~~~~-~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e  133 (167)
                      ++.+..+++ .+..|+..|...    ..|+|+++.+|||+|||.+++++++....                         
T Consensus        30 ~~~~~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~-------------------------   84 (237)
T d1gkub1          30 LKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL-------------------------   84 (237)
T ss_dssp             HHHHHHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT-------------------------
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH-------------------------
Confidence            444566665 667888888654    68899999999999999999988875442                         


Q ss_pred             HHHHhhhcchhhhhccccccceEEEccchhhhcC
Q psy11948        134 ELEEESANTTEFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                                       .+.++|||+|||+|+.|
T Consensus        85 -----------------~~~rvliv~Pt~~La~Q  101 (237)
T d1gkub1          85 -----------------KGKRCYVIFPTSLLVIQ  101 (237)
T ss_dssp             -----------------TSCCEEEEESCHHHHHH
T ss_pred             -----------------hcCeEEEEeccHHHHHH
Confidence                             12479999999999987

>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=96.91  E-value=3.5e-05  Score=54.84  Aligned_cols=40  Identities=25%  Similarity=0.293  Sum_probs=30.8

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhh
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGI  107 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~  107 (167)
                      ++..+.+.|..+    ..++|+++.+|||+|||.+|.+|++...
T Consensus        22 g~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~   65 (206)
T d1oywa2          22 GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN   65 (206)
T ss_dssp             CCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhcc
Confidence            444555556443    6689999999999999999999987543

>d2p6ra3 c.37.1.19 (A:1-202) 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=96.11  E-value=0.00028  Score=49.82  Aligned_cols=58  Identities=22%  Similarity=0.260  Sum_probs=44.7

Q ss_pred             ccCCCCcccccc----ccccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcch
Q psy11948         68 KLENPTEEDEND----SARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTT  143 (167)
Q Consensus        68 ~~~~~~~~~~~~----~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~  143 (167)
                      ++..+++.|..+    ..++++++++|||+|||.++.++++..+.                                   
T Consensus        22 g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~-----------------------------------   66 (202)
T d2p6ra3          22 GIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI-----------------------------------   66 (202)
T ss_dssp             ---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH-----------------------------------
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhh-----------------------------------
Confidence            555677777554    56899999999999999999888876653                                   


Q ss_pred             hhhhccccccceEEEccchhhhcC
Q psy11948        144 EFVKKTRNKLYALILAPTRELAIQ  167 (167)
Q Consensus       144 ~~~~~~~~~~~aLIl~PTRELa~Q  167 (167)
                             ...++|||+||++|+.|
T Consensus        67 -------~~~~vl~l~P~~~L~~q   83 (202)
T d2p6ra3          67 -------KGGKSLYVVPLRALAGE   83 (202)
T ss_dssp             -------TTCCEEEEESSHHHHHH
T ss_pred             -------ccCcceeecccHHHHHH
Confidence                   12478999999999976

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [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: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=95.59  E-value=0.0034  Score=46.18  Aligned_cols=32  Identities=22%  Similarity=0.118  Sum_probs=24.2

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCcccccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFG   58 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~   58 (167)
                      +++|-|.+++..  .. ..+++.|+.|||||...+
T Consensus         1 ~L~~eQ~~av~~--~~-~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VT-GPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             CCCHHHHHHHHC--CS-SEEEECCCTTSCHHHHHH
T ss_pred             CcCHHHHHHHhC--CC-CCEEEEeeCCccHHHHHH
Confidence            468899998853  22 468899999999998543

>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=94.91  E-value=0.0024  Score=47.13  Aligned_cols=30  Identities=17%  Similarity=0.251  Sum_probs=24.8

Q ss_pred             ccccceeeeecccCccceeeecchhhhhhh
Q psy11948         80 SARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        80 ~~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      ..++++++.++||+|||.+|+.+++.....
T Consensus         7 ~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~   36 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTKRYLPAIVREAIK   36 (305)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHH
T ss_pred             hcCCcEEEEECCCCCHHHHHHHHHHHHHHh
Confidence            467889999999999999998888765543

>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=93.12  E-value=0.0065  Score=42.04  Aligned_cols=46  Identities=28%  Similarity=0.266  Sum_probs=35.7

Q ss_pred             cccceeeeecccCccceeeecchhhhhhhccCCCCCCCCCCCcchhHHHHHHHHHHHhhhcchhhhhccccccceEEEcc
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSGLEEEAEEVLEELEEESANTTEFVKKTRNKLYALILAP  160 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~aLIl~P  160 (167)
                      .+++.++++|||+|||.++++++...+..                                         ..-++|||+|
T Consensus        22 ~~~n~lv~~pTGsGKT~i~~~~~~~~~~~-----------------------------------------~~~~il~i~P   60 (200)
T d1wp9a1          22 KETNCLIVLPTGLGKTLIAMMIAEYRLTK-----------------------------------------YGGKVLMLAP   60 (200)
T ss_dssp             GGSCEEEECCTTSCHHHHHHHHHHHHHHH-----------------------------------------SCSCEEEECS
T ss_pred             hcCCeEEEeCCCCcHHHHHHHHHHHHHHh-----------------------------------------cCCcEEEEcC
Confidence            45788999999999999888766544421                                         1236899999


Q ss_pred             chhhhcC
Q psy11948        161 TRELAIQ  167 (167)
Q Consensus       161 TRELa~Q  167 (167)
                      |++|+.|
T Consensus        61 ~~~L~~q   67 (200)
T d1wp9a1          61 TKPLVLQ   67 (200)
T ss_dssp             SHHHHHH
T ss_pred             chHHHHH
Confidence            9999976

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {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: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=93.09  E-value=0.032  Score=42.70  Aligned_cols=74  Identities=24%  Similarity=0.293  Sum_probs=46.0

Q ss_pred             CCHHHHHHHHHC--CCCCCchHHHhHHHHHHccCCcEEEEeecCCCcccccccchhhhhhcccCCCCcccccccccccee
Q psy11948          9 IPETIIRALYQK--GFKTPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGIPILTGIVNKLENPTEEDENDSARKDIV   86 (167)
Q Consensus         9 l~~~l~~~l~~~--g~~~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~lp~l~~~~~~~~~~~~~~~~~~~~~d~~   86 (167)
                      +.+..+....+.  .-...+..|..++-.++.+ +-+++.++.|+|||.... .++..+....         ...+..++
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~Q~~A~~~al~~-~~~vI~G~pGTGKTt~i~-~~l~~l~~~~---------~~~~~~I~  199 (359)
T d1w36d1         131 VDEALLAQTLDKLFPVSDEINWQKVAAAVALTR-RISVISGGPGTGKTTTVA-KLLAALIQMA---------DGERCRIR  199 (359)
T ss_dssp             CCHHHHHHHHHTTCCCTTSCCHHHHHHHHHHTB-SEEEEECCTTSTHHHHHH-HHHHHHHHTC---------SSCCCCEE
T ss_pred             CChHHHHHHHHHhccCcccccHHHHHHHHHHcC-CeEEEEcCCCCCceehHH-HHHHHHHHHH---------hccCCeEE
Confidence            444444433332  2334567899999988887 788999999999997632 2222222111         12345678


Q ss_pred             eeecccC
Q psy11948         87 GAAETGS   93 (167)
Q Consensus        87 ~~a~tgs   93 (167)
                      ++||||.
T Consensus       200 l~ApTgk  206 (359)
T d1w36d1         200 LAAPTGK  206 (359)
T ss_dssp             EEBSSHH
T ss_pred             EecCcHH
Confidence            8888863

>d1a1va1 c.37.1.14 (A:190-325) 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=93.05  E-value=0.0057  Score=39.88  Aligned_cols=20  Identities=30%  Similarity=0.165  Sum_probs=15.8

Q ss_pred             ccCCcEEEEeecCCCccccc
Q psy11948         38 LARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        38 ~~~~d~i~~a~tgsGKt~~~   57 (167)
                      .+.+..++.++||+|||+.+
T Consensus         6 ~~~~~~ll~apTGsGKT~~~   25 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKV   25 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHH
T ss_pred             cCCCEEEEEeCCCCCHHHHH
Confidence            34467799999999999754

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=92.85  E-value=0.049  Score=41.01  Aligned_cols=43  Identities=21%  Similarity=0.283  Sum_probs=29.6

Q ss_pred             HHHHHHCCCCC---CchHHHhHHHHHHccCCcEEEEeecCCCcccc
Q psy11948         14 IRALYQKGFKT---PTKIQSMVMPSALLARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        14 ~~~l~~~g~~~---pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~   56 (167)
                      +..+.+.|+-.   ..+-+...+-.+..++++++++++||||||..
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~  182 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY  182 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH
Confidence            34455655432   23455566666666669999999999999974

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

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: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=92.48  E-value=0.053  Score=39.84  Aligned_cols=33  Identities=24%  Similarity=0.182  Sum_probs=25.4

Q ss_pred             CCchHHHhHHHHHHccCCcEEEEeecCCCccccccc
Q psy11948         24 TPTKIQSMVMPSALLARKDIVGAAETGSGKTLAFGI   59 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~~~~d~i~~a~tgsGKt~~~~l   59 (167)
                      .+++=|.+++..  .+ ..+++.|+-|||||...+.
T Consensus        11 ~L~~eQ~~~v~~--~~-g~~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          11 HLNKEQQEAVRT--TE-GPLLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             TSCHHHHHHHHC--CS-SCEEEEECTTSCHHHHHHH
T ss_pred             hCCHHHHHHHhC--CC-CCEEEEecCCccHHHHHHH
Confidence            478889998853  23 5699999999999986543

>d1yksa1 c.37.1.14 (A:185-324) 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=92.24  E-value=0.013  Score=37.47  Aligned_cols=29  Identities=28%  Similarity=0.204  Sum_probs=22.4

Q ss_pred             cccceeeeecccCccceeeecchhhhhhh
Q psy11948         81 ARKDIVGAAETGSGKTLAFGIPILTGIVN  109 (167)
Q Consensus        81 ~~~d~~~~a~tgsgkt~~~~~p~i~~~~~  109 (167)
                      .++++++.++||+|||..++..++....+
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~~~   34 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAECAR   34 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHHHH
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHhhh
Confidence            46888999999999998876665555543

>d1t5la1 c.37.1.19 (A:2-414) 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=88.33  E-value=0.17  Score=39.30  Aligned_cols=32  Identities=25%  Similarity=0.255  Sum_probs=24.7

Q ss_pred             CCchHHHhHHHHHHc----cCCcEEEEeecCCCccc
Q psy11948         24 TPTKIQSMVMPSALL----ARKDIVGAAETGSGKTL   55 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l~----~~~d~i~~a~tgsGKt~   55 (167)
                      .|+.-|-++|..+..    |.++.++.+-||||||+
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~   46 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTF   46 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHH
Confidence            677788777766554    44678889999999986

>d1z63a1 c.37.1.19 (A:432-661) 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=85.71  E-value=0.4  Score=33.40  Aligned_cols=34  Identities=24%  Similarity=0.036  Sum_probs=25.0

Q ss_pred             CCchHHHhHHHHHH---ccCCcEEEEeecCCCccccc
Q psy11948         24 TPTKIQSMVMPSAL---LARKDIVGAAETGSGKTLAF   57 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l---~~~~d~i~~a~tgsGKt~~~   57 (167)
                      .+.|.|.+++.-+.   ..+..+++.-..|.|||...
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~   48 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT   48 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHH
Confidence            57799999986432   23356888889999999854

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=84.15  E-value=0.16  Score=39.83  Aligned_cols=16  Identities=44%  Similarity=0.495  Sum_probs=14.7

Q ss_pred             CcEEEEeecCCCcccc
Q psy11948         41 KDIVGAAETGSGKTLA   56 (167)
Q Consensus        41 ~d~i~~a~tgsGKt~~   56 (167)
                      +++++.+|||+|||+-
T Consensus        50 sNILliGPTGvGKTlL   65 (443)
T d1g41a_          50 KNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             ccEEEECCCCCCHHHH
Confidence            6899999999999974

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=83.01  E-value=0.4  Score=36.76  Aligned_cols=32  Identities=19%  Similarity=0.117  Sum_probs=20.2

Q ss_pred             hHHHhHHHHHHccCC-cEEEEeecCCCcccccc
Q psy11948         27 KIQSMVMPSALLARK-DIVGAAETGSGKTLAFG   58 (167)
Q Consensus        27 ~iQ~~~ip~~l~~~~-d~i~~a~tgsGKt~~~~   58 (167)
                      +-|...|..++...+ =++++++||||||.+..
T Consensus       144 ~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~  176 (401)
T d1p9ra_         144 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLY  176 (401)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHH
T ss_pred             HHHHHHHHHHHhhhhceEEEEcCCCCCccHHHH
Confidence            344444544443322 37899999999998643

>d1z3ix2 c.37.1.19 (X:92-389) 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=80.71  E-value=0.5  Score=34.36  Aligned_cols=33  Identities=24%  Similarity=0.074  Sum_probs=22.8

Q ss_pred             CCchHHHhHHHHHH--------ccCCcEEEEeecCCCcccc
Q psy11948         24 TPTKIQSMVMPSAL--------LARKDIVGAAETGSGKTLA   56 (167)
Q Consensus        24 ~pt~iQ~~~ip~~l--------~~~~d~i~~a~tgsGKt~~   56 (167)
                      .+.|+|..++.-+.        ..+...|+.-..|.|||+.
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~q   95 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQ   95 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHH
Confidence            57799999986442        1224577777888888863