Citrus Sinensis ID: 042526

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280----
Protein Sequence
MFHTNCATVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKLNSKKRKRSSANEEDSGDGDGDEDGRGVQKEEERNLKNEKGKKKKKKKKGKKIKTVEESVAG
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHHHcccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcccHHHHHHHHHHHHHHHHcccccEEEEEccccHHHHHHHHccccccccEEEEcccHHHHHHcccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHcccccccHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEcccccccccHcccccccccccccHHHccccHHHHHHHHHcccccccHHHHHccHHHHcccccEHEEHccccHHHHHHHHHHHHHHHHccccccccHHHccccccEEccccccEEEEEccHHHHHHHHHHHHHHHHHHccccEEEEEccHHccccEEEEEcccHHHHHHHcccccHHHHHHEEEEHHHHHHHHcccHHHHHHHHHHccccccccccEEEEcccccccEEEccccccEEEcccHHHHHHHHHHHHHHHHHcccEEEEEEHcccc
Coil and Loop (DISEMBL)
MFHTNCATVVVvgngpddaqEELVNEAEISTEFDawnelrlhplLMKSIYKLGFKESTSILKARIPALAHQRKDVigaaetesgktrafgLPALQRLLEEREKAAKMLEEKGeeaekyapkghlralIINPTRELALQVLMVAspslksnsLTLAMaagsplltsehsnrrkpnkrkrtrkggedekldslkwnplsqpktttllpsslalmnltegkpgkklnskkrkrssaneedsgdgdgdedgrgvqKEEERNLknekgkkkkkkkkgkkIKTVEESVAG
Flexible Loop (DISEMBL)
mfhtncatvvvvgngpddAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGaaetesgktrafgLPALQRLLEEREKAAKMLEEkgeeaekyapkghLRALIINPTRELALQVLMVASPSLKSNSLTLAMAagsplltsehsnrrkpnkrkrtrkggedekldslkwnplsqpktTTLLPSSLAlmnltegkpgkklnskkrkrssaneedsgdgdgdedgrgvqkeeernlknekgkkkkkkkkgkkiktveesvag
Low Complexity Region (SEG)
MFHTNCATVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSnrrkpnkrkrtrkGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEgkpgkklnskkrkrssANeedsgdgdgdedgrgVQkeeernlknekgkkkkkkkkgkkiktveeSVAG
Disordered region (IsUnstruct)
****NCATVVVVGNG*******LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIG********************************************GHLRALIINPTRELALQVLMVA*********************************************************************************************************************************************
Disordered Region (DISOPRED)
**********************************AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEER*****************APKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLT******RKPNKRKRTRKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKK********************************************************E*****
Disordered Region (DISEMBL)
MFHTNCATVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLT*********************EKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGK******************************************************************
Disordered Region (DISPRO)
*****CATVVVVGN*****************EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKLNSKKRKRSSANEEDSGDGDGDEDGRGVQKEEERNLKNEKGKKKKKKKKGKKIKTVEES***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFHTNCATVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGxxxxxxxxxxxxxxxxxxxxxxxxxxxxAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKLNSKKRKRSSANEEDSGDGDGDEDGRGVxxxxxxxxxxxxxxxxxxxxxGKKIKTVEESVAG
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	284	2.2.26 [Sep-21-2011]
Q93Y39	826	DEAD-box ATP-dependent RN	yes	no	0.450	0.154	0.671	6e-37
A3AVH5	832	DEAD-box ATP-dependent RN	yes	no	0.380	0.129	0.620	6e-29
A2XVF7	832	DEAD-box ATP-dependent RN	N/A	no	0.380	0.129	0.620	6e-29
Q54TD7	940	ATP-dependent RNA helicas	yes	no	0.489	0.147	0.315	4e-15
Q2GMX1	586	ATP-dependent RNA helicas	N/A	no	0.401	0.194	0.358	7e-13
Q03532	505	ATP-dependent RNA helicas	yes	no	0.433	0.243	0.346	2e-12
Q7S2N9	578	ATP-dependent RNA helicas	N/A	no	0.401	0.197	0.358	2e-12
Q09916	578	ATP-dependent RNA helicas	yes	no	0.408	0.200	0.353	3e-12
A4R8B5	587	ATP-dependent RNA helicas	N/A	no	0.394	0.190	0.364	3e-12
Q59W52	581	Pre-mRNA-splicing ATP-dep	N/A	no	0.327	0.160	0.432	5e-12

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

 Score =  154 bits (390), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 86/128 (67%), Positives = 94/128 (73%)

Query: 12  VGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ 71
           V    DD  EE V E EI  EF AW+ +RLHPLLMKSIY+L FKE T I KA     A+Q
Sbjct: 168 VSCDGDDTVEEQVEEEEIPPEFSAWSSMRLHPLLMKSIYRLDFKEPTKIQKACFNVAAYQ 227

Query: 72  RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP 131
            KDVIGAAET SGKT AFGLP LQRLL+EREK  K+   KGEEA+KYA  G+LRALII P
Sbjct: 228 GKDVIGAAETGSGKTLAFGLPILQRLLDEREKVGKLYALKGEEAQKYAADGYLRALIITP 287

Query: 132 TRELALQV 139
           TRELALQV
Sbjct: 288 TRELALQV 295

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

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

 Score =  128 bits (321), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 67/108 (62%), Positives = 79/108 (73%)

Query: 32  EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGL 91
           E  AW ELRLHPLL+ ++ +LGFKE T I KA  PA AHQ KDVIGAAET SGKT AFGL
Sbjct: 196 EVYAWRELRLHPLLITAVRRLGFKEPTPIQKACFPAAAHQGKDVIGAAETGSGKTLAFGL 255

Query: 92  PALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           P LQRLLEE+EKA ++  E     ++ + +  LRALI+ PTRELA QV
Sbjct: 256 PILQRLLEEQEKAMRLSREDESTQDENSRESPLRALILTPTRELAKQV 303

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 =  128 bits (321), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 67/108 (62%), Positives = 79/108 (73%)

Query: 32  EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGL 91
           E  AW ELRLHPLL+ ++ +LGFKE T I KA  PA AHQ KDVIGAAET SGKT AFGL
Sbjct: 196 EVYAWRELRLHPLLITAVRRLGFKEPTPIQKACFPAAAHQGKDVIGAAETGSGKTLAFGL 255

Query: 92  PALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           P LQRLLEE+EKA ++  E     ++ + +  LRALI+ PTRELA QV
Sbjct: 256 PILQRLLEEQEKAMRLSREDESTQDENSRESPLRALILTPTRELAKQV 303

Oryza sativa subsp. indica (taxid: 39946)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score = 82.0 bits (201), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 52/165 (31%), Positives = 80/165 (48%), Gaps = 26/165 (15%)

Query: 20  QEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAA 79
           Q+ +  E +   +   WN   L PL++K +  LGF + T I  + IP       DVIGAA
Sbjct: 280 QKTISKEEQDQLDMSEWNSYNLDPLILKGLRSLGFSKPTEIQSSVIPVAVSSGYDVIGAA 339

Query: 80  ETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGH---------------- 123
           +T SGKT AFG+P +QR+L+   K  + +E K  + +      +                
Sbjct: 340 QTGSGKTLAFGIPMVQRILQHLRKHGQNVENKANKQQNDNDDENEDVEEEEEEEEEEGRS 399

Query: 124 -----LRALIINPTRELALQVL-----MVASPSLKSNSLTLAMAA 158
                L +L+I PTRELA+QV      +++  +LK  S+   MA+
Sbjct: 400 KEYRKLFSLVICPTRELAIQVTNHIKSIISHTNLKVISIVGGMAS 444

ATP-dependent RNA helicase.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2GMX1|HAS1_CHAGB ATP-dependent RNA helicase HAS1 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=HAS1 PE=3 SV=1

 Score = 74.7 bits (182), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 47/131 (35%), Positives = 72/131 (54%), Gaps = 17/131 (12%)

Query: 29  ISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA 88
           +ST+  A++EL L    M SI ++GF + T I +  IP L    KDV+GAA+T SGKT A
Sbjct: 107 VSTDAQAFSELNLSDKTMMSINEMGFTKMTEIQRRGIPPLLAG-KDVLGAAKTGSGKTLA 165

Query: 89  FGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK 148
           F +PA++ L                 + ++ P+     +++ PTRELALQ+  VA   +K
Sbjct: 166 FLIPAIEML----------------NSLRFKPRNGTGVIVVTPTRELALQIFGVARELMK 209

Query: 149 SNSLTLAMAAG 159
           ++S T  +  G
Sbjct: 210 NHSQTYGVVIG 220

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (taxid: 306901)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q03532|HAS1_YEAST ATP-dependent RNA helicase HAS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HAS1 PE=1 SV=1

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/147 (34%), Positives = 76/147 (51%), Gaps = 24/147 (16%)

Query: 26  EAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGK 85
           E E +T  + + EL+L    +K+I K+GF   TS+    IP L   R DV+GAA+T SGK
Sbjct: 34  EGEQTTCVEKFEELKLSQPTLKAIEKMGFTTMTSVQARTIPPLLAGR-DVLGAAKTGSGK 92

Query: 86  TRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASP 145
           T AF +PA++ L                 + K+ P+     ++I PTRELALQ+  VA  
Sbjct: 93  TLAFLIPAIELL----------------HSLKFKPRNGTGIIVITPTRELALQIFGVARE 136

Query: 146 SLKSNSLTLAMAAGSPLLTSEHSNRRK 172
            ++ +S T  +  G        +NRR+
Sbjct: 137 LMEFHSQTFGIVIGG-------ANRRQ 156

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7S2N9|HAS1_NEUCR ATP-dependent RNA helicase has-1 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=has-1 PE=3 SV=1

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/131 (35%), Positives = 72/131 (54%), Gaps = 17/131 (12%)

Query: 29  ISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA 88
           I+T    ++EL L    MK+I ++GF + T I +  IP L    KDV+GAA+T SGKT A
Sbjct: 102 IATNATDFSELNLSDKTMKAIAEMGFTKMTEIQRRGIPPLL-AGKDVLGAAKTGSGKTLA 160

Query: 89  FGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK 148
           F +PA++ L                 + ++ P+    A+++ PTRELALQ+  VA   +K
Sbjct: 161 FLIPAIEML----------------SSLRFKPRNGTGAIVVTPTRELALQIFGVARELMK 204

Query: 149 SNSLTLAMAAG 159
           ++S T  +  G
Sbjct: 205 NHSQTYGVVIG 215

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q09916|HAS1_SCHPO ATP-dependent RNA helicase has1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=has1 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 47/133 (35%), Positives = 72/133 (54%), Gaps = 17/133 (12%)

Query: 27  AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKT 86
           A  +++ + +++L+L   + K+I ++GF+  T I K  IP L   R DV+GAA+T SGKT
Sbjct: 82  ASSTSDIEKFSDLQLSENIQKAIKEMGFETMTEIQKRSIPPLLAGR-DVLGAAKTGSGKT 140

Query: 87  RAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS 146
            AF +P ++ L                 A K+ P+     +II+PTRELALQ+  VA   
Sbjct: 141 LAFLIPTIEMLY----------------ALKFKPRNGTGVIIISPTRELALQIFGVAKEL 184

Query: 147 LKSNSLTLAMAAG 159
           LK +  T  +  G
Sbjct: 185 LKYHHQTFGIVIG 197

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A4R8B5|HAS1_MAGO7 ATP-dependent RNA helicase HAS1 OS=Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) GN=HAS1 PE=3 SV=2

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 47/129 (36%), Positives = 71/129 (55%), Gaps = 17/129 (13%)

Query: 31  TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFG 90
           +E  A++EL L    MK+I ++GF + T I +  IP L    KDV+GAA+T SGKT AF 
Sbjct: 109 SEAQAFSELNLSENTMKAIEEMGFTKMTEIQRRGIPPLLAG-KDVLGAAKTGSGKTLAFL 167

Query: 91  LPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN 150
           +PA++ L                 + K+ P+     ++++PTRELALQ+  VA   +K +
Sbjct: 168 IPAVEML----------------RSLKFKPRNGTGVIVVSPTRELALQIFGVARDLMKHH 211

Query: 151 SLTLAMAAG 159
           S T  +  G
Sbjct: 212 SQTYGIVIG 220

ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.

Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (taxid: 242507)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q59W52|PRP28_CANAL Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=PRP28 PE=3 SV=1

 Score = 72.0 bits (175), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 45/104 (43%), Positives = 62/104 (59%), Gaps = 11/104 (10%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           WNE  ++  L+  I +LG++E TS+ +A IP LA +++DV+G AET SGKT AF +P L 
Sbjct: 170 WNEGSINDKLVSIISQLGYEEPTSVQRASIP-LALKKRDVVGVAETGSGKTLAFLIPVLN 228

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            +L   E   K  +   E      P G    LI+ PTRELALQ+
Sbjct: 229 YILSIDENYLKYEKISNE------PVG----LILAPTRELALQI 262

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.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

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	284
255554328	496	dead box ATP-dependent RNA helicase, put	0.436	0.25	0.75	9e-44
224107545	847	predicted protein [Populus trichocarpa]	0.436	0.146	0.703	7e-42
449458872	848	PREDICTED: DEAD-box ATP-dependent RNA he	0.419	0.140	0.715	7e-41
449509127	784	PREDICTED: DEAD-box ATP-dependent RNA he	0.419	0.151	0.715	8e-41
356520440	810	PREDICTED: DEAD-box ATP-dependent RNA he	0.429	0.150	0.730	1e-40
297834580	831	DEAD-box ATP-dependent RNA helicase 13 [	0.450	0.154	0.648	2e-36
225433316	788	PREDICTED: DEAD-box ATP-dependent RNA he	0.429	0.154	0.679	4e-36
357505253	798	DEAD-box ATP-dependent RNA helicase [Med	0.419	0.149	0.693	4e-36
147810431	458	hypothetical protein VITISV_038405 [Viti	0.464	0.288	0.628	8e-36
227202696	827	AT3G16840 [Arabidopsis thaliana]	0.464	0.159	0.661	2e-35

>gi|255554328|ref|XP_002518204.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223542800|gb|EEF44337.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  183 bits (464), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 96/128 (75%), Positives = 100/128 (78%), Gaps = 4/128 (3%)

Query: 12  VGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ 71
           V NG DD   E V+EAE    F AWNELRLHPLLMKSIY+LGFKE T I KA IP  AHQ
Sbjct: 141 VSNGEDDTDGESVDEAE----FHAWNELRLHPLLMKSIYRLGFKEPTPIQKACIPPAAHQ 196

Query: 72  RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP 131
            KDVIGAAET SGKT AFGLP LQRLLEER+KAA  L+E GEEAEKY P G LRALII P
Sbjct: 197 GKDVIGAAETGSGKTLAFGLPILQRLLEERDKAANYLDEMGEEAEKYGPTGLLRALIITP 256

Query: 132 TRELALQV 139
           TRELALQV
Sbjct: 257 TRELALQV 264

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224107545|ref|XP_002314517.1| predicted protein [Populus trichocarpa] gi|222863557|gb|EEF00688.1| predicted protein [Populus trichocarpa]

 Score =  176 bits (447), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 90/128 (70%), Positives = 101/128 (78%), Gaps = 4/128 (3%)

Query: 12  VGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ 71
           V N  DD + E V+E    TEF  WNELRLHPLLMKSIY+LGFKE T I KA IPA AHQ
Sbjct: 144 VSNNKDDVEGESVDE----TEFYGWNELRLHPLLMKSIYRLGFKEPTPIQKACIPAAAHQ 199

Query: 72  RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP 131
            KDV+GAAET SGKT AFGLP LQRLLEE++KA+ M +  GEEAE++APKG LRALII P
Sbjct: 200 GKDVVGAAETGSGKTLAFGLPILQRLLEEQDKASNMGDNVGEEAERFAPKGLLRALIITP 259

Query: 132 TRELALQV 139
           TRELA+QV
Sbjct: 260 TRELAIQV 267

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458872|ref|XP_004147170.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 13-like [Cucumis sativus]

 Score =  173 bits (439), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 101/123 (82%), Gaps = 4/123 (3%)

Query: 17  DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
           D+ +++ V+E    TE+ AWNELRLHPLLMKSIYKLGFKE T+I KA IPA A+Q KDV+
Sbjct: 203 DEVEKDAVDE----TEYYAWNELRLHPLLMKSIYKLGFKEPTAIQKACIPAAAYQGKDVV 258

Query: 77  GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA 136
           GAAET SGKT AFGLP LQR L+EREK+ KM EEKG +A+KYAPK  LRALII PTRELA
Sbjct: 259 GAAETGSGKTLAFGLPILQRFLDEREKSGKMSEEKGVDAKKYAPKSLLRALIITPTRELA 318

Query: 137 LQV 139
           LQV
Sbjct: 319 LQV 321

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449509127|ref|XP_004163501.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 13-like, partial [Cucumis sativus]

 Score =  173 bits (438), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 101/123 (82%), Gaps = 4/123 (3%)

Query: 17  DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
           D+ +++ V+E    TE+ AWNELRLHPLLMKSIYKLGFKE T+I KA IPA A+Q KDV+
Sbjct: 183 DEVEKDAVDE----TEYYAWNELRLHPLLMKSIYKLGFKEPTAIQKACIPAAAYQGKDVV 238

Query: 77  GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA 136
           GAAET SGKT AFGLP LQR L+EREK+ KM EEKG +A+KYAPK  LRALII PTRELA
Sbjct: 239 GAAETGSGKTLAFGLPILQRFLDEREKSGKMSEEKGVDAKKYAPKSLLRALIITPTRELA 298

Query: 137 LQV 139
           LQV
Sbjct: 299 LQV 301

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520440|ref|XP_003528870.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 13-like [Glycine max]

 Score =  172 bits (437), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 92/126 (73%), Positives = 98/126 (77%), Gaps = 4/126 (3%)

Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRK 73
           N  DD  EE V+E    TEF AWNELRLHPLL+K+I KLGFKE T I KA IPA AHQ K
Sbjct: 159 NVKDDIGEEDVDE----TEFYAWNELRLHPLLLKAICKLGFKEPTPIQKACIPAAAHQGK 214

Query: 74  DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR 133
           DV+GAAET SGKT AFGLP LQRLLEEREKA  M+ E+GEE EKYA  G LRALII PTR
Sbjct: 215 DVVGAAETGSGKTLAFGLPILQRLLEEREKAGNMVGERGEEPEKYASTGLLRALIIAPTR 274

Query: 134 ELALQV 139
           ELALQV
Sbjct: 275 ELALQV 280

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297834580|ref|XP_002885172.1| DEAD-box ATP-dependent RNA helicase 13 [Arabidopsis lyrata subsp. lyrata] gi|297331012|gb|EFH61431.1| DEAD-box ATP-dependent RNA helicase 13 [Arabidopsis lyrata subsp. lyrata]

 Score =  158 bits (400), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 83/128 (64%), Positives = 91/128 (71%)

Query: 12  VGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ 71
           V    D   EE V   EI  EF AW  +RLHPLLMKSIY LGFK+ T I KA     A+Q
Sbjct: 166 VSCDDDYKVEEQVEGEEIPPEFSAWGLMRLHPLLMKSIYHLGFKQPTEIQKACFSIAAYQ 225

Query: 72  RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP 131
            KDVIGAAET SGKT AFGLP LQRLL+EREK  K+   KGE+A+KYA  G+LRALII P
Sbjct: 226 GKDVIGAAETGSGKTLAFGLPILQRLLDEREKVGKLYALKGEKAQKYAADGYLRALIITP 285

Query: 132 TRELALQV 139
           TRELALQV
Sbjct: 286 TRELALQV 293

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433316|ref|XP_002282504.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 13 [Vitis vinifera] gi|296083755|emb|CBI23744.3| unnamed protein product [Vitis vinifera]

 Score =  157 bits (398), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 87/128 (67%), Positives = 96/128 (75%), Gaps = 6/128 (4%)

Query: 12  VGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ 71
           V N  DD + + V+EAE    F  WNELRLHPLLMKSI++LGFK+ T I KA IPA AHQ
Sbjct: 137 VSNDKDDVEGDSVDEAE----FYEWNELRLHPLLMKSIHRLGFKQPTPIQKACIPAAAHQ 192

Query: 72  RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP 131
            KDV+GA+ET SGKT A GLP LQRLLEEREKAA+ L E  E  EKYA  G LRALII P
Sbjct: 193 GKDVVGASETGSGKTLALGLPILQRLLEEREKAAEPLAENSE--EKYAEGGILRALIITP 250

Query: 132 TRELALQV 139
           TRELALQV
Sbjct: 251 TRELALQV 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357505253|ref|XP_003622915.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|355497930|gb|AES79133.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  157 bits (398), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 86/124 (69%), Positives = 94/124 (75%), Gaps = 5/124 (4%)

Query: 17  DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
           D   EE ++E    TE+ AWNELRLHP LMK+I+KLGFKE T I KA +PA AHQ KDVI
Sbjct: 149 DSVDEENIDE----TEYYAWNELRLHPRLMKAIHKLGFKEPTPIQKACVPAAAHQGKDVI 204

Query: 77  GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE-AEKYAPKGHLRALIINPTREL 135
           GAAET SGKT AFGLP LQRLLEEREKA  +    GEE AEKYA  G LR+LII PTREL
Sbjct: 205 GAAETGSGKTLAFGLPILQRLLEEREKAESISGVNGEEAAEKYATTGLLRSLIIAPTREL 264

Query: 136 ALQV 139
           ALQV
Sbjct: 265 ALQV 268

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147810431|emb|CAN65340.1| hypothetical protein VITISV_038405 [Vitis vinifera]

 Score =  156 bits (395), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 88/140 (62%), Positives = 101/140 (72%), Gaps = 8/140 (5%)

Query: 3   HTNCATVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILK 62
            TN  +  VV    DD + + V+EAE    F  WNELR+HPLLMKSI++LGFK+ T I K
Sbjct: 143 QTNEESATVVDK--DDVEGDSVDEAE----FYEWNELRIHPLLMKSIHRLGFKQPTPIQK 196

Query: 63  ARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKG 122
           A IPA AHQ KDV+GA+ET SGKT A GLP LQRLLEEREKAA+ L E GE  EKYA  G
Sbjct: 197 ACIPAAAHQGKDVVGASETGSGKTLALGLPILQRLLEEREKAAEPLAENGE--EKYAEGG 254

Query: 123 HLRALIINPTRELALQVLMV 142
            LRALII PTRELALQ+  +
Sbjct: 255 ILRALIITPTRELALQITTI 274

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|227202696|dbj|BAH56821.1| AT3G16840 [Arabidopsis thaliana]

 Score =  155 bits (392), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/133 (66%), Positives = 98/133 (73%), Gaps = 1/133 (0%)

Query: 7   ATVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIP 66
           A+  V  +G DD  EE V E EI  EF AW+ +RLHPLLMKSIY+L FKE T I KA   
Sbjct: 165 ASAAVSCDG-DDTVEEQVEEEEIPPEFSAWSSMRLHPLLMKSIYRLDFKEPTKIQKACFN 223

Query: 67  ALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRA 126
             A+Q KDVIGAAET SGKT AFGLP LQRLL+EREK  K+   KGEEA+KYA  G+LRA
Sbjct: 224 VAAYQGKDVIGAAETGSGKTLAFGLPILQRLLDEREKVGKLYALKGEEAQKYAADGYLRA 283

Query: 127 LIINPTRELALQV 139
           LII PTRELALQV
Sbjct: 284 LIITPTRELALQV 296

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	284
TAIR|locus:2086775	826	AT3G16840 [Arabidopsis thalian	0.503	0.173	0.615	3.5e-37
DICTYBASE|DDB_G0281841	940	ddx24 "DEAD/DEAH box helicase"	0.341	0.103	0.371	7.5e-17
WB|WBGene00018890	746	F55F8.2 [Caenorhabditis elegan	0.482	0.183	0.353	3.5e-16
FB|FBgn0034496	813	CG9143 [Drosophila melanogaste	0.369	0.129	0.358	6.2e-13
ASPGD|ASPL0000042587	770	AN1750 [Emericella nidulans (t	0.380	0.140	0.449	2.1e-12
CGD|CAL0001091	581	orf19.672 [Candida albicans (t	0.359	0.175	0.424	7.5e-12
UNIPROTKB|Q59W52	581	PRP28 "Pre-mRNA-splicing ATP-d	0.359	0.175	0.424	7.5e-12
CGD|CAL0000625	631	SPB4 [Candida albicans (taxid:	0.397	0.179	0.347	2.9e-11
WB|WBGene00010280	959	F58G11.2a [Caenorhabditis eleg	0.394	0.116	0.36	1.1e-10
DICTYBASE|DDB_G0281711	783	ddx27 "DEAD/DEAH box helicase"	0.278	0.100	0.414	2.4e-09

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

 Score = 408 (148.7 bits), Expect = 3.5e-37, P = 3.5e-37
 Identities = 88/143 (61%), Positives = 100/143 (69%)

Query:    17 DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
             DD  EE V E EI  EF AW+ +RLHPLLMKSIY+L FKE T I KA     A+Q KDVI
Sbjct:   173 DDTVEEQVEEEEIPPEFSAWSSMRLHPLLMKSIYRLDFKEPTKIQKACFNVAAYQGKDVI 232

Query:    77 GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA 136
             GAAET SGKT AFGLP LQRLL+EREK  K+   KGEEA+KYA  G+LRALII PTRELA
Sbjct:   233 GAAETGSGKTLAFGLPILQRLLDEREKVGKLYALKGEEAQKYAADGYLRALIITPTRELA 292

Query:   137 LQVLMVASPSLKSNSLTLAMAAG 159
             LQV      + K+ S+ +    G
Sbjct:   293 LQVTEHLENAAKNLSVKVVPIVG 315

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

DICTYBASE|DDB_G0281841 ddx24 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 180 (68.4 bits), Expect = 7.5e-17, Sum P(2) = 7.5e-17
 Identities = 36/97 (37%), Positives = 54/97 (55%)

Query:    20 QEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAA 79
             Q+ +  E +   +   WN   L PL++K +  LGF + T I  + IP       DVIGAA
Sbjct:   280 QKTISKEEQDQLDMSEWNSYNLDPLILKGLRSLGFSKPTEIQSSVIPVAVSSGYDVIGAA 339

Query:    80 ETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAE 116
             +T SGKT AFG+P +QR+L+   K  + +E K  + +
Sbjct:   340 QTGSGKTLAFGIPMVQRILQHLRKHGQNVENKANKQQ 376

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

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0016787 "hydrolase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 212 (79.7 bits), Expect = 3.5e-16, P = 3.5e-16
 Identities = 52/147 (35%), Positives = 78/147 (53%)

Query:    14 NGPDDAQEELVNEAEISTEFDAWNELRLHPL-LMKSIYKLGFKESTSILKARIPALAHQR 72
             NG     ++   EA   T+  AW +    P  ++++I ++GF E T I  A +PA    R
Sbjct:   134 NGDTGKPKKSKKEASKKTDISAWKQFYFLPNEVLEAIEQMGFSEPTEIQSAVLPAAVRDR 193

Query:    73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT 132
             +DV+GAAET SGKT AFG+P + RLLE  + +     ++ E  E   P    RALI+ PT
Sbjct:   194 QDVLGAAETGSGKTLAFGIPLVARLLESSDDS-----QETESTEVRGP----RALIVAPT 244

Query:   133 RELALQVLMVASPSLKSNSLTLAMAAG 159
             REL +Q++   +  + +  L      G
Sbjct:   245 RELVIQIMKHINALISTTQLIATSIVG 271

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

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

 Score = 162 (62.1 bits), Expect = 6.2e-13, Sum P(2) = 6.2e-13
 Identities = 42/117 (35%), Positives = 65/117 (55%)

Query:    17 DDAQEELV----NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR 72
             D+   ELV     EAE   +  AWN L +   +++++ + GFK  T I    +PA  H +
Sbjct:   197 DEEAPELVPISTGEAE---DMSAWNGLGVPASILRALGEQGFKTPTQIQALTLPAAIHGK 253

Query:    73 KDVIGAAETESGKTRAFGLPALQRLLEEREK-----AAKMLEEKGEEAEKYAPKGHL 124
             KD++GAAET SGKT AFG+P L  ++E +++       K  + KG++ E  A +  L
Sbjct:   254 KDILGAAETGSGKTLAFGIPMLAGIMELKQRNIRSGIRKAPKVKGQQPEPAADEHEL 310

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0005524 "ATP binding" evidence=IEA

ASPGD|ASPL0000042587 AN1750 [Emericella nidulans (taxid:162425)]

 Score = 177 (67.4 bits), Expect = 2.1e-12, P = 2.1e-12
 Identities = 53/118 (44%), Positives = 69/118 (58%)

Query:    23 LVNEAEIS-TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAET 81
             L +EA+    +  AW  L L P  + S+ KL F   TS+ K+ IP +     DVIG A T
Sbjct:   185 LEDEADDDGADISAWEPLGLSPETLTSLSKLKFSTPTSVQKSCIPPILDGH-DVIGKAST 243

Query:    82 ESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
              SGKT AFGLP L+  LE RE+  K ++ + EE EK  P     ALI++PTRELA Q+
Sbjct:   244 GSGKTLAFGLPILEHYLE-RERR-KTIDSE-EEKEKI-PI----ALILSPTRELAHQL 293

GO:0008150 "biological_process" evidence=ND

GO:0005730 "nucleolus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

CGD|CAL0001091 orf19.672 [Candida albicans (taxid:5476)]

 Score = 170 (64.9 bits), Expect = 7.5e-12, P = 7.5e-12
 Identities = 48/113 (42%), Positives = 65/113 (57%)

Query:    36 WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
             WNE  ++  L+  I +LG++E TS+ +A IP LA +++DV+G AET SGKT AF +P L 
Sbjct:   170 WNEGSINDKLVSIISQLGYEEPTSVQRASIP-LALKKRDVVGVAETGSGKTLAFLIPVLN 228

Query:    96 RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK 148
              +L   E   K  E+   E     P G    LI+ PTRELALQ+   A    K
Sbjct:   229 YILSIDENYLKY-EKISNE-----PVG----LILAPTRELALQITKEAEKFCK 271

GO:0005682 "U5 snRNP" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q59W52 PRP28 "Pre-mRNA-splicing ATP-dependent RNA helicase PRP28" [Candida albicans SC5314 (taxid:237561)]

 Score = 170 (64.9 bits), Expect = 7.5e-12, P = 7.5e-12
 Identities = 48/113 (42%), Positives = 65/113 (57%)

Query:    36 WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
             WNE  ++  L+  I +LG++E TS+ +A IP LA +++DV+G AET SGKT AF +P L 
Sbjct:   170 WNEGSINDKLVSIISQLGYEEPTSVQRASIP-LALKKRDVVGVAETGSGKTLAFLIPVLN 228

Query:    96 RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK 148
              +L   E   K  E+   E     P G    LI+ PTRELALQ+   A    K
Sbjct:   229 YILSIDENYLKY-EKISNE-----PVG----LILAPTRELALQITKEAEKFCK 271

GO:0008150 "biological_process" evidence=ND

CGD|CAL0000625 SPB4 [Candida albicans (taxid:5476)]

 Score = 165 (63.1 bits), Expect = 2.9e-11, P = 2.9e-11
 Identities = 42/121 (34%), Positives = 69/121 (57%)

Query:    30 STEFDAWNELR--LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTR 87
             +TE  AW  LR  LHP + ++I  +G+   T +  + IP L+   KDV+  A T SGKT 
Sbjct:     4 NTESLAWENLRYDLHPWIKEAISSMGYPTMTPVQASTIPLLSGN-KDVVVEAVTGSGKTL 62

Query:    88 AFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL 147
             +F +P LQ++ +   K     +  G+  E    +GH+ +++++PTRELA Q+  V +  L
Sbjct:    63 SFVIPVLQKISDRLYKP----DSDGDLPEP-VKRGHMLSIVLSPTRELANQIQSVFNQVL 117

Query:   148 K 148
             +
Sbjct:   118 Q 118

GO:0030686 "90S preribosome" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0000027 "ribosomal large subunit assembly" evidence=IEA

WB|WBGene00010280 F58G11.2a [Caenorhabditis elegans (taxid:6239)]

 Score = 162 (62.1 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 45/125 (36%), Positives = 67/125 (53%)

Query:    15 GPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKD 74
             G D A E  +  AE      +W    LHP +++++ ++ +    +I  A IP +     D
Sbjct:   363 GQDRAVE--IRNAEKDVRLTSWTNSGLHPTILETLKRIKYNNVRTIQGAMIPQVLDGH-D 419

Query:    75 VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE 134
             V+G AET +GKT AFGLP + ++L       +M EE   +A +    G L ALI+ PTRE
Sbjct:   420 VLGQAETSAGKTAAFGLPIIDKIL-------RMDEETRNKARQ--DDGPL-ALILAPTRE 469

Query:   135 LALQV 139
             LA Q+
Sbjct:   470 LAAQI 474

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0043186 "P granule" evidence=IDA

DICTYBASE|DDB_G0281711 ddx27 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 138 (53.6 bits), Expect = 2.4e-09, Sum P(2) = 2.4e-09
 Identities = 34/82 (41%), Positives = 48/82 (58%)

Query:    29 ISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA 88
             +  E   + EL L   L+K++ KLGF + T I    IP LA   KD++ +A T SGKT A
Sbjct:   185 VEEELPTFEELHLSRPLLKAVQKLGFSQPTPIQAKAIP-LALNGKDILASASTGSGKTAA 243

Query:    89 FGLPALQRLL--EEREKAAKML 108
             F LP L+RLL  +   +A ++L
Sbjct:   244 FLLPVLERLLFRDSEYRAIRVL 265

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

GO:0005524 "ATP binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	284
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-24
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-16
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-13
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-12
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-11
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-10
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	1e-10
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	5e-10
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-09
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-07
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-07
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-07
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-07
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-06
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-04
pfam05786	719	pfam05786, Cnd2, Condensin complex subunit 2	0.002

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

 Score = 97.6 bits (244), Expect = 1e-24
 Identities = 44/110 (40%), Positives = 57/110 (51%), Gaps = 19/110 (17%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           + EL L P L++ IY LGF++ T I    IP L    +DVIG A+T SGKT AF +P L+
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLL-SGRDVIGQAQTGSGKTAAFLIPILE 59

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASP 145
           +L                       K   +ALI+ PTRELALQ+  VA  
Sbjct: 60  KLDPSP------------------KKDGPQALILAPTRELALQIAEVARK 91

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 = 77.9 bits (192), Expect = 3e-16
 Identities = 43/132 (32%), Positives = 62/132 (46%), Gaps = 22/132 (16%)

Query: 8   TVVVVGNGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPA 67
               V             E +   EF     L L P L++++  LGF+E T I  A IP 
Sbjct: 6   YDRFVKLKSAHNVALSRGEEKTPPEF---ASLGLSPELLQALKDLGFEEPTPIQLAAIPL 62

Query: 68  LAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL 127
           +    +DV+G A+T +GKT AF LP LQ++L+  E+                    + AL
Sbjct: 63  ILA-GRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKY------------------VSAL 103

Query: 128 IINPTRELALQV 139
           I+ PTRELA+Q+
Sbjct: 104 ILAPTRELAVQI 115

Length = 513

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

 Score = 68.4 bits (168), Expect = 4e-13
 Identities = 41/105 (39%), Positives = 57/105 (54%), Gaps = 19/105 (18%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++EL L   L++++   G+   T+I    IP  A   +DV+G+A T +GKT AF LPALQ
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPP-ALDGRDVLGSAPTGTGKTAAFLLPALQ 61

Query: 96  RLLE-EREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            LL+  R K+                 G  R LI+ PTRELA+QV
Sbjct: 62  HLLDFPRRKS-----------------GPPRILILTPTRELAMQV 89

Length = 434

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

 Score = 62.3 bits (152), Expect = 5e-12
 Identities = 35/96 (36%), Positives = 43/96 (44%), Gaps = 21/96 (21%)

Query: 65  IPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHL 124
           IPA+    KDV+  A T SGKT AF LP LQ LL                      KG  
Sbjct: 8   IPAI-LSGKDVLVQAPTGSGKTLAFLLPILQALLP--------------------KKGGP 46

Query: 125 RALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS 160
           +AL++ PTRELA Q+        K   L +A+  G 
Sbjct: 47  QALVLAPTRELAEQIYEELKKLFKILGLRVALLTGG 82

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

 Score = 64.4 bits (158), Expect = 1e-11
 Identities = 39/105 (37%), Positives = 57/105 (54%), Gaps = 21/105 (20%)

Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPAL 94
           A++ L L P L+ ++ +LG+ E T I    +PA+    KDVI  A+T SGKT AFGL  L
Sbjct: 5   AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAIL-AGKDVIAQAKTGSGKTAAFGLGLL 63

Query: 95  QRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           Q+L                + +++  +    AL++ PTRELA QV
Sbjct: 64  QKL----------------DVKRFRVQ----ALVLCPTRELADQV 88

Length = 460

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

 Score = 59.0 bits (143), Expect = 1e-10
 Identities = 35/104 (33%), Positives = 41/104 (39%), Gaps = 21/104 (20%)

Query: 49  IYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKML 108
           I K GF+      K  I AL    +DVI AA T SGKT A  LPAL+ L   +       
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGG----- 55

Query: 109 EEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSL 152
                           R L++ PTRELA Q          S  L
Sbjct: 56  ----------------RVLVLVPTRELAEQWAEELKKLGPSLGL 83

Length = 201

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

 Score = 61.1 bits (148), Expect = 1e-10
 Identities = 41/117 (35%), Positives = 58/117 (49%), Gaps = 17/117 (14%)

Query: 23  LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETE 82
           +V   E  T F   ++  L P LM +I+ LGF   T I +A++        D IG A+T 
Sbjct: 79  VVEPQEGKTRF---HDFNLAPELMHAIHDLGFPYCTPI-QAQVLGYTLAGHDAIGRAQTG 134

Query: 83  SGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +GKT AF +  + +LL+                E+Y   G  RALII PTREL +Q+
Sbjct: 135 TGKTAAFLISIINQLLQ-----------TPPPKERY--MGEPRALIIAPTRELVVQI 178

Length = 475

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

 Score = 59.2 bits (144), Expect = 5e-10
 Identities = 40/122 (32%), Positives = 58/122 (47%), Gaps = 14/122 (11%)

Query: 38  ELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL 97
           +  LHP +++++ K GF   T I    +P      +DV G A+T +GKT AF       L
Sbjct: 12  DFALHPQVVEALEKKGFHNCTPIQALALPLTL-AGRDVAGQAQTGTGKTMAFLTATFHYL 70

Query: 98  LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMA 157
           L              E+ +   P    RALI+ PTRELA+Q+   A P  ++  L L +A
Sbjct: 71  LSH---------PAPEDRKVNQP----RALIMAPTRELAVQIHADAEPLAQATGLKLGLA 117

Query: 158 AG 159
            G
Sbjct: 118 YG 119

Length = 423

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

 Score = 56.7 bits (137), Expect = 3e-09
 Identities = 35/107 (32%), Positives = 59/107 (55%), Gaps = 19/107 (17%)

Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPAL 94
           +++ L L P +++++ + G++E T I +  IPA+  + +D++ +A+T +GKT  F LP L
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVL-EGRDLMASAQTGTGKTAGFTLPLL 60

Query: 95  QRLLEEREKAAKMLEEKGEEAEKYAPKGH--LRALIINPTRELALQV 139
           Q L                   +   KG   +RALI+ PTRELA Q+
Sbjct: 61  QHL----------------ITRQPHAKGRRPVRALILTPTRELAAQI 91

Length = 456

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

 Score = 51.3 bits (123), Expect = 2e-07
 Identities = 36/95 (37%), Positives = 50/95 (52%), Gaps = 16/95 (16%)

Query: 45  LMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKA 104
           ++KS+   GF E T I     P +A   +D+IG AET SGKT AF LPA+  +       
Sbjct: 141 ILKSLKNAGFTEPTPIQVQGWP-IALSGRDMIGIAETGSGKTLAFLLPAIVHIN------ 193

Query: 105 AKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           A+ L   G+        G +  L++ PTRELA Q+
Sbjct: 194 AQPLLRYGD--------GPI-VLVLAPTRELAEQI 219

Length = 545

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

 Score = 51.4 bits (123), Expect = 3e-07
 Identities = 40/113 (35%), Positives = 58/113 (51%), Gaps = 24/113 (21%)

Query: 27  AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKT 86
           AE  T F    +L L   +++++  LG+++ + I    IP L + R DV+G A+T SGKT
Sbjct: 2   AEFETTF---ADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGR-DVLGMAQTGSGKT 57

Query: 87  RAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            AF LP L  L                + E  AP+     L++ PTRELA+QV
Sbjct: 58  AAFSLPLLHNL----------------DPELKAPQ----ILVLAPTRELAVQV 90

Length = 629

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

 Score = 48.5 bits (116), Expect = 3e-07
 Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 21/67 (31%)

Query: 73  KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT 132
           +DV+ AA T SGKT A  LP L+ L   +                       + L++ PT
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGG---------------------QVLVLAPT 39

Query: 133 RELALQV 139
           RELA QV
Sbjct: 40  RELANQV 46

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 = 50.3 bits (120), Expect = 4e-07
 Identities = 36/104 (34%), Positives = 51/104 (49%), Gaps = 14/104 (13%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++   LHP L+  +   GF   T I    +P +A    DV G A+T +GKT AF +  + 
Sbjct: 11  FSSFDLHPALLAGLESAGFTRCTPIQALTLP-VALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           RLL     A +  E+              RALI+ PTRELA+Q+
Sbjct: 70  RLLSRPALADRKPEDP-------------RALILAPTRELAIQI 100

Length = 572

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

 Score = 48.7 bits (116), Expect = 1e-06
 Identities = 40/120 (33%), Positives = 57/120 (47%), Gaps = 26/120 (21%)

Query: 25  NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARI-PALAHQRKDVIGAAETES 83
           N  EI   FDA   L+L+  L++ IY  GF++ ++I +  I P L     D IG A++ +
Sbjct: 22  NYDEIVDSFDA---LKLNEDLLRGIYSYGFEKPSAIQQRGIKPILD--GYDTIGQAQSGT 76

Query: 84  GKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA 143
           GKT  F + ALQ +                    Y      +ALI+ PTRELA Q+  V 
Sbjct: 77  GKTATFVIAALQLI-------------------DYDLNA-CQALILAPTRELAQQIQKVV 116

Length = 401

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

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 31/99 (31%), Positives = 50/99 (50%), Gaps = 14/99 (14%)

Query: 41  LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEE 100
           L P L+ ++   G++  T I    IPA A   + ++ +A+T SGKT +F +P + R    
Sbjct: 128 LPPKLLLNLETAGYEFPTPIQMQAIPA-ALSGRSLLVSADTGSGKTASFLVPIISRCCTI 186

Query: 101 REKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           R          G  +E+  P     A+++ PTREL +QV
Sbjct: 187 R---------SGHPSEQRNP----LAMVLTPTRELCVQV 212

Length = 518

>gnl|CDD|218747 pfam05786, Cnd2, Condensin complex subunit 2

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 5/58 (8%)

Query: 226 KKRKRSSANEEDSGDGDGDEDGRGVQKEEERNLKNEKGKKKKKKKKGKKIKTVEESVA 283
               + +      GD   D+D  G   EE+        KK KKK++ K   T+E++  
Sbjct: 151 DSDNKEAPETGREGDDGEDDDEEGSDGEEDGA-----KKKAKKKRQRKPESTLEKNFE 203

This family consists of several Barren protein homologues from several eukaryotic organisms. In Drosophila Barren (barr) is required for sister-chromatid segregation in mitosis. barr encodes a novel protein that is present in proliferating cells and has homologues in yeast and human. Mitotic defects in barr embryos become apparent during cycle 16, resulting in a loss of PNS and CNS neurons. Centromeres move apart at the metaphase-anaphase transition and Cyclin B is degraded, but sister chromatids remain connected, resulting in chromatin bridging. Barren protein localises to chromatin throughout mitosis. Colocalisation and biochemical experiments indicate that Barren associates with Topoisomerase II throughout mitosis and alters the activity of Topoisomerase II. It has been suggested that this association is required for proper chromosomal segregation by facilitating the decatenation of chromatids at anaphase. This family forms one of the three non-structural maintenance of chromosomes (SMC) subunits of the mitotic condensation complex along with Cnd1 and Cnd3. Length = 719

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	284
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.97
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.97
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	99.97
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.97
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.97
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.97
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.97
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.96
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.96
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.96
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.96
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.96
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	99.96
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.95
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	99.95
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.95
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.93
KOG0327	397	consensus Translation initiation factor 4F, helica	99.93
PTZ00424	401	helicase 45; Provisional	99.92
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.9
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.9
KOG4284	980	consensus DEAD box protein [Transcription]	99.9
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.9
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.89
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.89
PRK00254	720	ski2-like helicase; Provisional	99.85
PRK02362	737	ski2-like helicase; Provisional	99.85
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.82
PRK13767	876	ATP-dependent helicase; Provisional	99.81
PRK09401	1176	reverse gyrase; Reviewed	99.79
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.79
PRK01172	674	ski2-like helicase; Provisional	99.77
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.76
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.76
PRK14701	1638	reverse gyrase; Provisional	99.75
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.73
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.72
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.71
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.71
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.69
COG1205	851	Distinct helicase family with a unique C-terminal	99.68
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.68
PRK10689	1147	transcription-repair coupling factor; Provisional	99.65
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.63
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.62
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.62
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.62
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.59
PHA02653	675	RNA helicase NPH-II; Provisional	99.57
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.55
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.53
COG1204	766	Superfamily II helicase [General function predicti	99.52
PHA02558	501	uvsW UvsW helicase; Provisional	99.42
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.41
COG1202	830	Superfamily II helicase, archaea-specific [General	99.36
PRK05580	679	primosome assembly protein PriA; Validated	99.36
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.34
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.34
PRK13766	773	Hef nuclease; Provisional	99.23
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.19
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.18
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.18
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.15
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.14
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.11
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.11
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.08
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.08
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.03
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.82
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.82
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.82
KOG0354	746	consensus DEAD-box like helicase [General function	98.77
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.71
TIGR00595	505	priA primosomal protein N'. All proteins in this f	98.58
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.55
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.53
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.51
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.51
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.5
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.48
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.41
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.38
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.35
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.35
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	98.34
PRK09694	878	helicase Cas3; Provisional	98.28
KOG0353	695	consensus ATP-dependent DNA helicase [General func	98.25
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.23
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.22
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.21
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.2
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.18
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.18
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.13
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.1
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.02
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.83
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.8
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	97.77
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.68
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.67
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	97.65
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.65
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.62
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	97.56
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.55
PF13245	76	AAA_19: Part of AAA domain	97.55
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	97.49
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.26
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.17
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.02
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	96.98
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	96.78
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	96.72
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.71
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.61
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	96.59
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.42
KOG1803	649	consensus DNA helicase [Replication, recombination	96.42
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.4
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	96.39
PRK15483	986	type III restriction-modification system StyLTI en	96.24
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.14
KOG2340	698	consensus Uncharacterized conserved protein [Funct	96.08
PRK11054	684	helD DNA helicase IV; Provisional	96.07
PRK10875	615	recD exonuclease V subunit alpha; Provisional	96.05
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.0
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.95
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	95.93
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	95.83
PRK14873	665	primosome assembly protein PriA; Provisional	95.79
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.79
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	95.76
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	95.73
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.68
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	95.56
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	95.38
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	95.35
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.12
PRK05298	652	excinuclease ABC subunit B; Provisional	95.07
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.06
PRK10536	262	hypothetical protein; Provisional	94.95
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	94.91
COG3973	747	Superfamily I DNA and RNA helicases [General funct	94.87
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	94.86
COG4889	1518	Predicted helicase [General function prediction on	94.83
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	94.82
COG4096	875	HsdR Type I site-specific restriction-modification	94.8
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	94.73
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.63
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	94.6
PRK04914	956	ATP-dependent helicase HepA; Validated	94.49
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	94.47
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.32
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.2
PRK13889	988	conjugal transfer relaxase TraA; Provisional	94.15
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	93.97
PRK13764	602	ATPase; Provisional	93.89
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	93.88
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	93.68
PRK13851	344	type IV secretion system protein VirB11; Provision	93.66
PRK05973	237	replicative DNA helicase; Provisional	93.54
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	93.5
KOG1805	1100	consensus DNA replication helicase [Replication, r	93.44
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.25
PRK06921	266	hypothetical protein; Provisional	93.23
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	93.21
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.13
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.05
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	92.96
PRK10436	462	hypothetical protein; Provisional	92.89
PRK06835	329	DNA replication protein DnaC; Validated	92.79
COG1484	254	DnaC DNA replication protein [DNA replication, rec	92.74
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	92.68
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	92.66
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.65
PRK13897	606	type IV secretion system component VirD4; Provisio	92.64
PRK08181	269	transposase; Validated	92.59
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	92.55
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.39
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.3
PRK13826	1102	Dtr system oriT relaxase; Provisional	92.29
KOG4439	901	consensus RNA polymerase II transcription terminat	92.15
PRK13850	670	type IV secretion system protein VirD4; Provisiona	91.89
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	91.57
PF12846	304	AAA_10: AAA-like domain	91.49
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	91.47
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	91.4
TIGR02533	486	type_II_gspE general secretory pathway protein E.	90.96
PRK13876	663	conjugal transfer coupling protein TraG; Provision	90.56
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	90.53
PRK12377	248	putative replication protein; Provisional	90.5
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	90.23
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	90.21
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	90.19
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	89.92
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	89.84
PF10278	178	Med19: Mediator of RNA pol II transcription subuni	89.63
COG3587	985	Restriction endonuclease [Defense mechanisms]	89.55
PRK13880	636	conjugal transfer coupling protein TraG; Provision	89.32
PRK07952	244	DNA replication protein DnaC; Validated	89.31
PRK06526	254	transposase; Provisional	89.25
smart00382	148	AAA ATPases associated with a variety of cellular	89.25
PRK13822	641	conjugal transfer coupling protein TraG; Provision	89.19
PRK08939	306	primosomal protein DnaI; Reviewed	89.18
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	89.18
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	89.17
PRK08116	268	hypothetical protein; Validated	89.09
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	88.66
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	88.48
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	88.43
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	88.42
COG0610	962	Type I site-specific restriction-modification syst	88.34
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	88.25
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	88.12
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	87.78
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	87.64
PRK09183	259	transposase/IS protein; Provisional	87.57
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	87.53
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	87.44
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	87.29
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	87.08
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	86.66
KOG1533	290	consensus Predicted GTPase [General function predi	86.52
PRK08533	230	flagellar accessory protein FlaH; Reviewed	86.3
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	86.02
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	85.78
PRK08084	235	DNA replication initiation factor; Provisional	85.76
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	85.75
PRK08727	233	hypothetical protein; Validated	85.57
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	85.5
PRK04328	249	hypothetical protein; Provisional	85.5
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	85.12
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	85.06
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	84.91
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	84.59
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	84.5
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	84.41
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	84.36
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	84.27
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	84.25
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	84.23
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	84.17
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	83.9
KOG0387	923	consensus Transcription-coupled repair protein CSB	83.75
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	83.63
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	83.47
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	83.27
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	83.11
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	83.09
PF05729	166	NACHT: NACHT domain	83.02
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	82.75
PRK05595	444	replicative DNA helicase; Provisional	82.59
PHA02533	534	17 large terminase protein; Provisional	82.55
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	82.49
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	82.48
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	82.24
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	82.13
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	81.97
TIGR00665	434	DnaB replicative DNA helicase. This model describe	81.97
PF00004	132	AAA: ATPase family associated with various cellula	81.89
PRK05748	448	replicative DNA helicase; Provisional	81.87
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	81.68
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	81.67
PRK04296	190	thymidine kinase; Provisional	81.09
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	81.09
cd01394	218	radB RadB. The archaeal protein radB shares simila	81.09
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	81.0
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	80.84
KOG1002	791	consensus Nucleotide excision repair protein RAD16	80.84
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	80.63
TIGR02237	209	recomb_radB DNA repair and recombination protein R	80.56
PRK03992	389	proteasome-activating nucleotidase; Provisional	80.47
COG0606	490	Predicted ATPase with chaperone activity [Posttran	80.45
PHA02244	383	ATPase-like protein	80.32
PLN03025	319	replication factor C subunit; Provisional	80.29
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	80.23
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	80.18
PF13555	62	AAA_29: P-loop containing region of AAA domain	80.05

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.4e-37  Score=297.52  Aligned_cols=171  Identities=27%  Similarity=0.271  Sum_probs=151.8

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      .|++++|++.+..+|...||+.|||||+++||.+ +.|+|++++|.|||||||||+||+|.++....             
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~-l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~-------------  157 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIA-LSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQ-------------  157 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhccccee-ccCCceEEEeccCCcchhhhhhHHHHHHHhcc-------------
Confidence            6888999999999999999999999999999999 99999999999999999999999999998731             


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEe-CCCcchHHHHHhcCCCcccccc---------cCCc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAA-GSPLLTSEHSNRRKPNKRKRTR---------KGGE  184 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~-G~~~~~q~~~l~~~~~i~v~~~---------~~~~  184 (284)
                       .......+|++|||+||||||.||..++..++..+.++++|++ |.+...|...+.++.++++.+.         ....
T Consensus       158 -~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~  236 (519)
T KOG0331|consen  158 -GKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLN  236 (519)
T ss_pred             -ccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCcc
Confidence             1345567999999999999999999999999999888665555 5599999999999999988762         2235


Q ss_pred             cccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          185 DEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       185 ~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      +.+|.++|+||||+|++|||.|++..+++++++..+
T Consensus       237 l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  237 LSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             ccceeEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            779999999999999999999999999999966664

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.1e-36  Score=279.57  Aligned_cols=173  Identities=31%  Similarity=0.403  Sum_probs=159.2

Q ss_pred             CccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           30 STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      -....+|.+|++++.|++++...||..||+||+++||.+ +.|+|||+.|+||||||.||+||++++++...        
T Consensus        57 ~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~-L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p--------  127 (476)
T KOG0330|consen   57 DESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVA-LGGRDVIGLAETGSGKTGAFALPILQRLLQEP--------  127 (476)
T ss_pred             hhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchh-hCCCcEEEEeccCCCchhhhHHHHHHHHHcCC--------
Confidence            346678999999999999999999999999999999999 99999999999999999999999999998853        


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc---------
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT---------  179 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~---------  179 (284)
                                  ..++||||+||||||.||..+++.|+..+|++|+++.|| ....|..++.+.|+|+|.+         
T Consensus       128 ------------~~~~~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~  195 (476)
T KOG0330|consen  128 ------------KLFFALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLE  195 (476)
T ss_pred             ------------CCceEEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHH
Confidence                        348999999999999999999999999999999887766 7888899999999997766         


Q ss_pred             -ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          180 -RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       180 -~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                       .++..+..|.+||+||||+++||.|.+..=.++..+|+++|.-|
T Consensus       196 ~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~erqt~L  240 (476)
T KOG0330|consen  196 NTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPRERQTFL  240 (476)
T ss_pred             hccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcCccceEEE
Confidence             46667889999999999999999999999999999999998766

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.3e-36  Score=286.78  Aligned_cols=173  Identities=28%  Similarity=0.363  Sum_probs=159.1

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|.+|+|+.+|+++|..+||..|||||.++||.. +-|+|++++|-||||||.||.||+|++++-..           
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPva-llgkDIca~A~TGsGKTAAF~lPiLERLlYrP-----------  247 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVA-LLGKDICACAATGSGKTAAFALPILERLLYRP-----------  247 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHH-hhcchhhheecccCCchhhhHHHHHHHHhcCc-----------
Confidence            458999999999999999999999999999999988 88999999999999999999999999998742           


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc----------c
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR----------K  181 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~----------~  181 (284)
                            ......++||||||||||.||+++.+.|+.+..+.|++++|| +...|.+.|+..|||++.+.          .
T Consensus       248 ------k~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~  321 (691)
T KOG0338|consen  248 ------KKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSP  321 (691)
T ss_pred             ------ccCcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCC
Confidence                  334678999999999999999999999999999999988888 78889999999999988762          3


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ...+|.|..||+||||+|++-||..+.-.++..+|..+|+||
T Consensus       322 sf~ldsiEVLvlDEADRMLeegFademnEii~lcpk~RQTmL  363 (691)
T KOG0338|consen  322 SFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKNRQTML  363 (691)
T ss_pred             CccccceeEEEechHHHHHHHHHHHHHHHHHHhcccccccee
Confidence            346888999999999999999999999999999999999998

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

Probab=100.00  E-value=1.1e-34  Score=284.87  Aligned_cols=171  Identities=27%  Similarity=0.347  Sum_probs=150.5

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      .+|++|+|++.++++|.++||..|||||.++||.+ +.|+|++++|+||||||+||+||+|+++....            
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~-l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~------------   95 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLI-LAGRDVLGQAQTGTGKTAAFLLPLLQKILKSV------------   95 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHHhccc------------
Confidence            68999999999999999999999999999999999 99999999999999999999999999976420            


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCC-CcchHHHHHhcCCCcccccc---------cC
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------KG  182 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~~  182 (284)
                            ....+.||||+||||||.||++++..++.+. ++++++++|| +...|...+.++++++|.+.         ..
T Consensus        96 ------~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~  169 (513)
T COG0513          96 ------ERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGK  169 (513)
T ss_pred             ------ccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCC
Confidence                  0011129999999999999999999999998 7887776665 77888888888899988762         23


Q ss_pred             CccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          183 GEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       183 ~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ..++.+.++|+||||+|++|||.+++..++..+|...|..+
T Consensus       170 l~l~~v~~lVlDEADrmLd~Gf~~~i~~I~~~~p~~~qtll  210 (513)
T COG0513         170 LDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLL  210 (513)
T ss_pred             cchhhcCEEEeccHhhhhcCCCHHHHHHHHHhCCcccEEEE
Confidence            56889999999999999999999999999999999888766

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=4.3e-35  Score=295.18  Aligned_cols=187  Identities=24%  Similarity=0.301  Sum_probs=166.2

Q ss_pred             ccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHH
Q 042526           22 ELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEER  101 (284)
Q Consensus        22 ~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~  101 (284)
                      ..+.+..+|.|+.+|.+.|++..|+..|+++||..|||||.+|||+| +.|+|||++|.||||||++|+||++.++..++
T Consensus       353 i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~I-msGrdvIgvakTgSGKT~af~LPmirhi~dQr  431 (997)
T KOG0334|consen  353 IKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAI-MSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQR  431 (997)
T ss_pred             eeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchh-ccCcceEEeeccCCccchhhhcchhhhhhcCC
Confidence            56789999999999999999999999999999999999999999999 99999999999999999999999997666553


Q ss_pred             HHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc
Q 042526          102 EKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR  180 (284)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~  180 (284)
                                     ......+|.||||+||||||.||+..++.|++.+++++++++|+ ....|+..++++.+|+|++.
T Consensus       432 ---------------~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tp  496 (997)
T KOG0334|consen  432 ---------------PLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTP  496 (997)
T ss_pred             ---------------ChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEecc
Confidence                           33456699999999999999999999999999999988777666 67788889999988877662


Q ss_pred             ------------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCccc
Q 042526          181 ------------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKLN  224 (284)
Q Consensus       181 ------------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~~  224 (284)
                                  +.-.++|+.++|+||||+|++|||.|++..||++....+|.-+.
T Consensus       497 GRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlf  552 (997)
T KOG0334|consen  497 GRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLF  552 (997)
T ss_pred             chhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhcchhhhhhhh
Confidence                        22368899999999999999999999999999998777776553

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=3.4e-33  Score=276.20  Aligned_cols=183  Identities=21%  Similarity=0.205  Sum_probs=158.3

Q ss_pred             ccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHH
Q 042526           24 VNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK  103 (284)
Q Consensus        24 ~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~  103 (284)
                      +.+.++|.|+.+|++++|++.|+++|.++||+.|||||.+|||.+ ++|+|+|++||||||||+||+||++.++....  
T Consensus       120 ~~g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~-l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~--  196 (545)
T PTZ00110        120 IAGENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIA-LSGRDMIGIAETGSGKTLAFLLPAIVHINAQP--  196 (545)
T ss_pred             ecCCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hcCCCEEEEeCCCChHHHHHHHHHHHHHHhcc--
Confidence            468899999999999999999999999999999999999999999 99999999999999999999999999886532  


Q ss_pred             HHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc--
Q 042526          104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR--  180 (284)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~--  180 (284)
                                   ......+|++|||+||||||.||+..+..|+...++++++++|+ +...|...+..+++|++.+.  
T Consensus       197 -------------~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgr  263 (545)
T PTZ00110        197 -------------LLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGR  263 (545)
T ss_pred             -------------cccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHH
Confidence                         11224578999999999999999999999999888888666655 66778888888999877662  


Q ss_pred             -------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCc
Q 042526          181 -------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKK  222 (284)
Q Consensus       181 -------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~  222 (284)
                             ....+.++..+|+||||+|+++||.+++..++......+|..
T Consensus       264 L~d~l~~~~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~q~l  312 (545)
T PTZ00110        264 LIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTL  312 (545)
T ss_pred             HHHHHHcCCCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCCCCeEE
Confidence                   223578899999999999999999999999988776555543

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=8.8e-34  Score=267.48  Aligned_cols=185  Identities=22%  Similarity=0.257  Sum_probs=168.8

Q ss_pred             cccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHH
Q 042526           23 LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEERE  102 (284)
Q Consensus        23 ~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~  102 (284)
                      -+.+...|.|+.+|+.++++..|+.+++..-|+.|||||.+++|.. ++|+||+.+|.||||||.||+.|++.+++.+. 
T Consensus       212 rv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalpta-lsgrdvigIAktgSgktaAfi~pm~~himdq~-  289 (731)
T KOG0339|consen  212 RVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTA-LSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQP-  289 (731)
T ss_pred             eeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccc-cccccchheeeccCcchhHHHHHHHHHhcchh-
Confidence            4678889999999999999999999999999999999999999998 99999999999999999999999999998875 


Q ss_pred             HHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCcee-EEEeCCCcchHHHHHhcCCCccccc--
Q 042526          103 KAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTL-AMAAGSPLLTSEHSNRRKPNKRKRT--  179 (284)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v-~~~~G~~~~~q~~~l~~~~~i~v~~--  179 (284)
                                    ......+|.+||||||||||.||+.++++|++..++.+ ++++|++.-.|...|..++.++|++  
T Consensus       290 --------------eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPg  355 (731)
T KOG0339|consen  290 --------------ELKPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPG  355 (731)
T ss_pred             --------------hhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechH
Confidence                          44567899999999999999999999999999999876 5555668889999999899988776  


Q ss_pred             -------ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          180 -------RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       180 -------~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                             .+...+.|+.+|||||||+|++|||+|||.-|....-.++|..+
T Consensus       356 Rlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtll  406 (731)
T KOG0339|consen  356 RLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLL  406 (731)
T ss_pred             HHHHHHHhhcccceeeeEEEEechhhhhccccHHHHHHHHhhcCCcceEEE
Confidence                   34557889999999999999999999999999998888888877

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=9.8e-34  Score=269.31  Aligned_cols=177  Identities=29%  Similarity=0.312  Sum_probs=163.6

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      ..+..|++|+|+..++++|++.+|..||.||+.+||.. +.|+||++.|.|||||||||++|+|++|++.          
T Consensus        66 ~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~a-L~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~----------  134 (758)
T KOG0343|consen   66 TTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMA-LQGHDVLGAAKTGSGKTLAFLVPVLEALYRL----------  134 (758)
T ss_pred             hhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchh-ccCcccccccccCCCceeeehHHHHHHHHHc----------
Confidence            45668999999999999999999999999999999998 9999999999999999999999999999987          


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc----------c
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT----------R  180 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~----------~  180 (284)
                            .+....|.-||||+||||||.|++.++.+++++.++++.+++||....-...-..+.+|+|++          .
T Consensus       135 ------kWs~~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~~mNILVCTPGRLLQHmde~  208 (758)
T KOG0343|consen  135 ------KWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERISQMNILVCTPGRLLQHMDEN  208 (758)
T ss_pred             ------CCCCCCCceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhhcCCeEEechHHHHHHhhhc
Confidence                  677788999999999999999999999999999999999999998777777777788998877          3


Q ss_pred             cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCccc
Q 042526          181 KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKLN  224 (284)
Q Consensus       181 ~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~~  224 (284)
                      +......|..||+||||+|+||||--..-.+++++|..+|++|=
T Consensus       209 ~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLF  252 (758)
T KOG0343|consen  209 PNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKRQTLLF  252 (758)
T ss_pred             CCCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhheeeee
Confidence            45567789999999999999999999999999999999999983

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2e-33  Score=266.93  Aligned_cols=187  Identities=21%  Similarity=0.209  Sum_probs=161.1

Q ss_pred             ccccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           20 QEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        20 ~~~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      ....+.+.++|.++.+|.+-.+.+.|+.++...||+.|||||+.+||.+ ..|+|++++|+||||||.|||+|++.+++.
T Consensus        60 i~v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i-~~Grdl~acAqTGsGKT~aFLiPii~~~~~  138 (482)
T KOG0335|consen   60 IPVKVSGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPII-SGGRDLMACAQTGSGKTAAFLIPIISYLLD  138 (482)
T ss_pred             eeeeccCCccCCCcccccccchhHHHhhccccccccCCCcceeecccee-ecCCceEEEccCCCcchHHHHHHHHHHHHh
Confidence            3356789999999999999999999999999999999999999999999 999999999999999999999999999988


Q ss_pred             HHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeC-CCcchHHHHHhcCCCcccc
Q 042526          100 EREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAG-SPLLTSEHSNRRKPNKRKR  178 (284)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G-~~~~~q~~~l~~~~~i~v~  178 (284)
                      .....          ........+|++|||+||||||.||++++++|+...++.++..|| .+...|...+.++.+|+++
T Consensus       139 ~~~~~----------~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlva  208 (482)
T KOG0335|consen  139 EGPED----------RGESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVA  208 (482)
T ss_pred             cCccc----------CcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEe
Confidence            63210          001111257999999999999999999999999888887766555 5888899999999999887


Q ss_pred             cc---------cCCccccccccCCCCCCcccc-cccccchhhhcccCCC
Q 042526          179 TR---------KGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEG  217 (284)
Q Consensus       179 ~~---------~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r  217 (284)
                      +.         ....++.+.++|+||||+|+| |||.|++.+++++...
T Consensus       209 TpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~  257 (482)
T KOG0335|consen  209 TPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGM  257 (482)
T ss_pred             cCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCC
Confidence            72         233578899999999999999 9999999999997655

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=1.8e-32  Score=259.97  Aligned_cols=165  Identities=27%  Similarity=0.298  Sum_probs=140.8

Q ss_pred             cCcccCCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           34 DAWNELRLHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..|..|||++.|+..|.. |+|..||.||.+|||.+ ++|+|++|.|+||||||+||++|+++.|.....          
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~l-L~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~----------  204 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVL-LEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEP----------  204 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhh-hcCcceEEEcCCCCcccHHHHHHHHHHHHhcCc----------
Confidence            469999999999999986 99999999999999999 899999999999999999999999999987532          


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCcee--EEEeCCCcchHHHHHhcCCCcccccc----------
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTL--AMAAGSPLLTSEHSNRRKPNKRKRTR----------  180 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v--~~~~G~~~~~q~~~l~~~~~i~v~~~----------  180 (284)
                          ......|+.||||+||||||.|+|+.+++|.+...+-|  .+++|......-++|+++.+|+|.+.          
T Consensus       205 ----ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT  280 (708)
T KOG0348|consen  205 ----KIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNT  280 (708)
T ss_pred             ----cccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhcc
Confidence                33456899999999999999999999999999876544  44555566777788999999977652          


Q ss_pred             cCCccccccccCCCCCCcccccccccchhhhcc
Q 042526          181 KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMN  213 (284)
Q Consensus       181 ~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~  213 (284)
                      ....+.+|.+|||||||+++++||.-++-.|++
T Consensus       281 ~~i~~s~LRwlVlDEaDrlleLGfekdit~Il~  313 (708)
T KOG0348|consen  281 KSIKFSRLRWLVLDEADRLLELGFEKDITQILK  313 (708)
T ss_pred             chheeeeeeEEEecchhHHHhccchhhHHHHHH
Confidence            223455788999999999999999988866655

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=99.97  E-value=1.6e-32  Score=259.78  Aligned_cols=190  Identities=22%  Similarity=0.193  Sum_probs=161.9

Q ss_pred             cccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHH
Q 042526           21 EELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEE  100 (284)
Q Consensus        21 ~~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~  100 (284)
                      .....|..+|.|+++|++.+||.++++.|...||..|||||++|||.. ++.+|+|+.|.||||||+||++|++..+...
T Consensus       232 nis~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~-lQ~rD~igvaETgsGktaaf~ipLl~~Issl  310 (673)
T KOG0333|consen  232 NISIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLG-LQNRDPIGVAETGSGKTAAFLIPLLIWISSL  310 (673)
T ss_pred             eeeecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccch-hccCCeeeEEeccCCccccchhhHHHHHHcC
Confidence            345678899999999999999999999999999999999999999988 9999999999999999999999999998775


Q ss_pred             HHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc
Q 042526          101 REKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~  179 (284)
                      ....           .......+|+|+||+||||||+||..+...|++.+++++..++|| ....|--++..+..|++.+
T Consensus       311 P~~~-----------~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviat  379 (673)
T KOG0333|consen  311 PPMA-----------RLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIAT  379 (673)
T ss_pred             CCcc-----------hhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecC
Confidence            3111           012345689999999999999999999999999999988776666 6677777888888887765


Q ss_pred             c---------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCc
Q 042526          180 R---------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKK  222 (284)
Q Consensus       180 ~---------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~  222 (284)
                      .         ....+....++|+||||+|+||||.|++..+|+.+|-...+.
T Consensus       380 PgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~  431 (673)
T KOG0333|consen  380 PGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKP  431 (673)
T ss_pred             chHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCC
Confidence            2         122355678899999999999999999999999887665543

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

Probab=99.97  E-value=8.7e-32  Score=264.80  Aligned_cols=180  Identities=19%  Similarity=0.212  Sum_probs=153.8

Q ss_pred             cccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHH
Q 042526           23 LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEERE  102 (284)
Q Consensus        23 ~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~  102 (284)
                      .+.|.++|.|+.+|.+++|++.|+++|..+||..|||+|.+|||.+ +.|+|++++||||||||++|++|+|.++.....
T Consensus       110 ~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~i-l~g~dviv~ApTGSGKTlayllPil~~l~~~~~  188 (518)
T PLN00206        110 HVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAA-LSGRSLLVSADTGSGKTASFLVPIISRCCTIRS  188 (518)
T ss_pred             EecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hcCCCEEEEecCCCCccHHHHHHHHHHHHhhcc
Confidence            4578899999999999999999999999999999999999999999 899999999999999999999999998875321


Q ss_pred             HHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc-
Q 042526          103 KAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR-  180 (284)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~-  180 (284)
                      .             ......++++|||+||||||.|++..++.+.+..++.+++++|+ ....|...+..++++++.+. 
T Consensus       189 ~-------------~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPg  255 (518)
T PLN00206        189 G-------------HPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPG  255 (518)
T ss_pred             c-------------cccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHH
Confidence            0             11223578999999999999999999999999888877666555 66667777888888877652 


Q ss_pred             --------cCCccccccccCCCCCCcccccccccchhhhcccCC
Q 042526          181 --------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTE  216 (284)
Q Consensus       181 --------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~  216 (284)
                              ....++++..+|+||||.|+++||.+++..++...+
T Consensus       256 rL~~~l~~~~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l~  299 (518)
T PLN00206        256 RLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS  299 (518)
T ss_pred             HHHHHHHcCCccchheeEEEeecHHHHhhcchHHHHHHHHHhCC
Confidence                    234578899999999999999999999988877664

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=9.9e-32  Score=251.83  Aligned_cols=174  Identities=29%  Similarity=0.395  Sum_probs=144.2

Q ss_pred             cCcccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           34 DAWNELR--LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        34 ~~F~~l~--L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      .+|++|+  |+++|+++|..+||..+||+|..+||.+ +.++||++.|+||||||+||++|+++.+++...         
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPll-l~~KDVvveavTGSGKTlAFllP~le~i~rr~~---------   73 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLL-LKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREA---------   73 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHH-hcCCceEEEcCCCCCchhhHHHHHHHHHHhhcc---------
Confidence            4688875  6699999999999999999999999998 999999999999999999999999999977531         


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC-CCceeEEEeCC-CcchHHHHHhc-CCCcccccc--------
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS-NSLTLAMAAGS-PLLTSEHSNRR-KPNKRKRTR--------  180 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~-~~i~v~~~~G~-~~~~q~~~l~~-~~~i~v~~~--------  180 (284)
                            ......+.||||+||||||.||.+++..|..+ .++++.+++|| ........++. +|+|++.+.        
T Consensus        74 ------~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~  147 (567)
T KOG0345|consen   74 ------KTPPGQVGALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQ  147 (567)
T ss_pred             ------CCCccceeEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHh
Confidence                  12223578999999999999999999999988 47888776666 55555555555 577777652        


Q ss_pred             -cCCcc--ccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          181 -KGGED--EKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       181 -~~~~~--d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                       ....+  ..|..||+||||++++|||..++..|+..+|+-+.+-|
T Consensus       148 ~~~~~l~~rsLe~LVLDEADrLldmgFe~~~n~ILs~LPKQRRTGL  193 (567)
T KOG0345|consen  148 REAEKLSFRSLEILVLDEADRLLDMGFEASVNTILSFLPKQRRTGL  193 (567)
T ss_pred             chhhhccccccceEEecchHhHhcccHHHHHHHHHHhccccccccc
Confidence             11223  37888999999999999999999999999998887655

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=4.6e-32  Score=246.89  Aligned_cols=171  Identities=27%  Similarity=0.316  Sum_probs=151.8

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      .+..|+.|||++||.+.|+.+|+..|||||..|||.| +.|+|+|.+|.||||||+||.+|+++++.+.+          
T Consensus         5 t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkI-LeGrdcig~AkTGsGKT~AFaLPil~rLsedP----------   73 (442)
T KOG0340|consen    5 TAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKI-LEGRDCIGCAKTGSGKTAAFALPILNRLSEDP----------   73 (442)
T ss_pred             ccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHH-hcccccccccccCCCcchhhhHHHHHhhccCC----------
Confidence            4578999999999999999999999999999999999 99999999999999999999999999998763          


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccccc---------
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTRK---------  181 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~~---------  181 (284)
                                .+..||||+||||||.||...|..+++.+++++++++|| +...|...|.++|++++.+.-         
T Consensus        74 ----------~giFalvlTPTrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn  143 (442)
T KOG0340|consen   74 ----------YGIFALVLTPTRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSN  143 (442)
T ss_pred             ----------CcceEEEecchHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccC
Confidence                      688999999999999999999999999999999888877 566677778888998776521         


Q ss_pred             ----CCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          182 ----GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       182 ----~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                          --.+.++..+|+||||+|++-+|-...-.+.+-.|..+|+.+
T Consensus       144 ~~~~~~~~~rlkflVlDEADrvL~~~f~d~L~~i~e~lP~~RQtLl  189 (442)
T KOG0340|consen  144 LGVCSWIFQRLKFLVLDEADRVLAGCFPDILEGIEECLPKPRQTLL  189 (442)
T ss_pred             CccchhhhhceeeEEecchhhhhccchhhHHhhhhccCCCccceEE
Confidence                113678999999999999999887777777778888888877

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=99.97  E-value=6e-32  Score=254.45  Aligned_cols=175  Identities=29%  Similarity=0.370  Sum_probs=151.3

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      .....|.++.|++.++++|.+|||+.+|+||+.+||++ +.|+|+++.|.||||||+|||||+++.+....         
T Consensus        79 ~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pl-l~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~---------  148 (543)
T KOG0342|consen   79 TTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPL-LEGKDVLAAAKTGTGKTLAFLLPAIELLRKLK---------  148 (543)
T ss_pred             hhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCcc-CCCccceeeeccCCCceeeehhHHHHHHHhcc---------
Confidence            34556899999999999999999999999999999999 99999999999999999999999999998863         


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCC-cchHHHHHhcCCCcccccccCC-----
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSP-LLTSEHSNRRKPNKRKRTRKGG-----  183 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~~~~-----  183 (284)
                             ....++..+||||||||||.|++.+++.|.++. ++.|.+++||. .......+.++++|++.+ ++.     
T Consensus       149 -------~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliAT-PGRLlDHl  220 (543)
T KOG0342|consen  149 -------FKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIAT-PGRLLDHL  220 (543)
T ss_pred             -------cCCCCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeC-CchHHhHh
Confidence                   344578899999999999999999999999998 89998877774 444455666667776654 222     


Q ss_pred             ------ccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          184 ------EDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       184 ------~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                            ....+..+|+||||+.++|||--++.+++...|+.+|+++
T Consensus       221 qNt~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~rqt~L  266 (543)
T KOG0342|consen  221 QNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQTLL  266 (543)
T ss_pred             hcCCcchhhccceeEeecchhhhhcccHHHHHHHHHhccccceeeE
Confidence                  2334568999999999999999999999999999999998

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=2.8e-32  Score=252.15  Aligned_cols=179  Identities=21%  Similarity=0.223  Sum_probs=152.7

Q ss_pred             ccCccccCccc-CCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHH
Q 042526           28 EISTEFDAWNE-LRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAK  106 (284)
Q Consensus        28 ~~p~~~~~F~~-l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~  106 (284)
                      .+|.|.-+|.+ |.-.+++++++.++||..|||||++|||.+ ++|.|+++.|+||+|||++||+|-+.++..+..    
T Consensus       213 pIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~-LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~----  287 (629)
T KOG0336|consen  213 PIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPIL-LQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPK----  287 (629)
T ss_pred             cCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhccccee-ecCcceEEEEecCCCcCHHHhccceeeeeccch----
Confidence            48999999998 478899999999999999999999999998 999999999999999999999999988876543    


Q ss_pred             HHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccccc-----
Q 042526          107 MLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRK-----  181 (284)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~-----  181 (284)
                                ......+|.+|||+||||||.||.-++.......-..+++++|+....|...+.++.+|++.+.-     
T Consensus       288 ----------~~~qr~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL  357 (629)
T KOG0336|consen  288 ----------RREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDL  357 (629)
T ss_pred             ----------hhhccCCCceEEEeccHHHHHHHHhHHhHhhhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhh
Confidence                      22245789999999999999999999987765544567778888999999999999999776521     


Q ss_pred             ----CCccccccccCCCCCCcccccccccchhhhcccCCCCCCC
Q 042526          182 ----GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGK  221 (284)
Q Consensus       182 ----~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~  221 (284)
                          ...+..+.+||+||||+|+||||.|++..+|=+....+|.
T Consensus       358 ~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRqt  401 (629)
T KOG0336|consen  358 QMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQT  401 (629)
T ss_pred             hhcCeeeeeeeEEEEecchhhhhcccccHHHHHHhhhcCCccee
Confidence                1246678999999999999999999999987665555553

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=4.8e-31  Score=253.38  Aligned_cols=170  Identities=24%  Similarity=0.273  Sum_probs=145.8

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      .+|++|+|++.++++|.++||..|||||.+|||.+ +.|+|++++||||||||+||++|+++.+......          
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~i-l~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~----------   76 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLT-LAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAP----------   76 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCcEEEECCCCchHHHHHHHHHHHHHHhcccc----------
Confidence            58999999999999999999999999999999999 8999999999999999999999999998764210          


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc---------cCC
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------KGG  183 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~~~  183 (284)
                         ......++++|||+||||||.|+++++..++...++++.+++|+ ....+...+..+++|++.+.         ...
T Consensus        77 ---~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~  153 (423)
T PRK04837         77 ---EDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHI  153 (423)
T ss_pred             ---cccccCCceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCc
Confidence               11123568999999999999999999999999999998777766 55666777777889877662         234


Q ss_pred             ccccccccCCCCCCcccccccccchhhhcccCCC
Q 042526          184 EDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEG  217 (284)
Q Consensus       184 ~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r  217 (284)
                      .++++..+|+||||+|++.||..++..++...+.
T Consensus       154 ~l~~v~~lViDEad~l~~~~f~~~i~~i~~~~~~  187 (423)
T PRK04837        154 NLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPP  187 (423)
T ss_pred             ccccccEEEEecHHHHhhcccHHHHHHHHHhCCC
Confidence            5788999999999999999999998888776654

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.97  E-value=9.5e-32  Score=250.28  Aligned_cols=175  Identities=27%  Similarity=0.222  Sum_probs=151.7

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      .+|++|+|++.|++++.++||+.||.||..|||.+ +.|+||++.|.||||||+||+||+|+.++....           
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIpla-LEgKDvvarArTGSGKT~AYliPllqkll~~k~-----------   86 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLA-LEGKDVVARARTGSGKTAAYLIPLLQKLLAEKK-----------   86 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchh-hcCcceeeeeccCCCchHHHHHHHHHHHHHhhh-----------
Confidence            78999999999999999999999999999999998 999999999999999999999999999998752           


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCC--ceeEEEe-CCCcchHHHHHhcCCCccccc----------c
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNS--LTLAMAA-GSPLLTSEHSNRRKPNKRKRT----------R  180 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~--i~v~~~~-G~~~~~q~~~l~~~~~i~v~~----------~  180 (284)
                         ......+|.|+||+||||||.|+|+++..|..+.+  ++++-+. ..+...+..+|...|+|++.+          .
T Consensus        87 ---t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~  163 (569)
T KOG0346|consen   87 ---TNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAG  163 (569)
T ss_pred             ---cccccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhc
Confidence               22456789999999999999999999999998875  3433333 445556668889999998866          2


Q ss_pred             cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          181 KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       181 ~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ++..++.|..||.||||.|+.|||.-+...+...+||.-|.-+
T Consensus       164 ~~~~~~~l~~LVvDEADLllsfGYeedlk~l~~~LPr~~Q~~L  206 (569)
T KOG0346|consen  164 VLEYLDSLSFLVVDEADLLLSFGYEEDLKKLRSHLPRIYQCFL  206 (569)
T ss_pred             cchhhhheeeEEechhhhhhhcccHHHHHHHHHhCCchhhhee
Confidence            3356788999999999999999999999999999998887655

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=99.97  E-value=3.1e-32  Score=250.43  Aligned_cols=188  Identities=23%  Similarity=0.264  Sum_probs=164.5

Q ss_pred             cccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHH
Q 042526           23 LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEERE  102 (284)
Q Consensus        23 ~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~  102 (284)
                      .|+|..+|+|+.+|.++.+|..|++.|++.|+.+|||||-+.||.+ ++|||+|+.|-||||||+.|.||++-..++...
T Consensus       159 ~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvv-LsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~  237 (610)
T KOG0341|consen  159 LVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVV-LSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEM  237 (610)
T ss_pred             EeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceE-eecCceeeEEeecCCceEEEeHHHHHHHHHHHh
Confidence            7899999999999999999999999999999999999999999999 999999999999999999999999998877643


Q ss_pred             HHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC------CceeE-EEeCCCcchHHHHHhcCCCc
Q 042526          103 KAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN------SLTLA-MAAGSPLLTSEHSNRRKPNK  175 (284)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~------~i~v~-~~~G~~~~~q~~~l~~~~~i  175 (284)
                      .            .+.....+|.+||+||+||||.|++..+..+...+      .++++ |++|.+...|...++++.+|
T Consensus       238 ~------------lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHi  305 (610)
T KOG0341|consen  238 M------------LPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHI  305 (610)
T ss_pred             c------------CccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeE
Confidence            2            25566789999999999999999999998876543      24554 45566999999999999999


Q ss_pred             cccc---------ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          176 RKRT---------RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       176 ~v~~---------~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ++.+         .+...+|-..+|.+||||+|.||||..++.++..-...-+|+.+
T Consensus       306 vVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLL  362 (610)
T KOG0341|consen  306 VVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLL  362 (610)
T ss_pred             EEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheee
Confidence            8876         24457888899999999999999999999999887766667666

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.97  E-value=1.4e-31  Score=254.66  Aligned_cols=180  Identities=27%  Similarity=0.374  Sum_probs=150.6

Q ss_pred             cccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHH
Q 042526           27 AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAA  105 (284)
Q Consensus        27 ~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~  105 (284)
                      +.-+..++.|.+|+||.+++++|..+||..|||||+.+||++ ..| .||++.|.|||||||||.|||+.++......+.
T Consensus       174 ~~~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~a-i~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~  252 (731)
T KOG0347|consen  174 DSSKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAA-IRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQ  252 (731)
T ss_pred             cccccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHh-hccchhcccccccCCCceeeecchhhhhhhhccchHh
Confidence            344677888999999999999999999999999999999999 777 899999999999999999999998877644333


Q ss_pred             HHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc----
Q 042526          106 KMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR----  180 (284)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~----  180 (284)
                      ....       ....+..+.+||++||||||+||.+.+..++.+.+++++.++|| ....|++.|...|+|+|.+.    
T Consensus       253 e~~~-------~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlw  325 (731)
T KOG0347|consen  253 ELSN-------TSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLW  325 (731)
T ss_pred             hhhh-------HHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHH
Confidence            2222       11122334599999999999999999999999999999888887 77888888999999988762    


Q ss_pred             --------cCCccccccccCCCCCCcccccccccchhhhccc
Q 042526          181 --------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNL  214 (284)
Q Consensus       181 --------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~  214 (284)
                              -+..+..|..||+||||+|..-|.|...-++++.
T Consensus       326 eli~e~n~~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~  367 (731)
T KOG0347|consen  326 ELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKH  367 (731)
T ss_pred             HHHHhhhhhhhhhhhceEEEEccHHHHhhhccHHHHHHHHHH
Confidence                    2335778999999999999999988887777663

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.96  E-value=5.7e-30  Score=248.31  Aligned_cols=174  Identities=23%  Similarity=0.320  Sum_probs=147.7

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      +|++|+|++.|+++|.++||..|||+|.+|||.+ +.|+|+|++||||||||++|++|+++.+.....            
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i-l~g~dvlv~apTGsGKTla~~lpil~~l~~~~~------------   68 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAV-LEGRDLMASAQTGTGKTAGFTLPLLQHLITRQP------------   68 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCCcHHHHHHHHHHHHhhhccc------------
Confidence            7999999999999999999999999999999999 899999999999999999999999999865421            


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc---------cCCc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------KGGE  184 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~~~~  184 (284)
                        .......+++|||+||||||.|++..+..+..+.++.+..++|+ +...|...+...++|++.+.         ....
T Consensus        69 --~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~  146 (456)
T PRK10590         69 --HAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVK  146 (456)
T ss_pred             --ccccCCCceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcc
Confidence              11122356899999999999999999999999988888666665 55667777778889887762         2235


Q ss_pred             cccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          185 DEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       185 ~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      +.++..+|+||||.|++++|+.++..++..++...|...
T Consensus       147 l~~v~~lViDEah~ll~~~~~~~i~~il~~l~~~~q~l~  185 (456)
T PRK10590        147 LDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLL  185 (456)
T ss_pred             cccceEEEeecHHHHhccccHHHHHHHHHhCCccCeEEE
Confidence            788999999999999999999999888888877766443

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.96  E-value=5.2e-30  Score=248.65  Aligned_cols=170  Identities=28%  Similarity=0.328  Sum_probs=147.4

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      +.+|++|+|++.++++|.++||..|||+|.+|||.+ +.|+|++++||||||||+||++|+++++...            
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~-l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~------------   69 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAI-LAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK------------   69 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hcCCCEEEECCCCCcHHHHHHHHHHHHhhhc------------
Confidence            468999999999999999999999999999999999 8999999999999999999999999987542            


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCC-CcchHHHHHhcCCCcccccc---------c
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------K  181 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~  181 (284)
                              ...+++|||+||||||.|++..++.++... ++++..++|+ +...|...+..++++++.+.         .
T Consensus        70 --------~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~  141 (460)
T PRK11776         70 --------RFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKG  141 (460)
T ss_pred             --------cCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcC
Confidence                    135789999999999999999999998765 6888777766 66677788888889877662         2


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ...+.++..+|+||||+|+++||.++...++..++...|..+
T Consensus       142 ~~~l~~l~~lViDEad~~l~~g~~~~l~~i~~~~~~~~q~ll  183 (460)
T PRK11776        142 TLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLL  183 (460)
T ss_pred             CccHHHCCEEEEECHHHHhCcCcHHHHHHHHHhCCcccEEEE
Confidence            235778999999999999999999999988888887777544

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=9.7e-30  Score=252.76  Aligned_cols=171  Identities=23%  Similarity=0.220  Sum_probs=144.2

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|++|+|++.|+++|.++||+.|||||.+|||.+ +.|+|++++||||||||++|++|+++++......         
T Consensus         8 ~~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~-l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~---------   77 (572)
T PRK04537          8 DLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVA-LPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPAL---------   77 (572)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc---------
Confidence            347999999999999999999999999999999998 9999999999999999999999999988753200         


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc----------c
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR----------K  181 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~----------~  181 (284)
                          .......+++|||+||||||.|++..+..|+...++.+.+++|+ ....|...+..+++|+|.+.          .
T Consensus        78 ----~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~  153 (572)
T PRK04537         78 ----ADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHK  153 (572)
T ss_pred             ----cccccCCceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhcc
Confidence                01122358999999999999999999999999999988777766 55666667777788877762          1


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCC
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEG  217 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r  217 (284)
                      ...+..+..+|+||||.|+++||..++..++..++.
T Consensus       154 ~~~l~~v~~lViDEAh~lld~gf~~~i~~il~~lp~  189 (572)
T PRK04537        154 VVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPE  189 (572)
T ss_pred             ccchhheeeeEecCHHHHhhcchHHHHHHHHHhccc
Confidence            245677888999999999999999999888876664

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.96  E-value=1.1e-29  Score=254.40  Aligned_cols=170  Identities=25%  Similarity=0.313  Sum_probs=148.0

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|.+|+|++.|+++|.++||..|||+|.++||.+ +.|+|+|++||||||||+||++|+++.+...            
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~l-l~g~dvl~~ApTGsGKT~af~lpll~~l~~~------------   71 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHL-LNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE------------   71 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc------------
Confidence            357999999999999999999999999999999999 8999999999999999999999999987543            


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCC-CcchHHHHHhcCCCcccccc---------c
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------K  181 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~  181 (284)
                              ...+++|||+||||||.|++..+..+..+. ++.++.++|+ +...|...+..+++|+|.|.         .
T Consensus        72 --------~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~  143 (629)
T PRK11634         72 --------LKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRG  143 (629)
T ss_pred             --------cCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcC
Confidence                    146899999999999999999999998876 6777666555 67778888888899988772         2


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ...+..|..+|+||||.|+++||..++..++..+|...|..+
T Consensus       144 ~l~l~~l~~lVlDEAd~ml~~gf~~di~~Il~~lp~~~q~ll  185 (629)
T PRK11634        144 TLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTAL  185 (629)
T ss_pred             CcchhhceEEEeccHHHHhhcccHHHHHHHHHhCCCCCeEEE
Confidence            234778899999999999999999999999998888887655

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.96  E-value=3.4e-29  Score=241.12  Aligned_cols=170  Identities=27%  Similarity=0.343  Sum_probs=144.8

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      +|++|+|++.|+++|.++||..||++|.+|||.+ +.|+|++++||||||||++|++|+++++....             
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~-~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~-------------   67 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPA-LDGRDVLGSAPTGTGKTAAFLLPALQHLLDFP-------------   67 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHHhhcc-------------
Confidence            7999999999999999999999999999999999 89999999999999999999999999887531             


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc---------cCCc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------KGGE  184 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~~~~  184 (284)
                         ......+++|||+||||||.|+++.+..++...++.+..++|+ ....+...+..+++|++.+.         ....
T Consensus        68 ---~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~  144 (434)
T PRK11192         68 ---RRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFD  144 (434)
T ss_pred             ---ccCCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcC
Confidence               1122457899999999999999999999999999999888876 56666667777888877763         2234


Q ss_pred             cccccccCCCCCCcccccccccchhhhcccCCCCCCC
Q 042526          185 DEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGK  221 (284)
Q Consensus       185 ~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~  221 (284)
                      +..+..+|+||||+|+++||...+..+...++...|.
T Consensus       145 ~~~v~~lViDEah~~l~~~~~~~~~~i~~~~~~~~q~  181 (434)
T PRK11192        145 CRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQT  181 (434)
T ss_pred             cccCCEEEEECHHHHhCCCcHHHHHHHHHhCccccEE
Confidence            6788999999999999999998887776665554443

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=1.1e-29  Score=225.64  Aligned_cols=173  Identities=21%  Similarity=0.276  Sum_probs=147.2

Q ss_pred             cccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHH
Q 042526           27 AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAK  106 (284)
Q Consensus        27 ~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~  106 (284)
                      +.--.++.+|+++||.+.|++++++.||+.|+.||+.|||+| +.|+|||++|++|+|||.+|.+.+++.+....     
T Consensus        20 s~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~I-lkGrdViaQaqSGTGKTa~~si~vlq~~d~~~-----   93 (400)
T KOG0328|consen   20 SEKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQI-LKGRDVIAQAQSGTGKTATFSISVLQSLDISV-----   93 (400)
T ss_pred             ccCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhh-hcccceEEEecCCCCceEEEEeeeeeeccccc-----
Confidence            344567889999999999999999999999999999999999 99999999999999999999999998775542     


Q ss_pred             HHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc------
Q 042526          107 MLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT------  179 (284)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~------  179 (284)
                                     ...+||||+||||||.||..++..|+.++++.+..+.|| +....+..+..+.+.+..+      
T Consensus        94 ---------------r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~d  158 (400)
T KOG0328|consen   94 ---------------RETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLD  158 (400)
T ss_pred             ---------------ceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHH
Confidence                           357999999999999999999999999999999766665 5566666666666554432      


Q ss_pred             ---ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          180 ---RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       180 ---~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                         +.......+..||+||||.|++-||-.|...+...+|.+.|
T Consensus       159 mikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Q  202 (400)
T KOG0328|consen  159 MIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQ  202 (400)
T ss_pred             HHHhccccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCCce
Confidence               11123456888999999999999999999988888888887

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.95  E-value=5.3e-29  Score=231.00  Aligned_cols=171  Identities=25%  Similarity=0.319  Sum_probs=153.3

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|..+||+..++++|.+.||..|||||+.+||.| +.|+|++..|.||||||.||+||+++++....           
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipli-Le~~dvv~martgsgktaaf~ipm~e~Lk~~s-----------   87 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLI-LEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS-----------   87 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccce-eeccccceeeecCCcchhhHHHHHHHHHhhcc-----------
Confidence            568999999999999999999999999999999999 99999999999999999999999999987642           


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeC-CCcchHHHHHhcCCCcccccc---------cC
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAG-SPLLTSEHSNRRKPNKRKRTR---------KG  182 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G-~~~~~q~~~l~~~~~i~v~~~---------~~  182 (284)
                              ..+.+|||++||||||.|+.++++.+++.+++++++++| .....|-..+..+||+++.+.         ..
T Consensus        88 --------~~g~RalilsptreLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~  159 (529)
T KOG0337|consen   88 --------QTGLRALILSPTRELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMT  159 (529)
T ss_pred             --------ccccceeeccCcHHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehhee
Confidence                    368899999999999999999999999999998876555 567788888888999988552         12


Q ss_pred             CccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          183 GEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       183 ~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ..+.-+.|+||||||+++.|||.++.-.++.+.|..+|+.+
T Consensus       160 l~l~sveyVVfdEadrlfemgfqeql~e~l~rl~~~~QTll  200 (529)
T KOG0337|consen  160 LTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPESRQTLL  200 (529)
T ss_pred             ccccceeeeeehhhhHHHhhhhHHHHHHHHHhCCCcceEEE
Confidence            35778899999999999999999999999999999998776

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.95  E-value=1.4e-29  Score=228.25  Aligned_cols=171  Identities=21%  Similarity=0.293  Sum_probs=148.0

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      .-..|++++|.++|+..+.++||+.|+|||.++||.+ +.|+|+++.|.+|+|||.||++|+|+++....          
T Consensus        83 kG~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPia-LtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~----------  151 (459)
T KOG0326|consen   83 KGNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIA-LTGRDILARAKNGTGKTAAYCIPVLEKIDPKK----------  151 (459)
T ss_pred             cCccHHHhhhhHHHHHHHHHhccCCCCCcccccccee-ecchhhhhhccCCCCCccceechhhhhcCccc----------
Confidence            3445999999999999999999999999999999998 99999999999999999999999999886653          


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc--ccCC-----
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT--RKGG-----  183 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~--~~~~-----  183 (284)
                                ...+++||+||||||.|+..++..+++++++.|.+.+|| +....+.++...+++++.+  +++|     
T Consensus       152 ----------~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~Kg  221 (459)
T KOG0326|consen  152 ----------NVIQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKG  221 (459)
T ss_pred             ----------cceeEEEEeecchhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcc
Confidence                      578999999999999999999999999999999777766 5555555666666665544  2222     


Q ss_pred             --ccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          184 --EDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       184 --~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                        .++....+|+||||.+++..|-+.+-+++.-+|+.+|-.+
T Consensus       222 Va~ls~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~rQill  263 (459)
T KOG0326|consen  222 VADLSDCVILVMDEADKLLSVDFQPIVEKLISFLPKERQILL  263 (459)
T ss_pred             cccchhceEEEechhhhhhchhhhhHHHHHHHhCCccceeeE
Confidence              3556677999999999999999999999999999999776

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=1.5e-27  Score=232.48  Aligned_cols=174  Identities=25%  Similarity=0.271  Sum_probs=144.2

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      ....+|.+++|++.|+++|.++||..||++|.+|||.+ +.|+|+|++||||||||+||++|+++.+......       
T Consensus        84 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~-~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~-------  155 (475)
T PRK01297         84 EGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYT-LAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPP-------  155 (475)
T ss_pred             cCCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcc-------
Confidence            33467999999999999999999999999999999999 9999999999999999999999999998764210       


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhc-CCCcccccc--------
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRR-KPNKRKRTR--------  180 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~-~~~i~v~~~--------  180 (284)
                            .......+++|||+|||+||.|+++.++.|.+.+++.+..++|+ ....|...+.. .+++++.+.        
T Consensus       156 ------~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~  229 (475)
T PRK01297        156 ------KERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQ  229 (475)
T ss_pred             ------cccccCCceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHH
Confidence                  01112368999999999999999999999999999888777666 55666666654 477776652        


Q ss_pred             -cCCccccccccCCCCCCcccccccccchhhhcccCCCC
Q 042526          181 -KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGK  218 (284)
Q Consensus       181 -~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~  218 (284)
                       ....+.++..+|+||||.+.+++|++.+..++...+..
T Consensus       230 ~~~~~l~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~  268 (475)
T PRK01297        230 RGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRK  268 (475)
T ss_pred             cCCcccccCceEEechHHHHHhcccHHHHHHHHHhCCCC
Confidence             12357789999999999999999999998888877653

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

Probab=99.93  E-value=6.2e-26  Score=231.26  Aligned_cols=159  Identities=16%  Similarity=0.131  Sum_probs=133.7

Q ss_pred             ccccCccccCcccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHH
Q 042526           26 EAEISTEFDAWNELR--LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK  103 (284)
Q Consensus        26 ~~~~p~~~~~F~~l~--L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~  103 (284)
                      ...+|..-..|..++  |++.|.++|.++||+.||++|.+|||.+ +.|+|++++||||||||+||++|+|+.+...   
T Consensus         4 ~~~~p~~~a~~~~~~~~l~~~l~~~L~~~g~~~p~~~Q~~ai~~i-l~G~nvvv~apTGSGKTla~~LPiL~~l~~~---   79 (742)
T TIGR03817         4 VEHLPARAGRTAPWPAWAHPDVVAALEAAGIHRPWQHQARAAELA-HAGRHVVVATGTASGKSLAYQLPVLSALADD---   79 (742)
T ss_pred             eeecCCCCcccCCCCCcCCHHHHHHHHHcCCCcCCHHHHHHHHHH-HCCCCEEEECCCCCcHHHHHHHHHHHHHhhC---
Confidence            345666666666663  8999999999999999999999999999 9999999999999999999999999988653   


Q ss_pred             HHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---
Q 042526          104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---  180 (284)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---  180 (284)
                                        .++++|||+||||||.|++..++.++ ..++++.+++|+....|...++.++++++.+.   
T Consensus        80 ------------------~~~~aL~l~PtraLa~q~~~~l~~l~-~~~i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L  140 (742)
T TIGR03817        80 ------------------PRATALYLAPTKALAADQLRAVRELT-LRGVRPATYDGDTPTEERRWAREHARYVLTNPDML  140 (742)
T ss_pred             ------------------CCcEEEEEcChHHHHHHHHHHHHHhc-cCCeEEEEEeCCCCHHHHHHHhcCCCEEEEChHHH
Confidence                              35789999999999999999999997 45788888999888888778888888877653   


Q ss_pred             ---cC-------CccccccccCCCCCCcccccccccch
Q 042526          181 ---KG-------GEDEKLDSLKWNPLSQPKTTTLLPSS  208 (284)
Q Consensus       181 ---~~-------~~~d~l~~lv~dEAd~m~~~gflp~~  208 (284)
                         .+       ..+.+|.++|+||||.|.++ |-+.+
T Consensus       141 ~~~~L~~~~~~~~~l~~l~~vViDEah~~~g~-fg~~~  177 (742)
T TIGR03817       141 HRGILPSHARWARFLRRLRYVVIDECHSYRGV-FGSHV  177 (742)
T ss_pred             HHhhccchhHHHHHHhcCCEEEEeChhhccCc-cHHHH
Confidence               11       12678999999999999763 55554

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=99.93  E-value=1.4e-26  Score=213.00  Aligned_cols=189  Identities=23%  Similarity=0.300  Sum_probs=157.9

Q ss_pred             CCCCccccccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHH
Q 042526           14 NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPA   93 (284)
Q Consensus        14 ~~~~~~~~~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPi   93 (284)
                      +++...+.+.+.+++.-.-+.+|.+++|++.|++.++.+||+.||.||+.||+++ ..|.|++++|++|||||.||++++
T Consensus         6 ~g~~~~e~~~~iesn~~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~-i~G~dv~~qaqsgTgKt~af~i~i   84 (397)
T KOG0327|consen    6 NGPDGMEPEGVIESNWNEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPC-IKGHDVIAQAQSGTGKTAAFLISI   84 (397)
T ss_pred             CCCcccCccccccccHHHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhcccccc-ccCCceeEeeeccccchhhhHHHH
Confidence            4455555567778888888899999999999999999999999999999999999 899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeC-CCcchHHHHHhc-
Q 042526           94 LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAG-SPLLTSEHSNRR-  171 (284)
Q Consensus        94 l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G-~~~~~q~~~l~~-  171 (284)
                      ++.+.-..                    ...+|||++||||||.|+..+...+..+++++|+.++| .....+..++.. 
T Consensus        85 Lq~iD~~~--------------------ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~  144 (397)
T KOG0327|consen   85 LQQIDMSV--------------------KETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKD  144 (397)
T ss_pred             HhhcCcch--------------------HHHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhcc
Confidence            99885432                    24679999999999999999999999999999976655 466646555555 


Q ss_pred             CCCcccccc--cC-------CccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          172 KPNKRKRTR--KG-------GEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       172 ~~~i~v~~~--~~-------~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      .+++++.++  +.       ...+.+...++||||+|+..||..++..+...+|..-|--+
T Consensus       145 ~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l  205 (397)
T KOG0327|consen  145 KPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDVQVVL  205 (397)
T ss_pred             CceeecCCchhHHHhhccccccccceeEEeecchHhhhccchHHHHHHHHHHcCcchhhee
Confidence            477766553  22       24456788999999999999999999999888887776444

>PTZ00424 helicase 45; Provisional

Probab=99.92  E-value=2.5e-25  Score=211.51  Aligned_cols=168  Identities=21%  Similarity=0.236  Sum_probs=138.8

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      ...+|++|+|++.++++|.++||..|||+|.+|||.+ +.|+|++++||||||||++|++|+++.+...           
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i-~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~-----------   93 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPI-LDGYDTIGQAQSGTGKTATFVIAALQLIDYD-----------   93 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHhcCC-----------
Confidence            4578999999999999999999999999999999999 9999999999999999999999999876431           


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccccc---------
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTRK---------  181 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~~---------  181 (284)
                               ..+.++|||+|||+||.|++..+..++...++.+..++|+ ....+...+..++++++.+.-         
T Consensus        94 ---------~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~  164 (401)
T PTZ00424         94 ---------LNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKR  164 (401)
T ss_pred             ---------CCCceEEEECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhC
Confidence                     1357899999999999999999999998888877666665 455555666777788776531         


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      ...++++..+|+|||+.+.+.+|......++...+...+
T Consensus       165 ~~~l~~i~lvViDEah~~~~~~~~~~~~~i~~~~~~~~~  203 (401)
T PTZ00424        165 HLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQ  203 (401)
T ss_pred             CcccccccEEEEecHHHHHhcchHHHHHHHHhhCCCCcE
Confidence            235788999999999999988887766666655544443

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.90  E-value=3.8e-24  Score=202.18  Aligned_cols=153  Identities=24%  Similarity=0.267  Sum_probs=124.6

Q ss_pred             ccCcccCCCCHHHHHH----------HHHcCCCCCcHHHHHHHHHHH--------cCCCcEEEEccCCCCchHHhHHHHH
Q 042526           33 FDAWNELRLHPLLMKS----------IYKLGFKESTSILKARIPALA--------HQRKDVIGAAETESGKTRAFGLPAL   94 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~----------L~~~g~~~pT~iQ~~aip~il--------~~G~dviv~A~TGSGKTlafllPil   94 (284)
                      ..-|+.++++..+...          |..|++++.+|||.+++|.++        +.++||++.||||||||+||.|||+
T Consensus       126 lq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIV  205 (620)
T KOG0350|consen  126 LQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIV  205 (620)
T ss_pred             eeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHH
Confidence            3447888877655544          899999999999999999873        3478999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCc-chHHHHHhcCC
Q 042526           95 QRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPL-LTSEHSNRRKP  173 (284)
Q Consensus        95 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~-~~q~~~l~~~~  173 (284)
                      +.+...                   .....+||||+|||+||.||++++.++....|+.|+++.|..+ .....+|...+
T Consensus       206 Q~L~~R-------------------~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~  266 (620)
T KOG0350|consen  206 QLLSSR-------------------PVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDP  266 (620)
T ss_pred             HHHccC-------------------CccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCC
Confidence            987653                   2356899999999999999999999999999999999999854 44445555554


Q ss_pred             -----Cccccc----------ccCCccccccccCCCCCCccccccc
Q 042526          174 -----NKRKRT----------RKGGEDEKLDSLKWNPLSQPKTTTL  204 (284)
Q Consensus       174 -----~i~v~~----------~~~~~~d~l~~lv~dEAd~m~~~gf  204 (284)
                           ||++.+          .+...|..|.+||.||||+|++..|
T Consensus       267 ~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsf  312 (620)
T KOG0350|consen  267 PECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSF  312 (620)
T ss_pred             CccccceEEcCchHHHHhccCCCCcchhhceEEEechHHHHHHHHH
Confidence                 454443          3455688899999999999888765

>cd00268 DEADc DEAD-box helicases

Probab=99.90  E-value=4.1e-23  Score=178.49  Aligned_cols=166  Identities=32%  Similarity=0.405  Sum_probs=136.4

Q ss_pred             cccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 042526           36 WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEA  115 (284)
Q Consensus        36 F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~  115 (284)
                      |+++++++.+.+.|.++||+.|+++|.++|+.+ +.|+|+++.||||+|||++|++|+++.+....              
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~-~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~--------------   65 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPL-LSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP--------------   65 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc--------------
Confidence            789999999999999999999999999999999 88999999999999999999999999887751              


Q ss_pred             hhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcc-hHHHHHhcCCCcccccc---------cCCcc
Q 042526          116 EKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLL-TSEHSNRRKPNKRKRTR---------KGGED  185 (284)
Q Consensus       116 ~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~-~q~~~l~~~~~i~v~~~---------~~~~~  185 (284)
                          ...++++||++||++|+.|+...++.+....++.+..+.|+... .....+..+.++++.+.         ....+
T Consensus        66 ----~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~  141 (203)
T cd00268          66 ----KKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDL  141 (203)
T ss_pred             ----ccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCCh
Confidence                12478999999999999999999999988888888888776544 33344444667766552         11346


Q ss_pred             ccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          186 EKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       186 d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      ..+..+++||++.|.+.+|......++...+++.+
T Consensus       142 ~~l~~lIvDE~h~~~~~~~~~~~~~~~~~l~~~~~  176 (203)
T cd00268         142 SKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQ  176 (203)
T ss_pred             hhCCEEEEeChHHhhccChHHHHHHHHHhCCcccE
Confidence            77889999999999988888777766666555443

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.

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.90  E-value=1.2e-24  Score=210.46  Aligned_cols=176  Identities=18%  Similarity=0.182  Sum_probs=149.1

Q ss_pred             cccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHH
Q 042526           25 NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKA  104 (284)
Q Consensus        25 ~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~  104 (284)
                      +++-.|....+|++|.|..+++..|++.+|..||+||..|||.+ +.+.|+|++|.+|+|||+.|.+.+++.+...    
T Consensus        16 s~DV~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~-~~kmDliVQaKSGTGKTlVfsv~av~sl~~~----   90 (980)
T KOG4284|consen   16 SIDVQSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAI-FSKMDLIVQAKSGTGKTLVFSVLAVESLDSR----   90 (980)
T ss_pred             ccccccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhh-hcccceEEEecCCCCceEEEEeeeehhcCcc----
Confidence            44456778889999999999999999999999999999999999 9999999999999999999999998876553    


Q ss_pred             HHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCcchHHHHHhcCCCcccccc---
Q 042526          105 AKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---  180 (284)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---  180 (284)
                                      ...++++||+||||+|.||.+.+..++..+ |++|.+++||....+...-.+...|++.+.   
T Consensus        91 ----------------~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~~rIvIGtPGRi  154 (980)
T KOG4284|consen   91 ----------------SSHIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQTRIVIGTPGRI  154 (980)
T ss_pred             ----------------cCcceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhhceEEecCchHH
Confidence                            367999999999999999999999999865 899999999988887777777777665541   


Q ss_pred             ------cCCccccccccCCCCCCcccccc-cccchhhhcccCCCCCCC
Q 042526          181 ------KGGEDEKLDSLKWNPLSQPKTTT-LLPSSLALMNLTEGKPGK  221 (284)
Q Consensus       181 ------~~~~~d~l~~lv~dEAd~m~~~g-flp~~~~~~~~~~r~~~~  221 (284)
                            .......|.-+||||||++.+.+ |--++-.+++.+|..+|=
T Consensus       155 ~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~slP~~rQv  202 (980)
T KOG4284|consen  155 AQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIRQV  202 (980)
T ss_pred             HHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHhcchhhee
Confidence                  11234467779999999977744 888888888888887763

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.90  E-value=5.9e-24  Score=204.30  Aligned_cols=180  Identities=26%  Similarity=0.294  Sum_probs=142.9

Q ss_pred             ccccccccccCccccCcccC----CCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHH
Q 042526           20 QEELVNEAEISTEFDAWNEL----RLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ   95 (284)
Q Consensus        20 ~~~~~~~~~~p~~~~~F~~l----~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~   95 (284)
                      ....+.|.++|.|+-+|.+|    ..++.|++++...||..|||+|.+|||.+ +.++|+++|||||||||+||++|+++
T Consensus       118 ~k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvf-l~~r~~lAcapTGsgKtlaf~~Pil~  196 (593)
T KOG0344|consen  118 NKINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVF-LEKRDVLACAPTGSGKTLAFNLPILQ  196 (593)
T ss_pred             ceeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhh-hcccceEEeccCCCcchhhhhhHHHH
Confidence            34568899999999999984    69999999999999999999999999998 99999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh--cCCCceeEEEeCCCcchHHH------
Q 042526           96 RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL--KSNSLTLAMAAGSPLLTSEH------  167 (284)
Q Consensus        96 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~--~~~~i~v~~~~G~~~~~q~~------  167 (284)
                      +|....               ......+.+++||.||||||.|++.++..+.  ...++.++.+.......|..      
T Consensus       197 ~L~~~~---------------~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~  261 (593)
T KOG0344|consen  197 HLKDLS---------------QEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDE  261 (593)
T ss_pred             HHHHhh---------------cccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHH
Confidence            987764               2344578999999999999999999999999  66666666655543333311      


Q ss_pred             ---HHhcCCCcccccc----cCCccccccccCCCCCCccccc-ccccchhhhcccC
Q 042526          168 ---SNRRKPNKRKRTR----KGGEDEKLDSLKWNPLSQPKTT-TLLPSSLALMNLT  215 (284)
Q Consensus       168 ---~l~~~~~i~v~~~----~~~~~d~l~~lv~dEAd~m~~~-gflp~~~~~~~~~  215 (284)
                         .+...|.-++...    ..+.+..|.++|+||||+++.- +|.-|.-+++..+
T Consensus       262 k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac  317 (593)
T KOG0344|consen  262 KYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSAC  317 (593)
T ss_pred             HHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHh
Confidence               1222222222222    2357889999999999998887 8888887666543

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.89  E-value=6.1e-24  Score=186.95  Aligned_cols=180  Identities=19%  Similarity=0.231  Sum_probs=151.7

Q ss_pred             cccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHH
Q 042526           23 LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEERE  102 (284)
Q Consensus        23 ~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~  102 (284)
                      ...|+++....+.|.++-|.|+|++++-+.||++|+.+|..|||.. .-|.||+++|.+|.|||..|.|..|+.+-..  
T Consensus        31 d~kgsyv~ihssgfrdfllkpellraivdcgfehpsevqhecipqa-ilgmdvlcqaksgmgktavfvl~tlqqiepv--  107 (387)
T KOG0329|consen   31 DKKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQA-ILGMDVLCQAKSGMGKTAVFVLATLQQIEPV--  107 (387)
T ss_pred             cccCcEEEEeccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHH-hhcchhheecccCCCceeeeehhhhhhcCCC--
Confidence            4566677777888999999999999999999999999999999998 6799999999999999999999998876443  


Q ss_pred             HHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCC-CcchHHHHHhcCCCccccc-
Q 042526          103 KAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGS-PLLTSEHSNRRKPNKRKRT-  179 (284)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~-  179 (284)
                                        .+.+.+||+|.|||||.||.+++.+|++++ ++++++++|| ++......+.+-|+|++.+ 
T Consensus       108 ------------------~g~vsvlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTP  169 (387)
T KOG0329|consen  108 ------------------DGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTP  169 (387)
T ss_pred             ------------------CCeEEEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCc
Confidence                              356889999999999999999999999998 6888887777 6777777777778887755 


Q ss_pred             --------ccCCccccccccCCCCCCcccc-cccccchhhhcccCCCCCCCcc
Q 042526          180 --------RKGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       180 --------~~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~~~~  223 (284)
                              .+...+..+.+.|+||.|.|+. ...--++..+...+|...|-|-
T Consensus       170 GrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQEifr~tp~~KQvmm  222 (387)
T KOG0329|consen  170 GRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEIFRMTPHEKQVMM  222 (387)
T ss_pred             HHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHHHHhhcCcccceeee
Confidence                    2345688999999999998654 3366677777778888887554

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.89  E-value=5.8e-24  Score=195.15  Aligned_cols=175  Identities=24%  Similarity=0.276  Sum_probs=142.0

Q ss_pred             ccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcC--CCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           22 ELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ--RKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        22 ~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~--G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      ..++.+..-.++.+|++|+|.|+|+++|+.|+|..||.||..|+|.+ +.  -+++|++|++|||||.||.|.+|.++..
T Consensus        78 k~~dpnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPll-l~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~  156 (477)
T KOG0332|consen   78 KLADPNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLL-LAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDP  156 (477)
T ss_pred             eecCCCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchh-hcCCchhhhhhhcCCCchhHHHHHHHHHhcCc
Confidence            34444444467789999999999999999999999999999999998 44  5799999999999999999999998765


Q ss_pred             HHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCc----
Q 042526          100 EREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNK----  175 (284)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i----  175 (284)
                      .                    ...|+++.|+||||||.|+..++...+++.++++..+.-+.      ...++..+    
T Consensus       157 ~--------------------~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~s------k~~rG~~i~eqI  210 (477)
T KOG0332|consen  157 D--------------------VVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGS------KAKRGNKLTEQI  210 (477)
T ss_pred             c--------------------ccCCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCc------ccccCCcchhhe
Confidence            4                    35899999999999999999999999999888776655433      11112111    


Q ss_pred             cc----------ccccCCccccccccCCCCCCcccccc-cccchhhhcccCCCCCCCcc
Q 042526          176 RK----------RTRKGGEDEKLDSLKWNPLSQPKTTT-LLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       176 ~v----------~~~~~~~~d~l~~lv~dEAd~m~~~g-flp~~~~~~~~~~r~~~~~~  223 (284)
                      ++          ..++...+..+..+||||||.|++.. |-.++++++...|+..|-.+
T Consensus       211 viGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllL  269 (477)
T KOG0332|consen  211 VIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLL  269 (477)
T ss_pred             eeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEe
Confidence            11          11344567788999999999988765 99999999999998888776

>PRK00254 ski2-like helicase; Provisional

Probab=99.85  E-value=4.6e-21  Score=195.61  Aligned_cols=160  Identities=17%  Similarity=0.092  Sum_probs=129.5

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      +|++++|++.+++.|.++||+.|+|+|.+||+..++.|+|++++||||||||++|.+|++..+...              
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--------------   67 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--------------   67 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--------------
Confidence            689999999999999999999999999999997448999999999999999999999999877542              


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCcc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGED  185 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~  185 (284)
                              +.++|||+|||+||.|++..+..+. ..+++|..++|+....  ......+++++.+.         ....+
T Consensus        68 --------~~~~l~l~P~~aLa~q~~~~~~~~~-~~g~~v~~~~Gd~~~~--~~~~~~~~IiV~Tpe~~~~ll~~~~~~l  136 (720)
T PRK00254         68 --------GGKAVYLVPLKALAEEKYREFKDWE-KLGLRVAMTTGDYDST--DEWLGKYDIIIATAEKFDSLLRHGSSWI  136 (720)
T ss_pred             --------CCeEEEEeChHHHHHHHHHHHHHHh-hcCCEEEEEeCCCCCc--hhhhccCCEEEEcHHHHHHHHhCCchhh
Confidence                    4589999999999999999998875 3688998888875433  22345678776651         11346


Q ss_pred             ccccccCCCCCCcccccccccchhhhcccCCCCC
Q 042526          186 EKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKP  219 (284)
Q Consensus       186 d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~  219 (284)
                      .+|..+|+||++.+.+.++-+....++..+....
T Consensus       137 ~~l~lvViDE~H~l~~~~rg~~le~il~~l~~~~  170 (720)
T PRK00254        137 KDVKLVVADEIHLIGSYDRGATLEMILTHMLGRA  170 (720)
T ss_pred             hcCCEEEEcCcCccCCccchHHHHHHHHhcCcCC
Confidence            7899999999999988777666655555444333

>PRK02362 ski2-like helicase; Provisional

Probab=99.85  E-value=4.7e-21  Score=195.96  Aligned_cols=148  Identities=17%  Similarity=0.076  Sum_probs=122.0

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      .|++|+||+.++++|.+.||..|+|+|.+||+..++.|+|++++||||||||++|.+|++..+..               
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~---------------   66 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR---------------   66 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc---------------
Confidence            68999999999999999999999999999999855899999999999999999999999987742               


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCcc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGED  185 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~  185 (284)
                              +.++|||+|||+||.|++..++.+.. .++++.+++|+.....  .....++|++.+.         ....+
T Consensus        67 --------~~kal~i~P~raLa~q~~~~~~~~~~-~g~~v~~~tGd~~~~~--~~l~~~~IiV~Tpek~~~llr~~~~~l  135 (737)
T PRK02362         67 --------GGKALYIVPLRALASEKFEEFERFEE-LGVRVGISTGDYDSRD--EWLGDNDIIVATSEKVDSLLRNGAPWL  135 (737)
T ss_pred             --------CCcEEEEeChHHHHHHHHHHHHHhhc-CCCEEEEEeCCcCccc--cccCCCCEEEECHHHHHHHHhcChhhh
Confidence                    35799999999999999999998764 4888988888754332  2334567766652         11346


Q ss_pred             ccccccCCCCCCcccccccccch
Q 042526          186 EKLDSLKWNPLSQPKTTTLLPSS  208 (284)
Q Consensus       186 d~l~~lv~dEAd~m~~~gflp~~  208 (284)
                      ..+..+|+||++++.+.++-+..
T Consensus       136 ~~v~lvViDE~H~l~d~~rg~~l  158 (737)
T PRK02362        136 DDITCVVVDEVHLIDSANRGPTL  158 (737)
T ss_pred             hhcCEEEEECccccCCCcchHHH
Confidence            78899999999999876665444

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

Probab=99.82  E-value=2.9e-20  Score=189.00  Aligned_cols=139  Identities=13%  Similarity=-0.039  Sum_probs=112.2

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCC-cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEE-E
Q 042526           52 LGFKESTSILKARIPALAHQRK-DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALI-I  129 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~-dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLI-L  129 (284)
                      +||+ |||+|.++||.+ +.|+ +++++||||||||.+|+++++.. ..                    ....|++|| +
T Consensus        12 ~G~~-PtpiQ~~~i~~i-l~G~~~v~~~apTGSGKTaa~aafll~~-~~--------------------~~~~~~rLv~~   68 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERF-VAGQPPESCSTPTGLGKTSIIAAWLLAV-EI--------------------GAKVPRRLVYV   68 (844)
T ss_pred             hCCC-CCHHHHHHHHHH-HcCCCcceEecCCCCcccHHHHHhhccc-cc--------------------cccccceEEEe
Confidence            6998 999999999999 8898 68889999999999777665532 11                    124577887 5


Q ss_pred             ecCHHHHHHHHHHHhhhhcCC-----------------------CceeEEEeCC-CcchHHHHHhcCCCcccccc-----
Q 042526          130 NPTRELALQVLMVASPSLKSN-----------------------SLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR-----  180 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~~~~-----------------------~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~-----  180 (284)
                      +||||||.|++++++.+++.+                       .+++++++|| +...|...+..+++|+|.|.     
T Consensus        69 vPtReLa~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~s  148 (844)
T TIGR02621        69 VNRRTVVDQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGS  148 (844)
T ss_pred             CchHHHHHHHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcC
Confidence            599999999999999999865                       3777776666 67789999999999988773     


Q ss_pred             cCC----------------ccccccccCCCCCCcccccccccchhhhcccC
Q 042526          181 KGG----------------EDEKLDSLKWNPLSQPKTTTLLPSSLALMNLT  215 (284)
Q Consensus       181 ~~~----------------~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~  215 (284)
                      ...                .+.++..+||||||  +++||..++..++...
T Consensus       149 r~L~~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l  197 (844)
T TIGR02621       149 RLLFSGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQ  197 (844)
T ss_pred             CccccccccccccccchhhhhccceEEEEehhh--hccccHHHHHHHHHhc
Confidence            111                25788999999999  7899999999998854

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.

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.81  E-value=8.1e-20  Score=189.66  Aligned_cols=147  Identities=17%  Similarity=0.183  Sum_probs=112.3

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      |++.+.+.+.+ +|..|||+|.+|||.+ +.|+|++++||||||||+||++|+++.+.....              ....
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~i-l~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~--------------~~~~   81 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLI-HEGKNVLISSPTGSGKTLAAFLAIIDELFRLGR--------------EGEL   81 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHH-HcCCCEEEECCCCCcHHHHHHHHHHHHHHhhcc--------------ccCC
Confidence            67777777665 8999999999999998 999999999999999999999999998875421              1112


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHhh-------hh----cCC-CceeEEEeCCCcchHH-HHHhcCCCccccccc------
Q 042526          121 KGHLRALIINPTRELALQVLMVASP-------SL----KSN-SLTLAMAAGSPLLTSE-HSNRRKPNKRKRTRK------  181 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~~~~~-------l~----~~~-~i~v~~~~G~~~~~q~-~~l~~~~~i~v~~~~------  181 (284)
                      ..++++|||+|||+||.|++..+..       ++    ... ++++++.+|+....+. ..+...++|++++.-      
T Consensus        82 ~~~~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll  161 (876)
T PRK13767         82 EDKVYCLYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILL  161 (876)
T ss_pred             CCCeEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHh
Confidence            3578999999999999999886653       22    223 6778888887655444 455567888776521      


Q ss_pred             -----CCccccccccCCCCCCcccccc
Q 042526          182 -----GGEDEKLDSLKWNPLSQPKTTT  203 (284)
Q Consensus       182 -----~~~~d~l~~lv~dEAd~m~~~g  203 (284)
                           ...+.++..+|+||++.+.+..
T Consensus       162 ~~~~~~~~l~~l~~VVIDE~H~l~~~~  188 (876)
T PRK13767        162 NSPKFREKLRTVKWVIVDEIHSLAENK  188 (876)
T ss_pred             cChhHHHHHhcCCEEEEechhhhccCc
Confidence                 0135688999999999988643

>PRK09401 reverse gyrase; Reviewed

Probab=99.79  E-value=1.2e-19  Score=192.00  Aligned_cols=139  Identities=18%  Similarity=0.044  Sum_probs=104.7

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|+ .||++|..+||.+ +.|+|++++||||||||+ |++|++..+..                      .++++|||+|
T Consensus        77 ~G~-~pt~iQ~~~i~~i-l~g~dv~i~ApTGsGKT~-f~l~~~~~l~~----------------------~g~~alIL~P  131 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRL-LLGESFAIIAPTGVGKTT-FGLVMSLYLAK----------------------KGKKSYIIFP  131 (1176)
T ss_pred             cCC-CCcHHHHHHHHHH-HCCCcEEEEcCCCCCHHH-HHHHHHHHHHh----------------------cCCeEEEEec
Confidence            578 7999999999998 999999999999999995 77776654422                      2678999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCc------chHHHHHhc-CCCcccccc-------cCCccccccccCCCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPL------LTSEHSNRR-KPNKRKRTR-------KGGEDEKLDSLKWNPLS  197 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~------~~q~~~l~~-~~~i~v~~~-------~~~~~d~l~~lv~dEAd  197 (284)
                      ||+||.|++..++.++...++.+.+++|+..      ..+...+.+ .++|++.+.       ......++..+|+||||
T Consensus       132 TreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~l~~~~~~~lVvDEaD  211 (1176)
T PRK09401        132 TRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKFDFVFVDDVD  211 (1176)
T ss_pred             cHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccCEEEEEChH
Confidence            9999999999999999988888766655432      222334444 478877662       11234568889999999


Q ss_pred             cccc-----------ccccc-chhhhcccC
Q 042526          198 QPKT-----------TTLLP-SSLALMNLT  215 (284)
Q Consensus       198 ~m~~-----------~gflp-~~~~~~~~~  215 (284)
                      .|++           +||.. ++..++..+
T Consensus       212 ~~L~~~k~id~~l~~lGF~~~~i~~i~~~i  241 (1176)
T PRK09401        212 AVLKSSKNIDKLLYLLGFSEEDIEKAMELI  241 (1176)
T ss_pred             HhhhcccchhhHHHhCCCCHHHHHHHHHhc
Confidence            9986           89974 444444443

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=4.6e-19  Score=180.33  Aligned_cols=139  Identities=13%  Similarity=0.050  Sum_probs=111.7

Q ss_pred             ccCCCCHHHHHHHH-----HcCCCCC---cHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHH
Q 042526           37 NELRLHPLLMKSIY-----KLGFKES---TSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKML  108 (284)
Q Consensus        37 ~~l~L~~~Ll~~L~-----~~g~~~p---T~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~  108 (284)
                      +.|++.+++...+.     .+||..|   ||+|.++||.+ ..++|+|++++||||||+||++|++..++..        
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i-~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g--------  135 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAI-AMHKGFITEMQTGEGKTLTAVMPLYLNALTG--------  135 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhh-hcCCCeEEEeCCCCChHHHHHHHHHHHHhhc--------
Confidence            45678999998887     6899999   99999999999 8899999999999999999999999877542        


Q ss_pred             hhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccccCC----
Q 042526          109 EEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTRKGG----  183 (284)
Q Consensus       109 ~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~~~~----  183 (284)
                                     ..++||+|||+||.|+++++..+.+++++++++++|+ +...|...+  +++|++.|..-.    
T Consensus       136 ---------------~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDy  198 (970)
T PRK12899        136 ---------------KPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDY  198 (970)
T ss_pred             ---------------CCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHH
Confidence                           1389999999999999999999999999999887776 444444333  588876653211    


Q ss_pred             ------ccc-------cccccCCCCCCcccc
Q 042526          184 ------EDE-------KLDSLKWNPLSQPKT  201 (284)
Q Consensus       184 ------~~d-------~l~~lv~dEAd~m~~  201 (284)
                            .++       .+.++++||||.|+.
T Consensus       199 Lrd~~~~~~~~~~vqr~~~~~IIDEADsmLi  229 (970)
T PRK12899        199 LRDNSIATRKEEQVGRGFYFAIIDEVDSILI  229 (970)
T ss_pred             hhCCCCCcCHHHhhcccccEEEEechhhhhh
Confidence                  111       235789999999764

>PRK01172 ski2-like helicase; Provisional

Probab=99.77  E-value=1.8e-18  Score=175.41  Aligned_cols=144  Identities=15%  Similarity=0.083  Sum_probs=116.9

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      .|++|+|++.+++.+...+|. ++|+|.+|++.+ ..|+|++++||||||||++|.++++..+..               
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l-~~~~nvlv~apTGSGKTl~a~lail~~l~~---------------   64 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQL-RKGENVIVSVPTAAGKTLIAYSAIYETFLA---------------   64 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHH-hcCCcEEEECCCCchHHHHHHHHHHHHHHh---------------
Confidence            688999999999999999998 999999999998 999999999999999999999999876643               


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCcc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGED  185 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~  185 (284)
                              +.++|||+|||+||.|+++.+.++. ..++.+...+|+....  ....+.+++++.+.         ....+
T Consensus        65 --------~~k~v~i~P~raLa~q~~~~~~~l~-~~g~~v~~~~G~~~~~--~~~~~~~dIiv~Tpek~~~l~~~~~~~l  133 (674)
T PRK01172         65 --------GLKSIYIVPLRSLAMEKYEELSRLR-SLGMRVKISIGDYDDP--PDFIKRYDVVILTSEKADSLIHHDPYII  133 (674)
T ss_pred             --------CCcEEEEechHHHHHHHHHHHHHHh-hcCCeEEEEeCCCCCC--hhhhccCCEEEECHHHHHHHHhCChhHH
Confidence                    3479999999999999999999875 3678888887765432  12335567766552         11236


Q ss_pred             ccccccCCCCCCccccccccc
Q 042526          186 EKLDSLKWNPLSQPKTTTLLP  206 (284)
Q Consensus       186 d~l~~lv~dEAd~m~~~gflp  206 (284)
                      .++..+|+||++++.+.++-+
T Consensus       134 ~~v~lvViDEaH~l~d~~rg~  154 (674)
T PRK01172        134 NDVGLIVADEIHIIGDEDRGP  154 (674)
T ss_pred             hhcCEEEEecchhccCCCccH
Confidence            778899999999987655443

>TIGR01054 rgy reverse gyrase

Probab=99.76  E-value=1.3e-18  Score=184.18  Aligned_cols=140  Identities=19%  Similarity=0.037  Sum_probs=104.5

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCe
Q 042526           45 LMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHL  124 (284)
Q Consensus        45 Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (284)
                      +.+.+.+.....||++|+.+||.+ +.|+|++++||||||||+ |++|++..+..                      .++
T Consensus        67 f~~~f~~~~g~~p~~iQ~~~i~~i-l~G~d~vi~ApTGsGKT~-f~l~~~~~l~~----------------------~g~  122 (1171)
T TIGR01054        67 FEEFFKKAVGSEPWSIQKMWAKRV-LRGDSFAIIAPTGVGKTT-FGLAMSLFLAK----------------------KGK  122 (1171)
T ss_pred             HHHHHHHhcCCCCcHHHHHHHHHH-hCCCeEEEECCCCCCHHH-HHHHHHHHHHh----------------------cCC
Confidence            444455544457999999999998 999999999999999996 77888765432                      257


Q ss_pred             EEEEEecCHHHHHHHHHHHhhhhcCCCceeE---EEeCCCcc-hHH---HHHhc-CCCcccccccC-----Cccc-cccc
Q 042526          125 RALIINPTRELALQVLMVASPSLKSNSLTLA---MAAGSPLL-TSE---HSNRR-KPNKRKRTRKG-----GEDE-KLDS  190 (284)
Q Consensus       125 ~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~---~~~G~~~~-~q~---~~l~~-~~~i~v~~~~~-----~~~d-~l~~  190 (284)
                      ++|||+|||+||.|++..++.++...++.+.   +++|+... .+.   ..+.. .++|++.+.-.     ..+. ++..
T Consensus       123 ~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~~~~~~  202 (1171)
T TIGR01054       123 RCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDF  202 (1171)
T ss_pred             eEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhcCCCCE
Confidence            8999999999999999999999988776543   45566433 332   23344 47887766211     1122 6779


Q ss_pred             cCCCCCCcccc-----------cccccch
Q 042526          191 LKWNPLSQPKT-----------TTLLPSS  208 (284)
Q Consensus       191 lv~dEAd~m~~-----------~gflp~~  208 (284)
                      +++||||+|++           +||.++.
T Consensus       203 iVvDEaD~~L~~~k~vd~il~llGF~~e~  231 (1171)
T TIGR01054       203 IFVDDVDALLKASKNVDKLLKLLGFSEEL  231 (1171)
T ss_pred             EEEeChHhhhhccccHHHHHHHcCCCHHH
Confidence            99999999998           8998864

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.

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

Probab=99.76  E-value=2.3e-18  Score=174.51  Aligned_cols=141  Identities=21%  Similarity=0.233  Sum_probs=118.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      |++.+.+.+... |+.|||+|.+|||.| .+|+|+++.||||||||+|.+||+++.+....               ....
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i-~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~---------------~~~~   70 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEI-HSGENVLIIAPTGSGKTEAAFLPVINELLSLG---------------KGKL   70 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHH-hCCCceEEEcCCCCChHHHHHHHHHHHHHhcc---------------CCCC
Confidence            899999999988 999999999999999 89999999999999999999999999998851               1234


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhc-CCCccccccc-----------CCccccc
Q 042526          121 KGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRR-KPNKRKRTRK-----------GGEDEKL  188 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~-~~~i~v~~~~-----------~~~~d~l  188 (284)
                      ..++.+|+|+|.|+|+..+...+..++..+|+.+.+-.|+....+.+...+ .|||+++|.-           ...+..|
T Consensus        71 ~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~v  150 (814)
T COG1201          71 EDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDV  150 (814)
T ss_pred             CCceEEEEeCcHHHHHHHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCC
Confidence            467999999999999999999999999999999999899866666555555 4777766521           1235678


Q ss_pred             cccCCCCCCc
Q 042526          189 DSLKWNPLSQ  198 (284)
Q Consensus       189 ~~lv~dEAd~  198 (284)
                      .+++.||.-.
T Consensus       151 r~VIVDEiHe  160 (814)
T COG1201         151 RYVIVDEIHA  160 (814)
T ss_pred             cEEEeehhhh
Confidence            8888888444

>PRK14701 reverse gyrase; Provisional

Probab=99.75  E-value=6e-18  Score=182.97  Aligned_cols=142  Identities=17%  Similarity=0.007  Sum_probs=107.0

Q ss_pred             HHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCC
Q 042526           44 LLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKG  122 (284)
Q Consensus        44 ~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~  122 (284)
                      ++.+.+++ +|| .||++|+.+||.+ +.|+|++++||||||||++|+++++... .                      .
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~i-l~G~d~li~APTGsGKTl~~~~~al~~~-~----------------------~  121 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRI-LRGKSFSIVAPTGMGKSTFGAFIALFLA-L----------------------K  121 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHH-HcCCCEEEEEcCCCCHHHHHHHHHHHHH-h----------------------c
Confidence            44455665 899 5999999999999 9999999999999999996665554321 1                      2


Q ss_pred             CeEEEEEecCHHHHHHHHHHHhhhhcCCC--ceeEEEeCCCcchHH----HHHhcC-CCcccccccCC--cc-----ccc
Q 042526          123 HLRALIINPTRELALQVLMVASPSLKSNS--LTLAMAAGSPLLTSE----HSNRRK-PNKRKRTRKGG--ED-----EKL  188 (284)
Q Consensus       123 ~~~aLIL~PTReLa~Qi~~~~~~l~~~~~--i~v~~~~G~~~~~q~----~~l~~~-~~i~v~~~~~~--~~-----d~l  188 (284)
                      +.++|||+|||+||.|++..++.++..++  +.+++++|+....+.    ..+..+ ++|++.+.-..  .+     .++
T Consensus       122 g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l~~~~i  201 (1638)
T PRK14701        122 GKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEMKHLKF  201 (1638)
T ss_pred             CCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHHhhCCC
Confidence            56899999999999999999999988764  566677777544332    234444 78877663211  11     357


Q ss_pred             cccCCCCCCcccc-----------cccccchhh
Q 042526          189 DSLKWNPLSQPKT-----------TTLLPSSLA  210 (284)
Q Consensus       189 ~~lv~dEAd~m~~-----------~gflp~~~~  210 (284)
                      ..+++||||.|+.           +||.++.+.
T Consensus       202 ~~iVVDEAD~ml~~~knid~~L~llGF~~e~~~  234 (1638)
T PRK14701        202 DFIFVDDVDAFLKASKNIDRSLQLLGFYEEIIE  234 (1638)
T ss_pred             CEEEEECceeccccccccchhhhcCCChHHHHH
Confidence            7899999999986           799999874

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

Probab=99.73  E-value=6.5e-18  Score=141.02  Aligned_cols=135  Identities=25%  Similarity=0.264  Sum_probs=106.6

Q ss_pred             cHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHH
Q 042526           58 TSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELAL  137 (284)
Q Consensus        58 T~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~  137 (284)
                      ||+|.++|+.+ .+|+++++.||||||||++|++|+++.+...                     ...++||++||++|+.
T Consensus         1 t~~Q~~~~~~i-~~~~~~li~aptGsGKT~~~~~~~l~~~~~~---------------------~~~~~lii~P~~~l~~   58 (169)
T PF00270_consen    1 TPLQQEAIEAI-ISGKNVLISAPTGSGKTLAYILPALNRLQEG---------------------KDARVLIIVPTRALAE   58 (169)
T ss_dssp             -HHHHHHHHHH-HTTSEEEEECSTTSSHHHHHHHHHHHHHHTT---------------------SSSEEEEEESSHHHHH
T ss_pred             CHHHHHHHHHH-HcCCCEEEECCCCCccHHHHHHHHHhhhccC---------------------CCceEEEEeecccccc
Confidence            79999999999 7999999999999999999999999877663                     1348999999999999


Q ss_pred             HHHHHHhhhhcCCCceeEEEeCCCcch--HHHHHhcCCCcccccc----------cCCccccccccCCCCCCcccccccc
Q 042526          138 QVLMVASPSLKSNSLTLAMAAGSPLLT--SEHSNRRKPNKRKRTR----------KGGEDEKLDSLKWNPLSQPKTTTLL  205 (284)
Q Consensus       138 Qi~~~~~~l~~~~~i~v~~~~G~~~~~--q~~~l~~~~~i~v~~~----------~~~~~d~l~~lv~dEAd~m~~~gfl  205 (284)
                      |+...+..+....++.+..++|+....  +...+..++++++.+.          .. .+.++..+++||++.+.+.+|.
T Consensus        59 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~iViDE~h~l~~~~~~  137 (169)
T PF00270_consen   59 QQFERLRKFFSNTNVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKI-NISRLSLIVIDEAHHLSDETFR  137 (169)
T ss_dssp             HHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSS-TGTTESEEEEETHHHHHHTTHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccCcchhhcccccccc-ccccceeeccCcccccccccHH
Confidence            999999999988888888888876533  3344545688866551          12 3455889999999998887666


Q ss_pred             cchhhhcccC
Q 042526          206 PSSLALMNLT  215 (284)
Q Consensus       206 p~~~~~~~~~  215 (284)
                      .....++...
T Consensus       138 ~~~~~i~~~~  147 (169)
T PF00270_consen  138 AMLKSILRRL  147 (169)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHHHHHHHh
Confidence            6555555543

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 ....

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.72  E-value=4.8e-17  Score=168.78  Aligned_cols=135  Identities=15%  Similarity=0.058  Sum_probs=106.6

Q ss_pred             CCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCC------CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           40 RLHPLLMKSIYK-LGFKESTSILKARIPALAHQR------KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        40 ~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G------~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+..++..+.+ ++|+ |||+|..||+.+ ..+      +|++++|+||||||++|++|++..+..             
T Consensus       435 ~~~~~~~~~~~~~~~f~-~T~~Q~~aI~~I-~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~-------------  499 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPFE-ETPDQLKAIEEI-KADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD-------------  499 (926)
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHH-HhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh-------------
Confidence            345666666655 7995 999999999999 554      799999999999999999999876532             


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH----HHHHhc-CCCcccccc----cCC
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTS----EHSNRR-KPNKRKRTR----KGG  183 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q----~~~l~~-~~~i~v~~~----~~~  183 (284)
                                +.+++||+||++||.|++..++.+....++++.++.|+....+    ...+.. .+++++.|.    ...
T Consensus       500 ----------g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v  569 (926)
T TIGR00580       500 ----------GKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDV  569 (926)
T ss_pred             ----------CCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCC
Confidence                      4689999999999999999999988888899888887644322    223334 478877663    223


Q ss_pred             ccccccccCCCCCCcc
Q 042526          184 EDEKLDSLKWNPLSQP  199 (284)
Q Consensus       184 ~~d~l~~lv~dEAd~m  199 (284)
                      .+.+|..+|+||++++
T Consensus       570 ~f~~L~llVIDEahrf  585 (926)
T TIGR00580       570 KFKDLGLLIIDEEQRF  585 (926)
T ss_pred             CcccCCEEEeeccccc
Confidence            5778999999999983

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.71  E-value=3.6e-17  Score=166.04  Aligned_cols=131  Identities=20%  Similarity=0.134  Sum_probs=105.0

Q ss_pred             HHHHHHH-HHcCCCCCcHHHHHHHHHHHcCC------CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 042526           43 PLLMKSI-YKLGFKESTSILKARIPALAHQR------KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEA  115 (284)
Q Consensus        43 ~~Ll~~L-~~~g~~~pT~iQ~~aip~il~~G------~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~  115 (284)
                      ..+++.+ ..++|+ ||++|..||+.| ..+      ++++++|+||||||++|++|++..+.                 
T Consensus       248 ~~~~~~~~~~l~f~-lt~~Q~~ai~~I-~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~-----------------  308 (681)
T PRK10917        248 GELLKKFLASLPFE-LTGAQKRVVAEI-LADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE-----------------  308 (681)
T ss_pred             hHHHHHHHHhCCCC-CCHHHHHHHHHH-HHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH-----------------
Confidence            4455544 557885 999999999999 665      48999999999999999999987652                 


Q ss_pred             hhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH----HHHHhcC-CCccccccc----CCccc
Q 042526          116 EKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTS----EHSNRRK-PNKRKRTRK----GGEDE  186 (284)
Q Consensus       116 ~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q----~~~l~~~-~~i~v~~~~----~~~~d  186 (284)
                            .+.+++||+||++||.|++..++.+...+++++++++|+....+    ...+..+ +++++.|.-    ...+.
T Consensus       309 ------~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~  382 (681)
T PRK10917        309 ------AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFH  382 (681)
T ss_pred             ------cCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhc
Confidence                  26789999999999999999999999989999999999865432    3344443 777776521    12477


Q ss_pred             cccccCCCCCCc
Q 042526          187 KLDSLKWNPLSQ  198 (284)
Q Consensus       187 ~l~~lv~dEAd~  198 (284)
                      ++..+|+||+++
T Consensus       383 ~l~lvVIDE~Hr  394 (681)
T PRK10917        383 NLGLVIIDEQHR  394 (681)
T ss_pred             ccceEEEechhh
Confidence            899999999997

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.71  E-value=3e-17  Score=159.99  Aligned_cols=127  Identities=17%  Similarity=0.138  Sum_probs=95.9

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      .+||+.|+|+|.+|||.+ +.|+|+++++|||||||++|++|++..                          ...+|||+
T Consensus         6 ~~g~~~~r~~Q~~ai~~~-l~g~dvlv~apTGsGKTl~y~lp~l~~--------------------------~~~~lVi~   58 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAV-LLGRDCFVVMPTGGGKSLCYQLPALCS--------------------------DGITLVIS   58 (470)
T ss_pred             hcCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCCcHhHHHHHHHHHc--------------------------CCcEEEEe
Confidence            379999999999999999 899999999999999999999998741                          23589999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH----Hhc-CCCccccccc-----------CCccccccccCCC
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS----NRR-KPNKRKRTRK-----------GGEDEKLDSLKWN  194 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~----l~~-~~~i~v~~~~-----------~~~~d~l~~lv~d  194 (284)
                      |||+|+.|+...+..+    ++.++.+.|+....+...    +.. .+++++.+.-           +....++..+|+|
T Consensus        59 P~~~L~~dq~~~l~~~----gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViD  134 (470)
T TIGR00614        59 PLISLMEDQVLQLKAS----GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVD  134 (470)
T ss_pred             cHHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEe
Confidence            9999999988887653    677777777765543222    222 2455443310           0134677889999


Q ss_pred             CCCcccccc--cccch
Q 042526          195 PLSQPKTTT--LLPSS  208 (284)
Q Consensus       195 EAd~m~~~g--flp~~  208 (284)
                      ||+.+.+.|  |-++.
T Consensus       135 EaH~i~~~g~~fr~~~  150 (470)
T TIGR00614       135 EAHCISQWGHDFRPDY  150 (470)
T ss_pred             CCcccCccccccHHHH
Confidence            999998877  55543

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

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.69  E-value=9.8e-17  Score=161.59  Aligned_cols=131  Identities=20%  Similarity=0.120  Sum_probs=103.9

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHHcCC------CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 042526           43 PLLMKSIYKLGFKESTSILKARIPALAHQR------KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAE  116 (284)
Q Consensus        43 ~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G------~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~  116 (284)
                      ..+...+..++| .||++|..||+.| +.+      .+.+++|+||||||++|++|++..+..                 
T Consensus       223 ~~~~~~~~~lpf-~lt~~Q~~ai~~I-~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~-----------------  283 (630)
T TIGR00643       223 ELLTKFLASLPF-KLTRAQKRVVKEI-LQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA-----------------  283 (630)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHH-HHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc-----------------
Confidence            334556678999 5999999999999 554      368999999999999999999876532                 


Q ss_pred             hcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH----HHHHhc-CCCcccccccC----Ccccc
Q 042526          117 KYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTS----EHSNRR-KPNKRKRTRKG----GEDEK  187 (284)
Q Consensus       117 ~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q----~~~l~~-~~~i~v~~~~~----~~~d~  187 (284)
                            +.+++||+||++||.|++..++.+...+++++++++|+.....    ...+.. .+++++.+...    ..+.+
T Consensus       284 ------g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~  357 (630)
T TIGR00643       284 ------GYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKR  357 (630)
T ss_pred             ------CCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccc
Confidence                  5689999999999999999999999988999999988854433    223333 36776655221    34678


Q ss_pred             ccccCCCCCCc
Q 042526          188 LDSLKWNPLSQ  198 (284)
Q Consensus       188 l~~lv~dEAd~  198 (284)
                      +..+|+||+++
T Consensus       358 l~lvVIDEaH~  368 (630)
T TIGR00643       358 LALVIIDEQHR  368 (630)
T ss_pred             cceEEEechhh
Confidence            99999999997

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

Probab=99.68  E-value=8.4e-17  Score=165.92  Aligned_cols=136  Identities=22%  Similarity=0.214  Sum_probs=113.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      ....+..+|.+.|+..++++|.+|+..+ .+|+||||+++||||||.||++||++.+++..                   
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~-~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~-------------------  114 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLI-REGRNVVVTTGTGSGKTESFLLPILDHLLRDP-------------------  114 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHH-HCCCCEEEECCCCCchhHHHHHHHHHHHhhCc-------------------
Confidence            4556788899999999999999999999 99999999999999999999999999998863                   


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHhhhhcCCC--ceeEEEeCCCcchHH-HHHhcCCCcccccccC-------------Cc
Q 042526          121 KGHLRALIINPTRELALQVLMVASPSLKSNS--LTLAMAAGSPLLTSE-HSNRRKPNKRKRTRKG-------------GE  184 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~--i~v~~~~G~~~~~q~-~~l~~~~~i~v~~~~~-------------~~  184 (284)
                        .-+||+|.||++||+...+.++++...++  +.+..+.|....... ...+..|+|+++...+             ..
T Consensus       115 --~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~  192 (851)
T COG1205         115 --SARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWL  192 (851)
T ss_pred             --CccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHH
Confidence              22899999999999999999999998887  777888888766666 4455567776654222             24


Q ss_pred             cccccccCCCCCCc
Q 042526          185 DEKLDSLKWNPLSQ  198 (284)
Q Consensus       185 ~d~l~~lv~dEAd~  198 (284)
                      +.+|.++|+||+=-
T Consensus       193 ~~~Lk~lVvDElHt  206 (851)
T COG1205         193 LRNLKYLVVDELHT  206 (851)
T ss_pred             HhcCcEEEEeccee
Confidence            66799999999544

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

Probab=99.68  E-value=2.3e-16  Score=163.59  Aligned_cols=144  Identities=17%  Similarity=0.094  Sum_probs=103.0

Q ss_pred             Cccc--CCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           35 AWNE--LRLHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        35 ~F~~--l~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      .|..  ++....|...+.. +||..++|+|.++|+++ +.|+|+++++|||+|||+||+||+|..               
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~ai-L~GrDVLVimPTGSGKSLcYQLPAL~~---------------  499 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINAT-MSGYDVFVLMPTGGGKSLTYQLPALIC---------------  499 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCccHHHHHHHHHHHc---------------
Confidence            4775  4455667666665 89999999999999999 999999999999999999999999841               


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHh------cCCCcccccccC--
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNR------RKPNKRKRTRKG--  182 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~------~~~~i~v~~~~~--  182 (284)
                                 ...+|||+|+++|+.+....+..    .++.++.+.|+. ...|...++      ..+++++.+.-.  
T Consensus       500 -----------~GiTLVISPLiSLmqDQV~~L~~----~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~  564 (1195)
T PLN03137        500 -----------PGITLVISPLVSLIQDQIMNLLQ----ANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVA  564 (1195)
T ss_pred             -----------CCcEEEEeCHHHHHHHHHHHHHh----CCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhh
Confidence                       23599999999999843333322    477777777664 444444333      235554444210  


Q ss_pred             --C----------ccccccccCCCCCCcccccc--cccchh
Q 042526          183 --G----------EDEKLDSLKWNPLSQPKTTT--LLPSSL  209 (284)
Q Consensus       183 --~----------~~d~l~~lv~dEAd~m~~~g--flp~~~  209 (284)
                        +          ...+|..+|+|||+.+.+.|  |-|+..
T Consensus       565 ~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRpdYr  605 (1195)
T PLN03137        565 KSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQ  605 (1195)
T ss_pred             cchHHHHHHHhhhhccccceeccCcchhhhhcccchHHHHH
Confidence              0          12346778999999999988  666553

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.65  E-value=5.7e-16  Score=163.93  Aligned_cols=132  Identities=17%  Similarity=0.021  Sum_probs=102.8

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHHcCC------CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 042526           43 PLLMKSIYKLGFKESTSILKARIPALAHQR------KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAE  116 (284)
Q Consensus        43 ~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G------~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~  116 (284)
                      ....+....++| .||++|..|||.+ +.+      +|++++|+||||||.+|+.+++..+.                  
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~i-l~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~------------------  647 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAV-LSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE------------------  647 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHH-HHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH------------------
Confidence            344455677899 5999999999999 666      89999999999999999988765431                  


Q ss_pred             hcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHh----cCCCcccccccC----Ccccc
Q 042526          117 KYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNR----RKPNKRKRTRKG----GEDEK  187 (284)
Q Consensus       117 ~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~----~~~~i~v~~~~~----~~~d~  187 (284)
                           .+.+++||+||++||.|++..++......++++.++.|+ +...+...+.    ..++|++.|..+    ..+.+
T Consensus       648 -----~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~  722 (1147)
T PRK10689        648 -----NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKD  722 (1147)
T ss_pred             -----cCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhh
Confidence                 267899999999999999999998777778888777665 4434433332    357887777422    23578


Q ss_pred             ccccCCCCCCcc
Q 042526          188 LDSLKWNPLSQP  199 (284)
Q Consensus       188 l~~lv~dEAd~m  199 (284)
                      |..+|+||++++
T Consensus       723 L~lLVIDEahrf  734 (1147)
T PRK10689        723 LGLLIVDEEHRF  734 (1147)
T ss_pred             CCEEEEechhhc
Confidence            899999999996

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.63  E-value=9.4e-16  Score=153.91  Aligned_cols=138  Identities=14%  Similarity=0.098  Sum_probs=99.1

Q ss_pred             CCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhc
Q 042526           40 RLHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKY  118 (284)
Q Consensus        40 ~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~  118 (284)
                      .++......|++ +||..|+|+|.++|+.+ +.|+|+++.+|||||||++|++|++..                      
T Consensus         8 ~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~i-l~g~dvlv~apTGsGKTl~y~lpal~~----------------------   64 (607)
T PRK11057          8 NLESLAKQVLQETFGYQQFRPGQQEIIDAV-LSGRDCLVVMPTGGGKSLCYQIPALVL----------------------   64 (607)
T ss_pred             CchhHHHHHHHHHcCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCchHHHHHHHHHHHc----------------------
Confidence            344444555555 79999999999999999 899999999999999999999999742                      


Q ss_pred             CCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH----Hhc-CCCccccccc---------CCc
Q 042526          119 APKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS----NRR-KPNKRKRTRK---------GGE  184 (284)
Q Consensus       119 ~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~----l~~-~~~i~v~~~~---------~~~  184 (284)
                          ...+|||+||++|+.|+...+..+    ++.+.++.++........    +.. ..++++.+.-         ...
T Consensus        65 ----~g~tlVisPl~sL~~dqv~~l~~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~  136 (607)
T PRK11057         65 ----DGLTLVVSPLISLMKDQVDQLLAN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLA  136 (607)
T ss_pred             ----CCCEEEEecHHHHHHHHHHHHHHc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHh
Confidence                125899999999999998888754    666766666654443222    222 2333332211         011


Q ss_pred             cccccccCCCCCCcccccc--cccch
Q 042526          185 DEKLDSLKWNPLSQPKTTT--LLPSS  208 (284)
Q Consensus       185 ~d~l~~lv~dEAd~m~~~g--flp~~  208 (284)
                      ..++..+|+|||+.+.+.|  |-|+.
T Consensus       137 ~~~l~~iVIDEaH~i~~~G~~fr~~y  162 (607)
T PRK11057        137 HWNPALLAVDEAHCISQWGHDFRPEY  162 (607)
T ss_pred             hCCCCEEEEeCccccccccCcccHHH
Confidence            2357789999999998877  65554

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=99.62  E-value=2.9e-16  Score=147.15  Aligned_cols=68  Identities=37%  Similarity=0.436  Sum_probs=64.2

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHH
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEER  101 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~  101 (284)
                      |..|+++|+-|+|-.+..++.|+-||.+|+++||.| +.|-||+..|.||||||-||+||+|+.+.+..
T Consensus         1 m~af~e~gv~pel~~a~~e~dw~lptdvqaeaipli-lgggdvlmaaetgsgktgaf~lpilqiv~etl   68 (725)
T KOG0349|consen    1 MTAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLI-LGGGDVLMAAETGSGKTGAFCLPILQIVWETL   68 (725)
T ss_pred             CcchHhhCcchHhhhhhhhhccccccccccccccEE-ecCCcEEEEeccCCCCccceehhhHHHHHHHH
Confidence            467999999999999999999999999999999999 99999999999999999999999999987653

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.62  E-value=1.8e-15  Score=151.05  Aligned_cols=102  Identities=22%  Similarity=0.153  Sum_probs=89.2

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. .|||||..++|.+ +.|+  |+.++||+|||++|++|++....                       .+++++||+|
T Consensus       100 lg~-~p~~VQ~~~~~~l-l~G~--Iae~~TGeGKTla~~lp~~~~al-----------------------~G~~v~VvTp  152 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLAL-LSGR--LAEMQTGEGKTLTATLPAGTAAL-----------------------AGLPVHVITV  152 (656)
T ss_pred             hCC-CCChHHHHHHHHH-hCCC--eeeeeCCCCcHHHHHHHHHHHhh-----------------------cCCeEEEEcC
Confidence            566 5999999999999 8998  99999999999999999997543                       2678999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRK  181 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~  181 (284)
                      |++||.|++..+..|...++++|++++|+.. .+...+..+++|++.+..
T Consensus       153 treLA~qdae~~~~l~~~lGlsv~~i~gg~~-~~~r~~~y~~dIvygT~~  201 (656)
T PRK12898        153 NDYLAERDAELMRPLYEALGLTVGCVVEDQS-PDERRAAYGADITYCTNK  201 (656)
T ss_pred             cHHHHHHHHHHHHHHHhhcCCEEEEEeCCCC-HHHHHHHcCCCEEEECCC
Confidence            9999999999999999999999999998864 466777788899777643

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.62  E-value=2.8e-15  Score=152.52  Aligned_cols=130  Identities=17%  Similarity=0.084  Sum_probs=103.0

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|+ +|+++|..+++.+ +.|+  |+.++||+|||++|++|++...+.                       +.+++|++|
T Consensus        75 ~g~-~p~~vQl~~~~~l-~~G~--Iaem~TGeGKTL~a~lp~~l~al~-----------------------G~~v~VvTp  127 (790)
T PRK09200         75 LGM-RPYDVQLIGALVL-HEGN--IAEMQTGEGKTLTATMPLYLNALE-----------------------GKGVHLITV  127 (790)
T ss_pred             hCC-CCchHHHHhHHHH-cCCc--eeeecCCCcchHHHHHHHHHHHHc-----------------------CCCeEEEeC
Confidence            677 7999999999988 8887  999999999999999999854433                       568999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccCC----------------ccccccccCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGG----------------EDEKLDSLKWNP  195 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~~----------------~~d~l~~lv~dE  195 (284)
                      |++||.|.+..+..+...+|++|++++|+....+.......++|++.+..-.                -+..+.++++||
T Consensus       128 t~~LA~qd~e~~~~l~~~lGl~v~~i~g~~~~~~~r~~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDE  207 (790)
T PRK09200        128 NDYLAKRDAEEMGQVYEFLGLTVGLNFSDIDDASEKKAIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDE  207 (790)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCcHHHHHHhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEec
Confidence            9999999999999999999999999999876344445556788877652111                224567799999


Q ss_pred             CCccc-ccccccch
Q 042526          196 LSQPK-TTTLLPSS  208 (284)
Q Consensus       196 Ad~m~-~~gflp~~  208 (284)
                      ||.|+ |-.--|-+
T Consensus       208 aDsiLiDea~tpli  221 (790)
T PRK09200        208 IDSILLDEAQTPLI  221 (790)
T ss_pred             cccceeccCCCcee
Confidence            99954 33354533

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.59  E-value=4.2e-15  Score=148.77  Aligned_cols=131  Identities=11%  Similarity=0.089  Sum_probs=96.1

Q ss_pred             HHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeE
Q 042526           47 KSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLR  125 (284)
Q Consensus        47 ~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (284)
                      +.|++ +||..|+|+|.++|+.+ +.|+|+++++|||+|||++|++|++..                          .-.
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~i-l~g~dvlv~~PTG~GKTl~y~lpal~~--------------------------~g~   55 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHV-LDGRDVLVVMPTGGGKSLCYQVPALLL--------------------------KGL   55 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCccHhHHHHHHHHHc--------------------------CCc
Confidence            34554 89999999999999999 899999999999999999999998731                          124


Q ss_pred             EEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH----Hhc-CCCccccccc---------CCcccccccc
Q 042526          126 ALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS----NRR-KPNKRKRTRK---------GGEDEKLDSL  191 (284)
Q Consensus       126 aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~----l~~-~~~i~v~~~~---------~~~~d~l~~l  191 (284)
                      +|||+|+++|+.|....++.+    ++.+..+.|+....+...    +.. ..++++.+.-         .....++..+
T Consensus        56 ~lVisPl~sL~~dq~~~l~~~----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~i  131 (591)
T TIGR01389        56 TVVISPLISLMKDQVDQLRAA----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALV  131 (591)
T ss_pred             EEEEcCCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEE
Confidence            899999999999998888764    667777777654443222    222 3444433211         1123467889


Q ss_pred             CCCCCCcccccc--cccch
Q 042526          192 KWNPLSQPKTTT--LLPSS  208 (284)
Q Consensus       192 v~dEAd~m~~~g--flp~~  208 (284)
                      |+|||+.+.+.|  |-|..
T Consensus       132 ViDEaH~i~~~g~~frp~y  150 (591)
T TIGR01389       132 AVDEAHCVSQWGHDFRPEY  150 (591)
T ss_pred             EEeCCcccccccCccHHHH
Confidence            999999988866  55544

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.57  E-value=8.6e-15  Score=147.62  Aligned_cols=128  Identities=13%  Similarity=0.006  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHcCCCcEEEEccCCCCchHH---------hHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           59 SILKARIPALAHQRKDVIGAAETESGKTRA---------FGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        59 ~iQ~~aip~il~~G~dviv~A~TGSGKTla---------fllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      .+|.+++|.+ +.|+|+|++|+||||||.+         |++|.+..+....                 ......+++|+
T Consensus       167 ~iQ~qil~~i-~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~-----------------~~~~~~~ilvt  228 (675)
T PHA02653        167 DVQLKIFEAW-ISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID-----------------PNFIERPIVLS  228 (675)
T ss_pred             HHHHHHHHHH-HhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc-----------------cccCCcEEEEE
Confidence            4899999999 9999999999999999987         6667766554311                 11235689999


Q ss_pred             ecCHHHHHHHHHHHhhhhcC---CCceeEEEeCCCcchHHHHHhcCCCcccccc--cCCccccccccCCCCCCccccccc
Q 042526          130 NPTRELALQVLMVASPSLKS---NSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--KGGEDEKLDSLKWNPLSQPKTTTL  204 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~~~---~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--~~~~~d~l~~lv~dEAd~m~~~gf  204 (284)
                      +||||||.|+...+.....+   .+..+.+.+|+....+.....+..++++++.  ....+.++..+|+||||++..++.
T Consensus       229 ~PrreLa~qi~~~i~~~vg~~~~~g~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L~l~~L~~v~~VVIDEaHEr~~~~D  308 (675)
T PHA02653        229 LPRVALVRLHSITLLKSLGFDEIDGSPISLKYGSIPDELINTNPKPYGLVFSTHKLTLNKLFDYGTVIIDEVHEHDQIGD  308 (675)
T ss_pred             CcHHHHHHHHHHHHHHHhCccccCCceEEEEECCcchHHhhcccCCCCEEEEeCcccccccccCCEEEccccccCccchh
Confidence            99999999999998876655   3566777777765444344444667766653  234688999999999999988884

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.55  E-value=1.8e-14  Score=145.11  Aligned_cols=122  Identities=16%  Similarity=0.082  Sum_probs=97.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|+ +|+++|..+++.+ +.|+  |+.++||+|||++|++|++...+.                       +.+++|++|
T Consensus        53 lg~-~p~~vQlig~~~l-~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----------------------G~~V~VvTp  105 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIAL-HKGK--IAEMKTGEGKTLTATLPAYLNALT-----------------------GKGVHVVTV  105 (745)
T ss_pred             hCC-CccchHHhhhhhh-cCCc--eeeecCCCccHHHHHHHHHHHHHh-----------------------CCCEEEEcC
Confidence            676 5999999999987 7776  999999999999999999644332                       335999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccC----------------CccccccccCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKG----------------GEDEKLDSLKWNP  195 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~----------------~~~d~l~~lv~dE  195 (284)
                      |++||.|.+..+..|...+|++|++++|+.... .+.....++|++.+..-                ..+..+..+++||
T Consensus       106 t~~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~-~r~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDE  184 (745)
T TIGR00963       106 NDYLAQRDAEWMGQVYRFLGLSVGLILSGMSPE-ERREAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDE  184 (745)
T ss_pred             CHHHHHHHHHHHHHHhccCCCeEEEEeCCCCHH-HHHHhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeec
Confidence            999999999999999999999999998875543 34444567887766431                1345678899999


Q ss_pred             CCcccc
Q 042526          196 LSQPKT  201 (284)
Q Consensus       196 Ad~m~~  201 (284)
                      +|.|+-
T Consensus       185 aDs~LI  190 (745)
T TIGR00963       185 VDSILI  190 (745)
T ss_pred             HHHHhH
Confidence            998665

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.53  E-value=3.2e-14  Score=143.90  Aligned_cols=131  Identities=16%  Similarity=0.108  Sum_probs=100.1

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|..+++.+ ..|  .|++++||+|||++|++|++...+.                       +..++||+|
T Consensus        67 lgl-rpydVQlig~l~l-~~G--~Iaem~TGeGKTLta~Lpa~l~aL~-----------------------g~~V~VVTp  119 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVL-HQG--NIAEMKTGEGKTLTATMPLYLNALT-----------------------GKGAMLVTT  119 (762)
T ss_pred             cCC-CccHHHHHHHHHh-cCC--ceeEecCCcchHHHHHHHHHHHhhc-----------------------CCceEEeCC
Confidence            677 7888888888876 666  6999999999999999998654432                       346999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCC----CcchHHHHHhcCCCcccccccCC----------------cccccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGS----PLLTSEHSNRRKPNKRKRTRKGG----------------EDEKLDSL  191 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~----~~~~q~~~l~~~~~i~v~~~~~~----------------~~d~l~~l  191 (284)
                      |++||.|.+..+..|...+|++|.+++++    ....+......+++|++.+..-.                .+..+.++
T Consensus       120 n~yLA~Rdae~m~~l~~~LGLsv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~  199 (762)
T TIGR03714       120 NDYLAKRDAEEMGPVYEWLGLTVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYV  199 (762)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCcEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEE
Confidence            99999999999999999999999887665    23344455557788877663221                13457789


Q ss_pred             CCCCCCcc-cccccccchh
Q 042526          192 KWNPLSQP-KTTTLLPSSL  209 (284)
Q Consensus       192 v~dEAd~m-~~~gflp~~~  209 (284)
                      |.||||.| .|-.--|.++
T Consensus       200 IVDEaDsILiDeartplii  218 (762)
T TIGR03714       200 IVDEVDSVLLDSAQTPLVI  218 (762)
T ss_pred             EEecHhhHhhccCcCCeee
Confidence            99999997 4554666554

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.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.52  E-value=3.9e-14  Score=144.66  Aligned_cols=153  Identities=20%  Similarity=0.156  Sum_probs=126.0

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcC
Q 042526           40 RLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYA  119 (284)
Q Consensus        40 ~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~  119 (284)
                      .+++.+...+...|+....+-|+.++...+..|.|++++||||||||+..++.+++.+.+.                   
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~-------------------   75 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG-------------------   75 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc-------------------
Confidence            4888999999999998888888888887767789999999999999999999999988773                   


Q ss_pred             CCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccCCccccccccCCCCCCcc
Q 042526          120 PKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGGEDEKLDSLKWNPLSQP  199 (284)
Q Consensus       120 ~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~~~~d~l~~lv~dEAd~m  199 (284)
                         +-++|+|||+|.||.+++..+.+| ..+|++|...+|+.....  ....+.+++|.     +.+++.++..+..+++
T Consensus        76 ---~~k~vYivPlkALa~Ek~~~~~~~-~~~GirV~~~TgD~~~~~--~~l~~~~ViVt-----T~EK~Dsl~R~~~~~~  144 (766)
T COG1204          76 ---GGKVVYIVPLKALAEEKYEEFSRL-EELGIRVGISTGDYDLDD--ERLARYDVIVT-----TPEKLDSLTRKRPSWI  144 (766)
T ss_pred             ---CCcEEEEeChHHHHHHHHHHhhhH-HhcCCEEEEecCCcccch--hhhccCCEEEE-----chHHhhHhhhcCcchh
Confidence               346999999999999999999955 447999999999876543  34456677777     5667777777777777


Q ss_pred             cccc-cccchhhhcccCCCCCCCc
Q 042526          200 KTTT-LLPSSLALMNLTEGKPGKK  222 (284)
Q Consensus       200 ~~~g-flp~~~~~~~~~~r~~~~~  222 (284)
                      .+.+ ++.+.+|++.+..|++--+
T Consensus       145 ~~V~lvViDEiH~l~d~~RG~~lE  168 (766)
T COG1204         145 EEVDLVVIDEIHLLGDRTRGPVLE  168 (766)
T ss_pred             hcccEEEEeeeeecCCcccCceeh
Confidence            7777 7888899988877887543

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.42  E-value=7.1e-13  Score=130.39  Aligned_cols=122  Identities=13%  Similarity=-0.053  Sum_probs=85.5

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      ...|+++|..|++.+ +.+++.+++||||||||++++. ++..+...                     ...++||||||+
T Consensus       112 ~~~~r~~Q~~av~~~-l~~~~~il~apTGsGKT~i~~~-l~~~~~~~---------------------~~~~vLilvpt~  168 (501)
T PHA02558        112 KIEPHWYQYDAVYEG-LKNNRRLLNLPTSAGKSLIQYL-LSRYYLEN---------------------YEGKVLIIVPTT  168 (501)
T ss_pred             cCCCCHHHHHHHHHH-HhcCceEEEeCCCCCHHHHHHH-HHHHHHhc---------------------CCCeEEEEECcH
Confidence            357999999999998 7888999999999999987643 22222221                     234799999999


Q ss_pred             HHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc------ccCCccccccccCCCCCCccccccc
Q 042526          134 ELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT------RKGGEDEKLDSLKWNPLSQPKTTTL  204 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~------~~~~~~d~l~~lv~dEAd~m~~~gf  204 (284)
                      +|+.|+...+..+.......+..++|+....      ..+++++.+      .....++.+..+++|||+++..-.|
T Consensus       169 eL~~Q~~~~l~~~~~~~~~~~~~i~~g~~~~------~~~~I~VaT~qsl~~~~~~~~~~~~~iIvDEaH~~~~~~~  239 (501)
T PHA02558        169 SLVTQMIDDFVDYRLFPREAMHKIYSGTAKD------TDAPIVVSTWQSAVKQPKEWFDQFGMVIVDECHLFTGKSL  239 (501)
T ss_pred             HHHHHHHHHHHHhccccccceeEEecCcccC------CCCCEEEeeHHHHhhchhhhccccCEEEEEchhcccchhH
Confidence            9999999999988754444454444443221      234554443      1112367888999999999875443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.41  E-value=6.9e-13  Score=135.57  Aligned_cols=130  Identities=17%  Similarity=0.082  Sum_probs=95.7

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|...--.+ ..|+  |+.++||+|||++|++|++..++.                       +..++||+|
T Consensus        79 lg~-~~ydvQliGg~~L-h~G~--Iaem~TGeGKTL~a~Lpa~~~al~-----------------------G~~V~VvTp  131 (896)
T PRK13104         79 LGL-RHFDVQLIGGMVL-HEGN--IAEMRTGEGKTLVATLPAYLNAIS-----------------------GRGVHIVTV  131 (896)
T ss_pred             cCC-CcchHHHhhhhhh-ccCc--cccccCCCCchHHHHHHHHHHHhc-----------------------CCCEEEEcC
Confidence            455 5888888766554 5554  889999999999999999976543                       235899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccCC-----------cc-----ccccccCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGG-----------ED-----EKLDSLKWNP  195 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~~-----------~~-----d~l~~lv~dE  195 (284)
                      |++||.|++.++..|...+|++|++++|+..... +.....++|++.|..-.           .+     ..+.++++||
T Consensus       132 n~yLA~qd~e~m~~l~~~lGLtv~~i~gg~~~~~-r~~~y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDE  210 (896)
T PRK13104        132 NDYLAKRDSQWMKPIYEFLGLTVGVIYPDMSHKE-KQEAYKADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDE  210 (896)
T ss_pred             CHHHHHHHHHHHHHHhcccCceEEEEeCCCCHHH-HHHHhCCCEEEECChhhhHHHHhcCCccchHhhhccccceEEecc
Confidence            9999999999999999999999999888754433 23334678866653211           12     3577889999


Q ss_pred             CCccc-ccccccchh
Q 042526          196 LSQPK-TTTLLPSSL  209 (284)
Q Consensus       196 Ad~m~-~~gflp~~~  209 (284)
                      ||.|+ |-.--|.++
T Consensus       211 aDsiLIDeArtPLII  225 (896)
T PRK13104        211 VDSILIDEARTPLII  225 (896)
T ss_pred             HhhhhhhccCCceee
Confidence            99954 333444444

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

Probab=99.36  E-value=1.3e-12  Score=126.35  Aligned_cols=159  Identities=18%  Similarity=0.159  Sum_probs=118.9

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      ....+|.+|+.+.+-|...||+.++|+|..|+..-++.|.|+++.++|+|||||.--++=|.+++..             
T Consensus       194 ~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~-------------  260 (830)
T COG1202         194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG-------------  260 (830)
T ss_pred             ccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhC-------------
Confidence            4578899999999999999999999999999999989999999999999999999988888877663             


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHH-----HHhcCCCcccccccCCccccc
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEH-----SNRRKPNKRKRTRKGGEDEKL  188 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~-----~l~~~~~i~v~~~~~~~~d~l  188 (284)
                               +-..|+|+|..+||+|-|..|+.-...+++++++-+|........     .--...||++.+     .+-+
T Consensus       261 ---------g~KmlfLvPLVALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGT-----YEGi  326 (830)
T COG1202         261 ---------GKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGT-----YEGI  326 (830)
T ss_pred             ---------CCeEEEEehhHHhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEee-----chhH
Confidence                     457899999999999999999987788899998888864332211     111223455542     3333


Q ss_pred             cccCCCCCCcccccc-cccchhhhcccCCCCCC
Q 042526          189 DSLKWNPLSQPKTTT-LLPSSLALMNLTEGKPG  220 (284)
Q Consensus       189 ~~lv~dEAd~m~~~g-flp~~~~~~~~~~r~~~  220 (284)
                      .++..-. ..+-|+| .+.+.+|.+++.+|++.
T Consensus       327 D~lLRtg-~~lgdiGtVVIDEiHtL~deERG~R  358 (830)
T COG1202         327 DYLLRTG-KDLGDIGTVVIDEIHTLEDEERGPR  358 (830)
T ss_pred             HHHHHcC-CcccccceEEeeeeeeccchhcccc
Confidence            3333333 3344444 45555666666666653

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.36  E-value=6.6e-12  Score=127.60  Aligned_cols=116  Identities=15%  Similarity=0.039  Sum_probs=87.6

Q ss_pred             CCcHHHHHHHHHHHcC---CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPALAHQ---RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~---G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      .+|+.|.+|+..+ ..   +++++++|+||||||.+|+.++...+..                       +.++|||+||
T Consensus       144 ~Lt~~Q~~ai~~i-~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~-----------------------g~~vLvLvPt  199 (679)
T PRK05580        144 TLNPEQAAAVEAI-RAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ-----------------------GKQALVLVPE  199 (679)
T ss_pred             CCCHHHHHHHHHH-HhccCCCcEEEECCCCChHHHHHHHHHHHHHHc-----------------------CCeEEEEeCc
Confidence            4899999999999 55   4899999999999999999877654422                       4579999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH-HHH---Hh-cCCCccccccc--CCccccccccCCCCCCc
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTS-EHS---NR-RKPNKRKRTRK--GGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q-~~~---l~-~~~~i~v~~~~--~~~~d~l~~lv~dEAd~  198 (284)
                      ++|+.|++..++..   ++..++++.|+....+ ...   +. ..+++++.++.  ..-+.++..+|+||++.
T Consensus       200 ~~L~~Q~~~~l~~~---fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~~p~~~l~liVvDEeh~  269 (679)
T PRK05580        200 IALTPQMLARFRAR---FGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDEEHD  269 (679)
T ss_pred             HHHHHHHHHHHHHH---hCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhcccccCCCEEEEECCCc
Confidence            99999999988764   3567878877744332 222   22 34677776642  23467888899999875

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.34  E-value=1.2e-12  Score=140.59  Aligned_cols=116  Identities=22%  Similarity=0.222  Sum_probs=84.7

Q ss_pred             EEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhc--------
Q 042526           77 GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK--------  148 (284)
Q Consensus        77 v~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~--------  148 (284)
                      ++||||||||+||+||+|+++......          .........++++|||+|||+|+.|+++.++....        
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~----------~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~   70 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGE----------DTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRR   70 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccc----------cccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhh
Confidence            479999999999999999998864200          00001112468999999999999999999875221        


Q ss_pred             ----CCCceeEEEeCCCcchHHHHH-hcCCCcccccc---------c-CCccccccccCCCCCCccccc
Q 042526          149 ----SNSLTLAMAAGSPLLTSEHSN-RRKPNKRKRTR---------K-GGEDEKLDSLKWNPLSQPKTT  202 (284)
Q Consensus       149 ----~~~i~v~~~~G~~~~~q~~~l-~~~~~i~v~~~---------~-~~~~d~l~~lv~dEAd~m~~~  202 (284)
                          ..+++|.+++|+....+...+ ++.|+|++.|.         . ...+..|..+|+||++.|.+.
T Consensus        71 ~g~~~~~i~V~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~  139 (1490)
T PRK09751         71 RGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGS  139 (1490)
T ss_pred             cccccCceEEEEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhccc
Confidence                247889899988766665544 55788877661         1 124778999999999998865

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.34  E-value=4.6e-12  Score=106.34  Aligned_cols=143  Identities=27%  Similarity=0.175  Sum_probs=103.0

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           51 KLGFKESTSILKARIPALAHQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      ..++..|++.|..+++.+ ..+ +.+++.++||||||.+++.+++..+...                     ....+||+
T Consensus         3 ~~~~~~~~~~Q~~~~~~~-~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~---------------------~~~~~l~~   60 (201)
T smart00487        3 KFGFEPLRPYQKEAIEAL-LSGLRDVILAAPTGSGKTLAALLPALEALKRG---------------------KGKRVLVL   60 (201)
T ss_pred             ccCCCCCCHHHHHHHHHH-HcCCCcEEEECCCCCchhHHHHHHHHHHhccc---------------------CCCcEEEE
Confidence            457889999999999998 777 9999999999999999999998876543                     13469999


Q ss_pred             ecCHHHHHHHHHHHhhhhcCCC-ceeEEEeCCCcchHHHHHhcCC-Ccccccc---------cCCccccccccCCCCCCc
Q 042526          130 NPTRELALQVLMVASPSLKSNS-LTLAMAAGSPLLTSEHSNRRKP-NKRKRTR---------KGGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~~~~~-i~v~~~~G~~~~~q~~~l~~~~-~i~v~~~---------~~~~~d~l~~lv~dEAd~  198 (284)
                      +||+.++.|+...+..+..... .....+.|.........+..+. ++++.+.         ......++..+++||++.
T Consensus        61 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~  140 (201)
T smart00487       61 VPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHR  140 (201)
T ss_pred             eCCHHHHHHHHHHHHHHhccCCeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHH
Confidence            9999999999999998877655 3344444544455555555554 5544330         112345677899999999


Q ss_pred             ccccccccchhhhcccC
Q 042526          199 PKTTTLLPSSLALMNLT  215 (284)
Q Consensus       199 m~~~gflp~~~~~~~~~  215 (284)
                      +..-.+......++...
T Consensus       141 ~~~~~~~~~~~~~~~~~  157 (201)
T smart00487      141 LLDGGFGDQLEKLLKLL  157 (201)
T ss_pred             HhcCCcHHHHHHHHHhC
Confidence            87644555554444433

>PRK13766 Hef nuclease; Provisional

Probab=99.23  E-value=6.3e-11  Score=122.15  Aligned_cols=123  Identities=16%  Similarity=0.053  Sum_probs=95.7

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      .-.|.++|..++..+ +.+ |+++++|||+|||++|++++...+..                      .+.++|||+||+
T Consensus        13 ~~~~r~yQ~~~~~~~-l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~----------------------~~~~vLvl~Pt~   68 (773)
T PRK13766         13 TIEARLYQQLLAATA-LKK-NTLVVLPTGLGKTAIALLVIAERLHK----------------------KGGKVLILAPTK   68 (773)
T ss_pred             cCCccHHHHHHHHHH-hcC-CeEEEcCCCccHHHHHHHHHHHHHHh----------------------CCCeEEEEeCcH
Confidence            346899999998887 666 99999999999999999999887621                      245799999999


Q ss_pred             HHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCccccccccCCCCCCccc
Q 042526          134 ELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGEDEKLDSLKWNPLSQPK  200 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~d~l~~lv~dEAd~m~  200 (284)
                      +|+.|+...++.+....+..+..+.|+....+...+....++++.+.         ....++.+..+|||||.++.
T Consensus        69 ~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~  144 (773)
T PRK13766         69 PLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAV  144 (773)
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcccc
Confidence            99999999999886654557778888876666556666667765542         12245678889999999864

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.19  E-value=6.7e-11  Score=120.86  Aligned_cols=128  Identities=16%  Similarity=0.085  Sum_probs=92.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|....=.+ +.|+  |+.++||+|||++|++|++-..+.                       +..+-|++|
T Consensus        78 lg~-~~~dvQlig~l~L-~~G~--Iaem~TGeGKTLva~lpa~l~aL~-----------------------G~~V~IvTp  130 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVL-HEGK--IAEMKTGEGKTLVATLPAYLNALT-----------------------GKGVHVVTV  130 (830)
T ss_pred             hCC-CCCccHHHhhHHh-cCCc--hhhhhcCCCcHHHHHHHHHHHHHc-----------------------CCCEEEEec
Confidence            566 5999998887665 7775  899999999999999999643322                       223569999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccCC----------------ccccccccCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGG----------------EDEKLDSLKWNP  195 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~~----------------~~d~l~~lv~dE  195 (284)
                      |+.||.|.+..+..+...+|++|++++|+....+.... ..++|++.+..-.                -...+.++++||
T Consensus       131 n~yLA~rd~e~~~~l~~~LGlsv~~i~~~~~~~er~~~-y~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDE  209 (830)
T PRK12904        131 NDYLAKRDAEWMGPLYEFLGLSVGVILSGMSPEERREA-YAADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDE  209 (830)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCeEEEEcCCCCHHHHHHh-cCCCeEEECCcchhhhhhhcccccchhhhcccccceEEEec
Confidence            99999999999999999999999999887544443333 3577766552211                123455688899


Q ss_pred             CCcccc-cccccc
Q 042526          196 LSQPKT-TTLLPS  207 (284)
Q Consensus       196 Ad~m~~-~gflp~  207 (284)
                      ||.|+- -.--|-
T Consensus       210 aDsiLIDeArtpL  222 (830)
T PRK12904        210 VDSILIDEARTPL  222 (830)
T ss_pred             hhhheeccCCCce
Confidence            998543 334443

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

Probab=99.18  E-value=9.8e-11  Score=121.96  Aligned_cols=97  Identities=23%  Similarity=0.217  Sum_probs=77.7

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhh
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEK  117 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~  117 (284)
                      +++.+...+...||+ +.|.|.+.+..+   +..|+++++.||||||||+||++|++..+. .                 
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~-----------------  291 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-T-----------------  291 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-C-----------------
Confidence            445778888889998 789999866633   377999999999999999999999987543 1                 


Q ss_pred             cCCCCCeEEEEEecCHHHHHHHHH-HHhhhhcCCC--ceeEEEeCCC
Q 042526          118 YAPKGHLRALIINPTRELALQVLM-VASPSLKSNS--LTLAMAAGSP  161 (284)
Q Consensus       118 ~~~~~~~~aLIL~PTReLa~Qi~~-~~~~l~~~~~--i~v~~~~G~~  161 (284)
                           +-++||.+||++|..|+.. .+..+.+.++  ++++++.|..
T Consensus       292 -----~~~vvi~t~t~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~~  333 (850)
T TIGR01407       292 -----EKPVVISTNTKVLQSQLLEKDIPLLNEILNFKINAALIKGKS  333 (850)
T ss_pred             -----CCeEEEEeCcHHHHHHHHHHHHHHHHHHcCCCceEEEEEcch
Confidence                 2369999999999999865 6777777655  7777777763

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.18  E-value=5e-11  Score=112.61  Aligned_cols=74  Identities=20%  Similarity=0.211  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHcCCCc--EEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHH
Q 042526           60 ILKARIPALAHQRKD--VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELAL  137 (284)
Q Consensus        60 iQ~~aip~il~~G~d--viv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~  137 (284)
                      +|.++++.+ ..+.+  ++++||||||||++|++|++..                          ...+++++||++|+.
T Consensus         1 hQ~~~~~~~-~~~~~~~~~i~apTGsGKT~~~~~~~l~~--------------------------~~~~~~~~P~~aL~~   53 (357)
T TIGR03158         1 HQVATFEAL-QSKDADIIFNTAPTGAGKTLAWLTPLLHG--------------------------ENDTIALYPTNALIE   53 (357)
T ss_pred             CHHHHHHHH-HcCCCCEEEEECCCCCCHHHHHHHHHHHc--------------------------CCCEEEEeChHHHHH
Confidence            499999999 77764  7889999999999999998831                          235899999999999


Q ss_pred             HHHHHHhhhhcCC----CceeEEEeCC
Q 042526          138 QVLMVASPSLKSN----SLTLAMAAGS  160 (284)
Q Consensus       138 Qi~~~~~~l~~~~----~i~v~~~~G~  160 (284)
                      |+++.++.+...+    ++.+..+.|.
T Consensus        54 ~~~~~~~~~~~~~~~~~~~~v~~~~g~   80 (357)
T TIGR03158        54 DQTEAIKEFVDVFKPERDVNLLHVSKA   80 (357)
T ss_pred             HHHHHHHHHHHhcCCCCCceEEEecCC
Confidence            9999999887433    4556666665

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.15  E-value=8.9e-11  Score=121.22  Aligned_cols=106  Identities=14%  Similarity=0.057  Sum_probs=75.4

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHh-hhhc
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVAS-PSLK  148 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~-~l~~  148 (284)
                      .++++++++|+||||||++|.+|+++...                       ...++||++|||++|.|++..+. .+..
T Consensus        18 ~~~~~vvv~A~TGSGKTt~~pl~lL~~~~-----------------------~~~~ilvlqPrR~aA~qia~rva~~l~~   74 (812)
T PRK11664         18 KTAPQVLLKAPTGAGKSTWLPLQLLQHGG-----------------------INGKIIMLEPRRLAARNVAQRLAEQLGE   74 (812)
T ss_pred             HhCCCEEEEcCCCCCHHHHHHHHHHHcCC-----------------------cCCeEEEECChHHHHHHHHHHHHHHhCc
Confidence            67899999999999999999999986421                       12479999999999999999875 4555


Q ss_pred             CCCceeEEEeCCCcchHHHHHhcCCCccccc--------ccCCccccccccCCCCCCc-ccccc
Q 042526          149 SNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT--------RKGGEDEKLDSLKWNPLSQ-PKTTT  203 (284)
Q Consensus       149 ~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~--------~~~~~~d~l~~lv~dEAd~-m~~~g  203 (284)
                      ..+..|...+++....     .....|.+.|        .....++.+.++||||++. +++..
T Consensus        75 ~~g~~VGy~vr~~~~~-----~~~t~I~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHER~l~~D  133 (812)
T PRK11664         75 KPGETVGYRMRAESKV-----GPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQAD  133 (812)
T ss_pred             ccCceEEEEecCcccc-----CCCCcEEEEChhHHHHHHhhCCCcCcCcEEEEcCCCccccccc
Confidence            5677777666553221     1122333322        1123678899999999997 55543

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.14  E-value=1.4e-10  Score=119.69  Aligned_cols=114  Identities=16%  Similarity=0.098  Sum_probs=79.8

Q ss_pred             HHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHh
Q 042526           65 IPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVAS  144 (284)
Q Consensus        65 ip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~  144 (284)
                      +..+ ..+.++|++|+||||||.+|.+|+++...                       .+.++||+.|||++|.|++..+.
T Consensus        11 ~~~l-~~~~~vIi~a~TGSGKTT~vpl~lL~~~~-----------------------~~~~ilvlqPrR~aA~qiA~rva   66 (819)
T TIGR01970        11 RDAL-AAHPQVVLEAPPGAGKSTAVPLALLDAPG-----------------------IGGKIIMLEPRRLAARSAAQRLA   66 (819)
T ss_pred             HHHH-HcCCcEEEECCCCCCHHHHHHHHHHHhhc-----------------------cCCeEEEEeCcHHHHHHHHHHHH
Confidence            3444 77899999999999999999999987541                       13579999999999999999875


Q ss_pred             -hhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc--------ccCCccccccccCCCCCCc-ccccccccc
Q 042526          145 -PSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT--------RKGGEDEKLDSLKWNPLSQ-PKTTTLLPS  207 (284)
Q Consensus       145 -~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~--------~~~~~~d~l~~lv~dEAd~-m~~~gflp~  207 (284)
                       .+....+..|...+++..     .....+.|.+.+        .....+..+..+||||++. +++.+|+-.
T Consensus        67 ~~~~~~~g~~VGy~vr~~~-----~~s~~t~I~v~T~G~Llr~l~~d~~L~~v~~VIiDEaHER~L~~Dl~L~  134 (819)
T TIGR01970        67 SQLGEAVGQTVGYRVRGEN-----KVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLA  134 (819)
T ss_pred             HHhCCCcCcEEEEEEcccc-----ccCCCCcEEEECCcHHHHHHhhCcccccCCEEEEeccchhhhccchHHH
Confidence             444445666655444422     122334554433        1123577899999999994 777665433

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.

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

Probab=99.11  E-value=2.9e-10  Score=117.74  Aligned_cols=88  Identities=19%  Similarity=0.178  Sum_probs=70.6

Q ss_pred             HHHcCCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeE
Q 042526           49 IYKLGFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLR  125 (284)
Q Consensus        49 L~~~g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (284)
                      +.-.||+ +.+-|....-.+   +..+..+++.|+||||||+||++|++...                        .+.+
T Consensus       239 ~~~~~~e-~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~------------------------~~~~  293 (820)
T PRK07246        239 IALLGLE-ERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS------------------------DQRQ  293 (820)
T ss_pred             hccCCCc-cCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc------------------------CCCc
Confidence            3334675 888998844433   46789999999999999999999988632                        1457


Q ss_pred             EEEEecCHHHHHHH-HHHHhhhhcCCCceeEEEeCCC
Q 042526          126 ALIINPTRELALQV-LMVASPSLKSNSLTLAMAAGSP  161 (284)
Q Consensus       126 aLIL~PTReLa~Qi-~~~~~~l~~~~~i~v~~~~G~~  161 (284)
                      +||++|||+|+.|+ ...+..|.+.++++++++.|+.
T Consensus       294 vvI~t~T~~Lq~Ql~~~~i~~l~~~~~~~~~~~kg~~  330 (820)
T PRK07246        294 IIVSVPTKILQDQIMAEEVKAIQEVFHIDCHSLKGPQ  330 (820)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHHHhcCCcEEEEECCc
Confidence            99999999999999 5888889988888887777664

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.11  E-value=2.2e-10  Score=117.18  Aligned_cols=104  Identities=22%  Similarity=0.266  Sum_probs=87.0

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      -++|..+..+|+.++|.++.+.-|+|++||||||||..|+|.||..+.+..             .+.....+..+.++|+
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~-------------~~~~i~k~~fKiVYIa  171 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHE-------------EQGDIAKDDFKIVYIA  171 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhc-------------cccccccCCceEEEEe
Confidence            368899999999999999888999999999999999999999999887621             1133445678999999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHH
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEH  167 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~  167 (284)
                      |+++||..++.-+.+-...+|++|.-++|+.......
T Consensus       172 PmKALa~Em~~~~~kkl~~~gi~v~ELTGD~ql~~te  208 (1230)
T KOG0952|consen  172 PMKALAAEMVDKFSKKLAPLGISVRELTGDTQLTKTE  208 (1230)
T ss_pred             chHHHHHHHHHHHhhhcccccceEEEecCcchhhHHH
Confidence            9999999999988877777899999999986544333

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.08  E-value=1.3e-10  Score=109.06  Aligned_cols=53  Identities=28%  Similarity=0.170  Sum_probs=46.1

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh
Q 042526           74 DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL  147 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~  147 (284)
                      |+++.||||||||++|++|++..+...                     .+.+++|++|||+||.|+++.+..+.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~---------------------~~~~ii~v~P~~~L~~q~~~~l~~~f   53 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ---------------------KADRVIIALPTRATINAMYRRAKELF   53 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC---------------------CCCeEEEEeehHHHHHHHHHHHHHHh
Confidence            689999999999999999999765332                     35689999999999999999999874

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.

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.08  E-value=3.2e-10  Score=116.14  Aligned_cols=121  Identities=16%  Similarity=0.038  Sum_probs=88.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. .|+++|...--.+ ..|  -|+.++||+|||++|.+|++...+.                       +..+.||+|
T Consensus        79 lgm-~~ydVQliGgl~L-~~G--~IaEm~TGEGKTL~a~lp~~l~al~-----------------------g~~VhIvT~  131 (908)
T PRK13107         79 FEM-RHFDVQLLGGMVL-DSN--RIAEMRTGEGKTLTATLPAYLNALT-----------------------GKGVHVITV  131 (908)
T ss_pred             hCC-CcCchHHhcchHh-cCC--ccccccCCCCchHHHHHHHHHHHhc-----------------------CCCEEEEeC
Confidence            565 5888887655444 444  4889999999999999999866544                       334999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccCCcc----------------ccccccCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKGGED----------------EKLDSLKWNP  195 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~~~~----------------d~l~~lv~dE  195 (284)
                      |++||.|...++..|..++|++|.++.|+... +...-...++|+..+..-.-+                ..+.+.++||
T Consensus       132 ndyLA~RD~e~m~~l~~~lGlsv~~i~~~~~~-~~r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDE  210 (908)
T PRK13107        132 NDYLARRDAENNRPLFEFLGLTVGINVAGLGQ-QEKKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDE  210 (908)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCeEEEecCCCCH-HHHHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecc
Confidence            99999999999999999999999998887554 333334467876655322111                2334467788


Q ss_pred             CCccc
Q 042526          196 LSQPK  200 (284)
Q Consensus       196 Ad~m~  200 (284)
                      +|.|+
T Consensus       211 vDsiL  215 (908)
T PRK13107        211 VDSIL  215 (908)
T ss_pred             hhhhc
Confidence            88743

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

Probab=99.03  E-value=1.2e-09  Score=109.66  Aligned_cols=72  Identities=25%  Similarity=0.153  Sum_probs=60.1

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh-c
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL-K  148 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~-~  148 (284)
                      ..++.+++.|+||||||+||++|++..+...                     .+.++||++||++|+.|+...+..+. +
T Consensus        14 ~~~~~lliEA~TGtGKTlAYLlpal~~~~~~---------------------~~~rvlIstpT~~Lq~Ql~~~l~~l~~~   72 (636)
T TIGR03117        14 RQKRIGMLEASTGVGKTLAMIMAALTMLKER---------------------PDQKIAIAVPTLALMGQLWSELERLTAE   72 (636)
T ss_pred             hcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc---------------------cCceEEEECCcHHHHHHHHHHHHHHHHh
Confidence            7789999999999999999999999876532                     24679999999999999999999988 4


Q ss_pred             CC--CceeEEEeCCCc
Q 042526          149 SN--SLTLAMAAGSPL  162 (284)
Q Consensus       149 ~~--~i~v~~~~G~~~  162 (284)
                      .+  .++++++.|...
T Consensus        73 ~l~~~i~~~~lkGr~n   88 (636)
T TIGR03117        73 GLAGPVQAGFFPGSQE   88 (636)
T ss_pred             hcCCCeeEEEEECCcc
Confidence            43  566777777643

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.82  E-value=1.9e-08  Score=79.39  Aligned_cols=112  Identities=28%  Similarity=0.189  Sum_probs=76.9

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCc
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSL  152 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i  152 (284)
                      +++++.++||||||..++..+...+...                     ....+||++|++.|+.|....+...... .+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~---------------------~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~   58 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL---------------------KGGQVLVLAPTRELANQVAERLKELFGE-GI   58 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc---------------------cCCCEEEEcCcHHHHHHHHHHHHHHhhC-Cc
Confidence            4689999999999999988877654431                     3467999999999999999999887765 66


Q ss_pred             eeEEEeCCCcchH-HHHHhcCCCccccccc---------CCccccccccCCCCCCccccccccc
Q 042526          153 TLAMAAGSPLLTS-EHSNRRKPNKRKRTRK---------GGEDEKLDSLKWNPLSQPKTTTLLP  206 (284)
Q Consensus       153 ~v~~~~G~~~~~q-~~~l~~~~~i~v~~~~---------~~~~d~l~~lv~dEAd~m~~~gflp  206 (284)
                      .+..+.+.....+ ........++++.+.-         .........+++||++.+....+..
T Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~  122 (144)
T cd00046          59 KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGL  122 (144)
T ss_pred             EEEEEecCcchhHHHHHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHH
Confidence            6767666644333 2233344555443311         0123467779999998876655433

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

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.82  E-value=2.3e-08  Score=91.90  Aligned_cols=77  Identities=17%  Similarity=0.059  Sum_probs=59.4

Q ss_pred             CCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           53 GFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        53 g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      -|. |+|.|.+.+..+   +..|.++++.||||||||++|++|++.++.....                 .....+++|+
T Consensus         6 Py~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~-----------------~~~~~kvi~~   67 (289)
T smart00488        6 PYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE-----------------RIQKIKLIYL   67 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc-----------------cccccceeEE
Confidence            354 699999944433   2779999999999999999999999987654310                 0023479999


Q ss_pred             ecCHHHHHHHHHHHhhhh
Q 042526          130 NPTRELALQVLMVASPSL  147 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~  147 (284)
                      ++|..+..|....++++.
T Consensus        68 t~T~~~~~q~i~~l~~~~   85 (289)
T smart00488       68 SRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             eccHHHHHHHHHHHHhcc
Confidence            999999999888887764

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.82  E-value=2.3e-08  Score=91.90  Aligned_cols=77  Identities=17%  Similarity=0.059  Sum_probs=59.4

Q ss_pred             CCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           53 GFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        53 g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      -|. |+|.|.+.+..+   +..|.++++.||||||||++|++|++.++.....                 .....+++|+
T Consensus         6 Py~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~-----------------~~~~~kvi~~   67 (289)
T smart00489        6 PYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE-----------------RIQKIKLIYL   67 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc-----------------cccccceeEE
Confidence            354 699999944433   2779999999999999999999999987654310                 0023479999


Q ss_pred             ecCHHHHHHHHHHHhhhh
Q 042526          130 NPTRELALQVLMVASPSL  147 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~  147 (284)
                      ++|..+..|....++++.
T Consensus        68 t~T~~~~~q~i~~l~~~~   85 (289)
T smart00489       68 SRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             eccHHHHHHHHHHHHhcc
Confidence            999999999888887764

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=98.77  E-value=2.1e-08  Score=100.83  Aligned_cols=120  Identities=17%  Similarity=0.050  Sum_probs=82.7

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      .-.+...|....-.. + |+|+|+++|||+|||+..+.-+++++-..                     ..-++|+++||+
T Consensus        60 ~~~lR~YQ~eivq~A-L-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~---------------------p~~KiVF~aP~~  116 (746)
T KOG0354|consen   60 NLELRNYQEELVQPA-L-GKNTIIALPTGSGKTFIAAVIMKNHFEWR---------------------PKGKVVFLAPTR  116 (746)
T ss_pred             cccccHHHHHHhHHh-h-cCCeEEEeecCCCccchHHHHHHHHHhcC---------------------CcceEEEeeCCc
Confidence            335677899988887 7 99999999999999999998888877553                     236799999999


Q ss_pred             HHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc-------c---cCCccccccccCCCCCCc
Q 042526          134 ELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT-------R---KGGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~-------~---~~~~~d~l~~lv~dEAd~  198 (284)
                      -|+.|....+...+..  .++....|+ ....-...+-..+++.+.+       +   ..+++..+..+|||||=+
T Consensus       117 pLv~QQ~a~~~~~~~~--~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hr  190 (746)
T KOG0354|consen  117 PLVNQQIACFSIYLIP--YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHR  190 (746)
T ss_pred             hHHHHHHHHHhhccCc--ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEccccc
Confidence            9999988666655543  344333333 3333223333334443333       1   122345588899999988

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

Probab=98.71  E-value=5.9e-08  Score=93.43  Aligned_cols=119  Identities=17%  Similarity=0.058  Sum_probs=88.2

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|...|....-.. +. +|.+++-|||=|||+..++-+..++...                     .+ .+|+|+||+-|
T Consensus        15 e~R~YQ~~i~a~a-l~-~NtLvvlPTGLGKT~IA~~V~~~~l~~~---------------------~~-kvlfLAPTKPL   70 (542)
T COG1111          15 EPRLYQLNIAAKA-LF-KNTLVVLPTGLGKTFIAAMVIANRLRWF---------------------GG-KVLFLAPTKPL   70 (542)
T ss_pred             cHHHHHHHHHHHH-hh-cCeEEEecCCccHHHHHHHHHHHHHHhc---------------------CC-eEEEecCCchH
Confidence            4566777766665 43 4999999999999999888888777654                     34 79999999999


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc---------ccCCccccccccCCCCCCc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT---------RKGGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~---------~~~~~~d~l~~lv~dEAd~  198 (284)
                      +.|-+..|..+..-..-.++.+.|.........+-....+.+.|         .-..+++++..++||||-+
T Consensus        71 V~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHR  142 (542)
T COG1111          71 VLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHR  142 (542)
T ss_pred             HHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHhhCCEEEeccHHHHhHHhcCccChHHceEEEechhhh
Confidence            99999999998776556778888876555433333333443333         1223688999999999988

>TIGR00595 priA primosomal protein N'

Probab=98.58  E-value=1.3e-07  Score=93.43  Aligned_cols=97  Identities=14%  Similarity=0.019  Sum_probs=66.0

Q ss_pred             EEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeE
Q 042526           76 IGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLA  155 (284)
Q Consensus        76 iv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~  155 (284)
                      +++|+||||||.+|+..+ ..+..                      .+-++|||+|+++|+.|++..++..   ++..++
T Consensus         1 LL~g~TGsGKT~v~l~~i-~~~l~----------------------~g~~vLvlvP~i~L~~Q~~~~l~~~---f~~~v~   54 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAI-EKVLA----------------------LGKSVLVLVPEIALTPQMIQRFKYR---FGSQVA   54 (505)
T ss_pred             CccCCCCCCHHHHHHHHH-HHHHH----------------------cCCeEEEEeCcHHHHHHHHHHHHHH---hCCcEE
Confidence            468999999999996554 33332                      2457999999999999999988764   355677


Q ss_pred             EEeCCCcchHH----HHHhc-CCCccccccc--CCccccccccCCCCCCc
Q 042526          156 MAAGSPLLTSE----HSNRR-KPNKRKRTRK--GGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       156 ~~~G~~~~~q~----~~l~~-~~~i~v~~~~--~~~~d~l~~lv~dEAd~  198 (284)
                      ++.|+....+.    ..+.. ..++++.++.  ..-+.++..+++||+..
T Consensus        55 vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf~p~~~l~lIIVDEeh~  104 (505)
T TIGR00595        55 VLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALFLPFKNLGLIIVDEEHD  104 (505)
T ss_pred             EEECCCCHHHHHHHHHHHHcCCCCEEECChHHHcCcccCCCEEEEECCCc
Confidence            77776443322    12222 3566665532  23467788899999754

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).

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

Probab=98.55  E-value=1.7e-07  Score=97.66  Aligned_cols=89  Identities=18%  Similarity=0.186  Sum_probs=66.6

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEE
Q 042526           47 KSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRA  126 (284)
Q Consensus        47 ~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~a  126 (284)
                      ......+|+ |-++|+.|+-++ .+|.+|+++||||||||+..-.++-..+..                       +-++
T Consensus       111 ~~~~~~~F~-LD~fQ~~a~~~L-er~esVlV~ApTssGKTvVaeyAi~~al~~-----------------------~qrv  165 (1041)
T COG4581         111 PPAREYPFE-LDPFQQEAIAIL-ERGESVLVCAPTSSGKTVVAEYAIALALRD-----------------------GQRV  165 (1041)
T ss_pred             cHHHhCCCC-cCHHHHHHHHHH-hCCCcEEEEccCCCCcchHHHHHHHHHHHc-----------------------CCce
Confidence            334557886 889999999998 999999999999999998866665443332                       3359


Q ss_pred             EEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          127 LIINPTRELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       127 LIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      ++.+|.++|.+|.+..+...-...--.+.+++|+
T Consensus       166 iYTsPIKALsNQKyrdl~~~fgdv~~~vGL~TGD  199 (1041)
T COG4581         166 IYTSPIKALSNQKYRDLLAKFGDVADMVGLMTGD  199 (1041)
T ss_pred             EeccchhhhhhhHHHHHHHHhhhhhhhccceecc
Confidence            9999999999999998875543221123455554

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

Probab=98.53  E-value=3.7e-07  Score=91.01  Aligned_cols=145  Identities=19%  Similarity=0.103  Sum_probs=109.3

Q ss_pred             CCCCHHHHHH-HHHcCCCCCcHHHHHHHHHHHcCC------CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           39 LRLHPLLMKS-IYKLGFKESTSILKARIPALAHQR------KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        39 l~L~~~Ll~~-L~~~g~~~pT~iQ~~aip~il~~G------~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      +.....++.. +..+.|. +|..|..+|..| ...      .+=++++--|||||+..++.++..+..            
T Consensus       245 ~~~~~~l~~~~~~~LPF~-LT~aQ~~vi~EI-~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~------------  310 (677)
T COG1200         245 LPANGELLAKFLAALPFK-LTNAQKRVIKEI-LADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA------------  310 (677)
T ss_pred             CCccHHHHHHHHHhCCCC-ccHHHHHHHHHH-HhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc------------
Confidence            3445555555 4678896 999999999998 332      345889999999999999999876533            


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHH----HHhcC-CCcccccc--cC--
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEH----SNRRK-PNKRKRTR--KG--  182 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~----~l~~~-~~i~v~~~--~~--  182 (284)
                                 |.|+..++||--||.|-+..+..+...++++|++++|.....+..    .+..+ .+++|.|-  ..  
T Consensus       311 -----------G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~  379 (677)
T COG1200         311 -----------GYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDK  379 (677)
T ss_pred             -----------CCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcc
Confidence                       678999999999999999999999999999999999885544433    34444 56666652  22  


Q ss_pred             CccccccccCCCCCCc--------cccccc-ccch
Q 042526          183 GEDEKLDSLKWNPLSQ--------PKTTTL-LPSS  208 (284)
Q Consensus       183 ~~~d~l~~lv~dEAd~--------m~~~gf-lp~~  208 (284)
                      .++.+|-.++.||.-+        +...|. .|.+
T Consensus       380 V~F~~LgLVIiDEQHRFGV~QR~~L~~KG~~~Ph~  414 (677)
T COG1200         380 VEFHNLGLVIIDEQHRFGVHQRLALREKGEQNPHV  414 (677)
T ss_pred             eeecceeEEEEeccccccHHHHHHHHHhCCCCCcE
Confidence            3577888888888665        555665 4555

>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=98.51  E-value=2.1e-07  Score=77.88  Aligned_cols=67  Identities=21%  Similarity=0.114  Sum_probs=52.5

Q ss_pred             CCcHHHHHHHHHHHc------CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           56 ESTSILKARIPALAH------QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        56 ~pT~iQ~~aip~il~------~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      .|.+.|.+|+-.++.      ..+.+++.++||||||++++..+.... .                         .+||+
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-~-------------------------~~l~~   56 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA-R-------------------------KVLIV   56 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH-C-------------------------EEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc-c-------------------------ceeEe
Confidence            478999999998831      368999999999999988874333211 1                         69999


Q ss_pred             ecCHHHHHHHHHHHhhhhc
Q 042526          130 NPTRELALQVLMVASPSLK  148 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~~  148 (284)
                      ||+..|+.|....+..+..
T Consensus        57 ~p~~~l~~Q~~~~~~~~~~   75 (184)
T PF04851_consen   57 APNISLLEQWYDEFDDFGS   75 (184)
T ss_dssp             ESSHHHHHHHHHHHHHHST
T ss_pred             cCHHHHHHHHHHHHHHhhh
Confidence            9999999999999966554

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 ....

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

Probab=98.51  E-value=1.4e-07  Score=93.65  Aligned_cols=135  Identities=13%  Similarity=0.078  Sum_probs=95.1

Q ss_pred             HHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCe
Q 042526           46 MKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHL  124 (284)
Q Consensus        46 l~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (284)
                      ...|+. +||..+.|-|.++|..+ ++|+|+++.-|||.||++||-||.+-.                         .| 
T Consensus         6 ~~~L~~~fGy~~FR~gQ~evI~~~-l~g~d~lvvmPTGgGKSlCyQiPAll~-------------------------~G-   58 (590)
T COG0514           6 QQVLKQVFGYASFRPGQQEIIDAL-LSGKDTLVVMPTGGGKSLCYQIPALLL-------------------------EG-   58 (590)
T ss_pred             HHHHHHHhCccccCCCHHHHHHHH-HcCCcEEEEccCCCCcchHhhhHHHhc-------------------------CC-
Confidence            345665 79999999999999999 999999999999999999999999753                         13 


Q ss_pred             EEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcC-----CCccccc---------ccCCccccccc
Q 042526          125 RALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRK-----PNKRKRT---------RKGGEDEKLDS  190 (284)
Q Consensus       125 ~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~-----~~i~v~~---------~~~~~~d~l~~  190 (284)
                      -.|||+|...|-......++.    .|+.++++.++-...+...+...     .+++...         +....--++..
T Consensus        59 ~TLVVSPLiSLM~DQV~~l~~----~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l  134 (590)
T COG0514          59 LTLVVSPLISLMKDQVDQLEA----AGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISL  134 (590)
T ss_pred             CEEEECchHHHHHHHHHHHHH----cCceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCce
Confidence            489999999998766666554    36778777777555554443332     1221111         00011224556


Q ss_pred             cCCCCCCcccccc--cccchhhh
Q 042526          191 LKWNPLSQPKTTT--LLPSSLAL  211 (284)
Q Consensus       191 lv~dEAd~m~~~g--flp~~~~~  211 (284)
                      +++|||=.....|  |=|+-..+
T Consensus       135 ~vIDEAHCiSqWGhdFRP~Y~~l  157 (590)
T COG0514         135 VAIDEAHCISQWGHDFRPDYRRL  157 (590)
T ss_pred             EEechHHHHhhcCCccCHhHHHH
Confidence            7888888888777  77766444

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

Probab=98.50  E-value=9.4e-07  Score=91.08  Aligned_cols=103  Identities=23%  Similarity=0.138  Sum_probs=74.0

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|| .|+..|+.+...+ ..|+++-+.||||.||| +|.+.+-..+..                      .+-+++||+|
T Consensus        79 ~G~-~~ws~QR~WakR~-~rg~SFaiiAPTGvGKT-Tfg~~~sl~~a~----------------------kgkr~yii~P  133 (1187)
T COG1110          79 TGF-RPWSAQRVWAKRL-VRGKSFAIIAPTGVGKT-TFGLLMSLYLAK----------------------KGKRVYIIVP  133 (1187)
T ss_pred             hCC-CchHHHHHHHHHH-HcCCceEEEcCCCCchh-HHHHHHHHHHHh----------------------cCCeEEEEec
Confidence            355 7999999999998 99999999999999999 555444333322                      2467999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCC-ceeEE-EeCCCcchH----HHHHhc-CCCccccc
Q 042526          132 TRELALQVLMVASPSLKSNS-LTLAM-AAGSPLLTS----EHSNRR-KPNKRKRT  179 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~-i~v~~-~~G~~~~~q----~~~l~~-~~~i~v~~  179 (284)
                      |+-|+.|+++.+..|+...+ ..+.+ +.|.-...+    ..++.+ ..+|++.+
T Consensus       134 T~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitT  188 (1187)
T COG1110         134 TTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITT  188 (1187)
T ss_pred             CHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEe
Confidence            99999999999999997665 44433 555522222    223343 35666655

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

Probab=98.48  E-value=6.7e-07  Score=94.25  Aligned_cols=85  Identities=20%  Similarity=0.150  Sum_probs=63.1

Q ss_pred             CCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           53 GFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        53 g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      || .+.|-|.+.+..+   +..+..+++.|+||+|||+|||+|++......                      +-+++|.
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~----------------------~~~vvIs  311 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK----------------------EEPVVIS  311 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc----------------------CCeEEEE
Confidence            55 4889998855544   36788999999999999999999998654432                      3569999


Q ss_pred             ecCHHHHHHHHH-HHhhhhcCC--CceeEEEeCC
Q 042526          130 NPTRELALQVLM-VASPSLKSN--SLTLAMAAGS  160 (284)
Q Consensus       130 ~PTReLa~Qi~~-~~~~l~~~~--~i~v~~~~G~  160 (284)
                      ++|+.|-.|+.. .+-.|.+.+  .++++++-|.
T Consensus       312 T~T~~LQ~Ql~~kDiP~L~~~~~~~~~~~~lKGr  345 (928)
T PRK08074        312 TYTIQLQQQLLEKDIPLLQKIFPFPVEAALLKGR  345 (928)
T ss_pred             cCCHHHHHHHHHhhHHHHHHHcCCCceEEEEEcc
Confidence            999999999865 343343333  4566666665

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.41  E-value=2e-06  Score=88.19  Aligned_cols=100  Identities=17%  Similarity=0.108  Sum_probs=79.3

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|+ +|+++|..+-=.+ ..|+  |+.-.||+|||++..+|++.....                       +-++-|++|
T Consensus        77 ~g~-~~~dvQlig~l~l-~~G~--iaEm~TGEGKTLvA~l~a~l~al~-----------------------G~~v~vvT~  129 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVL-HEGN--IAEMKTGEGKTLTATLPVYLNALT-----------------------GKGVHVVTV  129 (796)
T ss_pred             hCC-CCchhHHHHHHHH-hcCC--cccccCCCCCcHHHHHHHHHHHHc-----------------------CCCeEEEec
Confidence            566 5999998887665 7776  889999999999999999876544                       556899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~  179 (284)
                      |--||.|=+..+..+...+|++|+++.|.....+. .-....+|.-.+
T Consensus       130 neyLA~Rd~e~~~~~~~~LGl~vg~i~~~~~~~~r-~~~y~~dI~Y~t  176 (796)
T PRK12906        130 NEYLSSRDATEMGELYRWLGLTVGLNLNSMSPDEK-RAAYNCDITYST  176 (796)
T ss_pred             cHHHHHhhHHHHHHHHHhcCCeEEEeCCCCCHHHH-HHHhcCCCeecC
Confidence            99999999999999999999999999887544433 333345664443

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.38  E-value=3.1e-06  Score=85.60  Aligned_cols=100  Identities=17%  Similarity=0.075  Sum_probs=79.7

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|+ +|+++|..+.-.+ +.|+  |+.-.||+|||++..+|++...+.                       +-.+-|++|
T Consensus        75 lg~-r~ydvQlig~l~L-l~G~--VaEM~TGEGKTLvA~l~a~l~AL~-----------------------G~~VhvvT~  127 (764)
T PRK12326         75 LGL-RPFDVQLLGALRL-LAGD--VIEMATGEGKTLAGAIAAAGYALQ-----------------------GRRVHVITV  127 (764)
T ss_pred             cCC-CcchHHHHHHHHH-hCCC--cccccCCCCHHHHHHHHHHHHHHc-----------------------CCCeEEEcC
Confidence            566 5999999999877 7773  668889999999999999865543                       556899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~  179 (284)
                      |--||.|=+..+..+...+|++|+++.+.....+ +.-....+|...+
T Consensus       128 NdyLA~RDae~m~~ly~~LGLsvg~i~~~~~~~e-rr~aY~~DItYgT  174 (764)
T PRK12326        128 NDYLARRDAEWMGPLYEALGLTVGWITEESTPEE-RRAAYACDVTYAS  174 (764)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCEEEEECCCCCHHH-HHHHHcCCCEEcC
Confidence            9999999999999999999999999988765444 3333356664443

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

Probab=98.35  E-value=1e-06  Score=93.96  Aligned_cols=71  Identities=21%  Similarity=0.221  Sum_probs=55.8

Q ss_pred             CCcHHHHHHHHHHH---c-CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALA---H-QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~-~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .+.+.|..||..+.   . ..+.++++.+||||||++. +.++.++....                    ...++|||+|
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~--------------------~~~rVLfLvD  471 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAK--------------------RFRRILFLVD  471 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcC--------------------ccCeEEEEec
Confidence            48999999998772   2 2468999999999999884 45556655431                    2458999999


Q ss_pred             CHHHHHHHHHHHhhhh
Q 042526          132 TRELALQVLMVASPSL  147 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~  147 (284)
                      +++|+.|..+.+..+.
T Consensus       472 R~~L~~Qa~~~F~~~~  487 (1123)
T PRK11448        472 RSALGEQAEDAFKDTK  487 (1123)
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999999998763

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

Probab=98.35  E-value=1.4e-06  Score=84.65  Aligned_cols=78  Identities=22%  Similarity=0.167  Sum_probs=56.9

Q ss_pred             CCCcHHHHHHHHHHHcC----CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           55 KESTSILKARIPALAHQ----RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~----G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      ..|.+.|.+|+..+ ..    ++..+++.|||+|||+.++..+-. +                         ...+||||
T Consensus        35 ~~lr~yQ~~al~a~-~~~~~~~~~gvivlpTGaGKT~va~~~~~~-~-------------------------~~~~Lvlv   87 (442)
T COG1061          35 FELRPYQEEALDAL-VKNRRTERRGVIVLPTGAGKTVVAAEAIAE-L-------------------------KRSTLVLV   87 (442)
T ss_pred             CCCcHHHHHHHHHH-HhhcccCCceEEEeCCCCCHHHHHHHHHHH-h-------------------------cCCEEEEE
Confidence            35899999999999 55    899999999999999877644321 1                         12299999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      ||++|+.|.+..+....... -.+..++|+
T Consensus        88 ~~~~L~~Qw~~~~~~~~~~~-~~~g~~~~~  116 (442)
T COG1061          88 PTKELLDQWAEALKKFLLLN-DEIGIYGGG  116 (442)
T ss_pred             CcHHHHHHHHHHHHHhcCCc-cccceecCc
Confidence            99999999986665543321 123445554

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=98.34  E-value=8.7e-07  Score=84.00  Aligned_cols=140  Identities=17%  Similarity=0.178  Sum_probs=94.0

Q ss_pred             HHHHHHHH-cCCCCC-cHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCC
Q 042526           44 LLMKSIYK-LGFKES-TSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPK  121 (284)
Q Consensus        44 ~Ll~~L~~-~g~~~p-T~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~  121 (284)
                      .+..+|++ +|+..+ |+.|..|+..++....||.++-|||+||+|||-||.|-.                         
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-------------------------   60 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-------------------------   60 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-------------------------
Confidence            45667776 688766 899999999997888899999999999999999998742                         


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH----HHHHhc-CCCcccc--c-------------cc
Q 042526          122 GHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTS----EHSNRR-KPNKRKR--T-------------RK  181 (284)
Q Consensus       122 ~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q----~~~l~~-~~~i~v~--~-------------~~  181 (284)
                      .+ ..||+.|...|.....+.+.+|-    +.+..+..--+...    +..|.+ +|.+.+.  +             ..
T Consensus        61 ~g-ITIV~SPLiALIkDQiDHL~~LK----Vp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~  135 (641)
T KOG0352|consen   61 GG-ITIVISPLIALIKDQIDHLKRLK----VPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNG  135 (641)
T ss_pred             CC-eEEEehHHHHHHHHHHHHHHhcC----CchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHH
Confidence            13 58999999999887777776652    22222222111111    112222 3444211  1             11


Q ss_pred             CCccccccccCCCCCCcccccc--cccchhhhcc
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTT--LLPSSLALMN  213 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~g--flp~~~~~~~  213 (284)
                      +..-+.|.+++.|||-....-|  |=|+-+.+-.
T Consensus       136 L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~  169 (641)
T KOG0352|consen  136 LANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGS  169 (641)
T ss_pred             HhhhceeeeEEechhhhHhhhccccCcchhhhhh
Confidence            1133568899999999877777  8888766533

>PRK09694 helicase Cas3; Provisional

Probab=98.28  E-value=2.6e-06  Score=88.77  Aligned_cols=86  Identities=23%  Similarity=0.069  Sum_probs=62.6

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      ...|+|+|..+.... ..+.-+|+.||||+|||.+.++.+. ++...                    ....+++|..||+
T Consensus       284 ~~~p~p~Q~~~~~~~-~~pgl~ileApTGsGKTEAAL~~A~-~l~~~--------------------~~~~gi~~aLPT~  341 (878)
T PRK09694        284 GYQPRQLQTLVDALP-LQPGLTIIEAPTGSGKTEAALAYAW-RLIDQ--------------------GLADSIIFALPTQ  341 (878)
T ss_pred             CCCChHHHHHHHhhc-cCCCeEEEEeCCCCCHHHHHHHHHH-HHHHh--------------------CCCCeEEEECcHH
Confidence            447999999886543 4566789999999999999876654 33332                    1235789999999


Q ss_pred             HHHHHHHHHHhhhhcCC--CceeEEEeCCC
Q 042526          134 ELALQVLMVASPSLKSN--SLTLAMAAGSP  161 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~--~i~v~~~~G~~  161 (284)
                      .+++|++..+..+....  ...+.+..|..
T Consensus       342 Atan~m~~Rl~~~~~~~f~~~~v~L~Hg~a  371 (878)
T PRK09694        342 ATANAMLSRLEALASKLFPSPNLILAHGNS  371 (878)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCceEeecCcc
Confidence            99999999998755432  34566666653

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=98.25  E-value=3.8e-06  Score=78.68  Aligned_cols=84  Identities=19%  Similarity=0.164  Sum_probs=70.2

Q ss_pred             ccCCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 042526           37 NELRLHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEA  115 (284)
Q Consensus        37 ~~l~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~  115 (284)
                      .+|+.+.+.-..|++ +..+.+.|.|.++|.+. +.|.|+++.-|||-||+|||-||+|-   .                
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~-ma~ed~~lil~tgggkslcyqlpal~---a----------------  133 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINAT-MAGEDAFLILPTGGGKSLCYQLPALC---A----------------  133 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhh-hccCceEEEEeCCCccchhhhhhHHh---c----------------
Confidence            346777777777766 67889999999999999 99999999999999999999999874   1                


Q ss_pred             hhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh
Q 042526          116 EKYAPKGHLRALIINPTRELALQVLMVASPSL  147 (284)
Q Consensus       116 ~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~  147 (284)
                             .-.+||+||...|.....-+++.|+
T Consensus       134 -------dg~alvi~plislmedqil~lkqlg  158 (695)
T KOG0353|consen  134 -------DGFALVICPLISLMEDQILQLKQLG  158 (695)
T ss_pred             -------CCceEeechhHHHHHHHHHHHHHhC
Confidence                   2359999999999887766777663

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.23  E-value=5.2e-06  Score=85.74  Aligned_cols=101  Identities=15%  Similarity=0.067  Sum_probs=77.2

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|...--.+ ..|  -|+.-.||+|||++..+|++-..+.                       +..+-|++|
T Consensus        79 lGm-~~ydVQliGg~~L-h~G--~iaEM~TGEGKTLvA~l~a~l~al~-----------------------G~~VhvvT~  131 (913)
T PRK13103         79 MGM-RHFDVQLIGGMTL-HEG--KIAEMRTGEGKTLVGTLAVYLNALS-----------------------GKGVHVVTV  131 (913)
T ss_pred             hCC-CcchhHHHhhhHh-ccC--ccccccCCCCChHHHHHHHHHHHHc-----------------------CCCEEEEeC
Confidence            564 6899998765444 444  5778899999999999999765443                       557899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR  180 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~  180 (284)
                      |--||.|=+..+..+...+|++|+++.|.....+.+ -....+|+..+.
T Consensus       132 ndyLA~RD~e~m~~l~~~lGl~v~~i~~~~~~~err-~~Y~~dI~YGT~  179 (913)
T PRK13103        132 NDYLARRDANWMRPLYEFLGLSVGIVTPFQPPEEKR-AAYAADITYGTN  179 (913)
T ss_pred             CHHHHHHHHHHHHHHhcccCCEEEEECCCCCHHHHH-HHhcCCEEEEcc
Confidence            999999999999999999999999998875544433 333366655553

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.22  E-value=1.4e-06  Score=93.27  Aligned_cols=113  Identities=19%  Similarity=0.140  Sum_probs=68.5

Q ss_pred             HHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe--c----CHHHHH
Q 042526           64 RIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN--P----TRELAL  137 (284)
Q Consensus        64 aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~--P----TReLa~  137 (284)
                      .|...+..++.+|++|+||||||.  .||.+..  ...                    .+..+.|+|  |    +++||.
T Consensus        81 ~Il~ai~~~~VviI~GeTGSGKTT--qlPq~ll--e~g--------------------~g~~g~I~~TQPRRlAArsLA~  136 (1294)
T PRK11131         81 DILEAIRDHQVVIVAGETGSGKTT--QLPKICL--ELG--------------------RGVKGLIGHTQPRRLAARTVAN  136 (1294)
T ss_pred             HHHHHHHhCCeEEEECCCCCCHHH--HHHHHHH--HcC--------------------CCCCCceeeCCCcHHHHHHHHH
Confidence            343333667778888999999998  5784432  210                    112223333  4    789999


Q ss_pred             HHHHHHhh-hhcCCCceeEEEeCCCcchHHHHHhcCCCccccc--------ccCCccccccccCCCCCC-cccccccccc
Q 042526          138 QVLMVASP-SLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT--------RKGGEDEKLDSLKWNPLS-QPKTTTLLPS  207 (284)
Q Consensus       138 Qi~~~~~~-l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~--------~~~~~~d~l~~lv~dEAd-~m~~~gflp~  207 (284)
                      ||..++.. ++...|+.+      ....|.   ...+.|++.|        .....+.++..+|+|||| ++++++|+.+
T Consensus       137 RVA~El~~~lG~~VGY~v------rf~~~~---s~~t~I~v~TpG~LL~~l~~d~~Ls~~~~IIIDEAHERsLn~DfLLg  207 (1294)
T PRK11131        137 RIAEELETELGGCVGYKV------RFNDQV---SDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILG  207 (1294)
T ss_pred             HHHHHHhhhhcceeceee------cCcccc---CCCCCEEEEChHHHHHHHhcCCccccCcEEEecCccccccccchHHH
Confidence            99999875 444444322      111111   2234443333        112347889999999999 5999999876


Q ss_pred             hh
Q 042526          208 SL  209 (284)
Q Consensus       208 ~~  209 (284)
                      .+
T Consensus       208 ~L  209 (1294)
T PRK11131        208 YL  209 (1294)
T ss_pred             HH
Confidence            44

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.21  E-value=5.7e-06  Score=84.41  Aligned_cols=79  Identities=8%  Similarity=-0.056  Sum_probs=59.9

Q ss_pred             CCcHHHHHHHHHHHcCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           56 ESTSILKARIPALAHQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      .+.|.|..|+..++..|  +.-+++.|||+|||+..+..+. ++                         .-.+||||||.
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~-~l-------------------------~k~tLILvps~  308 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAAC-TV-------------------------KKSCLVLCTSA  308 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHH-Hh-------------------------CCCEEEEeCcH
Confidence            47899999999884455  3778899999999988764332 21                         12489999999


Q ss_pred             HHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          134 ELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      +|+.|+.+.+..+.......+..++|+
T Consensus       309 ~Lv~QW~~ef~~~~~l~~~~I~~~tg~  335 (732)
T TIGR00603       309 VSVEQWKQQFKMWSTIDDSQICRFTSD  335 (732)
T ss_pred             HHHHHHHHHHHHhcCCCCceEEEEecC
Confidence            999999999998865444556666665

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).

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.20  E-value=1.1e-05  Score=82.83  Aligned_cols=85  Identities=22%  Similarity=0.228  Sum_probs=61.0

Q ss_pred             CCCCCcHHHHHHHHHHH---cC-----CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCe
Q 042526           53 GFKESTSILKARIPALA---HQ-----RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHL  124 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il---~~-----G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (284)
                      ||+ +.+-|.+.+-.+.   ..     ++.+++-|+||+|||+|||+|++-.....                      +-
T Consensus        23 ~~e-~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~----------------------~k   79 (697)
T PRK11747         23 GFI-PRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAE----------------------KK   79 (697)
T ss_pred             CCC-cCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHc----------------------CC
Confidence            664 8888988665552   33     36789999999999999999998655442                      34


Q ss_pred             EEEEEecCHHHHHHHH-HHHhhhhcCCC--ceeEEEeCC
Q 042526          125 RALIINPTRELALQVL-MVASPSLKSNS--LTLAMAAGS  160 (284)
Q Consensus       125 ~aLIL~PTReLa~Qi~-~~~~~l~~~~~--i~v~~~~G~  160 (284)
                      ++||-+.|..|=.|+. +.+-.|.+.++  ++++++=|.
T Consensus        80 ~vVIST~T~~LQeQL~~kDlP~l~~~l~~~~~~~llKGr  118 (697)
T PRK11747         80 KLVISTATVALQEQLVSKDLPLLLKISGLDFKFTLAKGR  118 (697)
T ss_pred             eEEEEcCCHHHHHHHHhhhhhHHHHHcCCCceEEEEcCc
Confidence            6999999999999984 45555555443  455555443

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.18  E-value=1.1e-05  Score=83.04  Aligned_cols=100  Identities=18%  Similarity=0.087  Sum_probs=76.2

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|+. |+++|..+.=.+ .  ..-|+...||.|||+++.+|+.-..+.                       +-.+-|+++
T Consensus        73 lG~r-~ydvQlig~l~L-~--~G~IaEm~TGEGKTL~a~l~ayl~aL~-----------------------G~~VhVvT~  125 (870)
T CHL00122         73 LGLR-HFDVQLIGGLVL-N--DGKIAEMKTGEGKTLVATLPAYLNALT-----------------------GKGVHIVTV  125 (870)
T ss_pred             hCCC-CCchHhhhhHhh-c--CCccccccCCCCchHHHHHHHHHHHhc-----------------------CCceEEEeC
Confidence            6775 999998876433 3  457889999999999999999633322                       456899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~  179 (284)
                      +..||.+-+..+..+...+|++|.++.++....+ +.-....+|.-.+
T Consensus       126 NdyLA~RD~e~m~pvy~~LGLsvg~i~~~~~~~e-rr~aY~~DItYgT  172 (870)
T CHL00122        126 NDYLAKRDQEWMGQIYRFLGLTVGLIQEGMSSEE-RKKNYLKDITYVT  172 (870)
T ss_pred             CHHHHHHHHHHHHHHHHHcCCceeeeCCCCChHH-HHHhcCCCCEecC
Confidence            9999999999999999999999998877654433 4444455664443

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

Probab=98.18  E-value=5.9e-06  Score=83.90  Aligned_cols=74  Identities=27%  Similarity=0.228  Sum_probs=60.8

Q ss_pred             HcCCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           51 KLGFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      .+..-.|.+.|.+++-.+   +..|+.+++.||||||||++||+|+|......                      +..++
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~----------------------~~~vi   67 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE----------------------GKKVI   67 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc----------------------CCcEE
Confidence            345557999999988655   25567799999999999999999999876553                      35799


Q ss_pred             EEecCHHHHHHHHHHHhhh
Q 042526          128 IINPTRELALQVLMVASPS  146 (284)
Q Consensus       128 IL~PTReLa~Qi~~~~~~l  146 (284)
                      |.++|+.|-.|+......+
T Consensus        68 ist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          68 ISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             EECCCHHHHHHHHHhhcch
Confidence            9999999999999888775

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=98.13  E-value=8.7e-06  Score=85.48  Aligned_cols=109  Identities=18%  Similarity=0.184  Sum_probs=85.1

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcC
Q 042526           40 RLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYA  119 (284)
Q Consensus        40 ~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~  119 (284)
                      .+|.+-..++.  |+..+.+||....++.+....++++|||||+|||...++-+|+.+......            -...
T Consensus       295 elP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~------------dgs~  360 (1674)
T KOG0951|consen  295 ELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLRE------------DGSV  360 (1674)
T ss_pred             CCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhccccc------------ccce
Confidence            46666666654  667799999999999855567999999999999999999999988664210            0222


Q ss_pred             CCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCc
Q 042526          120 PKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPL  162 (284)
Q Consensus       120 ~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~  162 (284)
                      +......++++|+..|+..+...+.+-...+|++|.-.+|...
T Consensus       361 nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~  403 (1674)
T KOG0951|consen  361 NLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQ  403 (1674)
T ss_pred             ecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEeccccc
Confidence            3345689999999999998888777777778999988888754

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.10  E-value=1.3e-05  Score=82.35  Aligned_cols=76  Identities=12%  Similarity=0.044  Sum_probs=62.8

Q ss_pred             cCCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEE
Q 042526           52 LGFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALI  128 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLI  128 (284)
                      +-|..+.|.|.+.+..+   +..|.++++.||||||||+|.|.|+|..+....                    ..++.++
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~--------------------~~~kIiy   65 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP--------------------EVRKIIY   65 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc--------------------ccccEEE
Confidence            34676789998877655   367999999999999999999999998765421                    2468999


Q ss_pred             EecCHHHHHHHHHHHhhhh
Q 042526          129 INPTRELALQVLMVASPSL  147 (284)
Q Consensus       129 L~PTReLa~Qi~~~~~~l~  147 (284)
                      .+.|..-..|+.++++++.
T Consensus        66 ~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604        66 ASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             EcccchHHHHHHHHHHhhh
Confidence            9999999999999999865

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).

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=98.02  E-value=8.7e-06  Score=83.54  Aligned_cols=80  Identities=20%  Similarity=0.225  Sum_probs=61.8

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +.|+ |-++|++||-++ .+|..|+|.|+|-+|||+..-.++...   +.                    .+.++++-+|
T Consensus       294 ~pFe-lD~FQk~Ai~~l-erg~SVFVAAHTSAGKTvVAEYAiala---q~--------------------h~TR~iYTSP  348 (1248)
T KOG0947|consen  294 YPFE-LDTFQKEAIYHL-ERGDSVFVAAHTSAGKTVVAEYAIALA---QK--------------------HMTRTIYTSP  348 (1248)
T ss_pred             CCCC-ccHHHHHHHHHH-HcCCeEEEEecCCCCcchHHHHHHHHH---Hh--------------------hccceEecch
Confidence            4564 778999999998 999999999999999998854443221   11                    2557999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      -++|.+|-++.++.-....|    +++|+
T Consensus       349 IKALSNQKfRDFk~tF~Dvg----LlTGD  373 (1248)
T KOG0947|consen  349 IKALSNQKFRDFKETFGDVG----LLTGD  373 (1248)
T ss_pred             hhhhccchHHHHHHhccccc----eeecc
Confidence            99999999999987655444    55555

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.83  E-value=8.8e-05  Score=76.64  Aligned_cols=100  Identities=17%  Similarity=0.103  Sum_probs=77.1

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|...--.+ +.|  -|+.-.||-||||++.+|+.-..+.                       +..+-|+++
T Consensus        82 lG~-r~ydVQliGgl~L-h~G--~IAEM~TGEGKTL~atlpaylnAL~-----------------------GkgVhVVTv  134 (939)
T PRK12902         82 LGM-RHFDVQLIGGMVL-HEG--QIAEMKTGEGKTLVATLPSYLNALT-----------------------GKGVHVVTV  134 (939)
T ss_pred             hCC-CcchhHHHhhhhh-cCC--ceeeecCCCChhHHHHHHHHHHhhc-----------------------CCCeEEEeC
Confidence            566 4899998766544 444  5789999999999999999764433                       445899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~  179 (284)
                      +--||..=+..+..+...+|++|+++.++. ..+.+......||...+
T Consensus       135 NdYLA~RDae~m~~vy~~LGLtvg~i~~~~-~~~err~aY~~DItYgT  181 (939)
T PRK12902        135 NDYLARRDAEWMGQVHRFLGLSVGLIQQDM-SPEERKKNYACDITYAT  181 (939)
T ss_pred             CHHHHHhHHHHHHHHHHHhCCeEEEECCCC-ChHHHHHhcCCCeEEec
Confidence            999999999999999999999999887654 33445555667775544

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

Probab=97.80  E-value=8.3e-05  Score=75.99  Aligned_cols=114  Identities=16%  Similarity=0.103  Sum_probs=77.8

Q ss_pred             CCcHHHHHHHHHHHcC---CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPALAHQ---RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~---G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      ..++-|+.|+..+..+   -.-.++.+.||||||-+|+=. +...+..                      +-++|||+|-
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~-i~~~L~~----------------------GkqvLvLVPE  254 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEA-IAKVLAQ----------------------GKQVLVLVPE  254 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHH-HHHHHHc----------------------CCEEEEEecc
Confidence            5678999999998433   267899999999999999644 4444442                      5689999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH-----HHHHhcCCCcccccccCCc--cccccccCCCC
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTS-----EHSNRRKPNKRKRTRKGGE--DEKLDSLKWNP  195 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q-----~~~l~~~~~i~v~~~~~~~--~d~l~~lv~dE  195 (284)
                      ..|..|+...++..   ++..++++.++-+..+     .+.......+++.++.-.+  +.+|--++.||
T Consensus       255 I~Ltpq~~~rf~~r---Fg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~Pf~~LGLIIvDE  321 (730)
T COG1198         255 IALTPQLLARFKAR---FGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFLPFKNLGLIIVDE  321 (730)
T ss_pred             ccchHHHHHHHHHH---hCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhcCchhhccEEEEec
Confidence            99999998888754   3456666666533222     2222334556666654433  56777766666

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=97.77  E-value=5e-05  Score=79.57  Aligned_cols=89  Identities=19%  Similarity=0.142  Sum_probs=69.6

Q ss_pred             HHHHH-HHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCC
Q 042526           45 LMKSI-YKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGH  123 (284)
Q Consensus        45 Ll~~L-~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (284)
                      ++..| ..+|+..+.|-|.+||-.+ +.|+|+++..|||.||.+||-||++-                          .+
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~-l~Gkd~fvlmpTG~GKSLCYQlPA~l--------------------------~~  304 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINAT-LSGKDCFVLMPTGGGKSLCYQLPALL--------------------------LG  304 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHH-HcCCceEEEeecCCceeeEeeccccc--------------------------cC
Confidence            44444 4589999999999999988 99999999999999999999999863                          12


Q ss_pred             eEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcch
Q 042526          124 LRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLT  164 (284)
Q Consensus       124 ~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~  164 (284)
                      ...|||.|...|.......+    ...+|..+.+.|+....
T Consensus       305 gitvVISPL~SLm~DQv~~L----~~~~I~a~~L~s~q~~~  341 (941)
T KOG0351|consen  305 GVTVVISPLISLMQDQVTHL----SKKGIPACFLSSIQTAA  341 (941)
T ss_pred             CceEEeccHHHHHHHHHHhh----hhcCcceeeccccccHH
Confidence            26899999999976544444    23477777777776554

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=97.68  E-value=0.00017  Score=65.57  Aligned_cols=87  Identities=20%  Similarity=0.198  Sum_probs=67.3

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|+ .|.++|..++=.+ ..|+  |+.=.||-|||++..+|++-..+.                       +-.+=|++.
T Consensus        74 ~g~-~p~~vQll~~l~L-~~G~--laEm~TGEGKTli~~l~a~~~AL~-----------------------G~~V~vvT~  126 (266)
T PF07517_consen   74 LGL-RPYDVQLLGALAL-HKGR--LAEMKTGEGKTLIAALPAALNALQ-----------------------GKGVHVVTS  126 (266)
T ss_dssp             TS-----HHHHHHHHHH-HTTS--EEEESTTSHHHHHHHHHHHHHHTT-----------------------SS-EEEEES
T ss_pred             cCC-cccHHHHhhhhhc-ccce--eEEecCCCCcHHHHHHHHHHHHHh-----------------------cCCcEEEec
Confidence            566 5999999999766 6676  889999999999998888654433                       456889999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTS  165 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q  165 (284)
                      +.-||..=+..+..|...+|++|.++.++....+
T Consensus       127 NdyLA~RD~~~~~~~y~~LGlsv~~~~~~~~~~~  160 (266)
T PF07517_consen  127 NDYLAKRDAEEMRPFYEFLGLSVGIITSDMSSEE  160 (266)
T ss_dssp             SHHHHHHHHHHHHHHHHHTT--EEEEETTTEHHH
T ss_pred             cHHHhhccHHHHHHHHHHhhhccccCccccCHHH
Confidence            9999999999999999999999999988766544

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.67  E-value=5.6e-05  Score=81.38  Aligned_cols=129  Identities=18%  Similarity=0.118  Sum_probs=68.9

Q ss_pred             cCCCCCcHHHH--HHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           52 LGFKESTSILK--ARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        52 ~g~~~pT~iQ~--~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      ..|....||..  ..|...+..+..+|++|+||||||.  .+|.+..  ...                 . ......++.
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~ll--e~~-----------------~-~~~~~I~~t  117 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKICL--ELG-----------------R-GSHGLIGHT  117 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHH--HcC-----------------C-CCCceEecC
Confidence            46766677766  3444443667788999999999997  4575532  210                 0 011122233


Q ss_pred             ecCHHHHHHHHHHHhhhhcCCCceeEEEeCC--CcchHHHHHhcCCCccccc--------ccCCccccccccCCCCCC-c
Q 042526          130 NPTRELALQVLMVASPSLKSNSLTLAMAAGS--PLLTSEHSNRRKPNKRKRT--------RKGGEDEKLDSLKWNPLS-Q  198 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~--~~~~q~~~l~~~~~i~v~~--------~~~~~~d~l~~lv~dEAd-~  198 (284)
                      -|-|--|..++.   +++..++..+...+|-  ....+.   .....|.+.|        .....+.++.++|+|||+ +
T Consensus       118 QPRRlAA~svA~---RvA~elg~~lG~~VGY~vR~~~~~---s~~T~I~~~TdGiLLr~l~~d~~L~~~~~IIIDEaHER  191 (1283)
T TIGR01967       118 QPRRLAARTVAQ---RIAEELGTPLGEKVGYKVRFHDQV---SSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHER  191 (1283)
T ss_pred             CccHHHHHHHHH---HHHHHhCCCcceEEeeEEcCCccc---CCCceeeeccccHHHHHhhhCcccccCcEEEEcCcchh
Confidence            355544444333   2333334333333332  111111   1223332222        122357889999999999 5


Q ss_pred             ccccccccch
Q 042526          199 PKTTTLLPSS  208 (284)
Q Consensus       199 m~~~gflp~~  208 (284)
                      +++++|+-+.
T Consensus       192 sL~~D~LL~l  201 (1283)
T TIGR01967       192 SLNIDFLLGY  201 (1283)
T ss_pred             hccchhHHHH
Confidence            9999988764

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.

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

Probab=97.65  E-value=0.00043  Score=73.14  Aligned_cols=135  Identities=12%  Similarity=0.018  Sum_probs=93.4

Q ss_pred             CCCHHHHHHHHH-cCCCCCcHHHHHHHHHH---HcCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           40 RLHPLLMKSIYK-LGFKESTSILKARIPAL---AHQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        40 ~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~i---l~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      ..+......+.+ ++|+ -||=|..||..+   +.++  .|=++|+--|-|||-..+=++.-.+                
T Consensus       578 ~~d~~~q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV----------------  640 (1139)
T COG1197         578 PPDTEWQEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAV----------------  640 (1139)
T ss_pred             CCChHHHHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHh----------------
Confidence            345555555544 6775 899999999988   2334  4889999999999977664443322                


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHh----c-CCCcccccccCC----c
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNR----R-KPNKRKRTRKGG----E  184 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~----~-~~~i~v~~~~~~----~  184 (284)
                             ..+.|+.|||||--||.|-++.++.=...++++|..+.-.....+.....    . ..||+|.|-.+.    .
T Consensus       641 -------~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~  713 (1139)
T COG1197         641 -------MDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVK  713 (1139)
T ss_pred             -------cCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcE
Confidence                   24689999999999999999999876677788888877665444443332    2 377887773332    3


Q ss_pred             cccccccCCCCCCc
Q 042526          185 DEKLDSLKWNPLSQ  198 (284)
Q Consensus       185 ~d~l~~lv~dEAd~  198 (284)
                      +..|--|+.||--+
T Consensus       714 FkdLGLlIIDEEqR  727 (1139)
T COG1197         714 FKDLGLLIIDEEQR  727 (1139)
T ss_pred             EecCCeEEEechhh
Confidence            44555566666433

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

Probab=97.65  E-value=0.00013  Score=74.46  Aligned_cols=71  Identities=17%  Similarity=0.138  Sum_probs=52.9

Q ss_pred             CcHHHHHHHHHHH---cC------CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           57 STSILKARIPALA---HQ------RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        57 pT~iQ~~aip~il---~~------G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      |.+.|..|+..++   ..      .+..++..+||||||++.+.-+. .+...                    ...+++|
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~-~l~~~--------------------~~~~~vl  297 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAAR-KALEL--------------------LKNPKVF  297 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHH-HHHhh--------------------cCCCeEE
Confidence            5678988887762   22      35688889999999987655443 22221                    1467899


Q ss_pred             EEecCHHHHHHHHHHHhhhhc
Q 042526          128 IINPTRELALQVLMVASPSLK  148 (284)
Q Consensus       128 IL~PTReLa~Qi~~~~~~l~~  148 (284)
                      ||+|+++|..|+.+.+..+..
T Consensus       298 ~lvdR~~L~~Q~~~~f~~~~~  318 (667)
T TIGR00348       298 FVVDRRELDYQLMKEFQSLQK  318 (667)
T ss_pred             EEECcHHHHHHHHHHHHhhCC
Confidence            999999999999999998753

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

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

Probab=97.62  E-value=0.00018  Score=62.24  Aligned_cols=73  Identities=12%  Similarity=0.140  Sum_probs=50.0

Q ss_pred             CcHHHHHHHHHHHcCCCc-EEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           57 STSILKARIPALAHQRKD-VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        57 pT~iQ~~aip~il~~G~d-viv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      +.+-|..||-.+ +.... .++++|+|||||. .+..++..+.....              ......+...||++||..-
T Consensus         2 ln~~Q~~Ai~~~-~~~~~~~~i~GpPGTGKT~-~l~~~i~~~~~~~~--------------~~~~~~~~~il~~~~sN~a   65 (236)
T PF13086_consen    2 LNESQREAIQSA-LSSNGITLIQGPPGTGKTT-TLASIIAQLLQRFK--------------SRSADRGKKILVVSPSNAA   65 (236)
T ss_dssp             --HHHHHHHHHH-CTSSE-EEEE-STTSSHHH-HHHHHHHHH---------------------HCCCSS-EEEEESSHHH
T ss_pred             CCHHHHHHHHHH-HcCCCCEEEECCCCCChHH-HHHHHHHHhccchh--------------hhhhhccccceeecCCchh
Confidence            568899999988 78888 9999999999993 33445554432100              0112356789999999999


Q ss_pred             HHHHHHHHhh
Q 042526          136 ALQVLMVASP  145 (284)
Q Consensus       136 a~Qi~~~~~~  145 (284)
                      +.++...+..
T Consensus        66 vd~~~~~l~~   75 (236)
T PF13086_consen   66 VDNILERLKK   75 (236)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHh
Confidence            9999998887

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=97.56  E-value=7.1e-05  Score=78.90  Aligned_cols=99  Identities=22%  Similarity=0.162  Sum_probs=75.8

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      |....|||.++++.+.....+|++.||+|||||.+.-+.++.   .                     ...-+|++++|.-
T Consensus      1141 f~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~---~---------------------~~~~~~vyi~p~~ 1196 (1674)
T KOG0951|consen 1141 FQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR---P---------------------DTIGRAVYIAPLE 1196 (1674)
T ss_pred             ccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC---C---------------------ccceEEEEecchH
Confidence            334489999999999777889999999999999999888775   1                     1356899999999


Q ss_pred             HHHHHHHHHHh-hhhcCCCceeEEEeCCCcchHHHHHhcCCCcccc
Q 042526          134 ELALQVLMVAS-PSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKR  178 (284)
Q Consensus       134 eLa~Qi~~~~~-~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~  178 (284)
                      +.+.-.+..+. +|....|..+.-++|.....  ..+....++++.
T Consensus      1197 ~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~~--lkl~~~~~vii~ 1240 (1674)
T KOG0951|consen 1197 EIADEQYRDWEKKFSKLLGLRIVKLTGETSLD--LKLLQKGQVIIS 1240 (1674)
T ss_pred             HHHHHHHHHHHHhhccccCceEEecCCccccc--hHHhhhcceEEe
Confidence            99998777765 56666788888888886554  333444444443

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

Probab=97.55  E-value=0.00046  Score=59.84  Aligned_cols=65  Identities=20%  Similarity=0.201  Sum_probs=44.3

Q ss_pred             CCcHHHHHHHHHHHcCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           56 ESTSILKARIPALAHQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ++|+-|..|+-.++.++ +-++++++.|||||.+  +-.+...+..                     .+..+++++||..
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~--l~~~~~~~~~---------------------~g~~v~~~apT~~   57 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL--LKALAEALEA---------------------AGKRVIGLAPTNK   57 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH--HHHHHHHHHH---------------------TT--EEEEESSHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH--HHHHHHHHHh---------------------CCCeEEEECCcHH
Confidence            46888999999984444 3477889999999953  3333333332                     2467999999999


Q ss_pred             HHHHHHHHH
Q 042526          135 LALQVLMVA  143 (284)
Q Consensus       135 La~Qi~~~~  143 (284)
                      .+..+...+
T Consensus        58 Aa~~L~~~~   66 (196)
T PF13604_consen   58 AAKELREKT   66 (196)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhh
Confidence            988877763

>PF13245 AAA_19: Part of AAA domain

Probab=97.55  E-value=0.00038  Score=51.24  Aligned_cols=53  Identities=25%  Similarity=0.304  Sum_probs=36.5

Q ss_pred             CCc-EEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHH
Q 042526           72 RKD-VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA  143 (284)
Q Consensus        72 G~d-viv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~  143 (284)
                      +.. +++.|++|||||...+- ++..+....                 ... +-++||++||+..+..+.+.+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~-~i~~l~~~~-----------------~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAA-RIAELLAAR-----------------ADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHH-HHHHHHHHh-----------------cCC-CCeEEEECCCHHHHHHHHHHH
Confidence            445 45599999999965543 333333221                 111 557999999999999998887

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=97.49  E-value=0.00013  Score=73.52  Aligned_cols=71  Identities=20%  Similarity=0.207  Sum_probs=58.6

Q ss_pred             CcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHH
Q 042526           57 STSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA  136 (284)
Q Consensus        57 pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa  136 (284)
                      +-|+|..||-.+ -++.+|++.|.|.+|||.+.-.+|...+...                       -++|+-+|-++|.
T Consensus       130 LDpFQ~~aI~Ci-dr~eSVLVSAHTSAGKTVVAeYAIA~sLr~k-----------------------QRVIYTSPIKALS  185 (1041)
T KOG0948|consen  130 LDPFQSTAIKCI-DRGESVLVSAHTSAGKTVVAEYAIAMSLREK-----------------------QRVIYTSPIKALS  185 (1041)
T ss_pred             cCchHhhhhhhh-cCCceEEEEeecCCCcchHHHHHHHHHHHhc-----------------------CeEEeeChhhhhc
Confidence            568999999999 9999999999999999998777776655443                       2699999999999


Q ss_pred             HHHHHHHhhhhcCCC
Q 042526          137 LQVLMVASPSLKSNS  151 (284)
Q Consensus       137 ~Qi~~~~~~l~~~~~  151 (284)
                      +|-|+++..=.+..|
T Consensus       186 NQKYREl~~EF~DVG  200 (1041)
T KOG0948|consen  186 NQKYRELLEEFKDVG  200 (1041)
T ss_pred             chhHHHHHHHhcccc
Confidence            999998865434333

>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=97.26  E-value=0.00091  Score=60.69  Aligned_cols=70  Identities=20%  Similarity=0.069  Sum_probs=50.2

Q ss_pred             CcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHH
Q 042526           57 STSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA  136 (284)
Q Consensus        57 pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa  136 (284)
                      +|+-|..+|-.   ...+++|.|..|||||.+.+--++..+...                   .....+.|+|++|+..|
T Consensus         1 l~~eQ~~~i~~---~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~-------------------~~~~~~Il~lTft~~aa   58 (315)
T PF00580_consen    1 LTDEQRRIIRS---TEGPLLVNAGAGSGKTTTLLERIAYLLYEG-------------------GVPPERILVLTFTNAAA   58 (315)
T ss_dssp             S-HHHHHHHHS----SSEEEEEE-TTSSHHHHHHHHHHHHHHTS-------------------SSTGGGEEEEESSHHHH
T ss_pred             CCHHHHHHHhC---CCCCEEEEeCCCCCchHHHHHHHHHhhccc-------------------cCChHHheecccCHHHH
Confidence            47889998864   477999999999999977655544333221                   12344699999999999


Q ss_pred             HHHHHHHhhhhc
Q 042526          137 LQVLMVASPSLK  148 (284)
Q Consensus       137 ~Qi~~~~~~l~~  148 (284)
                      ..+...+..+..
T Consensus        59 ~e~~~ri~~~l~   70 (315)
T PF00580_consen   59 QEMRERIRELLE   70 (315)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC
Confidence            999998887654

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 ....

>TIGR00376 DNA helicase, putative

Probab=97.17  E-value=0.0019  Score=65.77  Aligned_cols=67  Identities=16%  Similarity=0.210  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+++.|..|+..++.....+++++|+|||||.+. .-++..+..                      .+.++||++||..-
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~-~~ii~~~~~----------------------~g~~VLv~a~sn~A  213 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL-VELIRQLVK----------------------RGLRVLVTAPSNIA  213 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHH----------------------cCCCEEEEcCcHHH
Confidence            4588999999988333367889999999999544 344433333                      24589999999999


Q ss_pred             HHHHHHHHhh
Q 042526          136 ALQVLMVASP  145 (284)
Q Consensus       136 a~Qi~~~~~~  145 (284)
                      |.++...+..
T Consensus       214 vd~l~e~l~~  223 (637)
T TIGR00376       214 VDNLLERLAL  223 (637)
T ss_pred             HHHHHHHHHh
Confidence            9998887765

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=97.02  E-value=0.002  Score=63.15  Aligned_cols=72  Identities=18%  Similarity=0.152  Sum_probs=50.5

Q ss_pred             CCcHHHHHHHHHHH----cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALA----HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il----~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|+.=|-.||..+.    ..-+.-++.+-||||||++.. -+|.   +.                     +.| +|||+|
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~A-nVI~---~~---------------------~rP-tLV~Ah   65 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMA-NVIA---KV---------------------QRP-TLVLAH   65 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHH-HHHH---Hh---------------------CCC-eEEEec
Confidence            36666777776652    223467788899999996643 1222   21                     122 899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCce
Q 042526          132 TRELALQVLMVASPSLKSNSLT  153 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~  153 (284)
                      .+-||-|+|++++.|....-+.
T Consensus        66 NKTLAaQLy~Efk~fFP~NaVE   87 (663)
T COG0556          66 NKTLAAQLYSEFKEFFPENAVE   87 (663)
T ss_pred             chhHHHHHHHHHHHhCcCcceE
Confidence            9999999999999998765543

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=96.98  E-value=0.0021  Score=66.49  Aligned_cols=77  Identities=23%  Similarity=0.158  Sum_probs=60.3

Q ss_pred             CcHHHHHHHHHHH--cCCC-cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           57 STSILKARIPALA--HQRK-DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        57 pT~iQ~~aip~il--~~G~-dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      +.+.|..++..+.  .... .+++.||||.|||.+.+++++..+...                   .....+.+++.|+|
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~-------------------~~~~~r~i~vlP~~  256 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK-------------------IKLKSRVIYVLPFR  256 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc-------------------ccccceEEEEccHH
Confidence            3788888887762  1234 789999999999999999988765542                   12467899999999


Q ss_pred             HHHHHHHHHHhhhhcCCCc
Q 042526          134 ELALQVLMVASPSLKSNSL  152 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~~i  152 (284)
                      .++.++++.++......++
T Consensus       257 t~ie~~~~r~~~~~~~~~~  275 (733)
T COG1203         257 TIIEDMYRRAKEIFGLFSV  275 (733)
T ss_pred             HHHHHHHHHHHhhhccccc
Confidence            9999999999987665443

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=96.78  E-value=0.0042  Score=56.07  Aligned_cols=72  Identities=22%  Similarity=0.172  Sum_probs=44.3

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN  150 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~  150 (284)
                      ..+..+++-.+|+|||+..+.-+. .+....                 .....-.+|||||+ .+..|...++..+....
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~-----------------~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~   84 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALIS-YLKNEF-----------------PQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPD   84 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHHH-HHHHCC-----------------TTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-
T ss_pred             CCCCEEEEECCCCCchhhhhhhhh-hhhhcc-----------------ccccccceeEeecc-chhhhhhhhhccccccc
Confidence            457889999999999977654433 333311                 11111249999999 88899999999998655


Q ss_pred             CceeEEEeCCC
Q 042526          151 SLTLAMAAGSP  161 (284)
Q Consensus       151 ~i~v~~~~G~~  161 (284)
                      .+.+.++.|..
T Consensus        85 ~~~v~~~~~~~   95 (299)
T PF00176_consen   85 SLRVIIYDGDS   95 (299)
T ss_dssp             TS-EEEESSSC
T ss_pred             ccccccccccc
Confidence            66777777776

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=96.72  E-value=0.003  Score=65.41  Aligned_cols=108  Identities=19%  Similarity=0.148  Sum_probs=82.5

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHH--HHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARI--PALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKML  108 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~ai--p~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~  108 (284)
                      +....|..-+++....-.....|+..++..|..|+  |.+ +.+.++|..+||+-|||++.-|-++..++..+       
T Consensus       198 tl~~~~a~~~~~k~~~~~~~~kgi~~~fewq~ecls~~~~-~e~~nliys~Pts~gktlvaeilml~~~l~~r-------  269 (1008)
T KOG0950|consen  198 TLLFGFAKRLPTKVSHLYAKDKGILKLFEWQAECLSLPRL-LERKNLIYSLPTSAGKTLVAEILMLREVLCRR-------  269 (1008)
T ss_pred             hhhhhhhhcCchHHHHHHHHhhhHHHHHHHHHHHhcchhh-hcccceEEeCCCccchHHHHHHHHHHHHHHHh-------
Confidence            33334444333333334445689999999999988  677 78999999999999999999999998877653       


Q ss_pred             hhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC
Q 042526          109 EEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP  161 (284)
Q Consensus       109 ~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~  161 (284)
                                     -.++.+.|....+..-...+..|+...|+.|-.++|..
T Consensus       270 ---------------r~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g~~  307 (1008)
T KOG0950|consen  270 ---------------RNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAGRF  307 (1008)
T ss_pred             ---------------hceeEecceeehhHHHHhhhhhhccccCCcchhhcccC
Confidence                           13777778888877777788888888999998888764

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=96.71  E-value=0.0033  Score=52.03  Aligned_cols=54  Identities=20%  Similarity=0.246  Sum_probs=38.9

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      .|.=-++--.+|+|||--.+.-++.....                      .+.+.|||.|||.+|..++..++.+
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~----------------------~~~rvLvL~PTRvva~em~~aL~~~   56 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK----------------------RRLRVLVLAPTRVVAEEMYEALKGL   56 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH----------------------TT--EEEEESSHHHHHHHHHHTTTS
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH----------------------ccCeEEEecccHHHHHHHHHHHhcC
Confidence            45556778889999998777666654444                      2568999999999999999988755

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.61  E-value=0.0097  Score=61.83  Aligned_cols=100  Identities=12%  Similarity=-0.003  Sum_probs=74.3

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|...-=.+ ..|+  |+.-.||-||||+..+|+.-..+.                       |-.+-|++.
T Consensus        75 lG~-r~ydVQliGglvL-h~G~--IAEMkTGEGKTLvAtLpayLnAL~-----------------------GkgVhVVTv  127 (925)
T PRK12903         75 LGK-RPYDVQIIGGIIL-DLGS--VAEMKTGEGKTITSIAPVYLNALT-----------------------GKGVIVSTV  127 (925)
T ss_pred             hCC-CcCchHHHHHHHH-hcCC--eeeecCCCCccHHHHHHHHHHHhc-----------------------CCceEEEec
Confidence            566 6999998877655 6664  788999999999999998654333                       334778888


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~  179 (284)
                      +-=||..=...+..+...+|++|+++..+....+ +.-....+|...+
T Consensus       128 NdYLA~RDae~mg~vy~fLGLsvG~i~~~~~~~~-rr~aY~~DItYgT  174 (925)
T PRK12903        128 NEYLAERDAEEMGKVFNFLGLSVGINKANMDPNL-KREAYACDITYSV  174 (925)
T ss_pred             chhhhhhhHHHHHHHHHHhCCceeeeCCCCChHH-HHHhccCCCeeec
Confidence            8999999899999999999999988876543333 3334456664443

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

Probab=96.59  E-value=0.0061  Score=56.97  Aligned_cols=112  Identities=16%  Similarity=0.118  Sum_probs=75.0

Q ss_pred             CCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      ++||.|..+-..+   +.+..|++++|-||+|||-. +.+.++..+++                      |-++.|.+|-
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~----------------------G~~vciASPR  153 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQ----------------------GGRVCIASPR  153 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhc----------------------CCeEEEecCc
Confidence            6788887765544   26688999999999999953 45666666553                      5678888999


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc--ccCCccccccccCCCCCCc
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT--RKGGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~--~~~~~~d~l~~lv~dEAd~  198 (284)
                      .+.|..++..++.-..  ++.+.+++|++.....     . .+++.+  ..+.+-+...-+..||.|-
T Consensus       154 vDVclEl~~Rlk~aF~--~~~I~~Lyg~S~~~fr-----~-plvVaTtHQLlrFk~aFD~liIDEVDA  213 (441)
T COG4098         154 VDVCLELYPRLKQAFS--NCDIDLLYGDSDSYFR-----A-PLVVATTHQLLRFKQAFDLLIIDEVDA  213 (441)
T ss_pred             ccchHHHHHHHHHhhc--cCCeeeEecCCchhcc-----c-cEEEEehHHHHHHHhhccEEEEecccc
Confidence            9999988888775433  4677788887654432     2 333333  1223444555566677665

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.42  E-value=0.0089  Score=55.85  Aligned_cols=50  Identities=18%  Similarity=0.253  Sum_probs=37.1

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           45 LMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        45 Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      -+..|-..|+  +++.|...+..++..+.+++++++|||||| +++-.++..+
T Consensus       123 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~  172 (319)
T PRK13894        123 TLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEM  172 (319)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhh
Confidence            4455555665  567788888766588999999999999999 6666666544

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=96.42  E-value=0.0071  Score=60.11  Aligned_cols=64  Identities=20%  Similarity=0.163  Sum_probs=47.1

Q ss_pred             CCcHHHHHHHHHHHcCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           56 ESTSILKARIPALAHQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      .+.+-|.+|+... ... .-+++++|+|||||.+...-+.+ +...                      +-++||.+||++
T Consensus       185 ~ln~SQk~Av~~~-~~~k~l~~I~GPPGTGKT~TlvEiI~q-lvk~----------------------~k~VLVcaPSn~  240 (649)
T KOG1803|consen  185 NLNSSQKAAVSFA-INNKDLLIIHGPPGTGKTRTLVEIISQ-LVKQ----------------------KKRVLVCAPSNV  240 (649)
T ss_pred             cccHHHHHHHHHH-hccCCceEeeCCCCCCceeeHHHHHHH-HHHc----------------------CCeEEEEcCchH
Confidence            3456889999887 444 45688999999999776554444 4442                      357999999999


Q ss_pred             HHHHHHHHH
Q 042526          135 LALQVLMVA  143 (284)
Q Consensus       135 La~Qi~~~~  143 (284)
                      -+.-|.+.+
T Consensus       241 AVdNiverl  249 (649)
T KOG1803|consen  241 AVDNIVERL  249 (649)
T ss_pred             HHHHHHHHh
Confidence            888887753

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.40  E-value=0.03  Score=57.89  Aligned_cols=67  Identities=24%  Similarity=0.130  Sum_probs=46.7

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .++ .+++-|..|+-.+ ...+-+++.+.+|||||... -.++.. ....                   .....+++++|
T Consensus       320 ~~~-~l~~~Q~~Ai~~~-~~~~~~iitGgpGTGKTt~l-~~i~~~-~~~~-------------------~~~~~v~l~Ap  376 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTA-IQHKVVILTGGPGTGKTTIT-RAIIEL-AEEL-------------------GGLLPVGLAAP  376 (720)
T ss_pred             cCC-CCCHHHHHHHHHH-HhCCeEEEECCCCCCHHHHH-HHHHHH-HHHc-------------------CCCceEEEEeC
Confidence            454 5899999999998 78889999999999999432 223322 2210                   01145778899


Q ss_pred             CHHHHHHHHH
Q 042526          132 TRELALQVLM  141 (284)
Q Consensus       132 TReLa~Qi~~  141 (284)
                      |---|..+..
T Consensus       377 Tg~AA~~L~e  386 (720)
T TIGR01448       377 TGRAAKRLGE  386 (720)
T ss_pred             chHHHHHHHH
Confidence            9888776554

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=96.39  E-value=0.02  Score=57.83  Aligned_cols=68  Identities=18%  Similarity=0.195  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHH
Q 042526           59 SILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ  138 (284)
Q Consensus        59 ~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Q  138 (284)
                      ..|+.|+-.+ +..+-+++.+++|||||... ..++..+....                 .....+++++.+||---|..
T Consensus       148 ~~Qk~A~~~a-l~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~-----------------~~~~~~~I~l~APTGkAA~r  208 (586)
T TIGR01447       148 NWQKVAVALA-LKSNFSLITGGPGTGKTTTV-ARLLLALVKQS-----------------PKQGKLRIALAAPTGKAAAR  208 (586)
T ss_pred             HHHHHHHHHH-hhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhc-----------------cccCCCcEEEECCcHHHHHH
Confidence            6788899888 78889999999999999543 23333333221                 00013578899999888877


Q ss_pred             HHHHHhh
Q 042526          139 VLMVASP  145 (284)
Q Consensus       139 i~~~~~~  145 (284)
                      +...+..
T Consensus       209 L~e~~~~  215 (586)
T TIGR01447       209 LAESLRK  215 (586)
T ss_pred             HHHHHHh
Confidence            7666544

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

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

Probab=96.24  E-value=0.02  Score=60.50  Aligned_cols=51  Identities=18%  Similarity=0.158  Sum_probs=40.1

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVAS  144 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~  144 (284)
                      .++.+.-+||||||.+|+-.|+......                     +....||+||+.+.-..+.+-++
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~---------------------~~~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKY---------------------GLFKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHc---------------------CCcEEEEEeCCHHHHHHHHHHhh
Confidence            4789999999999999987776543221                     35679999999999888877665

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.14  E-value=0.014  Score=54.64  Aligned_cols=48  Identities=17%  Similarity=0.192  Sum_probs=34.7

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           47 KSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        47 ~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..+-..|.  .++-|...+-.++..+.+++++++|||||| +++-.++..+
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKT-Tll~aL~~~i  168 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKT-TLANAVIAEI  168 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHHH
Confidence            34445554  567788777777688899999999999999 4445555544

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.08  E-value=0.03  Score=55.08  Aligned_cols=93  Identities=18%  Similarity=0.255  Sum_probs=65.3

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccC-CCCc--hHHhHHHHHHHHHHHHHHHHHHHhh-hh-------hhhhhcCCCCC
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAET-ESGK--TRAFGLPALQRLLEEREKAAKMLEE-KG-------EEAEKYAPKGH  123 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~T-GSGK--TlafllPil~~l~~~~~~~~~~~~~-~~-------~~~~~~~~~~~  123 (284)
                      ..+|+.|.+.+-+. .+-+|++..-.| ++|.  +-.|++-+|+++++.+.+.-.+... .+       ...-.......
T Consensus       215 ~pltalQ~~L~~~m-~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tR  293 (698)
T KOG2340|consen  215 EPLTALQKELFKIM-FNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTR  293 (698)
T ss_pred             CcchHHHHHHHHHH-HhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCC
Confidence            46799999999887 889999764333 3455  5679999999998875532222111 11       11112234567


Q ss_pred             eEEEEEecCHHHHHHHHHHHhhhhc
Q 042526          124 LRALIINPTRELALQVLMVASPSLK  148 (284)
Q Consensus       124 ~~aLIL~PTReLa~Qi~~~~~~l~~  148 (284)
                      |.+|||||+||-|..|.+.+..++.
T Consensus       294 pkVLivvpfRe~A~riVn~lis~l~  318 (698)
T KOG2340|consen  294 PKVLIVVPFRESAYRIVNLLISLLS  318 (698)
T ss_pred             ceEEEEecchHHHHHHHHHHHHHhc
Confidence            9999999999999999999998854

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.07  E-value=0.035  Score=57.07  Aligned_cols=82  Identities=15%  Similarity=0.075  Sum_probs=55.2

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..+|+-|+.|+-   ....+++|.|..|||||.+.+ .-+.++....                  ....-++|+|+.||.
T Consensus       195 ~~L~~~Q~~av~---~~~~~~lV~agaGSGKT~vl~-~r~ayLl~~~------------------~~~~~~IL~ltft~~  252 (684)
T PRK11054        195 SPLNPSQARAVV---NGEDSLLVLAGAGSGKTSVLV-ARAGWLLARG------------------QAQPEQILLLAFGRQ  252 (684)
T ss_pred             CCCCHHHHHHHh---CCCCCeEEEEeCCCCHHHHHH-HHHHHHHHhC------------------CCCHHHeEEEeccHH
Confidence            468999999984   334578999999999996554 3333333321                  112336999999999


Q ss_pred             HHHHHHHHHhhhhcCCCceeEEEe
Q 042526          135 LALQVLMVASPSLKSNSLTLAMAA  158 (284)
Q Consensus       135 La~Qi~~~~~~l~~~~~i~v~~~~  158 (284)
                      .|..+...+.......++.+..+.
T Consensus       253 AA~em~eRL~~~lg~~~v~v~TFH  276 (684)
T PRK11054        253 AAEEMDERIRERLGTEDITARTFH  276 (684)
T ss_pred             HHHHHHHHHHHhcCCCCcEEEeHH
Confidence            999998887765543344444443

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=96.05  E-value=0.041  Score=55.83  Aligned_cols=70  Identities=17%  Similarity=0.145  Sum_probs=48.9

Q ss_pred             cHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHH
Q 042526           58 TSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELAL  137 (284)
Q Consensus        58 T~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~  137 (284)
                      ++.|+.|+-.. +..+-+++.+++|||||.+. .-++..+....                  ......+++.+||.--|.
T Consensus       154 ~d~Qk~Av~~a-~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~------------------~~~~~~i~l~APTgkAA~  213 (615)
T PRK10875        154 VDWQKVAAAVA-LTRRISVISGGPGTGKTTTV-AKLLAALIQLA------------------DGERCRIRLAAPTGKAAA  213 (615)
T ss_pred             CHHHHHHHHHH-hcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhc------------------CCCCcEEEEECCcHHHHH
Confidence            57899999887 88889999999999999543 22233222210                  012356888899998888


Q ss_pred             HHHHHHhhhh
Q 042526          138 QVLMVASPSL  147 (284)
Q Consensus       138 Qi~~~~~~l~  147 (284)
                      .+...+....
T Consensus       214 rL~e~~~~~~  223 (615)
T PRK10875        214 RLTESLGKAL  223 (615)
T ss_pred             HHHHHHHhhh
Confidence            8887665433

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.00  E-value=0.012  Score=60.00  Aligned_cols=68  Identities=19%  Similarity=0.143  Sum_probs=50.4

Q ss_pred             CCcHHHHHHHHHHH---cCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALA---HQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|+--|..+|..+.   ..| +..++.+-||||||+... -++    ...                     +..+|||+|
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a-~~~----~~~---------------------~~p~Lvi~~   62 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA-NVI----AQV---------------------NRPTLVIAH   62 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHH-HHH----HHh---------------------CCCEEEEEC
Confidence            48899999998772   223 366789999999996643 222    211                     123899999


Q ss_pred             CHHHHHHHHHHHhhhhcC
Q 042526          132 TRELALQVLMVASPSLKS  149 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~  149 (284)
                      +..+|.|+++.++.|...
T Consensus        63 n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631        63 NKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CHHHHHHHHHHHHHhCCC
Confidence            999999999999998754

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

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.95  E-value=0.019  Score=53.10  Aligned_cols=51  Identities=20%  Similarity=0.290  Sum_probs=35.0

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           44 LLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        44 ~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .-+..|...|.  +++-|...+..++..+.+++++++|||||| +++-.++..+
T Consensus       106 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~al~~~i  156 (299)
T TIGR02782       106 FTLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKT-TLANALLAEI  156 (299)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHHh
Confidence            34455555554  556667777666577889999999999999 4444555444

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.

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=95.93  E-value=0.032  Score=57.70  Aligned_cols=94  Identities=12%  Similarity=0.045  Sum_probs=59.8

Q ss_pred             CCcHHHHHHHHHHH---cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh--------------hhhhc
Q 042526           56 ESTSILKARIPALA---HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE--------------EAEKY  118 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~--------------~~~~~  118 (284)
                      .|+|.|...+-.++   ..+.+.++-+||||||||+.|...|........+..........              .....
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            48999988876662   55778999999999999999988887765543111111100000              00000


Q ss_pred             -----CCCCCeEEEEEecCHHHHHHHHHHHhhhhcC
Q 042526          119 -----APKGHLRALIINPTRELALQVLMVASPSLKS  149 (284)
Q Consensus       119 -----~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~  149 (284)
                           ....-|...+=+-|..-..|+.+++++....
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~  136 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYR  136 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcCCC
Confidence                 0123566677777777788888888877654

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=95.83  E-value=0.035  Score=55.97  Aligned_cols=76  Identities=11%  Similarity=-0.011  Sum_probs=58.0

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           48 SIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        48 ~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      .+...|+..+..-|..|+.++ ++..=-++++|+|||||++-.--+++.+..                      ..-.+|
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~V-L~rplsLIQGPPGTGKTvtsa~IVyhl~~~----------------------~~~~VL  458 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHV-LQRPLSLIQGPPGTGKTVTSATIVYHLARQ----------------------HAGPVL  458 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHH-HcCCceeeecCCCCCceehhHHHHHHHHHh----------------------cCCceE
Confidence            344567788889999999999 877788999999999998765444443222                      133489


Q ss_pred             EEecCHHHHHHHHHHHhhh
Q 042526          128 IINPTRELALQVLMVASPS  146 (284)
Q Consensus       128 IL~PTReLa~Qi~~~~~~l  146 (284)
                      |.+|+.--+.|++.-+.+.
T Consensus       459 vcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  459 VCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             EEcccchhHHHHHHHHHhc
Confidence            9999999999988777643

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.79  E-value=0.021  Score=58.40  Aligned_cols=98  Identities=15%  Similarity=0.045  Sum_probs=58.3

Q ss_pred             EEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeE
Q 042526           76 IGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLA  155 (284)
Q Consensus        76 iv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~  155 (284)
                      +..+.+|||||-.|+-.+-. .+.                      .+-++|||+|...|+.|+...++....  +..++
T Consensus       164 i~~~~~GSGKTevyl~~i~~-~l~----------------------~Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~  218 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAA-TLR----------------------AGRGALVVVPDQRDVDRLEAALRALLG--AGDVA  218 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHH-HHH----------------------cCCeEEEEecchhhHHHHHHHHHHHcC--CCcEE
Confidence            33444699999999754433 333                      245799999999999999999885432  14566


Q ss_pred             EEeCCCcchH----HHHHhcC-CCcccccccCCc--ccccccc-CCCCCCc
Q 042526          156 MAAGSPLLTS----EHSNRRK-PNKRKRTRKGGE--DEKLDSL-KWNPLSQ  198 (284)
Q Consensus       156 ~~~G~~~~~q----~~~l~~~-~~i~v~~~~~~~--~d~l~~l-v~dEAd~  198 (284)
                      ++.+.....+    ...+..+ ..|++.++...+  +.+|--+ ++||.|.
T Consensus       219 ~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAvFaP~~~LgLIIvdEEhd~  269 (665)
T PRK14873        219 VLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDLGLVAIWDDGDD  269 (665)
T ss_pred             EECCCCCHHHHHHHHHHHhCCCCcEEEEcceeEEeccCCCCEEEEEcCCch
Confidence            6766643332    2223333 567776654332  3344333 3444443

>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=95.79  E-value=0.019  Score=50.30  Aligned_cols=45  Identities=27%  Similarity=0.144  Sum_probs=32.8

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      +...|+-|..++.++ +...-+++.+|.|||||+..+...++.+..
T Consensus         2 I~p~~~~Q~~~~~al-~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~   46 (205)
T PF02562_consen    2 IKPKNEEQKFALDAL-LNNDLVIVNGPAGTGKTFLALAAALELVKE   46 (205)
T ss_dssp             ----SHHHHHHHHHH-HH-SEEEEE--TTSSTTHHHHHHHHHHHHT
T ss_pred             ccCCCHHHHHHHHHH-HhCCeEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            345688999999998 677888999999999998888887776654

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

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=95.76  E-value=0.053  Score=57.98  Aligned_cols=123  Identities=15%  Similarity=-0.006  Sum_probs=73.2

Q ss_pred             CCcHHHHHHHHHHH---cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPALA---HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      .+.|+|..++.-++   ..|.+.|++-..|.|||+-. +.++..+....                  ...+ ..|||||.
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~------------------~~~g-p~LIVvP~  228 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYR------------------GITG-PHMVVAPK  228 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhc------------------CCCC-CEEEEeCh
Confidence            57788998886542   36788899999999999764 34444443321                  0112 37999996


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHH--H-H-hcCCCcccccc--cC---Cccc--cccccCCCCCCcccc
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEH--S-N-RRKPNKRKRTR--KG---GEDE--KLDSLKWNPLSQPKT  201 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~--~-l-~~~~~i~v~~~--~~---~~~d--~l~~lv~dEAd~m~~  201 (284)
                       .|..|+..++.+++.  .+.+..++|........  . + ....++++.+-  ..   ..+.  .-..+|+|||-++.+
T Consensus       229 -SlL~nW~~Ei~kw~p--~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~L~k~~W~~VIvDEAHrIKN  305 (1033)
T PLN03142        229 -STLGNWMNEIRRFCP--VLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKN  305 (1033)
T ss_pred             -HHHHHHHHHHHHHCC--CCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHHhccCCCCEEEEcCccccCC
Confidence             556778888888865  45666777764332211  1 1 12234444321  00   0111  234689999877555

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=95.73  E-value=0.019  Score=58.87  Aligned_cols=71  Identities=14%  Similarity=0.038  Sum_probs=49.9

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+++-|.+|+-..   ...++|.|.+|||||.+..--+. ++....                  ....-+.|+|+.||..
T Consensus         2 ~Ln~~Q~~av~~~---~g~~lV~AgpGSGKT~vL~~Ria-~Li~~~------------------~v~p~~IL~lTFT~kA   59 (672)
T PRK10919          2 RLNPGQQQAVEFV---TGPCLVLAGAGSGKTRVITNKIA-HLIRGC------------------GYQARHIAAVTFTNKA   59 (672)
T ss_pred             CCCHHHHHHHhCC---CCCEEEEecCCCCHHHHHHHHHH-HHHHhc------------------CCCHHHeeeEechHHH
Confidence            3789999998643   45788899999999977543333 333221                  0112358999999999


Q ss_pred             HHHHHHHHhhhhc
Q 042526          136 ALQVLMVASPSLK  148 (284)
Q Consensus       136 a~Qi~~~~~~l~~  148 (284)
                      |..+...+..+..
T Consensus        60 A~em~~Rl~~~l~   72 (672)
T PRK10919         60 AREMKERVAQTLG   72 (672)
T ss_pred             HHHHHHHHHHHhC
Confidence            9999888877643

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

Probab=95.68  E-value=0.018  Score=53.16  Aligned_cols=54  Identities=19%  Similarity=0.224  Sum_probs=39.9

Q ss_pred             cccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHH
Q 042526           27 AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEE  100 (284)
Q Consensus        27 ~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~  100 (284)
                      ..+|..+.+|++|++|+-+.+.+..                   ..-=|+|.+|||||||.+ +.++|+++.+.
T Consensus        99 R~Ip~~i~~~e~LglP~i~~~~~~~-------------------~~GLILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805          99 RLIPSKIPTLEELGLPPIVRELAES-------------------PRGLILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             eccCccCCCHHHcCCCHHHHHHHhC-------------------CCceEEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            3578999999999999987773321                   112478999999999855 45778877664

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=95.56  E-value=0.039  Score=58.38  Aligned_cols=126  Identities=16%  Similarity=0.090  Sum_probs=85.7

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+++|...=-.+ ..|  -|+.-.||-||||+..+|+.-..+..                       -.+-|++.+-=|
T Consensus       169 ~~yDVQliGgivL-h~G--~IAEM~TGEGKTLvAtlp~yLnAL~G-----------------------kgVHvVTVNDYL  222 (1112)
T PRK12901        169 VHYDVQLIGGVVL-HQG--KIAEMATGEGKTLVATLPVYLNALTG-----------------------NGVHVVTVNDYL  222 (1112)
T ss_pred             cccchHHhhhhhh-cCC--ceeeecCCCCchhHHHHHHHHHHHcC-----------------------CCcEEEEechhh
Confidence            5777776654433 444  46788899999999999997655442                       236677888889


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc------------------------ccCCcccccccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT------------------------RKGGEDEKLDSL  191 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~------------------------~~~~~~d~l~~l  191 (284)
                      |..=...+..+...+|++|.|+.......+.+.-....||...+                        .-....|.+.|+
T Consensus       223 A~RDaewmgply~fLGLsvg~i~~~~~~~~~rr~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSI  302 (1112)
T PRK12901        223 AKRDSEWMGPLYEFHGLSVDCIDKHQPNSEARRKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSV  302 (1112)
T ss_pred             hhccHHHHHHHHHHhCCceeecCCCCCCHHHHHHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhh
Confidence            98888888888889999999887644445555555666664333                        112246677777


Q ss_pred             CCCCCCccccc-ccccc
Q 042526          192 KWNPLSQPKTT-TLLPS  207 (284)
Q Consensus       192 v~dEAd~m~~~-gflp~  207 (284)
                      ..|||--.+.+ |-.|.
T Consensus       303 LIDEARTPLIISGp~~~  319 (1112)
T PRK12901        303 LIDDARTPLIISGPVPK  319 (1112)
T ss_pred             hhccccCcEEEeCCCCC
Confidence            77887774444 34343

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=95.38  E-value=0.035  Score=56.69  Aligned_cols=70  Identities=14%  Similarity=0.033  Sum_probs=49.9

Q ss_pred             CcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHH
Q 042526           57 STSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA  136 (284)
Q Consensus        57 pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa  136 (284)
                      ++|-|.+|+-.   ...+++|.|..|||||.+.+--+. ++....                  .......|+|+.|+.-|
T Consensus         2 Ln~~Q~~av~~---~~~~~~V~Ag~GSGKT~~L~~ri~-~ll~~~------------------~~~p~~IL~vTFt~~Aa   59 (664)
T TIGR01074         2 LNPQQQEAVEY---VTGPCLVLAGAGSGKTRVITNKIA-YLIQNC------------------GYKARNIAAVTFTNKAA   59 (664)
T ss_pred             CCHHHHHHHhC---CCCCEEEEecCCCCHHHHHHHHHH-HHHHhc------------------CCCHHHeEEEeccHHHH
Confidence            67889998853   356899999999999966544333 333220                  01233589999999999


Q ss_pred             HHHHHHHhhhhc
Q 042526          137 LQVLMVASPSLK  148 (284)
Q Consensus       137 ~Qi~~~~~~l~~  148 (284)
                      .++...+..+..
T Consensus        60 ~em~~Rl~~~l~   71 (664)
T TIGR01074        60 REMKERVAKTLG   71 (664)
T ss_pred             HHHHHHHHHHhC
Confidence            999998877654

Designed to identify rep members of the uvrD/rep subfamily.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=95.35  E-value=0.057  Score=57.01  Aligned_cols=126  Identities=16%  Similarity=0.100  Sum_probs=84.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+++|...=-.+ ..|  -|+.-.||-||||+..+|+.-..+..                       -.+=|++.+-=|
T Consensus       138 ~~ydVQLiGgivL-h~G--~IAEM~TGEGKTLvatlp~yLnAL~G-----------------------~gVHvVTvNDYL  191 (1025)
T PRK12900        138 VPYDVQLIGGIVL-HSG--KISEMATGEGKTLVSTLPTFLNALTG-----------------------RGVHVVTVNDYL  191 (1025)
T ss_pred             cccchHHhhhHHh-hcC--CccccCCCCCcchHhHHHHHHHHHcC-----------------------CCcEEEeechHh
Confidence            5788887655444 444  46788899999999999997655442                       235677777889


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc------------------------cCCcccccccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR------------------------KGGEDEKLDSL  191 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~------------------------~~~~~d~l~~l  191 (284)
                      |..=...+..+...+|++|.|+..++.. ..++-....||...+.                        -....|.+.|+
T Consensus       192 A~RDaewm~p~y~flGLtVg~i~~~~~~-~~Rr~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSv  270 (1025)
T PRK12900        192 AQRDKEWMNPVFEFHGLSVGVILNTMRP-EERREQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSV  270 (1025)
T ss_pred             hhhhHHHHHHHHHHhCCeeeeeCCCCCH-HHHHHhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhh
Confidence            9988888899999999999988665433 3445555666643331                        11245667777


Q ss_pred             CCCCCCccccc-ccccch
Q 042526          192 KWNPLSQPKTT-TLLPSS  208 (284)
Q Consensus       192 v~dEAd~m~~~-gflp~~  208 (284)
                      ..|||--.+.+ |-.|..
T Consensus       271 LIDeARTPLIISgp~~~~  288 (1025)
T PRK12900        271 LIDEARTPLIISGPVPNA  288 (1025)
T ss_pred             hhccccCceEEeCCCCCc
Confidence            77777664444 344433

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.12  E-value=0.16  Score=52.83  Aligned_cols=77  Identities=10%  Similarity=0.092  Sum_probs=50.3

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      +++..+...-..++ .+++-|..|+-.++.+++-+++++++|||||.  ++-.+..+...                    
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTt--ll~~i~~~~~~--------------------  394 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKST--MLKAAREAWEA--------------------  394 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHH--HHHHHHHHHHh--------------------
Confidence            44444433322343 48999999999883335677999999999984  33333333332                    


Q ss_pred             CCCeEEEEEecCHHHHHHHHH
Q 042526          121 KGHLRALIINPTRELALQVLM  141 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~  141 (284)
                       .+..+++++||---|..+..
T Consensus       395 -~g~~V~~~ApTg~Aa~~L~~  414 (744)
T TIGR02768       395 -AGYRVIGAALSGKAAEGLQA  414 (744)
T ss_pred             -CCCeEEEEeCcHHHHHHHHh
Confidence             25678899999877766643

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=95.07  E-value=0.041  Score=56.27  Aligned_cols=68  Identities=18%  Similarity=0.129  Sum_probs=50.9

Q ss_pred             CCcHHHHHHHHHHH---cCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALA---HQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|++.|..+|..++   ..| +..++.+.+|||||+.+. .+    ....                     +..+|||+|
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l----~~~~---------------------~r~vLIVt~   65 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NV----IARL---------------------QRPTLVLAH   65 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HH----HHHh---------------------CCCEEEEEC
Confidence            59999999999872   123 256799999999997643 22    2211                     224999999


Q ss_pred             CHHHHHHHHHHHhhhhcC
Q 042526          132 TRELALQVLMVASPSLKS  149 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~  149 (284)
                      +.++|.|+++.+..+...
T Consensus        66 ~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298         66 NKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             CHHHHHHHHHHHHHhcCC
Confidence            999999999999888653

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.06  E-value=0.037  Score=52.79  Aligned_cols=27  Identities=26%  Similarity=0.145  Sum_probs=19.8

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      +..+++++||||||| +++-.++..+..
T Consensus       149 ~GlilI~G~TGSGKT-T~l~al~~~i~~  175 (372)
T TIGR02525       149 AGLGLICGETGSGKS-TLAASIYQHCGE  175 (372)
T ss_pred             CCEEEEECCCCCCHH-HHHHHHHHHHHh
Confidence            447899999999999 444566666543

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).

>PRK10536 hypothetical protein; Provisional

Probab=94.95  E-value=0.047  Score=49.50  Aligned_cols=45  Identities=16%  Similarity=0.149  Sum_probs=36.0

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .++..-+..|...+-.+ ..+.-+++.+++|||||+..+.-.++.+
T Consensus        55 ~~i~p~n~~Q~~~l~al-~~~~lV~i~G~aGTGKT~La~a~a~~~l   99 (262)
T PRK10536         55 SPILARNEAQAHYLKAI-ESKQLIFATGEAGCGKTWISAAKAAEAL   99 (262)
T ss_pred             ccccCCCHHHHHHHHHH-hcCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            45666788999999988 7788899999999999977666555544

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=94.91  E-value=0.063  Score=54.37  Aligned_cols=47  Identities=23%  Similarity=0.145  Sum_probs=39.1

Q ss_pred             CCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHH
Q 042526           56 ESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEERE  102 (284)
Q Consensus        56 ~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~  102 (284)
                      +|+.||...+..+   +..|+=-|.-+||||||||+.+..++.+|.....
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~ee   64 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDFEE   64 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHhHH
Confidence            4888998777655   3678888999999999999999999999877643

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.87  E-value=0.078  Score=53.12  Aligned_cols=92  Identities=15%  Similarity=0.014  Sum_probs=59.8

Q ss_pred             CCCCHH-HHHHHHHcCCCCC-------cHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           39 LRLHPL-LMKSIYKLGFKES-------TSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        39 l~L~~~-Ll~~L~~~g~~~p-------T~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      .++.++ |..+|.+.-=..+       -+=|-+.|..  -.+.-+||++..|||||.+.|--+.-.++..+         
T Consensus       187 ~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~--ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R---------  255 (747)
T COG3973         187 TGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRF--EKNKILVVQGAAGSGKTTIALHRVAYLLYGYR---------  255 (747)
T ss_pred             CchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhc--cCCCeEEEecCCCCCchhHHHHHHHHHHhccc---------
Confidence            445554 4456665433322       2334455542  44678899999999999877655544444432         


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS  149 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~  149 (284)
                             .....++ +|||.|.|-++.-|.+++-.|+..
T Consensus       256 -------~~l~~k~-vlvl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         256 -------GPLQAKP-VLVLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             -------cccccCc-eEEEcCcHHHHHHHHHhchhhccC
Confidence                   1111222 899999999999999999998764

>TIGR01075 uvrD DNA helicase II

Probab=94.86  E-value=0.093  Score=54.20  Aligned_cols=72  Identities=17%  Similarity=0.141  Sum_probs=52.0

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..++|-|.+|+-.   ....++|.|..|||||.+.. --+.++....                  ....-+.|+|+.|+.
T Consensus         3 ~~Ln~~Q~~av~~---~~g~~lV~AgaGSGKT~~L~-~Ria~Li~~~------------------~v~p~~IL~lTFTnk   60 (715)
T TIGR01075         3 DGLNDKQREAVAA---PPGNLLVLAGAGSGKTRVLT-HRIAWLLSVE------------------NASPHSIMAVTFTNK   60 (715)
T ss_pred             cccCHHHHHHHcC---CCCCEEEEecCCCCHHHHHH-HHHHHHHHcC------------------CCCHHHeEeeeccHH
Confidence            4589999999854   35689999999999997643 3333333320                  112336899999999


Q ss_pred             HHHHHHHHHhhhhc
Q 042526          135 LALQVLMVASPSLK  148 (284)
Q Consensus       135 La~Qi~~~~~~l~~  148 (284)
                      .|..+...+..+..
T Consensus        61 AA~em~~Rl~~~~~   74 (715)
T TIGR01075        61 AAAEMRHRIGALLG   74 (715)
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999998888765

Designed to identify uvrD members of the uvrD/rep subfamily.

>COG4889 Predicted helicase [General function prediction only]

Probab=94.83  E-value=0.071  Score=55.50  Aligned_cols=94  Identities=17%  Similarity=0.112  Sum_probs=60.5

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC-----CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR-----KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G-----~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      .|+.+.- .++..+|.-..=..|.|+|+.||... .+|     |.=++.| .|+|||++.| -+.+.+.           
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a-~~~F~~n~RGkLIMA-cGTGKTfTsL-kisEala-----------  205 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAA-KEGFSDNDRGKLIMA-CGTGKTFTSL-KISEALA-----------  205 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHH-HhhcccccCCcEEEe-cCCCccchHH-HHHHHHh-----------
Confidence            4555432 34455554445568999999999988 443     3445555 5899998765 2222222           


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEE
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMA  157 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~  157 (284)
                                   ..+.|+|+|+..|..|..+.+..=. .+.++...+
T Consensus       206 -------------~~~iL~LvPSIsLLsQTlrew~~~~-~l~~~a~aV  239 (1518)
T COG4889         206 -------------AARILFLVPSISLLSQTLREWTAQK-ELDFRASAV  239 (1518)
T ss_pred             -------------hhheEeecchHHHHHHHHHHHhhcc-CccceeEEE
Confidence                         2469999999999999988876432 245544333

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=94.82  E-value=0.047  Score=51.87  Aligned_cols=27  Identities=26%  Similarity=0.260  Sum_probs=19.5

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..+.-+++++|||||||... -.++..+
T Consensus       132 ~~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       132 PQEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             ccCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            35678999999999999543 4455444

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.

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

Probab=94.80  E-value=0.08  Score=54.64  Aligned_cols=73  Identities=18%  Similarity=0.135  Sum_probs=56.5

Q ss_pred             CCcHHHHHHHHHHH---cCCC-cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALA---HQRK-DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G~-dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|...|..||..+.   ..|+ -++++-.||||||.+. +.++.+|++..                    ..-++|+|+-
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~--------------------~~KRVLFLaD  223 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSG--------------------WVKRVLFLAD  223 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcc--------------------hhheeeEEec
Confidence            57789999997662   3333 3777777999999776 57888887753                    2347999999


Q ss_pred             CHHHHHHHHHHHhhhhcC
Q 042526          132 TRELALQVLMVASPSLKS  149 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~  149 (284)
                      .+.|+.|.+..+..+...
T Consensus       224 R~~Lv~QA~~af~~~~P~  241 (875)
T COG4096         224 RNALVDQAYGAFEDFLPF  241 (875)
T ss_pred             hHHHHHHHHHHHHHhCCC
Confidence            999999999988887664

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=94.73  E-value=0.068  Score=58.51  Aligned_cols=66  Identities=18%  Similarity=0.124  Sum_probs=48.9

Q ss_pred             CcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHH
Q 042526           57 STSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA  136 (284)
Q Consensus        57 pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa  136 (284)
                      .|+-|..||-   ..|++++|.|.-|||||.+..--++..+...                    ..--+.|||+-|+.-|
T Consensus         2 ~t~~Q~~ai~---~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~--------------------~~~~~il~~tFt~~aa   58 (1232)
T TIGR02785         2 WTDEQWQAIY---TRGQNILVSASAGSGKTAVLVERIIKKILRG--------------------VDIDRLLVVTFTNAAA   58 (1232)
T ss_pred             CCHHHHHHHh---CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC--------------------CCHhhEEEEeccHHHH
Confidence            5899999995   5699999999999999977665555544321                    0112589999999999


Q ss_pred             HHHHHHHhh
Q 042526          137 LQVLMVASP  145 (284)
Q Consensus       137 ~Qi~~~~~~  145 (284)
                      ..+...+..
T Consensus        59 ~e~~~ri~~   67 (1232)
T TIGR02785        59 REMKERIEE   67 (1232)
T ss_pred             HHHHHHHHH
Confidence            776665554

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.63  E-value=0.086  Score=54.53  Aligned_cols=72  Identities=15%  Similarity=0.104  Sum_probs=51.4

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..++|-|.+|+-..   ...++|.|..|||||.+..-=+ .++....                  ....-+.|+|+.|+.
T Consensus         8 ~~Ln~~Q~~av~~~---~g~~lV~AgaGSGKT~vl~~Ri-a~Li~~~------------------~v~p~~IL~lTFT~k   65 (721)
T PRK11773          8 DSLNDKQREAVAAP---LGNMLVLAGAGSGKTRVLVHRI-AWLMQVE------------------NASPYSIMAVTFTNK   65 (721)
T ss_pred             HhcCHHHHHHHhCC---CCCEEEEecCCCCHHHHHHHHH-HHHHHcC------------------CCChhHeEeeeccHH
Confidence            35899999998543   4589999999999996653332 2333210                  112236899999999


Q ss_pred             HHHHHHHHHhhhhc
Q 042526          135 LALQVLMVASPSLK  148 (284)
Q Consensus       135 La~Qi~~~~~~l~~  148 (284)
                      .|..+...+..+..
T Consensus        66 AA~Em~~Rl~~~~~   79 (721)
T PRK11773         66 AAAEMRHRIEQLLG   79 (721)
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999998887764

>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=94.60  E-value=0.059  Score=50.17  Aligned_cols=44  Identities=23%  Similarity=0.149  Sum_probs=33.7

Q ss_pred             CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           54 FKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        54 ~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      +..+++.|.+-+..++..+++++++++|||||| +++.+++..+-
T Consensus       125 ~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKT-t~lnall~~Ip  168 (312)
T COG0630         125 YGTISPEQAAYLWLAIEARKSIIICGGTASGKT-TLLNALLDFIP  168 (312)
T ss_pred             cCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHH-HHHHHHHHhCC
Confidence            456778887777666688999999999999999 55556555443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=94.49  E-value=0.15  Score=54.32  Aligned_cols=68  Identities=25%  Similarity=0.168  Sum_probs=48.7

Q ss_pred             CCcHHHHHHHHHHHc-CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           56 ESTSILKARIPALAH-QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        56 ~pT~iQ~~aip~il~-~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      .|.|+|..+.-.++. ....+++.-..|-|||+-.++-+-..+...                     ..-++|||||+ .
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g---------------------~~~rvLIVvP~-s  209 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG---------------------RAERVLILVPE-T  209 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC---------------------CCCcEEEEcCH-H
Confidence            489999998876522 234689999999999987755443332221                     22369999998 8


Q ss_pred             HHHHHHHHHhh
Q 042526          135 LALQVLMVASP  145 (284)
Q Consensus       135 La~Qi~~~~~~  145 (284)
                      |..|...++.+
T Consensus       210 L~~QW~~El~~  220 (956)
T PRK04914        210 LQHQWLVEMLR  220 (956)
T ss_pred             HHHHHHHHHHH
Confidence            99999888854

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=94.47  E-value=0.027  Score=55.65  Aligned_cols=97  Identities=21%  Similarity=0.197  Sum_probs=58.9

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCC
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNS  151 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~  151 (284)
                      .+=++-++||-||||.    -+|+++....                       .+++--|.|-||+.|++.++.+    |
T Consensus       191 RkIi~H~GPTNSGKTy----~ALqrl~~ak-----------------------sGvycGPLrLLA~EV~~r~na~----g  239 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTY----RALQRLKSAK-----------------------SGVYCGPLRLLAHEVYDRLNAL----G  239 (700)
T ss_pred             heEEEEeCCCCCchhH----HHHHHHhhhc-----------------------cceecchHHHHHHHHHHHhhhc----C
Confidence            3345667899999994    4566666542                       3778889999999999999875    6


Q ss_pred             ceeEEEeCCCcchHHHHHhcCC-CcccccccCCc-cccccccCCCCCCcccc
Q 042526          152 LTLAMAAGSPLLTSEHSNRRKP-NKRKRTRKGGE-DEKLDSLKWNPLSQPKT  201 (284)
Q Consensus       152 i~v~~~~G~~~~~q~~~l~~~~-~i~v~~~~~~~-~d~l~~lv~dEAd~m~~  201 (284)
                      +.|-+++|.........  ..+ ..+-++.-+.. -.....-|+||..||.|
T Consensus       240 ipCdL~TGeE~~~~~~~--~~~a~hvScTVEM~sv~~~yeVAViDEIQmm~D  289 (700)
T KOG0953|consen  240 IPCDLLTGEERRFVLDN--GNPAQHVSCTVEMVSVNTPYEVAVIDEIQMMRD  289 (700)
T ss_pred             CCccccccceeeecCCC--CCcccceEEEEEEeecCCceEEEEehhHHhhcC
Confidence            66777777643321110  111 11222222222 12344567788777665

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.32  E-value=0.5  Score=45.19  Aligned_cols=21  Identities=19%  Similarity=0.047  Sum_probs=17.4

Q ss_pred             cCCCcEEEEccCCCCchHHhH
Q 042526           70 HQRKDVIGAAETESGKTRAFG   90 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafl   90 (284)
                      ..|..+++.+|||+|||....
T Consensus       135 ~~g~ii~lvGptGvGKTTtia  155 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTA  155 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHH
Confidence            347789999999999996654

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=94.20  E-value=0.086  Score=44.98  Aligned_cols=29  Identities=14%  Similarity=0.187  Sum_probs=19.5

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      ..+.++++.+++|+|||... ..+...+..
T Consensus        45 ~~~~~l~l~G~~G~GKThLa-~ai~~~~~~   73 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLA-VAIANEAIR   73 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHH-HHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHH-HHHHHHhcc
Confidence            66899999999999999543 344444443

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=94.15  E-value=0.29  Score=52.33  Aligned_cols=64  Identities=11%  Similarity=0.033  Sum_probs=46.1

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCc-EEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           52 LGFKESTSILKARIPALAHQRKD-VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~d-viv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      .|+ .+++-|..|+..+ +.+++ +++++..|||||..  +-.+..+...                     .+..++.++
T Consensus       343 ~g~-~Ls~eQr~Av~~i-l~s~~v~vv~G~AGTGKTT~--l~~~~~~~e~---------------------~G~~V~~~A  397 (988)
T PRK13889        343 RGL-VLSGEQADALAHV-TDGRDLGVVVGYAGTGKSAM--LGVAREAWEA---------------------AGYEVRGAA  397 (988)
T ss_pred             cCC-CCCHHHHHHHHHH-hcCCCeEEEEeCCCCCHHHH--HHHHHHHHHH---------------------cCCeEEEec
Confidence            454 4899999999988 66554 68999999999964  3333333332                     256789999


Q ss_pred             cCHHHHHHHH
Q 042526          131 PTRELALQVL  140 (284)
Q Consensus       131 PTReLa~Qi~  140 (284)
                      ||---|..+.
T Consensus       398 pTGkAA~~L~  407 (988)
T PRK13889        398 LSGIAAENLE  407 (988)
T ss_pred             CcHHHHHHHh
Confidence            9987766554

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=93.97  E-value=0.047  Score=51.45  Aligned_cols=53  Identities=11%  Similarity=0.035  Sum_probs=37.1

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh
Q 042526           74 DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL  147 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~  147 (284)
                      -++|.+.+|||||+..+ -++..+..                    ...+..+++|+++..|...++..+..-.
T Consensus         3 v~~I~G~aGTGKTvla~-~l~~~l~~--------------------~~~~~~~~~l~~n~~l~~~l~~~l~~~~   55 (352)
T PF09848_consen    3 VILITGGAGTGKTVLAL-NLAKELQN--------------------SEEGKKVLYLCGNHPLRNKLREQLAKKY   55 (352)
T ss_pred             EEEEEecCCcCHHHHHH-HHHHHhhc--------------------cccCCceEEEEecchHHHHHHHHHhhhc
Confidence            37899999999996543 23322211                    1135678999999999998888876543

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK13764 ATPase; Provisional

Probab=93.89  E-value=0.11  Score=52.48  Aligned_cols=28  Identities=14%  Similarity=0.243  Sum_probs=21.2

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      ..+.+++++++|||||| +|+-.++..+.
T Consensus       255 ~~~~~ILIsG~TGSGKT-Tll~AL~~~i~  282 (602)
T PRK13764        255 ERAEGILIAGAPGAGKS-TFAQALAEFYA  282 (602)
T ss_pred             hcCCEEEEECCCCCCHH-HHHHHHHHHHh
Confidence            44678999999999999 45556666553

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=93.88  E-value=0.21  Score=51.69  Aligned_cols=72  Identities=18%  Similarity=0.128  Sum_probs=50.6

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..++|-|..|+-..   ...++|.|..|||||.+..-=+. ++....                  ....-+.|+|+-|+.
T Consensus         3 ~~Ln~~Q~~av~~~---~g~~lV~AgaGSGKT~~l~~ria-~Li~~~------------------~i~P~~IL~lTFT~k   60 (726)
T TIGR01073         3 AHLNPEQREAVKTT---EGPLLIMAGAGSGKTRVLTHRIA-HLIAEK------------------NVAPWNILAITFTNK   60 (726)
T ss_pred             cccCHHHHHHHhCC---CCCEEEEeCCCCCHHHHHHHHHH-HHHHcC------------------CCCHHHeeeeeccHH
Confidence            45889999998643   46899999999999966544333 333210                  011235899999999


Q ss_pred             HHHHHHHHHhhhhc
Q 042526          135 LALQVLMVASPSLK  148 (284)
Q Consensus       135 La~Qi~~~~~~l~~  148 (284)
                      -|..+...+..+..
T Consensus        61 AA~em~~Rl~~~~~   74 (726)
T TIGR01073        61 AAREMKERVEKLLG   74 (726)
T ss_pred             HHHHHHHHHHHHhc
Confidence            99988888877654

Designed to identify pcrA members of the uvrD/rep subfamily.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=93.68  E-value=0.048  Score=53.18  Aligned_cols=49  Identities=24%  Similarity=0.283  Sum_probs=38.0

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      .++++.|+||||||.+|++|.|-   ..                     .+ .+||.=|--||+......++..
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll---~~---------------------~~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL---NY---------------------PG-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH---hc---------------------cC-CEEEEECCCcHHHHHHHHHHHC
Confidence            36999999999999999999763   21                     12 4788889999988777766654

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

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=93.66  E-value=0.057  Score=51.01  Aligned_cols=32  Identities=22%  Similarity=0.185  Sum_probs=22.7

Q ss_pred             HHHHHHcCCCcEEEEccCCCCchHHhHHHHHHH
Q 042526           64 RIPALAHQRKDVIGAAETESGKTRAFGLPALQR   96 (284)
Q Consensus        64 aip~il~~G~dviv~A~TGSGKTlafllPil~~   96 (284)
                      .+..++..+.+++++++|||||| +++-.++..
T Consensus       154 ~l~~~v~~~~nilI~G~tGSGKT-Tll~aLl~~  185 (344)
T PRK13851        154 FLHACVVGRLTMLLCGPTGSGKT-TMSKTLISA  185 (344)
T ss_pred             HHHHHHHcCCeEEEECCCCccHH-HHHHHHHcc
Confidence            33333477999999999999999 444444443

>PRK05973 replicative DNA helicase; Provisional

Probab=93.54  E-value=0.17  Score=45.30  Aligned_cols=48  Identities=25%  Similarity=0.248  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHHcCCCC----------CcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           39 LRLHPLLMKSIYKLGFKE----------STSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        39 l~L~~~Ll~~L~~~g~~~----------pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      +.||..|=+.-.+.||..          +||... .+.-+ ..|.-+++.|++|+|||.-
T Consensus        23 ~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~-l~GGl-~~Gsl~LIaG~PG~GKT~l   80 (237)
T PRK05973         23 IPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEE-LFSQL-KPGDLVLLGARPGHGKTLL   80 (237)
T ss_pred             CcHHHHHHHHHHHhccchHHHHHHhccCCCCHHH-hcCCC-CCCCEEEEEeCCCCCHHHH
Confidence            345555555555567764          444322 33344 6788899999999999943

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=93.50  E-value=0.033  Score=58.56  Aligned_cols=89  Identities=19%  Similarity=0.092  Sum_probs=67.7

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ....|+|.+.+-.++....++++-+|||||||++|-+.+...+..                     ..+-++++++|-..
T Consensus       926 ~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~---------------------~p~~kvvyIap~ka  984 (1230)
T KOG0952|consen  926 KYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSY---------------------YPGSKVVYIAPDKA  984 (1230)
T ss_pred             cccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhcc---------------------CCCccEEEEcCCch
Confidence            355677877776655557788999999999999999888754433                     24578999999999


Q ss_pred             HHHHHHHHHhhhhcCCCceeEEEeCCCcch
Q 042526          135 LALQVLMVASPSLKSNSLTLAMAAGSPLLT  164 (284)
Q Consensus       135 La~Qi~~~~~~l~~~~~i~v~~~~G~~~~~  164 (284)
                      |+..-.+.+.......|+++.-+.|.....
T Consensus       985 lvker~~Dw~~r~~~~g~k~ie~tgd~~pd 1014 (1230)
T KOG0952|consen  985 LVKERSDDWSKRDELPGIKVIELTGDVTPD 1014 (1230)
T ss_pred             hhcccccchhhhcccCCceeEeccCccCCC
Confidence            998888887766555588887777775443

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=93.44  E-value=0.44  Score=50.16  Aligned_cols=87  Identities=14%  Similarity=0.059  Sum_probs=52.8

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      +.+..-....+.|.+...    -+..+..-|++|+-.++....-.++.+=+|||||...+  .|-+++-.          
T Consensus       648 P~f~~~~~~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~--~LIkiL~~----------  711 (1100)
T KOG1805|consen  648 PKFVDALSKVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTIS--LLIKILVA----------  711 (1100)
T ss_pred             chhhcccccccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHH--HHHHHHHH----------
Confidence            333333334455665553    23467789999999884445556889999999996543  22233332          


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHh
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVAS  144 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~  144 (284)
                                 .+-++|+.+-|..-+.-|.--+.
T Consensus       712 -----------~gkkVLLtsyThsAVDNILiKL~  734 (1100)
T KOG1805|consen  712 -----------LGKKVLLTSYTHSAVDNILIKLK  734 (1100)
T ss_pred             -----------cCCeEEEEehhhHHHHHHHHHHh
Confidence                       24567777777665555544444

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.25  E-value=0.035  Score=52.90  Aligned_cols=48  Identities=23%  Similarity=0.187  Sum_probs=36.8

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           74 DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      ++++.|+||||||.+|++|-+-..                         .-.+||+=|--|+........+.+
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-------------------------~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-------------------------PGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-------------------------CCCEEEEccchhHHHHHHHHHHHc
Confidence            478999999999999999976421                         124788889999998777666543

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.

>PRK06921 hypothetical protein; Provisional

Probab=93.23  E-value=0.53  Score=42.77  Aligned_cols=27  Identities=22%  Similarity=0.343  Sum_probs=19.0

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      .+..+++.+++|+|||... ..+...+.
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~  142 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELM  142 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHh
Confidence            4778999999999999432 34444443

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=93.21  E-value=0.22  Score=52.42  Aligned_cols=67  Identities=19%  Similarity=0.220  Sum_probs=51.7

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|-..|...+..+ =.+..+++.|||-+|||++- .-+++.+++..                    ..=-+|+++||..|
T Consensus       511 ~Pd~WQ~elLDsv-Dr~eSavIVAPTSaGKTfis-fY~iEKVLRes--------------------D~~VVIyvaPtKaL  568 (1330)
T KOG0949|consen  511 CPDEWQRELLDSV-DRNESAVIVAPTSAGKTFIS-FYAIEKVLRES--------------------DSDVVIYVAPTKAL  568 (1330)
T ss_pred             CCcHHHHHHhhhh-hcccceEEEeeccCCceecc-HHHHHHHHhhc--------------------CCCEEEEecchHHH
Confidence            4778899999887 88999999999999999642 34456666643                    22347889999999


Q ss_pred             HHHHHHHHh
Q 042526          136 ALQVLMVAS  144 (284)
Q Consensus       136 a~Qi~~~~~  144 (284)
                      +.|+...+.
T Consensus       569 VnQvsa~Vy  577 (1330)
T KOG0949|consen  569 VNQVSANVY  577 (1330)
T ss_pred             hhhhhHHHH
Confidence            999866554

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.13  E-value=0.21  Score=47.06  Aligned_cols=27  Identities=19%  Similarity=0.298  Sum_probs=19.0

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..+..+++++|||||||... -.++..+
T Consensus       120 ~~~g~ili~G~tGSGKTT~l-~al~~~i  146 (343)
T TIGR01420       120 RPRGLILVTGPTGSGKSTTL-ASMIDYI  146 (343)
T ss_pred             hcCcEEEEECCCCCCHHHHH-HHHHHhh
Confidence            34668999999999999543 3444443

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.05  E-value=0.13  Score=48.40  Aligned_cols=33  Identities=27%  Similarity=0.386  Sum_probs=23.7

Q ss_pred             HHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           64 RIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        64 aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .+..++..+.+++++++|||||| +++-.++..+
T Consensus       152 ~L~~~v~~~~nili~G~tgSGKT-Tll~aL~~~i  184 (332)
T PRK13900        152 FLEHAVISKKNIIISGGTSTGKT-TFTNAALREI  184 (332)
T ss_pred             HHHHHHHcCCcEEEECCCCCCHH-HHHHHHHhhC
Confidence            33433477999999999999999 5555555544

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

Probab=92.96  E-value=0.18  Score=47.36  Aligned_cols=36  Identities=19%  Similarity=0.127  Sum_probs=30.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchH
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTR   87 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTl   87 (284)
                      ..|..+++-|+..+..++..+.++++++-||||||.
T Consensus       153 i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTT  188 (355)
T COG4962         153 IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTT  188 (355)
T ss_pred             HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHH
Confidence            357889999999999885555699999999999993

>PRK10436 hypothetical protein; Provisional

Probab=92.89  E-value=0.18  Score=49.53  Aligned_cols=26  Identities=35%  Similarity=0.379  Sum_probs=18.8

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .+.-+++++|||||||.+. ..+|..+
T Consensus       217 ~~GliLvtGpTGSGKTTtL-~a~l~~~  242 (462)
T PRK10436        217 PQGLILVTGPTGSGKTVTL-YSALQTL  242 (462)
T ss_pred             cCCeEEEECCCCCChHHHH-HHHHHhh
Confidence            3457899999999999654 4455554

>PRK06835 DNA replication protein DnaC; Validated

Probab=92.79  E-value=0.36  Score=45.36  Aligned_cols=47  Identities=19%  Similarity=0.163  Sum_probs=30.4

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHH
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLM  141 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~  141 (284)
                      .+.++++.++||+|||+ .+..+...+...                      +..+ +..+..+|..++..
T Consensus       182 ~~~~Lll~G~~GtGKTh-La~aIa~~l~~~----------------------g~~V-~y~t~~~l~~~l~~  228 (329)
T PRK06835        182 NNENLLFYGNTGTGKTF-LSNCIAKELLDR----------------------GKSV-IYRTADELIEILRE  228 (329)
T ss_pred             cCCcEEEECCCCCcHHH-HHHHHHHHHHHC----------------------CCeE-EEEEHHHHHHHHHH
Confidence            46899999999999995 333444444331                      3334 45566777777654

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=92.74  E-value=0.26  Score=44.48  Aligned_cols=70  Identities=14%  Similarity=0.191  Sum_probs=45.5

Q ss_pred             cCCCCCcHHHHHHHHHH------HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeE
Q 042526           52 LGFKESTSILKARIPAL------AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLR  125 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~i------l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (284)
                      +.|.....++..++-.+      +.++.++++.+++|+|||.-. .++...+..                      .+. 
T Consensus        79 ~d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa-~Ai~~~l~~----------------------~g~-  134 (254)
T COG1484          79 FDFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLA-IAIGNELLK----------------------AGI-  134 (254)
T ss_pred             ccccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH-HHHHHHHHH----------------------cCC-
Confidence            34445555555544433      246889999999999999433 334444442                      133 


Q ss_pred             EEEEecCHHHHHHHHHHHhh
Q 042526          126 ALIINPTRELALQVLMVASP  145 (284)
Q Consensus       126 aLIL~PTReLa~Qi~~~~~~  145 (284)
                      .++++++.+|+.++...+..
T Consensus       135 sv~f~~~~el~~~Lk~~~~~  154 (254)
T COG1484         135 SVLFITAPDLLSKLKAAFDE  154 (254)
T ss_pred             eEEEEEHHHHHHHHHHHHhc
Confidence            56677999999999887664

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=92.68  E-value=0.26  Score=44.75  Aligned_cols=46  Identities=26%  Similarity=0.213  Sum_probs=27.8

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHHc-CCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           48 SIYKLGFKESTSILKARIPALAH-QRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        48 ~L~~~g~~~pT~iQ~~aip~il~-~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .|..+||   ++-|.+.|-.++. .+.-+++.++||||||. ++-.++..+
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT-~l~all~~i  104 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTT-TLYSALSEL  104 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHH-HHHHHHhhh
Confidence            3555564   2445555544423 34468999999999994 444555554

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.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=92.66  E-value=0.18  Score=47.56  Aligned_cols=42  Identities=19%  Similarity=0.187  Sum_probs=30.9

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchH
Q 042526           44 LLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTR   87 (284)
Q Consensus        44 ~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTl   87 (284)
                      .-+..|.+.|+  +++-+...+..++..+.+++++++||||||.
T Consensus       152 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTT  193 (340)
T TIGR03819       152 FTLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTT  193 (340)
T ss_pred             CCHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHH
Confidence            34555666666  4456666666665778899999999999984

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.

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

Probab=92.65  E-value=0.16  Score=43.39  Aligned_cols=34  Identities=24%  Similarity=0.249  Sum_probs=27.3

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      ..++-|...+...+..|..+++.++||||||..+
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            3566677777767688999999999999999543

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.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=92.64  E-value=0.078  Score=53.72  Aligned_cols=49  Identities=18%  Similarity=0.036  Sum_probs=39.0

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      ..+++.||||||||.+|++|-|...                         .-.+||+=|--|+........++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~-------------------------~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW-------------------------EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC-------------------------CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            4789999999999999999987542                         123788889999998777766653

>PRK08181 transposase; Validated

Probab=92.59  E-value=0.38  Score=43.89  Aligned_cols=18  Identities=11%  Similarity=0.206  Sum_probs=16.4

Q ss_pred             cCCCcEEEEccCCCCchH
Q 042526           70 HQRKDVIGAAETESGKTR   87 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTl   87 (284)
                      ..+.++++.+|+|+|||.
T Consensus       104 ~~~~nlll~Gp~GtGKTH  121 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSH  121 (269)
T ss_pred             hcCceEEEEecCCCcHHH
Confidence            578899999999999994

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=92.55  E-value=1.2  Score=39.60  Aligned_cols=96  Identities=15%  Similarity=0.140  Sum_probs=67.5

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHc--CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAH--QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~--~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      ..|.-+..|.+|+=.+.. ++ ...+.|......++.  +|.|.+.+--.|.||| +-++|++..++.+.          
T Consensus         3 ~~w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKT-sVI~Pmla~~LAdg----------   69 (229)
T PF12340_consen    3 RNWDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKT-SVIVPMLALALADG----------   69 (229)
T ss_pred             CCCCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCcc-chHHHHHHHHHcCC----------
Confidence            357777778888766653 34 367889988877732  3789999999999999 66789998777642          


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhh-hhcCCCcee
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASP-SLKSNSLTL  154 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~-l~~~~~i~v  154 (284)
                                 .-.+.++|| +.|..|....++. |+.-++..|
T Consensus        70 -----------~~LvrviVp-k~Ll~q~~~~L~~~lg~l~~r~i  101 (229)
T PF12340_consen   70 -----------SRLVRVIVP-KALLEQMRQMLRSRLGGLLNRRI  101 (229)
T ss_pred             -----------CcEEEEEcC-HHHHHHHHHHHHHHHHHHhCCee
Confidence                       234555555 5588998888875 444334444

There are two conserved sequence motifs: LLE and NMG.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=92.39  E-value=0.2  Score=50.49  Aligned_cols=46  Identities=37%  Similarity=0.375  Sum_probs=28.5

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHHc-CCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           48 SIYKLGFKESTSILKARIPALAH-QRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        48 ~L~~~g~~~pT~iQ~~aip~il~-~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .|.++||.   +-|...|-.++. ...-+++++|||||||.+. ..++..+
T Consensus       294 ~l~~lg~~---~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       294 DIDKLGFE---PDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             CHHHcCCC---HHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            35566653   445555554423 2346789999999999653 4555554

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.

>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=92.30  E-value=0.13  Score=46.27  Aligned_cols=27  Identities=26%  Similarity=0.338  Sum_probs=20.6

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..+.+++++++|||||| +++-.++..+
T Consensus       125 ~~~~~ili~G~tGSGKT-T~l~all~~i  151 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKT-TLLNALLEEI  151 (270)
T ss_dssp             HTTEEEEEEESTTSSHH-HHHHHHHHHC
T ss_pred             ccceEEEEECCCccccc-hHHHHHhhhc
Confidence            56889999999999999 4445555443

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 ....

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=92.29  E-value=1  Score=48.66  Aligned_cols=78  Identities=13%  Similarity=0.055  Sum_probs=53.2

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcC
Q 042526           40 RLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYA  119 (284)
Q Consensus        40 ~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~  119 (284)
                      ++++..+.+....++ .+|+-|..|+..+...++-++++++.|||||..  +-.+..+...                   
T Consensus       366 ~v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~--l~~~~~~~e~-------------------  423 (1102)
T PRK13826        366 GVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTM--MKAAREAWEA-------------------  423 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHH--HHHHHHHHHH-------------------
Confidence            455666655444444 589999999998744466789999999999943  3333333332                   


Q ss_pred             CCCCeEEEEEecCHHHHHHHHH
Q 042526          120 PKGHLRALIINPTRELALQVLM  141 (284)
Q Consensus       120 ~~~~~~aLIL~PTReLa~Qi~~  141 (284)
                        .+..++.++||---|..+..
T Consensus       424 --~G~~V~g~ApTgkAA~~L~e  443 (1102)
T PRK13826        424 --AGYRVVGGALAGKAAEGLEK  443 (1102)
T ss_pred             --cCCeEEEEcCcHHHHHHHHH
Confidence              35678899999777766544

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=92.15  E-value=0.61  Score=47.65  Aligned_cols=109  Identities=22%  Similarity=0.148  Sum_probs=67.0

Q ss_pred             CcHHHHHHHHHHHc----CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           57 STSILKARIPALAH----QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        57 pT~iQ~~aip~il~----~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      +-|.|.+++.-++.    .+..-|+.-.-|=|||++.+--++..=.....+            ........ ..|||||-
T Consensus       326 LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~------------~~~~~~a~-~TLII~Pa  392 (901)
T KOG4439|consen  326 LMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAR------------EKKGESAS-KTLIICPA  392 (901)
T ss_pred             cchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhh------------cccccccC-CeEEeCcH
Confidence            45788887765421    234456677789999976543333321111100            01111111 38999996


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~  179 (284)
                      + |.+|++.++.+-....-++|.+++|.........-.+..|+++.+
T Consensus       393 S-li~qW~~Ev~~rl~~n~LsV~~~HG~n~r~i~~~~L~~YDvViTT  438 (901)
T KOG4439|consen  393 S-LIHQWEAEVARRLEQNALSVYLYHGPNKREISAKELRKYDVVITT  438 (901)
T ss_pred             H-HHHHHHHHHHHHHhhcceEEEEecCCccccCCHHHHhhcceEEEe
Confidence            5 667888888776666678999999988655555666677776655

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=91.89  E-value=0.11  Score=53.29  Aligned_cols=48  Identities=17%  Similarity=0.147  Sum_probs=37.6

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASP  145 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~  145 (284)
                      .++++.||||||||.+|++|-|-..                         .-.+||+=|--|+........+.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~-------------------------~gS~VV~DpKGE~~~~Ta~~R~~  187 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF-------------------------KGSVIALDVKGELFELTSRARKA  187 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC-------------------------CCCEEEEeCCchHHHHHHHHHHh
Confidence            4899999999999999999986532                         11478888999998877666654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=91.57  E-value=1.4  Score=40.30  Aligned_cols=19  Identities=26%  Similarity=0.197  Sum_probs=15.4

Q ss_pred             CCCcEEEEccCCCCchHHh
Q 042526           71 QRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlaf   89 (284)
                      .++.+++.+|||+|||.+.
T Consensus       193 ~~~vi~~vGptGvGKTTt~  211 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTL  211 (282)
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3567889999999999554

>PF12846 AAA_10: AAA-like domain

Probab=91.49  E-value=0.54  Score=42.09  Aligned_cols=42  Identities=24%  Similarity=0.361  Sum_probs=30.8

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHH
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELAL  137 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~  137 (284)
                      +++++.|+||||||.+.. .++..+...                      ++.++|+=|..+...
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~~----------------------g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIRR----------------------GPRVVIFDPKGDYSP   43 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHHc----------------------CCCEEEEcCCchHHH
Confidence            578999999999996555 555555442                      567788878777666

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=91.47  E-value=0.37  Score=40.40  Aligned_cols=48  Identities=21%  Similarity=0.174  Sum_probs=29.6

Q ss_pred             EEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           75 VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        75 viv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      +++.+++|||||. +++-++.....                      .+..+++++ +-+-+.++...+..+
T Consensus         2 ~li~G~~G~GKT~-l~~~~~~~~~~----------------------~g~~v~~~s-~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTT-FALQFLYAGLA----------------------RGEPGLYVT-LEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHH-HHHHHHHHHHH----------------------CCCcEEEEE-CCCCHHHHHHHHHHc
Confidence            6889999999994 33333222222                      244566664 556677777777665

A related protein is found in archaea.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=91.40  E-value=0.39  Score=45.56  Aligned_cols=60  Identities=15%  Similarity=0.217  Sum_probs=42.7

Q ss_pred             CcHHHHHHHHHHH-----cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           57 STSILKARIPALA-----HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        57 pT~iQ~~aip~il-----~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +++=|+.++..++     ..+..+++.++-|||||  |++=.|......                     .+..+++++|
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs--~l~~~i~~~~~~---------------------~~~~~~~~a~   58 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKS--FLIKAIIDYLRS---------------------RGKKVLVTAP   58 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChh--HHHHHHHHHhcc---------------------ccceEEEecc
Confidence            4566777766551     56889999999999999  555444443332                     2456899999


Q ss_pred             CHHHHHHH
Q 042526          132 TRELALQV  139 (284)
Q Consensus       132 TReLa~Qi  139 (284)
                      |---|..|
T Consensus        59 tg~AA~~i   66 (364)
T PF05970_consen   59 TGIAAFNI   66 (364)
T ss_pred             hHHHHHhc
Confidence            98877776

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=90.96  E-value=0.36  Score=47.75  Aligned_cols=46  Identities=30%  Similarity=0.413  Sum_probs=27.3

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHHcCCC-cEEEEccCCCCchHHhHHHHHHHH
Q 042526           48 SIYKLGFKESTSILKARIPALAHQRK-DVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        48 ~L~~~g~~~pT~iQ~~aip~il~~G~-dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .|..+||.   +-|.+.|-.++...+ -+++++|||||||.+. -.++..+
T Consensus       220 ~l~~Lg~~---~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l  266 (486)
T TIGR02533       220 DLETLGMS---PELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRL  266 (486)
T ss_pred             CHHHcCCC---HHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhcc
Confidence            34555652   445555544433344 4689999999999543 3445544

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.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=90.56  E-value=0.18  Score=51.73  Aligned_cols=48  Identities=21%  Similarity=0.104  Sum_probs=37.2

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASP  145 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~  145 (284)
                      .++++.||||||||.+|++|-|-...                         -.+||+=|--||........++
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~~-------------------------~S~VV~D~KGEl~~~Ta~~R~~  192 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTWP-------------------------GSAIVHDIKGENWQLTAGFRAR  192 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhCC-------------------------CCEEEEeCcchHHHHHHHHHHh
Confidence            58999999999999999999875321                         1377888889987766665544

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=90.53  E-value=0.29  Score=49.89  Aligned_cols=123  Identities=18%  Similarity=0.152  Sum_probs=63.3

Q ss_pred             cHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe--cCHHH
Q 042526           58 TSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN--PTREL  135 (284)
Q Consensus        58 T~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~--PTReL  135 (284)
                      +.++.+.+..| ...+-||+.+.||||||.-    +-++|+..                 ....+   .+|-|  |-|.-
T Consensus       358 f~~R~~ll~~i-r~n~vvvivgETGSGKTTQ----l~QyL~ed-----------------GY~~~---GmIGcTQPRRvA  412 (1042)
T KOG0924|consen  358 FACRDQLLSVI-RENQVVVIVGETGSGKTTQ----LAQYLYED-----------------GYADN---GMIGCTQPRRVA  412 (1042)
T ss_pred             HHHHHHHHHHH-hhCcEEEEEecCCCCchhh----hHHHHHhc-----------------ccccC---CeeeecCchHHH
Confidence            44555555555 6677889999999999943    33455553                 12222   34444  77777


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcc-----hHHHHHhc--CCCcccccccCCccccccccCCCCCCc-----ccccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLL-----TSEHSNRR--KPNKRKRTRKGGEDEKLDSLKWNPLSQ-----PKTTT  203 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~-----~q~~~l~~--~~~i~v~~~~~~~~d~l~~lv~dEAd~-----m~~~g  203 (284)
                      |..++..+   +..++..+...+|=.+.     .+.-.++.  ..-++...+.-..|++-..+++|||-.     ..-||
T Consensus       413 AiSVAkrV---a~EM~~~lG~~VGYsIRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfG  489 (1042)
T KOG0924|consen  413 AISVAKRV---AEEMGVTLGDTVGYSIRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFG  489 (1042)
T ss_pred             HHHHHHHH---HHHhCCccccccceEEEeeecCCCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHH
Confidence            77665544   33333222222221110     00000000  000111223445677778888999876     45566


Q ss_pred             cccch
Q 042526          204 LLPSS  208 (284)
Q Consensus       204 flp~~  208 (284)
                      ||-.+
T Consensus       490 llk~~  494 (1042)
T KOG0924|consen  490 LLKKV  494 (1042)
T ss_pred             HHHHH
Confidence            66555

>PRK12377 putative replication protein; Provisional

Probab=90.50  E-value=0.91  Score=40.89  Aligned_cols=48  Identities=13%  Similarity=0.166  Sum_probs=30.5

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHH
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA  143 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~  143 (284)
                      ..++++.+++|+|||. .+..+...+...                      +.. ++.++..+|..++...+
T Consensus       101 ~~~l~l~G~~GtGKTh-La~AIa~~l~~~----------------------g~~-v~~i~~~~l~~~l~~~~  148 (248)
T PRK12377        101 CTNFVFSGKPGTGKNH-LAAAIGNRLLAK----------------------GRS-VIVVTVPDVMSRLHESY  148 (248)
T ss_pred             CCeEEEECCCCCCHHH-HHHHHHHHHHHc----------------------CCC-eEEEEHHHHHHHHHHHH
Confidence            4689999999999993 223444444331                      223 35556778888776543

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=90.23  E-value=0.19  Score=45.20  Aligned_cols=49  Identities=18%  Similarity=0.075  Sum_probs=29.1

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHH
Q 042526           44 LLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPAL   94 (284)
Q Consensus        44 ~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil   94 (284)
                      +++++|..-|+.+..+.--..+--+ ..|.-+++.|++|+|||. |++-++
T Consensus         3 ~~~~~~~~~~~~tg~~~Ld~~~gG~-~~g~~~~i~g~~G~GKT~-l~~~~~   51 (271)
T cd01122           3 EIREALSNEEVWWPFPVLNKLTKGL-RKGELIILTAGTGVGKTT-FLREYA   51 (271)
T ss_pred             hhhccccccCCCCCcceeeeeeEEE-cCCcEEEEEcCCCCCHHH-HHHHHH
Confidence            4555665444443333222233334 678899999999999994 433333

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

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

Probab=90.21  E-value=0.24  Score=51.96  Aligned_cols=20  Identities=45%  Similarity=0.449  Sum_probs=16.9

Q ss_pred             cCCCcEEEEccCCCCchHHh
Q 042526           70 HQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlaf   89 (284)
                      ....-+|+.|+||||||...
T Consensus        63 ~~~~vvii~getGsGKTTql   82 (845)
T COG1643          63 EQNQVVIIVGETGSGKTTQL   82 (845)
T ss_pred             HhCCEEEEeCCCCCChHHHH
Confidence            66778999999999999553

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=90.19  E-value=0.73  Score=40.49  Aligned_cols=29  Identities=31%  Similarity=0.361  Sum_probs=21.4

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      ..|.-+++.|+||+||| +|++-++..+..
T Consensus        11 ~~G~l~lI~G~~G~GKT-~~~~~~~~~~~~   39 (242)
T cd00984          11 QPGDLIIIAARPSMGKT-AFALNIAENIAK   39 (242)
T ss_pred             CCCeEEEEEeCCCCCHH-HHHHHHHHHHHH
Confidence            56888999999999999 555555544433

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=89.92  E-value=0.66  Score=45.74  Aligned_cols=47  Identities=30%  Similarity=0.328  Sum_probs=29.5

Q ss_pred             HHHcCCCCCcHHHHHHHHHHHcCCC-cEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           49 IYKLGFKESTSILKARIPALAHQRK-DVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        49 L~~~g~~~pT~iQ~~aip~il~~G~-dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      |.++||.   +.|...+-.++...+ =+++.+|||||||.+ +..+|+.+..
T Consensus       237 l~~Lg~~---~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~  284 (500)
T COG2804         237 LEKLGMS---PFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNT  284 (500)
T ss_pred             HHHhCCC---HHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcC
Confidence            4444543   666666666534433 367889999999955 4566665544

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=89.84  E-value=0.41  Score=42.99  Aligned_cols=23  Identities=26%  Similarity=0.229  Sum_probs=18.1

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHH
Q 042526           74 DVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .+++.|++||||| +|++-+|..+
T Consensus        15 r~viIG~sGSGKT-~li~~lL~~~   37 (241)
T PF04665_consen   15 RMVIIGKSGSGKT-TLIKSLLYYL   37 (241)
T ss_pred             eEEEECCCCCCHH-HHHHHHHHhh
Confidence            7899999999999 6666666443

This is thought to be an ATPase involved in viral DNA packaging [].

>PF10278 Med19: Mediator of RNA pol II transcription subunit 19 ; InterPro: IPR019403 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=89.63  E-value=0.54  Score=40.10  Aligned_cols=15  Identities=27%  Similarity=-0.013  Sum_probs=9.2

Q ss_pred             CcchHHHHHhcCCCc
Q 042526          161 PLLTSEHSNRRKPNK  175 (284)
Q Consensus       161 ~~~~q~~~l~~~~~i  175 (284)
                      ......+.|..+|.|
T Consensus        60 ~d~ssLrslIekPPi   74 (178)
T PF10278_consen   60 QDNSSLRSLIEKPPI   74 (178)
T ss_pred             cCcchHHHHhhCCCC
Confidence            344445677777777

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=89.55  E-value=0.57  Score=48.78  Aligned_cols=48  Identities=19%  Similarity=0.237  Sum_probs=33.8

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHH
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLM  141 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~  141 (284)
                      -++=|.-.||||||.+|+=-|......                     ..-...||+|||.+.-.-+..
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~---------------------YG~~KFIivVPs~AIkeGv~~  122 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKK---------------------YGLFKFIIVVPSLAIKEGVFL  122 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHH---------------------hCceeEEEEeccHHHHhhhHH
Confidence            467778899999999998666543222                     245678999999776554433

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=89.32  E-value=0.2  Score=51.11  Aligned_cols=46  Identities=24%  Similarity=0.176  Sum_probs=35.4

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHH
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA  143 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~  143 (284)
                      ..+++.||||||||.+|++|.|-..                         +-.+||+=|-.|+..-+....
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~~-------------------------~~S~VV~D~KGE~~~~Tag~R  221 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLSW-------------------------GHSSVITDLKGELWALTAGWR  221 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhhC-------------------------CCCEEEEeCcHHHHHHHHHHH
Confidence            5799999999999999999987521                         224788889999976555443

>PRK07952 DNA replication protein DnaC; Validated

Probab=89.31  E-value=1.4  Score=39.69  Aligned_cols=25  Identities=20%  Similarity=0.214  Sum_probs=17.6

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      ..+++.+++|+|||... ..+...+.
T Consensus       100 ~~~~l~G~~GtGKThLa-~aia~~l~  124 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLA-AAICNELL  124 (244)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            47999999999999433 34444443

>PRK06526 transposase; Provisional

Probab=89.25  E-value=0.5  Score=42.66  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=17.1

Q ss_pred             cCCCcEEEEccCCCCchHHh
Q 042526           70 HQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlaf   89 (284)
                      ..+.++++.+|+|+|||...
T Consensus        96 ~~~~nlll~Gp~GtGKThLa  115 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLA  115 (254)
T ss_pred             hcCceEEEEeCCCCchHHHH
Confidence            56789999999999999543

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=89.25  E-value=0.26  Score=37.94  Aligned_cols=18  Identities=22%  Similarity=0.167  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCchHHh
Q 042526           72 RKDVIGAAETESGKTRAF   89 (284)
Q Consensus        72 G~dviv~A~TGSGKTlaf   89 (284)
                      +..+++.+|+|||||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            567999999999999443

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=89.19  E-value=0.26  Score=50.40  Aligned_cols=49  Identities=16%  Similarity=0.108  Sum_probs=36.6

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhh
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASP  145 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~  145 (284)
                      ...+++.|+||||||.++++|-+-..                         +-.++|+=|-.|++..+....++
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~~-------------------------~gS~VV~DpKgEl~~~Ta~~R~~  272 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALKW-------------------------GGPLVVLDPSTEVAPMVSEHRRD  272 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhcC-------------------------CCCEEEEeCcHHHHHHHHHHHHH
Confidence            35789999999999999999975311                         12367777999998766665544

>PRK08939 primosomal protein DnaI; Reviewed

Probab=89.18  E-value=1.5  Score=40.67  Aligned_cols=17  Identities=18%  Similarity=0.120  Sum_probs=14.8

Q ss_pred             CCCcEEEEccCCCCchH
Q 042526           71 QRKDVIGAAETESGKTR   87 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTl   87 (284)
                      .++.+++.+++|+|||.
T Consensus       155 ~~~gl~L~G~~G~GKTh  171 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSY  171 (306)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            46789999999999993

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=89.18  E-value=0.25  Score=50.25  Aligned_cols=49  Identities=18%  Similarity=0.129  Sum_probs=37.5

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      ..+++.||||||||.++++|-+-..                         +-.++|+=|..|++..+...-++.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~~-------------------------~gS~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALKY-------------------------GGPLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhcC-------------------------CCCEEEEEChHHHHHHHHHHHHHc
Confidence            5899999999999999999964321                         113788889999987777655544

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=89.17  E-value=0.45  Score=41.06  Aligned_cols=22  Identities=23%  Similarity=0.368  Sum_probs=15.8

Q ss_pred             EEEEccCCCCchHHhHHHHHHHH
Q 042526           75 VIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        75 viv~A~TGSGKTlafllPil~~l   97 (284)
                      +++++|||||||... -.++..+
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~   25 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYI   25 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHh
Confidence            688999999999553 4444444

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK08116 hypothetical protein; Validated

Probab=89.09  E-value=1.6  Score=39.59  Aligned_cols=48  Identities=15%  Similarity=0.076  Sum_probs=29.9

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHH
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA  143 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~  143 (284)
                      +..+++.+++|||||... ..+.+.+...                      +.. ++..+..+|...+...+
T Consensus       114 ~~gl~l~G~~GtGKThLa-~aia~~l~~~----------------------~~~-v~~~~~~~ll~~i~~~~  161 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLA-ACIANELIEK----------------------GVP-VIFVNFPQLLNRIKSTY  161 (268)
T ss_pred             CceEEEECCCCCCHHHHH-HHHHHHHHHc----------------------CCe-EEEEEHHHHHHHHHHHH
Confidence            345999999999999433 3455544432                      222 44556677777775543

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=88.66  E-value=0.9  Score=35.27  Aligned_cols=16  Identities=25%  Similarity=0.322  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCCchH
Q 042526           72 RKDVIGAAETESGKTR   87 (284)
Q Consensus        72 G~dviv~A~TGSGKTl   87 (284)
                      ++.+++.+++|+|||.
T Consensus        19 ~~~v~i~G~~G~GKT~   34 (151)
T cd00009          19 PKNLLLYGPPGTGKTT   34 (151)
T ss_pred             CCeEEEECCCCCCHHH
Confidence            7889999999999993

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=88.48  E-value=0.25  Score=46.22  Aligned_cols=18  Identities=28%  Similarity=0.335  Sum_probs=15.3

Q ss_pred             cCCCcEEEEccCCCCchH
Q 042526           70 HQRKDVIGAAETESGKTR   87 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTl   87 (284)
                      ++-.|+++.+|||||||+
T Consensus        95 L~KSNILLiGPTGsGKTl  112 (408)
T COG1219          95 LSKSNILLIGPTGSGKTL  112 (408)
T ss_pred             eeeccEEEECCCCCcHHH
Confidence            345689999999999995

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=88.43  E-value=1.3  Score=41.74  Aligned_cols=29  Identities=17%  Similarity=0.132  Sum_probs=21.8

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      .-.|=+++++|+||||| +.+=.+.|++.-
T Consensus       175 t~NRliLlhGPPGTGKT-SLCKaLaQkLSI  203 (423)
T KOG0744|consen  175 TWNRLILLHGPPGTGKT-SLCKALAQKLSI  203 (423)
T ss_pred             eeeeEEEEeCCCCCChh-HHHHHHHHhhee
Confidence            33567899999999999 666666666643

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=88.42  E-value=0.65  Score=44.47  Aligned_cols=49  Identities=22%  Similarity=0.272  Sum_probs=32.6

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLM  141 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~  141 (284)
                      ...+++++.+.||||||. ++-++|..+...                      +-++||.=|.-++....++
T Consensus        13 ~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~----------------------g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   13 SENRHILIIGATGSGKTQ-AIRHLLDQIRAR----------------------GDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             GGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT----------------------T-EEEEEEETTHHHHHH--
T ss_pred             hhhCcEEEECCCCCCHHH-HHHHHHHHHHHc----------------------CCEEEEEECCchHHHHhcC
Confidence            567899999999999996 445666665443                      4468888888887665544

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=88.34  E-value=2.3  Score=45.64  Aligned_cols=91  Identities=18%  Similarity=0.002  Sum_probs=58.3

Q ss_pred             CCCCHHHHHHHHHc-CCC------CCcHHHHHHHHHHHc-------------CCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           39 LRLHPLLMKSIYKL-GFK------ESTSILKARIPALAH-------------QRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        39 l~L~~~Ll~~L~~~-g~~------~pT~iQ~~aip~il~-------------~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      +.=++.|+.-|..+ =|.      ..-++|.++-+.++.             .++.-+|.--+|||||++-+..+- .+.
T Consensus       220 ~l~~~~ll~~i~~f~vf~~~~~~~~~k~~~~~~q~~av~~~i~~~~~~~~~~~~~~G~IWHtqGSGKTlTm~~~A~-~l~  298 (962)
T COG0610         220 FLAPERLLDIIRNFIVFDKSDDGLVKKKYQRYAQYRAVQKAIKRILKASNPGDGKGGYIWHTQGSGKTLTMFKLAR-LLL  298 (962)
T ss_pred             HhCHHHHHHHHHheEEEeecCCcccchhHHHHHHHHHHHHHHHHHHhccCCCcCCceEEEeecCCchHHHHHHHHH-HHH
Confidence            34456677777552 122      344566555553311             134567777799999987543221 111


Q ss_pred             HHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC
Q 042526           99 EEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN  150 (284)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~  150 (284)
                      ..                    ...|.++|||--++|-.|+.+.+..+....
T Consensus       299 ~~--------------------~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~  330 (962)
T COG0610         299 EL--------------------PKNPKVLFVVDRKDLDDQTSDEFQSFGKVA  330 (962)
T ss_pred             hc--------------------cCCCeEEEEechHHHHHHHHHHHHHHHHhh
Confidence            11                    367899999999999999999999987754

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=88.25  E-value=0.52  Score=45.48  Aligned_cols=51  Identities=20%  Similarity=0.213  Sum_probs=33.3

Q ss_pred             HHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHH
Q 042526           65 IPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV  139 (284)
Q Consensus        65 ip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi  139 (284)
                      ||.- ...+++++.|+||||||.. +..++..+...                      +-+++|+=|..++....
T Consensus        36 ~~~~-~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~----------------------~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          36 FPKD-AEEAHTMIIGTTGTGKTTQ-IRELLASIRAR----------------------GDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             CCcc-hhhccEEEEcCCCCCHHHH-HHHHHHHHHhc----------------------CCCEEEEeCCcchhHhh
Confidence            4544 5578999999999999964 44444444332                      33577777777765443

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=88.12  E-value=1  Score=39.96  Aligned_cols=54  Identities=15%  Similarity=0.004  Sum_probs=34.2

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL  147 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~  147 (284)
                      ..|.-+++.+++|||||.-.+--+...+ .                      .+-.+++++ +-+-+.|+.+.+..+.
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~~~-~----------------------~ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWNGL-Q----------------------MGEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHHHH-H----------------------cCCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            4578999999999999953322222222 1                      234567666 5666777777666554

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=87.78  E-value=0.78  Score=47.74  Aligned_cols=51  Identities=18%  Similarity=0.149  Sum_probs=37.0

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           74 DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      =.++.||.|||||.+..-+ |.....                     ...-.+|+|+.-|.|+.++...++.-
T Consensus        51 V~vVRSpMGTGKTtaLi~w-Lk~~l~---------------------~~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRW-LKDALK---------------------NPDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             eEEEECCCCCCcHHHHHHH-HHHhcc---------------------CCCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            4578999999999666433 322211                     13457999999999999999988743

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>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=87.64  E-value=0.55  Score=42.85  Aligned_cols=25  Identities=20%  Similarity=0.242  Sum_probs=20.0

Q ss_pred             HHHHHHcCCCcEEEEccCCCCchHH
Q 042526           64 RIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        64 aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .+..++..++.+++++|+|||||..
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            3344457899999999999999953

>PRK09183 transposase/IS protein; Provisional

Probab=87.57  E-value=1.3  Score=40.09  Aligned_cols=19  Identities=16%  Similarity=0.310  Sum_probs=16.8

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|.++++.+|+|+|||..
T Consensus       100 ~~~~~v~l~Gp~GtGKThL  118 (259)
T PRK09183        100 ERNENIVLLGPSGVGKTHL  118 (259)
T ss_pred             hcCCeEEEEeCCCCCHHHH
Confidence            6789999999999999943

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=87.53  E-value=1.3  Score=38.72  Aligned_cols=55  Identities=15%  Similarity=-0.029  Sum_probs=32.0

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhh
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSL  147 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~  147 (284)
                      -.|.-+++.+++|||||.-.+--+.+.+...                      +-.+++++ +-+-..++.+.++.+.
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~~~~~~----------------------ge~vlyvs-~ee~~~~l~~~~~s~g   71 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYNGLKNF----------------------GEKVLYVS-FEEPPEELIENMKSFG   71 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHHHHHH----------------------T--EEEEE-SSS-HHHHHHHHHTTT
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHHhhhhc----------------------CCcEEEEE-ecCCHHHHHHHHHHcC
Confidence            4578999999999999943322222222220                      22355555 5555677777777664

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=87.44  E-value=0.4  Score=48.34  Aligned_cols=69  Identities=13%  Similarity=0.137  Sum_probs=47.5

Q ss_pred             CCCccccccccccccCccccCcccCC-CCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchH
Q 042526           15 GPDDAQEELVNEAEISTEFDAWNELR-LHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTR   87 (284)
Q Consensus        15 ~~~~~~~~~~~~~~~p~~~~~F~~l~-L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTl   87 (284)
                      ...+.....+.+...|.+-.+|+++| ++..+..-+.- .-+.+|-.++..-+    .--+.|++|+|+|+|||.
T Consensus       168 ~a~~~~r~~~~~~~~~~snv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv----~PprGvLlHGPPGCGKT~  238 (802)
T KOG0733|consen  168 LARGILRQFVEGLEFPESNVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGV----RPPRGVLLHGPPGCGKTS  238 (802)
T ss_pred             hcchhhhhhhcccCCCCCCcchhhccChHHHHHHHHHHHHHhcCchhHhhcCC----CCCCceeeeCCCCccHHH
Confidence            33344455677788888888999996 55544443322 23777877776654    345789999999999994

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=87.29  E-value=0.61  Score=43.20  Aligned_cols=20  Identities=40%  Similarity=0.431  Sum_probs=17.3

Q ss_pred             HcCCCcEEEEccCCCCchHH
Q 042526           69 AHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        69 l~~G~dviv~A~TGSGKTla   88 (284)
                      +..|.++++.++||||||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            36789999999999999943

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=87.08  E-value=0.75  Score=41.53  Aligned_cols=20  Identities=20%  Similarity=0.054  Sum_probs=17.7

Q ss_pred             cCCCcEEEEccCCCCchHHh
Q 042526           70 HQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlaf   89 (284)
                      ..|+++++.+++|+|||...
T Consensus        19 ~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        19 KSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             hcCCeEEEEcCCCCCHHHHH
Confidence            77999999999999999544

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=86.66  E-value=2.7  Score=47.30  Aligned_cols=63  Identities=21%  Similarity=0.180  Sum_probs=43.8

Q ss_pred             CCcHHHHHHHHHHHcC--CCcEEEEccCCCCchHHh--HHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALAHQ--RKDVIGAAETESGKTRAF--GLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~--G~dviv~A~TGSGKTlaf--llPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .+|+-|..|+-.+ +.  .+-+++++..|||||...  ++.++..+..                     ..+..++.++|
T Consensus       835 ~Lt~~Qr~Av~~i-Lts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e---------------------~~g~~V~glAP  892 (1623)
T PRK14712        835 KLTSGQRAATRMI-LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE---------------------SERPRVVGLGP  892 (1623)
T ss_pred             ccCHHHHHHHHHH-HhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh---------------------ccCceEEEEec
Confidence            6899999999988 54  478999999999999543  1222221111                     13467888999


Q ss_pred             CHHHHHHHH
Q 042526          132 TRELALQVL  140 (284)
Q Consensus       132 TReLa~Qi~  140 (284)
                      |---|..+.
T Consensus       893 TgkAa~~L~  901 (1623)
T PRK14712        893 THRAVGEMR  901 (1623)
T ss_pred             hHHHHHHHH
Confidence            977666553

>KOG1533 consensus Predicted GTPase [General function prediction only]

Probab=86.52  E-value=0.74  Score=41.33  Aligned_cols=25  Identities=20%  Similarity=0.073  Sum_probs=19.9

Q ss_pred             EEEEccCCCCchHHhHHHHHHHHHHH
Q 042526           75 VIGAAETESGKTRAFGLPALQRLLEE  100 (284)
Q Consensus        75 viv~A~TGSGKTlafllPil~~l~~~  100 (284)
                      .++.+|+||||| +|+..+.+.+...
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~~   29 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSAI   29 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHHh
Confidence            478899999999 8888877766543

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=86.30  E-value=1.5  Score=38.78  Aligned_cols=19  Identities=11%  Similarity=0.137  Sum_probs=16.4

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|.-+++.+++|+|||..
T Consensus        22 ~~g~~~~i~G~~G~GKTtl   40 (230)
T PRK08533         22 PAGSLILIEGDESTGKSIL   40 (230)
T ss_pred             CCCcEEEEECCCCCCHHHH
Confidence            5688999999999999944

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=86.02  E-value=0.57  Score=46.94  Aligned_cols=72  Identities=10%  Similarity=-0.103  Sum_probs=55.5

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           48 SIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        48 ~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      .+..+-.+....+|..+|..+ ..|+++++...|-+||.++|-+..+..+...                     .....+
T Consensus       278 ~~~~~~~E~~~~~~~~~~~~~-~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~---------------------~~s~~~  335 (1034)
T KOG4150|consen  278 LLNKNTGESGIAISLELLKFA-SEGRADGGNEARQAGKGTCPTSGSRKFQTLC---------------------HATNSL  335 (1034)
T ss_pred             HHhcccccchhhhhHHHHhhh-hhcccccccchhhcCCccCcccchhhhhhcC---------------------ccccee
Confidence            345566777889999999988 9999999999999999999998877655442                     123467


Q ss_pred             EEecCHHHHHHHHH
Q 042526          128 IINPTRELALQVLM  141 (284)
Q Consensus       128 IL~PTReLa~Qi~~  141 (284)
                      ++.||.+|+..-..
T Consensus       336 ~~~~~~~~~~~~~~  349 (1034)
T KOG4150|consen  336 LPSEMVEHLRNGSK  349 (1034)
T ss_pred             cchhHHHHhhccCC
Confidence            77888888765433

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=85.78  E-value=2.6  Score=45.27  Aligned_cols=89  Identities=21%  Similarity=0.081  Sum_probs=60.2

Q ss_pred             cHHHHHHHHHHH-------cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           58 TSILKARIPALA-------HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        58 T~iQ~~aip~il-------~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      +..|-.|+..+.       ..|--+|-.|.||+|||+|=+     +++..                -.....+++..|-.
T Consensus       410 F~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA-----RImya----------------Lsd~~~g~RfsiAL  468 (1110)
T TIGR02562       410 FRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA-----RAMYA----------------LRDDKQGARFAIAL  468 (1110)
T ss_pred             cchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH-----HHHHH----------------hCCCCCCceEEEEc
Confidence            346766766551       225557778999999997753     22221                11223567888888


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHH
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEH  167 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~  167 (284)
                      -.|.|..|..+.++.-..-..-.+++++|+....+..
T Consensus       469 GLRTLTLQTGda~r~rL~L~~ddLAVlIGs~Av~~L~  505 (1110)
T TIGR02562       469 GLRSLTLQTGHALKTRLNLSDDDLAVLIGGTAVQTLF  505 (1110)
T ss_pred             cccceeccchHHHHHhcCCCccceEEEECHHHHHHHH
Confidence            9999999999999986655455778888886555444

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

>PRK08084 DNA replication initiation factor; Provisional

Probab=85.76  E-value=3.3  Score=36.66  Aligned_cols=17  Identities=6%  Similarity=0.092  Sum_probs=14.7

Q ss_pred             CCCcEEEEccCCCCchH
Q 042526           71 QRKDVIGAAETESGKTR   87 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTl   87 (284)
                      .+..+++.+|+|+|||.
T Consensus        44 ~~~~l~l~Gp~G~GKTh   60 (235)
T PRK08084         44 HSGYIYLWSREGAGRSH   60 (235)
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            45689999999999994

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=85.75  E-value=2.8  Score=48.33  Aligned_cols=66  Identities=18%  Similarity=0.133  Sum_probs=43.9

Q ss_pred             CCCcHHHHHHHHHHHcC--CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           55 KESTSILKARIPALAHQ--RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~--G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      ..+|+-|..|+-.+ +.  ++-+++++..|||||... ..++..+....                  ...+..++.++||
T Consensus      1018 ~~Lt~~Q~~Ai~~i-l~~~~~~~~i~G~AGtGKTt~l-~~~~~~i~~~~------------------~~~g~~v~glApT 1077 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLI-ISTKDRFVAVQGLAGVGKTTML-ESRYKPVLQAF------------------ESEQLQVIGLAPT 1077 (1960)
T ss_pred             CCCCHHHHHHHHHH-HhCCCcEEEEEeCCCCCHHHhH-HHHHHHHHHHH------------------HhcCCeEEEEeCh
Confidence            36899999999998 54  356788999999999443 22222222210                  0135678889999


Q ss_pred             HHHHHHHH
Q 042526          133 RELALQVL  140 (284)
Q Consensus       133 ReLa~Qi~  140 (284)
                      -.-|.++.
T Consensus      1078 ~~Aa~~L~ 1085 (1960)
T TIGR02760      1078 HEAVGELK 1085 (1960)
T ss_pred             HHHHHHHH
Confidence            77776553

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK08727 hypothetical protein; Validated

Probab=85.57  E-value=2  Score=38.01  Aligned_cols=15  Identities=20%  Similarity=0.164  Sum_probs=13.2

Q ss_pred             CcEEEEccCCCCchH
Q 042526           73 KDVIGAAETESGKTR   87 (284)
Q Consensus        73 ~dviv~A~TGSGKTl   87 (284)
                      ..+++.+++|||||.
T Consensus        42 ~~l~l~G~~G~GKTh   56 (233)
T PRK08727         42 DWLYLSGPAGTGKTH   56 (233)
T ss_pred             CeEEEECCCCCCHHH
Confidence            459999999999994

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=85.50  E-value=1.3  Score=45.97  Aligned_cols=108  Identities=19%  Similarity=0.058  Sum_probs=65.7

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS  149 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~  149 (284)
                      ..+-+-|+.-.-|=||| +-.|+.+..|.+..                   ..+| -|||||+--|    .++++.|.++
T Consensus       416 k~~l~gILADEMGLGKT-iQvIaFlayLkq~g-------------------~~gp-HLVVvPsSTl----eNWlrEf~kw  470 (941)
T KOG0389|consen  416 KKKLNGILADEMGLGKT-IQVIAFLAYLKQIG-------------------NPGP-HLVVVPSSTL----ENWLREFAKW  470 (941)
T ss_pred             HccccceehhhccCcch-hHHHHHHHHHHHcC-------------------CCCC-cEEEecchhH----HHHHHHHHHh
Confidence            44566689999999999 45566666665531                   2455 4889997766    4455566655


Q ss_pred             C-CceeEEEeCCCcch-HHH-HHhcC---CCccccc----------ccCCccccccccCCCCCCccccc
Q 042526          150 N-SLTLAMAAGSPLLT-SEH-SNRRK---PNKRKRT----------RKGGEDEKLDSLKWNPLSQPKTT  202 (284)
Q Consensus       150 ~-~i~v~~~~G~~~~~-q~~-~l~~~---~~i~v~~----------~~~~~~d~l~~lv~dEAd~m~~~  202 (284)
                      . .++|..|+|..... +.+ .+.++   .++++++          +...---++.+++|||+-++-++
T Consensus       471 CPsl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~  539 (941)
T KOG0389|consen  471 CPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNR  539 (941)
T ss_pred             CCceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhcc
Confidence            5 68899999985322 222 22222   2333333          11111236888999998875544

>PRK04328 hypothetical protein; Provisional

Probab=85.50  E-value=1.8  Score=38.83  Aligned_cols=18  Identities=22%  Similarity=0.289  Sum_probs=15.4

Q ss_pred             cCCCcEEEEccCCCCchH
Q 042526           70 HQRKDVIGAAETESGKTR   87 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTl   87 (284)
                      -.|.-+++.+++|+|||.
T Consensus        21 p~gs~ili~G~pGsGKT~   38 (249)
T PRK04328         21 PERNVVLLSGGPGTGKSI   38 (249)
T ss_pred             cCCcEEEEEcCCCCCHHH
Confidence            357889999999999984

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=85.12  E-value=0.83  Score=43.43  Aligned_cols=27  Identities=19%  Similarity=0.309  Sum_probs=21.2

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      +.|+-+++.+|+||||| |..+.+.+-|
T Consensus        63 ~aGrgiLi~GppgTGKT-AlA~gIa~eL   89 (450)
T COG1224          63 MAGRGILIVGPPGTGKT-ALAMGIAREL   89 (450)
T ss_pred             ccccEEEEECCCCCcHH-HHHHHHHHHh
Confidence            56899999999999999 5555555544

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.06  E-value=4.1  Score=39.17  Aligned_cols=19  Identities=26%  Similarity=0.303  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCchHHhH
Q 042526           72 RKDVIGAAETESGKTRAFG   90 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafl   90 (284)
                      ++.+++.+|||+|||.+..
T Consensus       174 ~~vi~lvGptGvGKTTT~a  192 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIA  192 (388)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4578999999999997654

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=84.91  E-value=2.9  Score=40.33  Aligned_cols=20  Identities=25%  Similarity=0.320  Sum_probs=17.1

Q ss_pred             CCCcEEEEccCCCCchHHhH
Q 042526           71 QRKDVIGAAETESGKTRAFG   90 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafl   90 (284)
                      .++-+.+.+|||.|||.+..
T Consensus       202 ~~~vi~LVGPTGVGKTTTlA  221 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLA  221 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHH
Confidence            37889999999999997654

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=84.59  E-value=0.54  Score=45.34  Aligned_cols=55  Identities=11%  Similarity=0.030  Sum_probs=35.5

Q ss_pred             ccccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      .|-.+|.+++-.....+.|.+.   -+.+|.-++..-+    ...+.+++.+|+|||||+..
T Consensus       139 ~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl----~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        139 KPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGI----DPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCC----CCCceEEEECCCCCCHHHHH
Confidence            4456799997666666666542   3344443333222    34678999999999999643

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=84.50  E-value=2  Score=46.98  Aligned_cols=54  Identities=24%  Similarity=0.238  Sum_probs=38.1

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLM  141 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~  141 (284)
                      -.+.+++|.|..|||||.+...-+|..+....                  ...-...|||+.|+.=|..+..
T Consensus        14 ~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~------------------~~~v~~ILvvTFT~aAa~Emk~   67 (1139)
T COG1074          14 PPGQSVLVEASAGTGKTFVLAERVLRLLLEGG------------------PLDVDEILVVTFTKAAAAEMKE   67 (1139)
T ss_pred             CCCCcEEEEEcCCCCchhHHHHHHHHHHhhcC------------------CCChhHeeeeeccHHHHHHHHH
Confidence            45789999999999999887777766665520                  1223468999998755554433

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=84.41  E-value=8.1  Score=38.82  Aligned_cols=20  Identities=20%  Similarity=0.192  Sum_probs=16.9

Q ss_pred             cCCCcEEEEccCCCCchHHh
Q 042526           70 HQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlaf   89 (284)
                      ..|.-+++.++||+|||...
T Consensus       348 ~~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            45788999999999999654

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=84.36  E-value=2.5  Score=40.30  Aligned_cols=59  Identities=19%  Similarity=0.238  Sum_probs=44.3

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH-HHHHHHHHHhhhhcCCCc
Q 042526           74 DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE-LALQVLMVASPSLKSNSL  152 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe-La~Qi~~~~~~l~~~~~i  152 (284)
                      -.++.+..|||||.+.++-++..+....                    .+.++||+-||.. |..-++..+......+++
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~--------------------~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~   62 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINK--------------------KQQNILAARKVQNSIRDSVFKDIENLLSIEGI   62 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcC--------------------CCcEEEEEehhhhHHHHHHHHHHHHHHHHcCC
Confidence            3578899999999999988887776630                    2467899999965 777788888766655444

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=84.27  E-value=1.8  Score=39.01  Aligned_cols=18  Identities=11%  Similarity=0.075  Sum_probs=15.8

Q ss_pred             cCCCcEEEEccCCCCchH
Q 042526           70 HQRKDVIGAAETESGKTR   87 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTl   87 (284)
                      ..|.-+++.+++|+|||.
T Consensus        34 p~gs~~lI~G~pGtGKT~   51 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSL   51 (259)
T ss_pred             ECCcEEEEEcCCCCCHHH
Confidence            457889999999999994

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=84.25  E-value=1.1  Score=37.09  Aligned_cols=27  Identities=30%  Similarity=0.381  Sum_probs=13.6

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..++.+++.+++|+|||. ++--++.++
T Consensus        22 ~~~~~~ll~G~~G~GKT~-ll~~~~~~~   48 (185)
T PF13191_consen   22 GSPRNLLLTGESGSGKTS-LLRALLDRL   48 (185)
T ss_dssp             -----EEE-B-TTSSHHH-HHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHH-HHHHHHHHH
Confidence            346789999999999993 333344433

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=84.23  E-value=2.4  Score=43.40  Aligned_cols=55  Identities=16%  Similarity=0.142  Sum_probs=38.1

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH--HHHHHHHHHhhhhcC
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE--LALQVLMVASPSLKS  149 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe--La~Qi~~~~~~l~~~  149 (284)
                      ..++++.|+||+|||..+ ..++......                      +..++|+=|-.+  |...++..++..+..
T Consensus       176 ~~H~lv~G~TGsGKT~l~-~~l~~q~i~~----------------------g~~viv~DpKgD~~l~~~~~~~~~~~G~~  232 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLA-ELLITQDIRR----------------------GDVVIVIDPKGDADLKRRMRAEAKRAGRP  232 (634)
T ss_pred             CCcEEEECCCCCCHHHHH-HHHHHHHHHc----------------------CCeEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence            467899999999999666 4454444332                      345667777754  888888888776543

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=84.17  E-value=1.6  Score=38.13  Aligned_cols=19  Identities=26%  Similarity=0.072  Sum_probs=16.2

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|..+++.+++|+|||..
T Consensus        18 ~~G~~~~i~G~~G~GKT~l   36 (229)
T TIGR03881        18 PRGFFVAVTGEPGTGKTIF   36 (229)
T ss_pred             cCCeEEEEECCCCCChHHH
Confidence            4588999999999999843

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=83.90  E-value=1.4  Score=39.50  Aligned_cols=55  Identities=22%  Similarity=0.103  Sum_probs=36.3

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhc
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK  148 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~  148 (284)
                      -.|+.+++.+++||||| .|++=.+......                      +- -++.+.|.|...++...+..+.-
T Consensus        21 p~g~~~lI~G~pGsGKT-~f~~qfl~~~~~~----------------------ge-~vlyvs~~e~~~~l~~~~~~~g~   75 (260)
T COG0467          21 PRGSVVLITGPPGTGKT-IFALQFLYEGARE----------------------GE-PVLYVSTEESPEELLENARSFGW   75 (260)
T ss_pred             cCCcEEEEEcCCCCcHH-HHHHHHHHHHHhc----------------------CC-cEEEEEecCCHHHHHHHHHHcCC
Confidence            45889999999999999 3433332222221                      22 35566788888888888877654

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=83.75  E-value=2.1  Score=44.44  Aligned_cols=84  Identities=19%  Similarity=0.091  Sum_probs=51.0

Q ss_pred             CCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      .+.|+|+.++.-+   ..++..=|+.-.-|=|||.- .+..|..|....                  . ..-.||||||.
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQ-iisFLaaL~~S~------------------k-~~~paLIVCP~  264 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQ-IISFLAALHHSG------------------K-LTKPALIVCPA  264 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchh-HHHHHHHHhhcc------------------c-ccCceEEEccH
Confidence            3457788776544   24566667788899999932 122222222210                  0 01239999997


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCc
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPL  162 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~  162 (284)
                      - +..|+.+++..+..  .++|.+++|...
T Consensus       265 T-ii~qW~~E~~~w~p--~~rv~ilh~t~s  291 (923)
T KOG0387|consen  265 T-IIHQWMKEFQTWWP--PFRVFILHGTGS  291 (923)
T ss_pred             H-HHHHHHHHHHHhCc--ceEEEEEecCCc
Confidence            5 45677777777744  567777777644

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=83.63  E-value=0.78  Score=43.78  Aligned_cols=26  Identities=19%  Similarity=0.307  Sum_probs=17.7

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQR   96 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~   96 (284)
                      ..|+-+++.+|+||||| |..+.+.+.
T Consensus        48 ~aGr~iLiaGppGtGKT-AlA~~ia~e   73 (398)
T PF06068_consen   48 IAGRAILIAGPPGTGKT-ALAMAIAKE   73 (398)
T ss_dssp             -TT-EEEEEE-TTSSHH-HHHHHHHHH
T ss_pred             ccCcEEEEeCCCCCCch-HHHHHHHHH
Confidence            46999999999999999 444555443

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=83.47  E-value=0.67  Score=36.29  Aligned_cols=18  Identities=22%  Similarity=0.270  Sum_probs=11.6

Q ss_pred             CCCcEEEEccCCCCchHH
Q 042526           71 QRKDVIGAAETESGKTRA   88 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTla   88 (284)
                      +++-+++.|++|+|||..
T Consensus         3 ~~~~~~i~G~~G~GKT~~   20 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTL   20 (131)
T ss_dssp             ----EEEEE-TTSSHHHH
T ss_pred             CCcccEEEcCCCCCHHHH
Confidence            466789999999999944

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=83.27  E-value=7.1  Score=37.95  Aligned_cols=20  Identities=30%  Similarity=0.200  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCCchHHhH
Q 042526           71 QRKDVIGAAETESGKTRAFG   90 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafl   90 (284)
                      .|+.+++.+|||+|||.+.+
T Consensus       220 ~~~~i~~vGptGvGKTTt~~  239 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLA  239 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            36788999999999996543

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=83.11  E-value=0.74  Score=44.95  Aligned_cols=54  Identities=13%  Similarity=0.105  Sum_probs=30.2

Q ss_pred             cccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           32 EFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      |..+|.+++=-...++.|.+.   -+.+|--+...-   + ..++.+++.+|+|||||+..
T Consensus       178 p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~g---i-~~p~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        178 PLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIG---I-KPPKGVILYGPPGTGKTLLA  234 (438)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcC---C-CCCcEEEEECCCCCCHHHHH
Confidence            446788885333444444432   122222111111   2 45678999999999999654

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=83.09  E-value=5.8  Score=45.13  Aligned_cols=65  Identities=15%  Similarity=0.102  Sum_probs=43.5

Q ss_pred             CCcHHHHHHHHHHHcC--CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           56 ESTSILKARIPALAHQ--RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~--G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      .+|+-|..|+-.+ +.  .+-+++++..|+|||... -.++..+...                  ....+..++.++||-
T Consensus       967 ~Lt~~Q~~Av~~i-l~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l------------------~~~~~~~V~glAPTg 1026 (1747)
T PRK13709        967 GLTSGQRAATRMI-LESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTL------------------PESERPRVVGLGPTH 1026 (1747)
T ss_pred             CCCHHHHHHHHHH-HhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHh------------------hcccCceEEEECCcH
Confidence            5899999999998 55  467899999999999442 2333222111                  011345688899997


Q ss_pred             HHHHHHH
Q 042526          134 ELALQVL  140 (284)
Q Consensus       134 eLa~Qi~  140 (284)
                      --|..+.
T Consensus      1027 rAAk~L~ 1033 (1747)
T PRK13709       1027 RAVGEMR 1033 (1747)
T ss_pred             HHHHHHH
Confidence            6665543

>PF05729 NACHT: NACHT domain

Probab=83.02  E-value=2.8  Score=33.75  Aligned_cols=25  Identities=28%  Similarity=0.181  Sum_probs=17.1

Q ss_pred             cEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           74 DVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      =+++.|++|+|||. ++--++..+..
T Consensus         2 ~l~I~G~~G~GKSt-ll~~~~~~~~~   26 (166)
T PF05729_consen    2 VLWISGEPGSGKST-LLRKLAQQLAE   26 (166)
T ss_pred             EEEEECCCCCChHH-HHHHHHHHHHh
Confidence            47899999999994 44444444443

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=82.75  E-value=4.2  Score=36.29  Aligned_cols=29  Identities=28%  Similarity=0.188  Sum_probs=19.9

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      ..|.=+++.|+||.||| +|++-++..+..
T Consensus        17 ~~g~L~vi~a~pg~GKT-~~~l~ia~~~a~   45 (259)
T PF03796_consen   17 RPGELTVIAARPGVGKT-AFALQIALNAAL   45 (259)
T ss_dssp             -TT-EEEEEESTTSSHH-HHHHHHHHHHHH
T ss_pred             CcCcEEEEEecccCCch-HHHHHHHHHHHH
Confidence            45666888999999999 566666555544

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK05595 replicative DNA helicase; Provisional

Probab=82.59  E-value=4.1  Score=39.68  Aligned_cols=27  Identities=26%  Similarity=0.309  Sum_probs=19.8

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..|.=+++.|+||+||| +|++-++..+
T Consensus       199 ~~g~liviaarpg~GKT-~~al~ia~~~  225 (444)
T PRK05595        199 QKGDMILIAARPSMGKT-TFALNIAEYA  225 (444)
T ss_pred             CCCcEEEEEecCCCChH-HHHHHHHHHH
Confidence            45666778999999999 6666665543

>PHA02533 17 large terminase protein; Provisional

Probab=82.55  E-value=6.6  Score=39.38  Aligned_cols=72  Identities=14%  Similarity=0.113  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|.|.|...+-.+ ..++-.++..+-..|||.+.++-++-.....                     .+..+++++|+++-
T Consensus        59 ~L~p~Q~~i~~~~-~~~R~~ii~~aRq~GKStl~a~~al~~a~~~---------------------~~~~v~i~A~~~~Q  116 (534)
T PHA02533         59 QMRDYQKDMLKIM-HKNRFNACNLSRQLGKTTVVAIFLLHYVCFN---------------------KDKNVGILAHKASM  116 (534)
T ss_pred             CCcHHHHHHHHHH-hcCeEEEEEEcCcCChHHHHHHHHHHHHHhC---------------------CCCEEEEEeCCHHH
Confidence            4788999988876 5566667777789999977665444333221                     24589999999999


Q ss_pred             HHHHHHHHhhhhcC
Q 042526          136 ALQVLMVASPSLKS  149 (284)
Q Consensus       136 a~Qi~~~~~~l~~~  149 (284)
                      |..+.+.++.+...
T Consensus       117 A~~vF~~ik~~ie~  130 (534)
T PHA02533        117 AAEVLDRTKQAIEL  130 (534)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99998888765543

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=82.49  E-value=4.1  Score=41.50  Aligned_cols=72  Identities=15%  Similarity=0.001  Sum_probs=51.1

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+++-|.+|+...   ...++|.|..|||||-+..-=+...+...                   ....-+.|.++-|+--
T Consensus         2 ~Ln~~Q~~av~~~---~gp~lV~AGaGsGKT~vlt~Ria~li~~~-------------------~v~p~~Il~vTFTnkA   59 (655)
T COG0210           2 KLNPEQREAVLHP---DGPLLVLAGAGSGKTRVLTERIAYLIAAG-------------------GVDPEQILAITFTNKA   59 (655)
T ss_pred             CCCHHHHHHHhcC---CCCeEEEECCCCCchhhHHHHHHHHHHcC-------------------CcChHHeeeeechHHH
Confidence            5789999999654   56888889999999966554443333221                   0112248999999999


Q ss_pred             HHHHHHHHhhhhcC
Q 042526          136 ALQVLMVASPSLKS  149 (284)
Q Consensus       136 a~Qi~~~~~~l~~~  149 (284)
                      |..+...+..+...
T Consensus        60 A~em~~Rl~~~~~~   73 (655)
T COG0210          60 AAEMRERLLKLLGL   73 (655)
T ss_pred             HHHHHHHHHHHhCc
Confidence            99988888888763

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=82.48  E-value=4.2  Score=39.23  Aligned_cols=43  Identities=19%  Similarity=0.234  Sum_probs=27.9

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           53 GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      |+.+..+---..+.-+ ..|.=+++.|+||+||| +|++-++..+
T Consensus       176 gi~tG~~~LD~~~~G~-~~g~liviag~pg~GKT-~~al~ia~~~  218 (421)
T TIGR03600       176 GLSTGLPKLDRLTNGL-VKGDLIVIGARPSMGKT-TLALNIAENV  218 (421)
T ss_pred             ceeCCChhHHHHhcCC-CCCceEEEEeCCCCCHH-HHHHHHHHHH
Confidence            4444444444444444 66778899999999999 6666665443

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=82.24  E-value=1.4  Score=38.57  Aligned_cols=20  Identities=20%  Similarity=0.172  Sum_probs=14.5

Q ss_pred             HcCCCcEEEEccCCCCchHH
Q 042526           69 AHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        69 l~~G~dviv~A~TGSGKTla   88 (284)
                      +..+.++++.+|+|||||+.
T Consensus        19 AaG~h~lLl~GppGtGKTml   38 (206)
T PF01078_consen   19 AAGGHHLLLIGPPGTGKTML   38 (206)
T ss_dssp             HHCC--EEEES-CCCTHHHH
T ss_pred             HcCCCCeEEECCCCCCHHHH
Confidence            46789999999999999954

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=82.13  E-value=7.2  Score=40.70  Aligned_cols=90  Identities=16%  Similarity=0.024  Sum_probs=56.8

Q ss_pred             CCcHHHHHHHHHHH--c-------CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEE
Q 042526           56 ESTSILKARIPALA--H-------QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRA  126 (284)
Q Consensus        56 ~pT~iQ~~aip~il--~-------~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~a  126 (284)
                      .+.|+|++.+.-+.  +       .....|+.-..|+|||+- +|++|..+++..+               .....--++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq-~IsflwtlLrq~P---------------~~~~~~~k~  301 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQ-CISFIWTLLRQFP---------------QAKPLINKP  301 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHH-HHHHHHHHHHhCc---------------Ccccccccc
Confidence            46689999886551  1       223455666689999964 4677777776531               111122568


Q ss_pred             EEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCc
Q 042526          127 LIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPL  162 (284)
Q Consensus       127 LIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~  162 (284)
                      |||+|. -|+.-+++++.++.....+.+..++|...
T Consensus       302 lVV~P~-sLv~nWkkEF~KWl~~~~i~~l~~~~~~~  336 (776)
T KOG0390|consen  302 LVVAPS-SLVNNWKKEFGKWLGNHRINPLDFYSTKK  336 (776)
T ss_pred             EEEccH-HHHHHHHHHHHHhccccccceeeeecccc
Confidence            999996 45566777777766654556666677654

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=81.97  E-value=4.8  Score=33.81  Aligned_cols=27  Identities=26%  Similarity=0.233  Sum_probs=19.9

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      .|.=+++.|++|+||| +|++-++..+.
T Consensus        31 ~g~l~~i~g~~g~GKT-~~~~~l~~~~~   57 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKT-TLALQLAAALA   57 (193)
T ss_dssp             TTSEEEEEECSTSSHH-HHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHH-HHHHHHHHHHH
Confidence            5777899999999999 45555555444

>TIGR00665 DnaB replicative DNA helicase

Probab=81.97  E-value=4.4  Score=39.17  Aligned_cols=28  Identities=32%  Similarity=0.323  Sum_probs=20.9

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      ..|.=+++.|+||+||| +|++-++.++.
T Consensus       193 ~~G~l~vi~g~pg~GKT-~~~l~~a~~~a  220 (434)
T TIGR00665       193 QPSDLIILAARPSMGKT-AFALNIAENAA  220 (434)
T ss_pred             CCCeEEEEEeCCCCChH-HHHHHHHHHHH
Confidence            55777889999999999 66665555443

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=81.89  E-value=0.93  Score=35.25  Aligned_cols=14  Identities=21%  Similarity=0.297  Sum_probs=12.0

Q ss_pred             EEEEccCCCCchHH
Q 042526           75 VIGAAETESGKTRA   88 (284)
Q Consensus        75 viv~A~TGSGKTla   88 (284)
                      |++.+|+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            68999999999943

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK05748 replicative DNA helicase; Provisional

Probab=81.87  E-value=4.7  Score=39.30  Aligned_cols=27  Identities=37%  Similarity=0.423  Sum_probs=21.0

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..|.=+++.|+||+||| +|++-++..+
T Consensus       201 ~~G~livIaarpg~GKT-~~al~ia~~~  227 (448)
T PRK05748        201 QPNDLIIVAARPSVGKT-AFALNIAQNV  227 (448)
T ss_pred             CCCceEEEEeCCCCCch-HHHHHHHHHH
Confidence            56777899999999999 6666665544

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=81.68  E-value=1.5  Score=42.65  Aligned_cols=55  Identities=27%  Similarity=0.175  Sum_probs=33.6

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHH----HHHHHHHhhh
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA----LQVLMVASPS  146 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa----~Qi~~~~~~l  146 (284)
                      .-.|||+.+||||||||-  .-.|.+++                       +-|.||.=|.|---|    ..|..++.+|
T Consensus       225 eKSNvLllGPtGsGKTll--aqTLAr~l-----------------------dVPfaIcDcTtLTQAGYVGeDVEsvi~KL  279 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLL--AQTLARVL-----------------------DVPFAICDCTTLTQAGYVGEDVESVIQKL  279 (564)
T ss_pred             ecccEEEECCCCCchhHH--HHHHHHHh-----------------------CCCeEEecccchhhcccccccHHHHHHHH
Confidence            345899999999999943  23333333                       245666666554433    3466677777


Q ss_pred             hcCC
Q 042526          147 LKSN  150 (284)
Q Consensus       147 ~~~~  150 (284)
                      ....
T Consensus       280 l~~A  283 (564)
T KOG0745|consen  280 LQEA  283 (564)
T ss_pred             HHHc
Confidence            6543

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=81.67  E-value=4  Score=41.78  Aligned_cols=55  Identities=18%  Similarity=0.160  Sum_probs=39.9

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH--HHHHHHHHHHhhhhcC
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR--ELALQVLMVASPSLKS  149 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR--eLa~Qi~~~~~~l~~~  149 (284)
                      ....++.++||+|||..+.+-+.+.+ .                      .+..++|+=|-.  +|..-++..++..++.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i-~----------------------~g~~vi~fDpkgD~el~~~~~~~~~~~GR~  236 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDI-R----------------------RGDVVIVFDPKGDADLLKRMYAEAKRAGRL  236 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHH-H----------------------cCCeEEEEeCCCCHHHHHHHHHHHHHhCCC
Confidence            45789999999999977665444433 2                      144677777885  7888888888887764

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PRK04296 thymidine kinase; Provisional

Probab=81.09  E-value=2.3  Score=36.34  Aligned_cols=25  Identities=20%  Similarity=-0.032  Sum_probs=16.9

Q ss_pred             CCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           72 RKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        72 G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      |.=+++.+++|+|||. .++-++.++
T Consensus         2 g~i~litG~~GsGKTT-~~l~~~~~~   26 (190)
T PRK04296          2 AKLEFIYGAMNSGKST-ELLQRAYNY   26 (190)
T ss_pred             cEEEEEECCCCCHHHH-HHHHHHHHH
Confidence            4456889999999994 344444443

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=81.09  E-value=1.5  Score=40.80  Aligned_cols=27  Identities=33%  Similarity=0.379  Sum_probs=21.2

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      +.||-+++.+|+||||| |..+.+-+-+
T Consensus        62 maGravLlaGppgtGKT-AlAlaisqEL   88 (456)
T KOG1942|consen   62 MAGRAVLLAGPPGTGKT-ALALAISQEL   88 (456)
T ss_pred             ccCcEEEEecCCCCchh-HHHHHHHHHh
Confidence            67999999999999999 4455555444

>cd01394 radB RadB

Probab=81.09  E-value=7.2  Score=33.66  Aligned_cols=19  Identities=16%  Similarity=0.060  Sum_probs=15.3

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|.-+++.+++|||||..
T Consensus        17 ~~g~i~~i~G~~GsGKT~l   35 (218)
T cd01394          17 ERGTVTQVYGPPGTGKTNI   35 (218)
T ss_pred             cCCeEEEEECCCCCCHHHH
Confidence            3466789999999999943

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=81.00  E-value=1.9  Score=37.31  Aligned_cols=19  Identities=21%  Similarity=0.148  Sum_probs=16.0

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..+..+++.+++|||||..
T Consensus        36 ~~~~~lll~G~~G~GKT~l   54 (226)
T TIGR03420        36 KGDRFLYLWGESGSGKSHL   54 (226)
T ss_pred             CCCCeEEEECCCCCCHHHH
Confidence            4567999999999999944

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=80.84  E-value=6  Score=45.69  Aligned_cols=64  Identities=17%  Similarity=0.065  Sum_probs=45.6

Q ss_pred             CCcHHHHHHHHHHHcC-CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           56 ESTSILKARIPALAHQ-RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~-G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      .+++-|..|+-.++.+ .+=++++++.|+|||.  ++-.+-.+.+.                     .+..+++++||.-
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt--~l~~l~~~~~~---------------------~G~~V~~lAPTgr  485 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTE--IAQLLLHLASE---------------------QGYEIQIITAGSL  485 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHH--HHHHHHHHHHh---------------------cCCeEEEEeCCHH
Confidence            4789999999988433 3678899999999993  33333333332                     3567999999987


Q ss_pred             HHHHHHHH
Q 042526          135 LALQVLMV  142 (284)
Q Consensus       135 La~Qi~~~  142 (284)
                      -|.++...
T Consensus       486 AA~~L~e~  493 (1960)
T TIGR02760       486 SAQELRQK  493 (1960)
T ss_pred             HHHHHHHH
Confidence            77666554

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=80.84  E-value=2.6  Score=41.76  Aligned_cols=88  Identities=20%  Similarity=0.081  Sum_probs=54.1

Q ss_pred             CCcHHHHHHHHHHHc----CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALAH----QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il~----~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .+.|+|.+.+--+..    .-..-|+.-.-|.|||.-.+.-+    +...                    .+...|||+|
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLl----lae~--------------------~ra~tLVvaP  239 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALL----LAEV--------------------DRAPTLVVAP  239 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHH----Hhcc--------------------ccCCeeEEcc
Confidence            345777765532211    11223667789999995433222    2221                    2233899999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHH
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSN  169 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l  169 (284)
                      +.+| .|..+++.++.. ...++.+++|.........+
T Consensus       240 ~VAl-mQW~nEI~~~T~-gslkv~~YhG~~R~~nikel  275 (791)
T KOG1002|consen  240 TVAL-MQWKNEIERHTS-GSLKVYIYHGAKRDKNIKEL  275 (791)
T ss_pred             HHHH-HHHHHHHHHhcc-CceEEEEEecccccCCHHHh
Confidence            9998 678888888877 45778888887544444443

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

Probab=80.63  E-value=1.8  Score=39.81  Aligned_cols=47  Identities=30%  Similarity=0.380  Sum_probs=29.0

Q ss_pred             cCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHH
Q 042526           29 ISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ   95 (284)
Q Consensus        29 ~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~   95 (284)
                      +...+++|++|+||+-+-+-               |   + ...-=||+.++|||||+.+. ..++.
T Consensus       103 I~~~IPt~eeL~LPevlk~l---------------a---~-~kRGLviiVGaTGSGKSTtm-AaMi~  149 (375)
T COG5008         103 IETKIPTFEELKLPEVLKDL---------------A---L-AKRGLVIIVGATGSGKSTTM-AAMIG  149 (375)
T ss_pred             hhccCCcHHhcCCcHHHHHh---------------h---c-ccCceEEEECCCCCCchhhH-HHHhc
Confidence            34567778888887754331               1   1 22225778899999998554 34443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=80.56  E-value=3.9  Score=35.02  Aligned_cols=21  Identities=19%  Similarity=-0.035  Sum_probs=16.6

Q ss_pred             cCCCcEEEEccCCCCchHHhH
Q 042526           70 HQRKDVIGAAETESGKTRAFG   90 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafl   90 (284)
                      ..|.=+.+.+++|||||...+
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~   30 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICM   30 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHH
Confidence            346778999999999995443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=80.47  E-value=0.89  Score=43.58  Aligned_cols=53  Identities=13%  Similarity=0.106  Sum_probs=30.3

Q ss_pred             cccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      |-.+|.+++--+...+.|...   .+.+|-.++..-+    ..-+.+++.+|+|||||+.
T Consensus       126 p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~----~~p~gvLL~GppGtGKT~l  181 (389)
T PRK03992        126 PNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGI----EPPKGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCC----CCCCceEEECCCCCChHHH
Confidence            345678876444445555442   2333332222211    2346799999999999954

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=80.45  E-value=1.6  Score=42.90  Aligned_cols=20  Identities=20%  Similarity=0.217  Sum_probs=17.8

Q ss_pred             HcCCCcEEEEccCCCCchHH
Q 042526           69 AHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        69 l~~G~dviv~A~TGSGKTla   88 (284)
                      +..|+++++.+|+|||||+.
T Consensus       195 AAGgHnLl~~GpPGtGKTml  214 (490)
T COG0606         195 AAGGHNLLLVGPPGTGKTML  214 (490)
T ss_pred             HhcCCcEEEecCCCCchHHh
Confidence            46799999999999999954

>PHA02244 ATPase-like protein

Probab=80.32  E-value=1.8  Score=41.39  Aligned_cols=20  Identities=20%  Similarity=0.228  Sum_probs=17.5

Q ss_pred             HHcCCCcEEEEccCCCCchH
Q 042526           68 LAHQRKDVIGAAETESGKTR   87 (284)
Q Consensus        68 il~~G~dviv~A~TGSGKTl   87 (284)
                      ++..+.+|++.+|||+|||.
T Consensus       115 ~l~~~~PVLL~GppGtGKTt  134 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNH  134 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHH
Confidence            34779999999999999993

>PLN03025 replication factor C subunit; Provisional

Probab=80.29  E-value=2.4  Score=39.29  Aligned_cols=40  Identities=10%  Similarity=0.070  Sum_probs=25.0

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      +|.++--++.++..|+.+           +.  - .....+++.+|+|+|||..
T Consensus        11 ~l~~~~g~~~~~~~L~~~-----------~~--~-~~~~~lll~Gp~G~GKTtl   50 (319)
T PLN03025         11 KLDDIVGNEDAVSRLQVI-----------AR--D-GNMPNLILSGPPGTGKTTS   50 (319)
T ss_pred             CHHHhcCcHHHHHHHHHH-----------Hh--c-CCCceEEEECCCCCCHHHH
Confidence            466665566666665542           00  0 1224689999999999943

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=80.23  E-value=2.3  Score=40.41  Aligned_cols=54  Identities=17%  Similarity=0.115  Sum_probs=35.5

Q ss_pred             cccCcccCC-CCHHHHHHHH--HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           32 EFDAWNELR-LHPLLMKSIY--KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        32 ~~~~F~~l~-L~~~Ll~~L~--~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      |-.+|+++| |...|.+.=.  ++-..+|=-++..-|.    .-+.|++.+|+||||||..
T Consensus       146 PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~----PPKGVLLYGPPGTGKTLLA  202 (406)
T COG1222         146 PDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGID----PPKGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCC----CCCceEeeCCCCCcHHHHH
Confidence            446799995 7666554322  2455566555555443    3468999999999999644

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=80.18  E-value=4.5  Score=32.23  Aligned_cols=14  Identities=36%  Similarity=0.361  Sum_probs=11.9

Q ss_pred             EEEEccCCCCchHH
Q 042526           75 VIGAAETESGKTRA   88 (284)
Q Consensus        75 viv~A~TGSGKTla   88 (284)
                      +++.+++|+|||..
T Consensus         2 ~~i~G~~G~GKT~l   15 (165)
T cd01120           2 ILVFGPTGSGKTTL   15 (165)
T ss_pred             eeEeCCCCCCHHHH
Confidence            57899999999943

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=80.05  E-value=1.5  Score=30.99  Aligned_cols=17  Identities=18%  Similarity=0.145  Sum_probs=14.4

Q ss_pred             CCcEEEEccCCCCchHH
Q 042526           72 RKDVIGAAETESGKTRA   88 (284)
Q Consensus        72 G~dviv~A~TGSGKTla   88 (284)
                      |...++.+++|||||..
T Consensus        23 g~~tli~G~nGsGKSTl   39 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTL   39 (62)
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            56799999999999943

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	284
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		2e-10
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-09
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		3e-09
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-09
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-08
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		3e-07
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-07
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-06
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-06
3ly5_A	262	Ddx18 Dead-Domain Length = 262		2e-06
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		2e-06
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-06
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-06
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		5e-06
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		5e-06
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		8e-06
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		9e-06
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-05
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-05
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-05
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-05
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-05
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		2e-05
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-05
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-05
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		2e-05
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		3e-05
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-05
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		4e-05
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		4e-05
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		4e-05
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		4e-05
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		5e-05
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-04
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		2e-04
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-04
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-04
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		3e-04
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		8e-04
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		8e-04

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/126 (35%), Positives = 65/126 (51%), Gaps = 25/126 (19%)
Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRK 73
           + P +A + +V E E  T    + +L +  +L ++  +LG+ + T I    IP LA Q +
Sbjct: 27  DSPTEASQPIVEEEETKT----FKDLGVTDVLCEACDQLGWTKPTKIQIEAIP-LALQGR 81
Query: 74  DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR 133
           D+IG AET SGKT AF LP L  LLE  ++                    L AL++ PTR
Sbjct: 82  DIIGLAETGSGKTGAFALPILNALLETPQR--------------------LFALVLTPTR 121
Query: 134 ELALQV 139
           ELA Q+
Sbjct: 122 ELAFQI 127

>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 = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 57/105 (54%), Gaps = 12/105 (11%)
Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++EL+L P +  +I    ++  T I K  IPA+   R D++  A+T SGKT AF +P + 
Sbjct: 25  FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHR-DIMACAQTGSGKTAAFLIPIIN 83
Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVL 140
            L+ +               ++Y+   + + LI+ PTRELA+Q+L
Sbjct: 84  HLVCQ-----------DLNQQRYSKTAYPKCLILAPTRELAIQIL 117

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 42/116 (36%), Positives = 60/116 (51%), Gaps = 21/116 (18%)
Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           + +  L P ++++++  G    T I  A +P LA + KD+IG A T +GKT AF LP  +
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALP-LALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV---LMVASPSLK 148
           RL   +E+  K                  RAL++ PTRELALQV   L   +P LK
Sbjct: 62  RLAPSQERGRKP-----------------RALVLTPTRELALQVASELTAVAPHLK 100

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 42/116 (36%), Positives = 60/116 (51%), Gaps = 21/116 (18%)
Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           + +  L P ++++++  G    T I  A +P LA + KD+IG A T +GKT AF LP  +
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALP-LALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV---LMVASPSLK 148
           RL   +E+  K                  RAL++ PTRELALQV   L   +P LK
Sbjct: 62  RLAPSQERGRKP-----------------RALVLTPTRELALQVASELTAVAPHLK 100

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 67/136 (49%), Gaps = 16/136 (11%)
Query: 24  VNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETES 83
           V  +++      +    L  +++ ++ K G+K  T I K  IP ++  R D++  A+T S
Sbjct: 46  VTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGR-DLMACAQTGS 104
Query: 84  GKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA 143
           GKT AF LP L +LLE+  +    LE            G  + +I++PTRELA+Q+   A
Sbjct: 105 GKTAAFLLPILSKLLEDPHE----LE-----------LGRPQVVIVSPTRELAIQIFNEA 149
Query: 144 SPSLKSNSLTLAMAAG 159
                 + L + +  G
Sbjct: 150 RKFAFESYLKIGIVYG 165

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/127 (30%), Positives = 67/127 (52%), Gaps = 23/127 (18%)
Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSI-LKARIPALAHQR 72
           NGPD  + E V E+  +   D+++++ L   L++ IY  GF++ ++I  +A +P +  + 
Sbjct: 20  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCI--KG 77
Query: 73  KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT 132
            DVI  A++ +GKT  F +  LQ+ +E   KA +                   AL++ PT
Sbjct: 78  YDVIAQAQSGTGKTATFAISILQQ-IELDLKATQ-------------------ALVLAPT 117
Query: 133 RELALQV 139
           RELA Q+
Sbjct: 118 RELAQQI 124

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/102 (34%), Positives = 52/102 (50%), Gaps = 20/102 (19%)
Query: 38  ELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL 97
           E +++  L+++I   GF+  T I    IP + H R +++ +A T SGKT AF +P L +L
Sbjct: 33  EYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGR-ELLASAPTGSGKTLAFSIPILMQL 91
Query: 98  LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            +   K                     RALII+PTRELA Q+
Sbjct: 92  KQPANKG-------------------FRALIISPTRELASQI 114

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 51/109 (46%), Gaps = 21/109 (19%)
Query: 31  TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFG 90
            E+  +NEL L   ++ +I   GF++ T I    IP   +   +++  A T SGKT +F 
Sbjct: 3   VEYXNFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFA 62
Query: 91  LPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +P ++ + E                        + A+I+ PTRELA+QV
Sbjct: 63  IPLIELVNEN---------------------NGIEAIILTPTRELAIQV 90

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/121 (29%), Positives = 67/121 (55%), Gaps = 27/121 (22%)
Query: 24  VNEAEISTEFDA----WNELRLHPLLMKSIYKLGFKESTSIL-KARIPALAHQRKDVIGA 78
           + E++I T +D     ++++ L   L++ ++  GF+E ++I  +A +P +  +  DV+  
Sbjct: 8   IEESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPII--EGHDVLAQ 65
Query: 79  AETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           A++ +GKT  F + ALQR+    + + K            AP+    AL++ PTRELALQ
Sbjct: 66  AQSGTGKTGTFSIAALQRI----DTSVK------------APQ----ALMLAPTRELALQ 105
Query: 139 V 139
           +
Sbjct: 106 I 106

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 56/114 (49%), Gaps = 17/114 (14%)
Query: 46  MKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAA 105
           +K+I ++GF   T I    I  L   R D++ AA+T SGKT AF +PA++ +++ R    
Sbjct: 66  LKAIKEMGFTNMTEIQHKSIRPLLEGR-DLLAAAKTGSGKTLAFLIPAVELIVKLR---- 120
Query: 106 KMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAG 159
                       + P+     LI++PTRELA+Q   V    +  +  T  +  G
Sbjct: 121 ------------FMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMG 162

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/119 (29%), Positives = 64/119 (53%), Gaps = 27/119 (22%)
Query: 26  EAEISTEFDA----WNELRLHPLLMKSIYKLGFKESTSIL-KARIPALAHQRKDVIGAAE 80
           E++I T +D     ++++ L   L++ ++  GF+E ++I  +A +P +  +  DV+  A+
Sbjct: 2   ESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPII--EGHDVLAQAQ 59
Query: 81  TESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           + +GKT  F + ALQR+                +    AP+    AL++ PTRELALQ+
Sbjct: 60  SGTGKTGTFSIAALQRI----------------DTSVKAPQ----ALMLAPTRELALQI 98

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/135 (31%), Positives = 61/135 (45%), Gaps = 17/135 (12%)
Query: 32  EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGL 91
           E   +++  L    +K + +  ++  T I K  I  LA Q KDV+GAA+T SGKT AF +
Sbjct: 23  EITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTI-GLALQGKDVLGAAKTGSGKTLAFLV 81
Query: 92  PALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNS 151
           P L+ L                   ++     L  LII+PTRELA Q   V     K++ 
Sbjct: 82  PVLEALYR----------------LQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHD 125
Query: 152 LTLAMAAGSPLLTSE 166
            +  +  G   L  E
Sbjct: 126 FSAGLIIGGKDLKHE 140

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 62/107 (57%), Gaps = 5/107 (4%)
Query: 34  DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++++++ +  ++M +I    +   T + K  IP +  +R D++  A+T SGKT AF LP 
Sbjct: 15  ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKR-DLMACAQTGSGKTAAFLLPI 73
Query: 94  LQRLLEERE-KAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           L ++  +   +A + ++E G    +   K +  +L++ PTRELA+Q+
Sbjct: 74  LSQIYSDGPGEALRAMKENGRYGRR---KQYPISLVLAPTRELAVQI 117

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 34/121 (28%), Positives = 64/121 (52%), Gaps = 27/121 (22%)
Query: 24  VNEAEISTEFDA----WNELRLHPLLMKSIYKLGFKESTSIL-KARIPALAHQRKDVIGA 78
           + E++I T +      ++++ L   L++ ++  GF+E ++I  +A +P +  +  DV+  
Sbjct: 7   IEESQIQTNYQKVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPII--EGHDVLAQ 64
Query: 79  AETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           A++ +GKT  F + ALQR+                +    AP+    AL++ PTRELALQ
Sbjct: 65  AQSGTGKTGTFSIAALQRI----------------DTSVKAPQ----ALMLAPTRELALQ 104
Query: 139 V 139
           +
Sbjct: 105 I 105

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 64/124 (51%), Gaps = 25/124 (20%)
Query: 24  VNEAEISTEFDA----WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAA 79
           + E++I T +D     +++  L   L++ ++  GF+E ++I +  I  +  +  DV+  A
Sbjct: 7   IEESQIQTNYDKVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPII-EGHDVLAQA 65
Query: 80  ETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           ++ +GKT  F + ALQR+    + + K            AP+    AL + PTRELALQ+
Sbjct: 66  QSGTGKTGTFSIAALQRI----DTSVK------------APQ----ALXLAPTRELALQI 105
Query: 140 LMVA 143
             V 
Sbjct: 106 QKVV 109

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 21/105 (20%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++ ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           L ++               E A KY      + L ++PT ELALQ
Sbjct: 86  LSQV---------------EPANKYP-----QCLCLSPTYELALQ 110

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 21/105 (20%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++ ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           L ++               E A KY      + L ++PT ELALQ
Sbjct: 153 LSQV---------------EPANKYP-----QCLCLSPTYELALQ 177

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 21/105 (20%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++ ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  
Sbjct: 93  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           L ++               E A KY      + L ++PT ELALQ
Sbjct: 153 LSQV---------------EPANKYP-----QCLCLSPTYELALQ 177

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 21/105 (20%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++ ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  
Sbjct: 63  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 122
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           L ++               E A KY      + L ++PT ELALQ
Sbjct: 123 LSQV---------------EPANKYP-----QCLCLSPTYELALQ 147

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 21/105 (20%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++ ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  
Sbjct: 26  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 85
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           L ++               E A KY      + L ++PT ELALQ
Sbjct: 86  LSQV---------------EPANKYP-----QCLCLSPTYELALQ 110

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 54/105 (51%), Gaps = 21/105 (20%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPA 93
           ++ ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  
Sbjct: 42  SFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 101
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           L ++               E A KY      + L ++PT ELALQ
Sbjct: 102 LSQV---------------EPANKYP-----QCLCLSPTYELALQ 126

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 17/96 (17%)
Query: 45  LMKSIYKLGFKESTSILKARI-PALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK 103
           + K+I ++ F   T + +  I P L+ +  DVI  A+T +GKT AF +P  Q L+     
Sbjct: 32  IHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN---- 87
Query: 104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
                        K+  +  ++A+I+ PTR+LALQ+
Sbjct: 88  ------------TKFDSQYMVKAVIVAPTRDLALQI 111

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 63/132 (47%), Gaps = 23/132 (17%)
Query: 29  ISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA 88
           ++T+ + + +  L   L+  I++ GF++ + I +  IP +A   +D++  A+  +GKT A
Sbjct: 16  LNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIP-VAITGRDILARAKNGTGKTAA 74
Query: 89  FGLPALQRLLEEREKAAKMLEEKGEEAEKYAPK-GHLRALIINPTRELALQVLMVASPSL 147
           F +P L                     EK  PK   ++ALI+ PTRELALQ   V     
Sbjct: 75  FVIPTL---------------------EKVKPKLNKIQALIMVPTRELALQTSQVVRTLG 113
Query: 148 KSNSLTLAMAAG 159
           K   ++  +  G
Sbjct: 114 KHCGISCMVTTG 125

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 17/96 (17%)
Query: 45  LMKSIYKLGFKESTSILKARI-PALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK 103
           + K+I ++ F   T + +  I P L+ +  DVI  A+T +GKT AF +P  Q L+     
Sbjct: 83  IHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN---- 138
Query: 104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
                        K+  +  ++A+I+ PTR+LALQ+
Sbjct: 139 ------------TKFDSQYMVKAVIVAPTRDLALQI 162

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 17/96 (17%)
Query: 45  LMKSIYKLGFKESTSILKARI-PALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK 103
           + K+I ++ F   T + +  I P L+ +  DVI  A+T +GKT AF +P  Q L+     
Sbjct: 32  IHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN---- 87
Query: 104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
                        K+  +  ++A+I+ PTR+LALQ+
Sbjct: 88  ------------TKFDSQYMVKAVIVAPTRDLALQI 111

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 57/108 (52%), Gaps = 25/108 (23%)
Query: 34  DAWNELRLHPLLMKSIYKLGFKESTSIL-KARIPALAHQRKDVIGAAETESGKTRAFGLP 92
           D ++++ L   L++ IY  GF++ ++I  +A IP +  +  DVI  A++ +GKT  F + 
Sbjct: 30  DNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCI--KGYDVIAQAQSGTGKTATFAIS 87
Query: 93  ALQRL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            LQ+L +E +E                      +AL++ PTRELA Q+
Sbjct: 88  ILQQLEIEFKET---------------------QALVLAPTRELAQQI 114

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 59/120 (49%), Gaps = 21/120 (17%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ-RKDVIGAAETESGKTRAFGLPA 93
           +++EL L P L+K IY + F++ + I +  +P L H   +++I  +++ +GKT AF L  
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLT 153
           L R+                  E  +P+    A+ + P+RELA Q L V     K   +T
Sbjct: 66  LTRV----------------NPEDASPQ----AICLAPSRELARQTLEVVQEMGKFTKIT 105

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 59/120 (49%), Gaps = 21/120 (17%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ-RKDVIGAAETESGKTRAFGLPA 93
           +++EL L P L+K IY + F++ + I +  +P L H   +++I  +++ +GKT AF L  
Sbjct: 6   SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLT 153
           L R+                  E  +P+    A+ + P+RELA Q L V     K   +T
Sbjct: 66  LTRV----------------NPEDASPQ----AICLAPSRELARQTLEVVQEMGKFTKIT 105

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 59/120 (49%), Gaps = 21/120 (17%)
Query: 35  AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQ-RKDVIGAAETESGKTRAFGLPA 93
           +++EL L P L+K IY + F++ + I +  +P L H   +++I  +++ +GKT AF L  
Sbjct: 23  SFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 82
Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLT 153
           L R+                  E  +P+    A+ + P+RELA Q L V     K   +T
Sbjct: 83  LTRV----------------NPEDASPQ----AICLAPSRELARQTLEVVQEMGKFTKIT 122

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 58/118 (49%), Gaps = 26/118 (22%)
Query: 26  EAEISTEFDA---WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETE 82
           E E S E D    ++ + L   L++ IY  GF++ ++I +  I  +   R DVI  +++ 
Sbjct: 27  EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSG 85
Query: 83  SGKTRAFGLPALQRL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +GKT  F +  LQ L ++ RE                      +ALI+ PTRELA+Q+
Sbjct: 86  TGKTATFSISVLQCLDIQVRET---------------------QALILAPTRELAVQI 122

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 58/118 (49%), Gaps = 26/118 (22%)
Query: 26  EAEISTEFDA---WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETE 82
           E E S E D    ++ + L   L++ IY  GF++ ++I +  I  +   R DVI  +++ 
Sbjct: 26  EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSG 84
Query: 83  SGKTRAFGLPALQRL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +GKT  F +  LQ L ++ RE                      +ALI+ PTRELA+Q+
Sbjct: 85  TGKTATFSISVLQCLDIQVRET---------------------QALILAPTRELAVQI 121

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 58/118 (49%), Gaps = 26/118 (22%)
Query: 26  EAEISTEFDA---WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETE 82
           E E S E D    ++ + L   L++ IY  GF++ ++I +  I  +   R DVI  +++ 
Sbjct: 27  EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSG 85
Query: 83  SGKTRAFGLPALQRL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +GKT  F +  LQ L ++ RE                      +ALI+ PTRELA+Q+
Sbjct: 86  TGKTATFSISVLQCLDIQVRET---------------------QALILAPTRELAVQI 122

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 58/118 (49%), Gaps = 26/118 (22%)
Query: 26  EAEISTEFDA---WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETE 82
           E E S E D    ++ + L   L++ IY  GF++ ++I +  I  +   R DVI  +++ 
Sbjct: 5   EFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSG 63
Query: 83  SGKTRAFGLPALQRL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +GKT  F +  LQ L ++ RE                      +ALI+ PTRELA+Q+
Sbjct: 64  TGKTATFSISVLQCLDIQVRET---------------------QALILAPTRELAVQI 100

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/107 (29%), Positives = 57/107 (53%), Gaps = 23/107 (21%)
Query: 34  DAWNELRLHPLLMKSIYKLGFKESTSIL-KARIPALAHQRKDVIGAAETESGKTRAFGLP 92
           D+++++ L   L++ IY  GF++ ++I  +A +P +  +  DVI  A++ +GKT  F + 
Sbjct: 14  DSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCI--KGYDVIAQAQSGTGKTATFAIS 71
Query: 93  ALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            LQ+ +E   KA +                   AL++ PTRELA Q+
Sbjct: 72  ILQQ-IELDLKATQ-------------------ALVLAPTRELAQQI 98

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 52/95 (54%), Gaps = 21/95 (22%)
Query: 45  LMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKA 104
           L+  I+++G+++ + I +  IP +A   +D++  A+  +GK+ A+ +P L+RL       
Sbjct: 14  LLMGIFEMGWEKPSPIQEESIP-IALSGRDILARAKNGTGKSGAYLIPLLERL------- 65
Query: 105 AKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
                           K +++A++I PTRELALQV
Sbjct: 66  -------------DLKKDNIQAMVIVPTRELALQV 87

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 23/105 (21%)
Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++ + L   L++ IY  GF++ ++I +  I  +   R DVI  +++ +GKT  F +  LQ
Sbjct: 3   FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSVSVLQ 61
Query: 96  RL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            L ++ RE                      +ALI+ PTRELA+QV
Sbjct: 62  CLDIQVRET---------------------QALILAPTRELAVQV 85

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 23/105 (21%)
Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++ + L   L++ IY  GF++ ++I +  I  +   R DVI  +++ +GKT  F +  LQ
Sbjct: 3   FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGR-DVIAQSQSGTGKTATFSVSVLQ 61
Query: 96  RL-LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            L ++ RE                      +ALI+ PTRELA+QV
Sbjct: 62  CLDIQVRET---------------------QALILAPTRELAVQV 85

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/111 (27%), Positives = 55/111 (49%), Gaps = 23/111 (20%)
Query: 34  DAWNELRLHPLLMKSIYKLGFKESTSI-LKARIPALAHQRKDVIGAAETESGKTRAFGLP 92
           D+++++ L   L++ IY  GF+  ++I  +A +P +     DVI  A++ +G T  F + 
Sbjct: 15  DSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXG--YDVIAQAQSGTGXTATFAIS 72
Query: 93  ALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA 143
            LQ++  E +  A                   +AL++ PTRELA Q+  V 
Sbjct: 73  ILQQI--ELDLXAT------------------QALVLAPTRELAQQIQXVV 103

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 49/104 (47%), Gaps = 21/104 (20%)
Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           +      P ++++I  L F + T I +  IP  A + +  +G ++T +GKT A+ LP  +
Sbjct: 6   FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPG-ALRGESXVGQSQTGTGKTHAYLLPIXE 64
Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           ++  ER                      ++A+I  PTRELA Q+
Sbjct: 65  KIKPER--------------------AEVQAVITAPTRELATQI 88

>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 = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 59/118 (50%), Gaps = 17/118 (14%)
Query: 45  LMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKA 104
           +M  I +  F E T+I     P +A    D++G A+T SGKT ++ LPA+  +  +    
Sbjct: 54  VMDVIARQNFTEPTAIQAQGWP-VALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQ---- 108
Query: 105 AKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSL-TLAMAAGSP 161
                E+G+        G +  L++ PTRELA QV  VA+   ++  L +  +  G+P
Sbjct: 109 --PFLERGD--------GPI-CLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAP 155

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	284
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-23
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-23
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	4e-23
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-22
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	8e-22
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-21
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	7e-21
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-20
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	4e-20
3bor_A	237	Human initiation factor 4A-II; translation initiat	4e-20
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	7e-20
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	8e-20
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	7e-19
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	7e-19
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	7e-19
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	8e-19
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-18
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-18
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-18
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-18
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	3e-18
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	3e-18
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-17
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-17
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-17
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-17
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-17
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-17
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	6e-14
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-13

>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 =  101 bits (255), Expect = 3e-26
 Identities = 45/159 (28%), Positives = 68/159 (42%), Gaps = 18/159 (11%)

Query: 17  DDAQEELVNEAEIST-EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDV 75
           +     + N  +I+  E   +++  L    +K + +  ++  T I K  I  LA Q KDV
Sbjct: 7   ESISRLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIG-LALQGKDV 65

Query: 76  IGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL 135
           +GAA+T SGKT AF +P L+ L   +                +     L  LII+PTREL
Sbjct: 66  LGAAKTGSGKTLAFLVPVLEALYRLQ----------------WTSTDGLGVLIISPTREL 109

Query: 136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPN 174
           A Q   V     K++  +  +  G   L  E       N
Sbjct: 110 AYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNIN 148

>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 = 98.7 bits (246), Expect = 2e-23
 Identities = 33/125 (26%), Positives = 58/125 (46%), Gaps = 20/125 (16%)

Query: 16  PDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKD 74
               +E+   E  + +  +   E  L   + K+I ++ F   T + +  I   L+ +  D
Sbjct: 57  IHVPKEDNSKEVTLDSLLE---EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHD 113

Query: 75  VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE 134
           VI  A+T +GKT AF +P  Q L+                  K+  +  ++A+I+ PTR+
Sbjct: 114 VIARAKTGTGKTFAFLIPIFQHLI----------------NTKFDSQYMVKAVIVAPTRD 157

Query: 135 LALQV 139
           LALQ+
Sbjct: 158 LALQI 162

>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 = 98.0 bits (244), Expect = 3e-23
 Identities = 33/121 (27%), Positives = 58/121 (47%), Gaps = 20/121 (16%)

Query: 20  QEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGA 78
           +E+   E  + +  +   E  L   + K+I ++ F   T + +  I   L+ +  DVI  
Sbjct: 10  KEDNSKEVTLDSLLE---EGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIAR 66

Query: 79  AETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQ 138
           A+T +GKT AF +P  Q L+                  K+  +  ++A+I+ PTR+LALQ
Sbjct: 67  AKTGTGKTFAFLIPIFQHLIN----------------TKFDSQYMVKAVIVAPTRDLALQ 110

Query: 139 V 139
           +
Sbjct: 111 I 111

>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 = 94.3 bits (235), Expect = 4e-23
 Identities = 42/123 (34%), Positives = 59/123 (47%), Gaps = 21/123 (17%)

Query: 17  DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
            D+  E         E   + +L +  +L ++  +LG+ + T I    IP LA Q +D+I
Sbjct: 26  HDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIP-LALQGRDII 84

Query: 77  GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA 136
           G AET SGKT AF LP L  LLE  ++                    L AL++ PTRELA
Sbjct: 85  GLAETGSGKTGAFALPILNALLETPQR--------------------LFALVLTPTRELA 124

Query: 137 LQV 139
            Q+
Sbjct: 125 FQI 127

>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 = 92.0 bits (229), Expect = 3e-22
 Identities = 36/145 (24%), Positives = 65/145 (44%), Gaps = 19/145 (13%)

Query: 17  DDAQEELVNEAEISTEFDAWNEL--RLHPLLMKSIYKLGFKESTSILKARIPALAHQRKD 74
           +     L      + E  ++  L   ++   +K+I ++GF   T I    I     + +D
Sbjct: 35  ESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIR-PLLEGRD 93

Query: 75  VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE 134
           ++ AA+T SGKT AF +PA++ +++ R                + P+     LI++PTRE
Sbjct: 94  LLAAAKTGSGKTLAFLIPAVELIVKLR----------------FMPRNGTGVLILSPTRE 137

Query: 135 LALQVLMVASPSLKSNSLTLAMAAG 159
           LA+Q   V    +  +  T  +  G
Sbjct: 138 LAMQTFGVLKELMTHHVHTYGLIMG 162

>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 = 90.7 bits (226), Expect = 8e-22
 Identities = 33/108 (30%), Positives = 58/108 (53%), Gaps = 12/108 (11%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++EL+L P +  +I    ++  T I K  IPA   + +D++  A+T SGKT AF +P + 
Sbjct: 25  FDELKLDPTIRNNILLASYQRPTPIQKNAIPA-ILEHRDIMACAQTGSGKTAAFLIPIIN 83

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA 143
            L+ +               ++Y+   + + LI+ PTRELA+Q+L  +
Sbjct: 84  HLVCQ-----------DLNQQRYSKTAYPKCLILAPTRELAIQILSES 120

>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 = 89.1 bits (222), Expect = 1e-21
 Identities = 35/103 (33%), Positives = 51/103 (49%), Gaps = 18/103 (17%)

Query: 37  NELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQR 96
            +  L P ++++++  G    T I  A +P    + KD+IG A T +GKT AF LP  +R
Sbjct: 4   KDFPLKPEILEALHGRGLTTPTPIQAAALPLAL-EGKDLIGQARTGTGKTLAFALPIAER 62

Query: 97  LLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           L   +E+                     RAL++ PTRELALQV
Sbjct: 63  LAPSQERG-----------------RKPRALVLTPTRELALQV 88

>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 = 89.9 bits (224), Expect = 7e-21
 Identities = 29/103 (28%), Positives = 47/103 (45%), Gaps = 21/103 (20%)

Query: 37  NELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQR 96
           NEL L   ++ +I   GF++ T I    IP   +   +++  A T SGKT +F +P ++ 
Sbjct: 9   NELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIEL 68

Query: 97  LLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +                          + A+I+ PTRELA+QV
Sbjct: 69  V---------------------NENNGIEAIILTPTRELAIQV 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 = 89.2 bits (222), Expect = 2e-20
 Identities = 35/126 (27%), Positives = 62/126 (49%), Gaps = 21/126 (16%)

Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRK 73
           NGPD  + E V E+  +   D+++++ L   L++ IY  GF++ ++I +  I     +  
Sbjct: 20  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCI-KGY 78

Query: 74  DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR 133
           DVI  A++ +GKT  F +  LQ++  +                        +AL++ PTR
Sbjct: 79  DVIAQAQSGTGKTATFAISILQQIELD--------------------LKATQALVLAPTR 118

Query: 134 ELALQV 139
           ELA Q+
Sbjct: 119 ELAQQI 124

>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 = 86.1 bits (214), Expect = 4e-20
 Identities = 34/106 (32%), Positives = 51/106 (48%), Gaps = 20/106 (18%)

Query: 34  DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPA 93
               E +++  L+++I   GF+  T I    IP + H R +++ +A T SGKT AF +P 
Sbjct: 29  QLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGR-ELLASAPTGSGKTLAFSIPI 87

Query: 94  LQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           L +L +                         RALII+PTRELA Q+
Sbjct: 88  LMQLKQ-------------------PANKGFRALIISPTRELASQI 114

>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 = 85.7 bits (213), Expect = 4e-20
 Identities = 35/126 (27%), Positives = 56/126 (44%), Gaps = 24/126 (19%)

Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRK 73
           N          N  EI   FD   ++ L   L++ IY  GF++ ++I +  I     +  
Sbjct: 13  NLYFQGGVIESNWNEIVDNFD---DMNLKESLLRGIYAYGFEKPSAIQQRAIIPCI-KGY 68

Query: 74  DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR 133
           DVI  A++ +GKT  F +  LQ+L  E ++                     +AL++ PTR
Sbjct: 69  DVIAQAQSGTGKTATFAISILQQLEIEFKE--------------------TQALVLAPTR 108

Query: 134 ELALQV 139
           ELA Q+
Sbjct: 109 ELAQQI 114

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score = 84.5 bits (210), Expect = 7e-20
 Identities = 27/103 (26%), Positives = 49/103 (47%), Gaps = 21/103 (20%)

Query: 37  NELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQR 96
                 P ++++I  L F + T I +  IP    + + ++G ++T +GKT A+ LP +++
Sbjct: 7   TRFPFQPFIIEAIKTLRFYKPTEIQERIIPGAL-RGESMVGQSQTGTGKTHAYLLPIMEK 65

Query: 97  LLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +  ER                      ++A+I  PTRELA Q+
Sbjct: 66  IKPERA--------------------EVQAVITAPTRELATQI 88

>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 = 84.5 bits (210), Expect = 8e-20
 Identities = 30/119 (25%), Positives = 56/119 (47%), Gaps = 21/119 (17%)

Query: 21  EELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAE 80
           EE   +         ++++ L   L++ ++  GF+E ++I +  I  +  +  DV+  A+
Sbjct: 1   EESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPII-EGHDVLAQAQ 59

Query: 81  TESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           + +GKT  F + ALQR+    +                      +AL++ PTRELALQ+
Sbjct: 60  SGTGKTGTFSIAALQRIDTSVKA--------------------PQALMLAPTRELALQI 98

>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 = 82.3 bits (204), Expect = 7e-19
 Identities = 28/123 (22%), Positives = 48/123 (39%), Gaps = 21/123 (17%)

Query: 17  DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
           D +         +  E   +  L L   +++ +   GF+  + +    IP L     D+I
Sbjct: 7   DLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIP-LGRCGLDLI 65

Query: 77  GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA 136
             A++ +GKT  F   AL  L+ E                        + LI+ PTRE+A
Sbjct: 66  VQAKSGTGKTCVFSTIALDSLVLE--------------------NLSTQILILAPTREIA 105

Query: 137 LQV 139
           +Q+
Sbjct: 106 VQI 108

>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 = 84.5 bits (210), Expect = 7e-19
 Identities = 32/108 (29%), Positives = 55/108 (50%), Gaps = 21/108 (19%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPAL 94
           ++EL L P L+K IY + F++ + I +  +P  L +  +++I  +++ +GKT AF L  L
Sbjct: 7   FDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTML 66

Query: 95  QRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMV 142
            R+                  E  +P+    A+ + P+RELA Q L V
Sbjct: 67  TRV----------------NPEDASPQ----AICLAPSRELARQTLEV 94

>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 = 84.5 bits (210), Expect = 7e-19
 Identities = 32/123 (26%), Positives = 57/123 (46%), Gaps = 24/123 (19%)

Query: 17  DDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVI 76
              + E   E +++  FD    + L   L++ IY  GF++ ++I +  I  +  + +DVI
Sbjct: 23  TKVEFETSEEVDVTPTFD---TMGLREDLLRGIYAYGFEKPSAIQQRAIKQII-KGRDVI 78

Query: 77  GAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA 136
             +++ +GKT  F +  LQ L  +                        +ALI+ PTRELA
Sbjct: 79  AQSQSGTGKTATFSISVLQCLDIQ--------------------VRETQALILAPTRELA 118

Query: 137 LQV 139
           +Q+
Sbjct: 119 VQI 121

>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 = 81.4 bits (202), Expect = 8e-19
 Identities = 29/109 (26%), Positives = 57/109 (52%), Gaps = 24/109 (22%)

Query: 31  TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFG 90
            EF+   +  L   L+  I+++G+++ + I +  IP      +D++  A+  +GK+ A+ 
Sbjct: 3   NEFE---DYCLKRELLMGIFEMGWEKPSPIQEESIPIAL-SGRDILARAKNGTGKSGAYL 58

Query: 91  LPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           +P L+RL  +++                    +++A++I PTRELALQV
Sbjct: 59  IPLLERLDLKKD--------------------NIQAMVIVPTRELALQV 87

>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 = 81.8 bits (203), Expect = 1e-18
 Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 16/116 (13%)

Query: 36  WNE-LRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPAL 94
           + +  + +P L+KSI ++G  + T I     P    Q  D+I  A+T +GKT ++ +P  
Sbjct: 21  FKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPI-ILQGIDLIVVAQTGTGKTLSYLMPGF 79

Query: 95  QRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN 150
             L  +                    +     L++ PTRELAL V    S      
Sbjct: 80  IHLDSQPISR--------------EQRNGPGMLVLTPTRELALHVEAECSKYSYKG 121

>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 = 83.8 bits (208), Expect = 1e-18
 Identities = 31/126 (24%), Positives = 55/126 (43%), Gaps = 24/126 (19%)

Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRK 73
              D   +           F+   +  L   L+  I++ GF++ + I +  IP +A   +
Sbjct: 4   GSKDTRPQTDDVLNTKGNTFE---DFYLKRELLMGIFEAGFEKPSPIQEEAIP-VAITGR 59

Query: 74  DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR 133
           D++  A+  +GKT AF +P L+++  +                       ++ALI+ PTR
Sbjct: 60  DILARAKNGTGKTAAFVIPTLEKVKPK--------------------LNKIQALIMVPTR 99

Query: 134 ELALQV 139
           ELALQ 
Sbjct: 100 ELALQT 105

>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 = 83.7 bits (208), Expect = 1e-18
 Identities = 31/115 (26%), Positives = 56/115 (48%), Gaps = 24/115 (20%)

Query: 25  NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESG 84
           N  ++  +FD   ++ L   L++ ++  GF+E ++I +  I  +  +  DV+  A++ +G
Sbjct: 15  NYDKVVYKFD---DMELDENLLRGVFGYGFEEPSAIQQRAIMPII-EGHDVLAQAQSGTG 70

Query: 85  KTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           KT  F + ALQR+                           +AL++ PTRELALQ+
Sbjct: 71  KTGTFSIAALQRIDTS--------------------VKAPQALMLAPTRELALQI 105

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 83.7 bits (208), Expect = 1e-18
 Identities = 31/108 (28%), Positives = 56/108 (51%), Gaps = 3/108 (2%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           ++++ +  ++M +I    +   T + K  IP    +++D++  A+T SGKT AF LP L 
Sbjct: 17  FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPI-IKEKRDLMACAQTGSGKTAAFLLPILS 75

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA 143
           ++  +    A  L    E       K +  +L++ PTRELA+Q+   A
Sbjct: 76  QIYSDGPGEA--LRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEA 121

>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 = 83.0 bits (206), Expect = 3e-18
 Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 21/108 (19%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPAL 94
           + ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  L
Sbjct: 27  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 86

Query: 95  QRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMV 142
            ++                E     P+     L ++PT ELALQ   V
Sbjct: 87  SQV----------------EPANKYPQ----CLCLSPTYELALQTGKV 114

>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 = 80.7 bits (200), Expect = 3e-18
 Identities = 35/117 (29%), Positives = 54/117 (46%), Gaps = 16/117 (13%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           + E      +M  I +  F E T+I     P  A    D++G A+T SGKT ++ LPA+ 
Sbjct: 31  FYEANFPANVMDVIARQNFTEPTAIQAQGWPV-ALSGLDMVGVAQTGSGKTLSYLLPAIV 89

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSL 152
            +  +         E+G+      P      L++ PTRELA QV  VA+   ++  L
Sbjct: 90  HINHQPFL------ERGD-----GP----ICLVLAPTRELAQQVQQVAAEYCRACRL 131

>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 = 81.4 bits (202), Expect = 1e-17
 Identities = 34/108 (31%), Positives = 54/108 (50%), Gaps = 16/108 (14%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQ 95
           +    L  +++ ++ K G+K  T I K  IP      +D++  A+T SGKT AF LP L 
Sbjct: 58  FTSADLRDIIIDNVNKSGYKIPTPIQKCSIPV-ISSGRDLMACAQTGSGKTAAFLLPILS 116

Query: 96  RLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVA 143
           +LLE+  +                  G  + +I++PTRELA+Q+   A
Sbjct: 117 KLLEDPHE---------------LELGRPQVVIVSPTRELAIQIFNEA 149

>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 = 78.0 bits (193), Expect = 2e-17
 Identities = 30/110 (27%), Positives = 46/110 (41%), Gaps = 24/110 (21%)

Query: 30  STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF 89
           S+ F    +  L P L+++I   GF+  + +    IP  A    DV+  A++  GKT  F
Sbjct: 13  SSGFR---DFLLKPELLRAIVDCGFEHPSEVQHECIP-QAILGMDVLCQAKSGMGKTAVF 68

Query: 90  GLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
            L  LQ+L                        G +  L++  TRELA Q+
Sbjct: 69  VLATLQQLEPV--------------------TGQVSVLVMCHTRELAFQI 98

>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 = 79.9 bits (198), Expect = 2e-17
 Identities = 27/99 (27%), Positives = 47/99 (47%), Gaps = 27/99 (27%)

Query: 41  LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEE 100
           ++  + ++I ++GFK  T +    IP +  Q K+V+  A+T SGKT A+ +P L+     
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLML-QGKNVVVRAKTGSGKTAAYAIPILEL---- 55

Query: 101 REKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
                                  +++L++ PTREL  QV
Sbjct: 56  ----------------------GMKSLVVTPTRELTRQV 72

>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 = 80.3 bits (199), Expect = 2e-17
 Identities = 30/115 (26%), Positives = 48/115 (41%), Gaps = 24/115 (20%)

Query: 25  NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESG 84
           +   +S+ F    +  L P L+++I   GF+  + +    IP  A    DV+  A++  G
Sbjct: 2   SPGHMSSGFR---DFLLKPELLRAIVDCGFEHPSEVQHECIP-QAILGMDVLCQAKSGMG 57

Query: 85  KTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
           KT  F L  LQ+L                        G +  L++  TRELA Q+
Sbjct: 58  KTAVFVLATLQQLEPV--------------------TGQVSVLVMCHTRELAFQI 92

>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 = 80.8 bits (200), Expect = 2e-17
 Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 21/108 (19%)

Query: 36  WNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQRKDVIGAAETESGKTRAFGLPAL 94
           + ELRL P L++ +Y +GF   + I +  +P  LA   +++I  +++ +GKT AF L  L
Sbjct: 94  FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAML 153

Query: 95  QRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMV 142
            ++                E     P+     L ++PT ELALQ   V
Sbjct: 154 SQV----------------EPANKYPQ----CLCLSPTYELALQTGKV 181

>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 = 78.6 bits (194), Expect = 4e-17
 Identities = 35/130 (26%), Positives = 58/130 (44%), Gaps = 24/130 (18%)

Query: 14  NGPDDAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIP-ALAHQR 72
           N  +  Q +  +       F+   ELRL P L++ +Y +GF   + I +  +P  LA   
Sbjct: 75  NQVEVLQRDPNSPLYSVKSFE---ELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPP 131

Query: 73  KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT 132
           +++I  +++ +GKT AF L  L ++                E     P+     L ++PT
Sbjct: 132 QNLIAQSQSGTGKTAAFVLAMLSQV----------------EPANKYPQ----CLCLSPT 171

Query: 133 RELALQVLMV 142
            ELALQ   V
Sbjct: 172 YELALQTGKV 181

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 70.1 bits (172), Expect = 6e-14
 Identities = 16/103 (15%), Positives = 27/103 (26%), Gaps = 24/103 (23%)

Query: 37  NELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQR 96
                +        K   K+ T   +     +  Q K     A T  GKT    + AL  
Sbjct: 2   EFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIV-QGKSFTMVAPTGVGKTTFGMMTALWL 60

Query: 97  LLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQV 139
             + +                       ++ ++ PT  L  Q 
Sbjct: 61  ARKGK-----------------------KSALVFPTVTLVKQT 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	284
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.97
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.97
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.96
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.96
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.96
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.96
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.96
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.95
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.95
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.95
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.95
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.95
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.95
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.95
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.95
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.94
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.94
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.93
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.92
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.91
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.91
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.9
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.9
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.9
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.9
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.9
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.89
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.89
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.86
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.85
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.83
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.81
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.79
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.79
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.79
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.79
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.79
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.78
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.78
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.77
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.77
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.77
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.76
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.75
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.75
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.74
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.74
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.73
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.7
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.69
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.68
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.62
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.62
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.62
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.62
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.61
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.58
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.58
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.57
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.55
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.55
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.55
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.54
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.5
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.48
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.46
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.44
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.42
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.4
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.38
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.31
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.3
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.27
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.17
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.11
3h1t_A	590	Type I site-specific restriction-modification syst	99.1
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.76
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.7
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.57
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.41
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.4
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.15
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.01
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.99
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.98
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	96.9
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.82
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.75
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.71
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.52
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.39
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	95.76
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.74
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	94.59
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.44
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	94.11
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	93.06
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	92.29
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	90.19
3co5_A	143	Putative two-component system transcriptional RES	89.58
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	89.2
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	88.73
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	88.55
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	88.54
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	88.47
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	88.42
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	88.27
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	87.52
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	87.35
2eyu_A	261	Twitching motility protein PILT; pilus retraction	87.17
1p9r_A	418	General secretion pathway protein E; bacterial typ	87.08
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	86.62
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	86.48
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	86.09
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	86.01
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	85.21
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	84.67
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	84.55
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	84.15
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	84.13
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	84.07
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	83.85
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	83.52
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	83.28
1tue_A	212	Replication protein E1; helicase, replication, E1E	83.09
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	82.93
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	82.04
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	81.5
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	80.89
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	80.47
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	80.32
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	80.28

>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=99.97  E-value=6.8e-32  Score=238.21  Aligned_cols=186  Identities=21%  Similarity=0.185  Sum_probs=158.7

Q ss_pred             cccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHH
Q 042526           21 EELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEE  100 (284)
Q Consensus        21 ~~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~  100 (284)
                      ...+.+.+.|.|+.+|.+++|++.++++|.++||..|||+|.++||.+ +.|+|++++||||||||++|++|++.++...
T Consensus        16 ~i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~   94 (242)
T 3fe2_A           16 EITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVA-LSGLDMVGVAQTGSGKTLSYLLPAIVHINHQ   94 (242)
T ss_dssp             TEEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHH-HHTCCEEEEECTTSCHHHHHHHHHHHHHHTS
T ss_pred             ceEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCcCHHHHHHHHHHHHHHHhc
Confidence            346678889999999999999999999999999999999999999998 8999999999999999999999999987643


Q ss_pred             HHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc
Q 042526          101 REKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT  179 (284)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~  179 (284)
                      .               ......++++|||+|||+||.|+++.++.+....++.+.+++|+ ....+...+..++++++.+
T Consensus        95 ~---------------~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~T  159 (242)
T 3fe2_A           95 P---------------FLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIAT  159 (242)
T ss_dssp             C---------------CCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEEC
T ss_pred             c---------------ccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEEC
Confidence            1               11223578899999999999999999999999889988888776 4555667777888887766


Q ss_pred             c---------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCc
Q 042526          180 R---------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKK  222 (284)
Q Consensus       180 ~---------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~  222 (284)
                      .         ....+.++..+|+|||++|.+.||.+....++...+...|..
T Consensus       160 p~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~  211 (242)
T 3fe2_A          160 PGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTL  211 (242)
T ss_dssp             HHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEE
T ss_pred             HHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEE
Confidence            2         223577889999999999999999999999988876665543

>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=99.97  E-value=1.1e-31  Score=256.47  Aligned_cols=178  Identities=23%  Similarity=0.296  Sum_probs=154.2

Q ss_pred             ccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHH
Q 042526           22 ELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEER  101 (284)
Q Consensus        22 ~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~  101 (284)
                      ..+.+.++|.|+.+|.+++|++.++++|.++||..|||+|.+|||.+ +.|+|++++|+||||||++|++|+++++....
T Consensus        44 ~~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i-~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~  122 (434)
T 2db3_A           44 VKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVI-SSGRDLMACAQTGSGKTAAFLLPILSKLLEDP  122 (434)
T ss_dssp             EEEESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC
T ss_pred             eEecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hcCCCEEEECCCCCCchHHHHHHHHHHHHhcc
Confidence            45788899999999999999999999999999999999999999999 89999999999999999999999999887642


Q ss_pred             HHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc
Q 042526          102 EKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR  180 (284)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~  180 (284)
                                     ......++++|||+|||+||.|++++++.++...++++++++|+ ....|...+..++++++.+.
T Consensus       123 ---------------~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp  187 (434)
T 2db3_A          123 ---------------HELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATP  187 (434)
T ss_dssp             ---------------CCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECH
T ss_pred             ---------------cccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEECh
Confidence                           11234578999999999999999999999999888888777776 45556677778888877661


Q ss_pred             ---------cCCccccccccCCCCCCcccccccccchhhhcccC
Q 042526          181 ---------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLT  215 (284)
Q Consensus       181 ---------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~  215 (284)
                               ....+.++..+|+||||+|.++||.++...++...
T Consensus       188 ~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~  231 (434)
T 2db3_A          188 GRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHV  231 (434)
T ss_dssp             HHHHHHHHTTSCCCTTCCEEEEETHHHHTSTTTHHHHHHHHHCT
T ss_pred             HHHHHHHHhCCcccccCCeEEEccHhhhhccCcHHHHHHHHHhc
Confidence                     12347788999999999999999999998888764

>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=99.96  E-value=2.3e-30  Score=236.65  Aligned_cols=169  Identities=23%  Similarity=0.289  Sum_probs=140.8

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      ++.+|.+++|++.|+++|..+||..|||+|.+|||.+ +.|  +|++++||||||||+||++|+++++...         
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i-l~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~---------  159 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLM-LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA---------  159 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHH-TSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTT---------
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-HcCCCCeEEEECCCCCCccHHHHHHHHHhhhcc---------
Confidence            4678999999999999999999999999999999999 776  9999999999999999999999876432         


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCcchHHHHHhcCCCcccccc--------
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--------  180 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--------  180 (284)
                                 ..++++|||+|||+||.|++.+++.++... ++.+.+++|+.....  .....++|++.+.        
T Consensus       160 -----------~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~IlV~TP~~l~~~l~  226 (300)
T 3fmo_B          160 -----------NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER--GQKISEQIVIGTPGTVLDWCS  226 (300)
T ss_dssp             -----------SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCT--TCCCCCSEEEECHHHHHHHHT
T ss_pred             -----------CCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhh--hhcCCCCEEEECHHHHHHHHH
Confidence                       247899999999999999999999998875 678877777654332  1245677766651        


Q ss_pred             --cCCccccccccCCCCCCcccc-cccccchhhhcccCCCCCCCcc
Q 042526          181 --KGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       181 --~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~~~~  223 (284)
                        ....+.++..+|+||||+|++ .||......++...++..|..+
T Consensus       227 ~~~~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~  272 (300)
T 3fmo_B          227 KLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLL  272 (300)
T ss_dssp             TTCCCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEE
T ss_pred             hcCCCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEE
Confidence              234578999999999999998 6899999888888877666444

>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=99.96  E-value=7.7e-30  Score=222.47  Aligned_cols=180  Identities=19%  Similarity=0.176  Sum_probs=144.2

Q ss_pred             cccccCccccCccc-CCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHH
Q 042526           25 NEAEISTEFDAWNE-LRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK  103 (284)
Q Consensus        25 ~~~~~p~~~~~F~~-l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~  103 (284)
                      .+..+|.|+.+|.+ +++++.++++|.++||..|||+|.++||.+ +.|+|++++||||||||++|++|++..+..... 
T Consensus        10 ~~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~-   87 (228)
T 3iuy_A           10 EKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPII-LQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPI-   87 (228)
T ss_dssp             SCCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHC-----
T ss_pred             ccCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHHHhccc-
Confidence            45668999999999 799999999999999999999999999998 899999999999999999999999998765321 


Q ss_pred             HHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc--
Q 042526          104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR--  180 (284)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~--  180 (284)
                                   ......++++|||+|||+||.|+++.++.+. ..++.+.+++|+ ....+...+..++++++.+.  
T Consensus        88 -------------~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~  153 (228)
T 3iuy_A           88 -------------SREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGR  153 (228)
T ss_dssp             ------------------CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHH
T ss_pred             -------------hhhccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHH
Confidence                         1112357889999999999999999999987 356777666665 55566677778888877662  


Q ss_pred             -------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          181 -------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 -------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                             ....+.++..+|+|||+.+.+.+|.+....++...+...+
T Consensus       154 l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~  200 (228)
T 3iuy_A          154 LNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQ  200 (228)
T ss_dssp             HHHHHHTTCCCCTTCCEEEECCHHHHHHTTCHHHHHHHHHHSCSSCE
T ss_pred             HHHHHHcCCcCcccceEEEEECHHHHhccchHHHHHHHHHhCCcCCe
Confidence                   2234678899999999999999999999888877765544

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.96  E-value=5.6e-29  Score=218.11  Aligned_cols=175  Identities=26%  Similarity=0.277  Sum_probs=145.9

Q ss_pred             CccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           30 STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      +.++.+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+....        
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~-~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~--------   91 (236)
T 2pl3_A           21 VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLA-LQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQ--------   91 (236)
T ss_dssp             GGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHHHTT--------
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhc--------
Confidence            466788999999999999999999999999999999999 89999999999999999999999999887531        


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------  180 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------  180 (284)
                              .....++++|||+|||+||.|++..++.+....++.+.+++|+...........++++++.+.         
T Consensus        92 --------~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~l~~  163 (236)
T 2pl3_A           92 --------WTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDE  163 (236)
T ss_dssp             --------CCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHHTTCSEEEECHHHHHHHHHH
T ss_pred             --------ccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhCCCCCEEEECHHHHHHHHHh
Confidence                    112246789999999999999999999999888899988888865554444456778766551         


Q ss_pred             -cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCC
Q 042526          181 -KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGK  221 (284)
Q Consensus       181 -~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~  221 (284)
                       ....+.++..+|+|||+++.+.+|.+....++...+...+.
T Consensus       164 ~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~  205 (236)
T 2pl3_A          164 TVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQT  205 (236)
T ss_dssp             CSSCCCTTCCEEEETTHHHHHHTTTHHHHHHHHHTSCTTSEE
T ss_pred             cCCcccccccEEEEeChHHHhcCCcHHHHHHHHHhCCCCCeE
Confidence             12346788899999999999999999988888877765553

>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=99.96  E-value=3e-29  Score=219.60  Aligned_cols=176  Identities=18%  Similarity=0.164  Sum_probs=141.0

Q ss_pred             ccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHH
Q 042526           24 VNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK  103 (284)
Q Consensus        24 ~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~  103 (284)
                      ..++..|.+..+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|++..+...   
T Consensus        14 ~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~---   89 (230)
T 2oxc_A           14 RTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLG-RCGLDLIVQAKSGTGKTCVFSTIALDSLVLE---   89 (230)
T ss_dssp             ----------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHCCTT---
T ss_pred             ccCCCCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCCcHHHHHHHHHHHHHHhc---
Confidence            346677888899999999999999999999999999999999998 8999999999999999999999999876432   


Q ss_pred             HHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCcchHHHHHhcCCCcccccc--
Q 042526          104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--  180 (284)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--  180 (284)
                                       ..++++|||+|||+||.|+++.++.+.... ++.+.+++|+....+......++++++.+.  
T Consensus        90 -----------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~Iiv~Tp~~  152 (230)
T 2oxc_A           90 -----------------NLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGR  152 (230)
T ss_dssp             -----------------SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTTSCSEEEECHHH
T ss_pred             -----------------CCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhccCCCEEEECHHH
Confidence                             246789999999999999999999998765 788988888866655555556778876552  


Q ss_pred             -------cCCccccccccCCCCCCcccccc-cccchhhhcccCCCCCC
Q 042526          181 -------KGGEDEKLDSLKWNPLSQPKTTT-LLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 -------~~~~~d~l~~lv~dEAd~m~~~g-flp~~~~~~~~~~r~~~  220 (284)
                             ....+.++..+|+|||+++.+.| |.+....++...+...+
T Consensus       153 l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~  200 (230)
T 2oxc_A          153 IKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQ  200 (230)
T ss_dssp             HHHHHHTTSSCGGGCCEEEESSHHHHHSTTSSHHHHHHHHHHSCSSCE
T ss_pred             HHHHHhcCCcccccCCEEEeCCchHhhcCcchHHHHHHHHHhCCCCCe
Confidence                   22346788899999999999998 88888777777765554

>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=99.96  E-value=3.4e-29  Score=222.62  Aligned_cols=171  Identities=28%  Similarity=0.334  Sum_probs=146.9

Q ss_pred             CccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           30 STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      +.+..+|++++|++.++++|..+||..|+++|.++|+.+ +.|+|++++||||||||++|++|++..+...         
T Consensus        39 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i-~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~---------  108 (249)
T 3ber_A           39 EEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLA-LQGRDIIGLAETGSGKTGAFALPILNALLET---------  108 (249)
T ss_dssp             HHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHHHS---------
T ss_pred             ccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCCEEEEcCCCCCchhHhHHHHHHHHhcC---------
Confidence            456788999999999999999999999999999999999 8999999999999999999999999887653         


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc--------
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR--------  180 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~--------  180 (284)
                                 ..++++|||+|||+||.|+++.++.++...++.+.+++|+. ...+...+..++++++.+.        
T Consensus       109 -----------~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~  177 (249)
T 3ber_A          109 -----------PQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLE  177 (249)
T ss_dssp             -----------CCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHH
T ss_pred             -----------CCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHH
Confidence                       13678999999999999999999999998889888888774 4555666777888877651        


Q ss_pred             --cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCC
Q 042526          181 --KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGK  221 (284)
Q Consensus       181 --~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~  221 (284)
                        ....+.++..+|+|||+++.+.+|.+....++...++..+.
T Consensus       178 ~~~~~~l~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~  220 (249)
T 3ber_A          178 NTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKT  220 (249)
T ss_dssp             HSTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSSEE
T ss_pred             cCCCcCccccCEEEEcChhhhhccChHHHHHHHHHhCCCCCeE
Confidence              22356788899999999999999999998888877665543

>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=99.95  E-value=2.6e-29  Score=222.67  Aligned_cols=181  Identities=22%  Similarity=0.299  Sum_probs=147.5

Q ss_pred             ccccccccCc--cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHH
Q 042526           22 ELVNEAEIST--EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        22 ~~~~~~~~p~--~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~   99 (284)
                      ..+.+...|.  ++.+|.+|+|++.++++|..+||..|+|+|.++||.+ +.|+|++++||||||||++|++|+++.+..
T Consensus         9 ~~~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i-~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~   87 (253)
T 1wrb_A            9 VSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAI-LEHRDIMACAQTGSGKTAAFLIPIINHLVC   87 (253)
T ss_dssp             CCEECCSSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             eeeeCCCCCCCCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            3456677777  8999999999999999999999999999999999999 899999999999999999999999998765


Q ss_pred             HHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccc
Q 042526          100 EREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKR  178 (284)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~  178 (284)
                      ....           ........++++|||+|||+||.|+++.++.+....++.+++++|+. ...+...+..++++++.
T Consensus        88 ~~~~-----------~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~  156 (253)
T 1wrb_A           88 QDLN-----------QQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVA  156 (253)
T ss_dssp             TCC-----------------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEE
T ss_pred             hccc-----------cccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEE
Confidence            3100           00111234678999999999999999999999988888887777764 45556666777888776


Q ss_pred             cc---------cCCccccccccCCCCCCcccccccccchhhhccc
Q 042526          179 TR---------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNL  214 (284)
Q Consensus       179 ~~---------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~  214 (284)
                      +.         ....+.++..+|+|||++|.+.+|.++...++..
T Consensus       157 Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~  201 (253)
T 1wrb_A          157 TPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEE  201 (253)
T ss_dssp             CHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHS
T ss_pred             CHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCchHHHHHHHHhh
Confidence            51         1234677889999999999999999988888774

>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=99.95  E-value=2.9e-29  Score=220.88  Aligned_cols=178  Identities=21%  Similarity=0.246  Sum_probs=135.9

Q ss_pred             ccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHH
Q 042526           22 ELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEER  101 (284)
Q Consensus        22 ~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~  101 (284)
                      ..+...+.|.++.+|++++|++.++++|..+||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+... 
T Consensus        18 ~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i-~~~~~~li~apTGsGKT~~~~l~~l~~l~~~-   95 (237)
T 3bor_A           18 GGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPC-IKGYDVIAQAQSGTGKTATFAISILQQLEIE-   95 (237)
T ss_dssp             ---------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEECCCSSHHHHHHHHHHHHHHCCTT-
T ss_pred             CCcccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-
Confidence            45566778899999999999999999999999999999999999999 8999999999999999999999999876432 


Q ss_pred             HHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcC-CCccccc
Q 042526          102 EKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRK-PNKRKRT  179 (284)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~-~~i~v~~  179 (284)
                                         ..++++|||+|||+||.|++..++.++...++.+..++|+ ....+...+..+ +++++.+
T Consensus        96 -------------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~T  156 (237)
T 3bor_A           96 -------------------FKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGT  156 (237)
T ss_dssp             -------------------SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEEC
T ss_pred             -------------------CCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEEC
Confidence                               2467899999999999999999999998888888777766 444455555555 7776655


Q ss_pred             ---------ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          180 ---------RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       180 ---------~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                               .....+.++..+|+|||+.|.+.+|......++...+...+
T Consensus       157 p~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~  206 (237)
T 3bor_A          157 PGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQ  206 (237)
T ss_dssp             HHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCE
T ss_pred             HHHHHHHHHhCCcCcccCcEEEECCchHhhccCcHHHHHHHHHhCCCCCe
Confidence                     12235677899999999999999999888887776655544

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

Probab=99.95  E-value=2.4e-28  Score=229.29  Aligned_cols=189  Identities=19%  Similarity=0.210  Sum_probs=150.0

Q ss_pred             cccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHH
Q 042526           23 LVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEERE  102 (284)
Q Consensus        23 ~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~  102 (284)
                      .+.+.++|.++.+|++++|++.++++|..+||..|||+|.++||.+ +.|+|++++||||||||++|++|+++.+.....
T Consensus         4 ~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i-~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~   82 (417)
T 2i4i_A            4 EATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPII-KEKRDLMACAQTGSGKTAAFLLPILSQIYSDGP   82 (417)
T ss_dssp             EEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCC
T ss_pred             ccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-ccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccc
Confidence            3567789999999999999999999999999999999999999998 899999999999999999999999998876421


Q ss_pred             HHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc-
Q 042526          103 KAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR-  180 (284)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~-  180 (284)
                      ....  ..............++++|||+|||+||.|+++.++.+....++.+++++|+ ....+...+..++++++.+. 
T Consensus        83 ~~~~--~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~  160 (417)
T 2i4i_A           83 GEAL--RAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPG  160 (417)
T ss_dssp             CHHH--HHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHH
T ss_pred             cchh--hccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChH
Confidence            0000  0000000011223457899999999999999999999998888888887776 45556666777788877652 


Q ss_pred             --------cCCccccccccCCCCCCcccccccccchhhhccc
Q 042526          181 --------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNL  214 (284)
Q Consensus       181 --------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~  214 (284)
                              ....++.+..+|+|||+.+.+.+|.+....++..
T Consensus       161 ~l~~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~  202 (417)
T 2i4i_A          161 RLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQ  202 (417)
T ss_dssp             HHHHHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTS
T ss_pred             HHHHHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHh
Confidence                    1124677888999999999999999988887763

>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=99.95  E-value=9.4e-29  Score=214.57  Aligned_cols=176  Identities=19%  Similarity=0.293  Sum_probs=141.4

Q ss_pred             ccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHH
Q 042526           24 VNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK  103 (284)
Q Consensus        24 ~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~  103 (284)
                      ....++|.++.+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+...   
T Consensus         4 ~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~---   79 (224)
T 1qde_A            4 QIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPI-IEGHDVLAQAQSGTGKTGTFSIAALQRIDTS---   79 (224)
T ss_dssp             -CCBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHCCTT---
T ss_pred             ccccccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHH-hcCCCEEEECCCCCcHHHHHHHHHHHHHhcc---
Confidence            345667888999999999999999999999999999999999999 8999999999999999999999999876432   


Q ss_pred             HHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---
Q 042526          104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---  180 (284)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---  180 (284)
                                       ..++++|||+|||+||.|+++.+..+....++.+..+.|+............+++++.+.   
T Consensus        80 -----------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l  142 (224)
T 1qde_A           80 -----------------VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRV  142 (224)
T ss_dssp             -----------------CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHH
T ss_pred             -----------------CCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCCCCEEEECHHHH
Confidence                             246789999999999999999999999888898888888755444333334477766551   


Q ss_pred             ------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          181 ------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 ------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                            ....+.++..+|+|||+.+.+.+|......++...+...+
T Consensus       143 ~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~l~~i~~~~~~~~~  188 (224)
T 1qde_A          143 FDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQ  188 (224)
T ss_dssp             HHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCE
T ss_pred             HHHHHhCCcchhhCcEEEEcChhHHhhhhhHHHHHHHHHhCCccCe
Confidence                  2234677899999999999999999888888776655544

>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=99.95  E-value=1.5e-28  Score=219.97  Aligned_cols=171  Identities=24%  Similarity=0.309  Sum_probs=140.6

Q ss_pred             cCcccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           34 DAWNELR--LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        34 ~~F~~l~--L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      .+|++++  |++.++++|.++||..|+|+|.++||.+ +.|+|++++||||||||++|++|+++.+....          
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~----------  120 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPL-LEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR----------  120 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHH-HHTCCCEECCCTTSCHHHHHHHHHHHHHHHTT----------
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCcEEEEccCCCCchHHHHHHHHHHHHhcc----------
Confidence            4577776  9999999999999999999999999999 88999999999999999999999999887631          


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc----------
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR----------  180 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~----------  180 (284)
                            .....++++|||+|||+||.|++..++.+....++.+.+++|+. ...+...+..+++|++.+.          
T Consensus       121 ------~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~  194 (262)
T 3ly5_A          121 ------FMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNT  194 (262)
T ss_dssp             ------CCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHC
T ss_pred             ------ccccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHcc
Confidence                  11224678999999999999999999999998888888877764 4555566677788877661          


Q ss_pred             cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCC
Q 042526          181 KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGK  221 (284)
Q Consensus       181 ~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~  221 (284)
                      ....+.++..+|+|||++|.+.||.++...++..++...|.
T Consensus       195 ~~~~~~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~~q~  235 (262)
T 3ly5_A          195 PGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQT  235 (262)
T ss_dssp             TTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHHSCSSSEE
T ss_pred             CCcccccCCEEEEcChHHHhhhhHHHHHHHHHHhCCCCCeE
Confidence            22356788999999999999999999998888877665543

>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=99.95  E-value=3.6e-28  Score=208.07  Aligned_cols=166  Identities=19%  Similarity=0.273  Sum_probs=138.9

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      .+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|++..+...             
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-------------   68 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIA-LSGRDILARAKNGTGKSGAYLIPLLERLDLK-------------   68 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHH-HTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-------------
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-ccCCCEEEECCCCCchHHHHHHHHHHHhccc-------------
Confidence            47999999999999999999999999999999998 8999999999999999999999999865332             


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCc-chHHHHHhcCCCcccccc---------cC
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPL-LTSEHSNRRKPNKRKRTR---------KG  182 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~-~~q~~~l~~~~~i~v~~~---------~~  182 (284)
                             ..++++|||+|||+|+.|+++.+..+.... ++.+.+++|+.. ..+...+..++++++.+.         ..
T Consensus        69 -------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~  141 (206)
T 1vec_A           69 -------KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGV  141 (206)
T ss_dssp             -------SCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTC
T ss_pred             -------CCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCC
Confidence                   246789999999999999999999998877 788877777644 444455566777766552         22


Q ss_pred             CccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          183 GEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       183 ~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      ..+.++..+|+|||+.+.+.+|.+....++...++..+
T Consensus       142 ~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~  179 (206)
T 1vec_A          142 AKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQ  179 (206)
T ss_dssp             SCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCE
T ss_pred             cCcccCCEEEEEChHHhHhhCcHHHHHHHHHhCCccce
Confidence            35678899999999999999999888888877765544

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.95  E-value=1.3e-28  Score=213.71  Aligned_cols=168  Identities=18%  Similarity=0.232  Sum_probs=138.1

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      +..+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+...           
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~-----------   69 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGA-LRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----------   69 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----------
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHHHhC-----------
Confidence            3468999999999999999999999999999999999 8999999999999999999999999876432           


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC----CceeEEEeCCCcch-HHHHHhcCCCcccccc------
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN----SLTLAMAAGSPLLT-SEHSNRRKPNKRKRTR------  180 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~----~i~v~~~~G~~~~~-q~~~l~~~~~i~v~~~------  180 (284)
                               ..++++|||+|||+||.|+++.++.+....    ++.+.+++|+.... +...+..++++++.+.      
T Consensus        70 ---------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~  140 (219)
T 1q0u_A           70 ---------RAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDF  140 (219)
T ss_dssp             ---------SCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHH
T ss_pred             ---------cCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHH
Confidence                     246789999999999999999999998876    67787777775433 3333445677766552      


Q ss_pred             ---cCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          181 ---KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 ---~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                         ....+.++..+|+|||+.+.+.+|......++...+...+
T Consensus       141 l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~  183 (219)
T 1q0u_A          141 IREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQ  183 (219)
T ss_dssp             HHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCE
T ss_pred             HHcCCCCcCcceEEEEcCchHHhhhChHHHHHHHHHhCCcccE
Confidence               1235678899999999999999999888888887765554

>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=99.95  E-value=2e-28  Score=215.72  Aligned_cols=173  Identities=23%  Similarity=0.312  Sum_probs=141.4

Q ss_pred             cccccccCccccCcccC----CCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           23 LVNEAEISTEFDAWNEL----RLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        23 ~~~~~~~p~~~~~F~~l----~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      .+.+.++|.|+.+|.++    +|++.++++|.++||..|||+|.++||.+ +.|+|++++||||||||++|++|++..+.
T Consensus        14 ~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~l~~a~TGsGKT~~~~l~~l~~l~   92 (245)
T 3dkp_A           14 HVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVM-LHGRELLASAPTGSGKTLAFSIPILMQLK   92 (245)
T ss_dssp             EEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHC
T ss_pred             EecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            45677899999999998    89999999999999999999999999999 89999999999999999999999998764


Q ss_pred             HHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchH--HHHHhcCCCcc
Q 042526           99 EEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTS--EHSNRRKPNKR  176 (284)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q--~~~l~~~~~i~  176 (284)
                      .                   ....++++|||+|||+||.|+++.+..+....++.+.++.|+....+  ......+++++
T Consensus        93 ~-------------------~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~  153 (245)
T 3dkp_A           93 Q-------------------PANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDIL  153 (245)
T ss_dssp             S-------------------CCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEE
T ss_pred             h-------------------cccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEE
Confidence            3                   12346789999999999999999999999988888877766532222  12234456776


Q ss_pred             cccc-----------cCCccccccccCCCCCCcccc---cccccchhhhcccC
Q 042526          177 KRTR-----------KGGEDEKLDSLKWNPLSQPKT---TTLLPSSLALMNLT  215 (284)
Q Consensus       177 v~~~-----------~~~~~d~l~~lv~dEAd~m~~---~gflp~~~~~~~~~  215 (284)
                      +.+.           ....+.++..+|+|||+.|.+   .+|......++...
T Consensus       154 v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~  206 (245)
T 3dkp_A          154 VTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLAC  206 (245)
T ss_dssp             EECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHC
T ss_pred             EECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhc
Confidence            6551           124577889999999999988   78888888776543

>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=99.94  E-value=2.2e-27  Score=205.60  Aligned_cols=176  Identities=21%  Similarity=0.255  Sum_probs=135.7

Q ss_pred             ccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHH
Q 042526           24 VNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREK  103 (284)
Q Consensus        24 ~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~  103 (284)
                      +.+...+....+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|++..+...   
T Consensus         4 ~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~---   79 (220)
T 1t6n_A            4 VKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQA-ILGMDVLCQAKSGMGKTAVFVLATLQQLEPV---   79 (220)
T ss_dssp             ----------CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHCCCC---
T ss_pred             CCCCcccccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hCCCCEEEECCCCCchhhhhhHHHHHhhhcc---
Confidence            345556667788999999999999999999999999999999999 8999999999999999999999999765321   


Q ss_pred             HHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCc-chHHHHHhc-CCCcccccc
Q 042526          104 AAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPL-LTSEHSNRR-KPNKRKRTR  180 (284)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~-~~q~~~l~~-~~~i~v~~~  180 (284)
                                       ..++++|||+|||+|+.|+++.++.+.... ++++.+++|+.. ..+...+.. .+++++.+.
T Consensus        80 -----------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~  142 (220)
T 1t6n_A           80 -----------------TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTP  142 (220)
T ss_dssp             -----------------TTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECH
T ss_pred             -----------------CCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCH
Confidence                             235689999999999999999999998876 788888888754 444444444 457766551


Q ss_pred             ---------cCCccccccccCCCCCCcccc-cccccchhhhcccCCCCCC
Q 042526          181 ---------KGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 ---------~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~  220 (284)
                               ....+.++..+|+|||+.+.+ .+|......++...+.+.+
T Consensus       143 ~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~  192 (220)
T 1t6n_A          143 GRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ  192 (220)
T ss_dssp             HHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSE
T ss_pred             HHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHHHHHHHHHhCCCcCe
Confidence                     223567889999999999886 6888777777766655444

>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=99.94  E-value=7.1e-27  Score=199.86  Aligned_cols=166  Identities=25%  Similarity=0.297  Sum_probs=137.4

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      +|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+...              
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~-~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~--------------   66 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLA-LEGKDLIGQARTGTGKTLAFALPIAERLAPS--------------   66 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--------------
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-cCCCCEEEECCCCChHHHHHHHHHHHHHhhc--------------
Confidence            6999999999999999999999999999999999 8999999999999999999999999876431              


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc---------cCCc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR---------KGGE  184 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~---------~~~~  184 (284)
                         .....++++||++|||+|+.|+++.+..+...  +.+..++|+ ....+...+..++++++.+.         ....
T Consensus        67 ---~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~  141 (207)
T 2gxq_A           67 ---QERGRKPRALVLTPTRELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLD  141 (207)
T ss_dssp             ---CCTTCCCSEEEECSSHHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSC
T ss_pred             ---cccCCCCcEEEEECCHHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcc
Confidence               11235688999999999999999999998765  566666665 45556666677788876652         1234


Q ss_pred             cccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          185 DEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       185 ~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      +.++..+|+|||+.+.+.+|......++...+...+
T Consensus       142 ~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~  177 (207)
T 2gxq_A          142 LSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQ  177 (207)
T ss_dssp             CTTCSEEEEESHHHHHHTTCHHHHHHHHHTSCTTSE
T ss_pred             hhhceEEEEEChhHhhccchHHHHHHHHHhCCccCe
Confidence            678899999999999999999988888877665544

>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=99.93  E-value=1.8e-26  Score=216.65  Aligned_cols=173  Identities=18%  Similarity=0.215  Sum_probs=144.5

Q ss_pred             cccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHH
Q 042526           27 AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAK  106 (284)
Q Consensus        27 ~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~  106 (284)
                      ...+.+..+|++++|++.++++|..+||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+...      
T Consensus        30 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i-~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~------  102 (410)
T 2j0s_A           30 SEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQI-IKGRDVIAQSQSGTGKTATFSISVLQCLDIQ------  102 (410)
T ss_dssp             CTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHTCCTT------
T ss_pred             CCCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCCEEEECCCCCCchHHHHHHHHHHHhhc------
Confidence            344566789999999999999999999999999999999999 8999999999999999999999999765321      


Q ss_pred             HHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc-----
Q 042526          107 MLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR-----  180 (284)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~-----  180 (284)
                                    ..++++|||+|||+||.|+++.+..++...++.+..++|+. ...+...+..++++++.+.     
T Consensus       103 --------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~  168 (410)
T 2j0s_A          103 --------------VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFD  168 (410)
T ss_dssp             --------------SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHH
T ss_pred             --------------cCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHH
Confidence                          24678999999999999999999999998899888877764 4555566667788876552     


Q ss_pred             ----cCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          181 ----KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 ----~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                          ....+..+..+|+|||+.|.+.+|......++...+...+
T Consensus       169 ~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~~  212 (410)
T 2j0s_A          169 MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQ  212 (410)
T ss_dssp             HHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCE
T ss_pred             HHHhCCccHhheeEEEEccHHHHHhhhhHHHHHHHHHhCccCce
Confidence                1234567889999999999999999888888776665554

>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=99.92  E-value=2.9e-25  Score=207.83  Aligned_cols=182  Identities=19%  Similarity=0.249  Sum_probs=146.0

Q ss_pred             ccccccccccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           18 DAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        18 ~~~~~~~~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      ..+.......+.+....+|.+++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|+++.+
T Consensus        24 ~~~~~~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~-~~~~~~lv~a~TGsGKT~~~~~~~~~~~  102 (414)
T 3eiq_A           24 GMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPC-IKGYDVIAQAQSGTGKTATFAISILQQI  102 (414)
T ss_dssp             ------CCCCCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEECCCSCSSSHHHHHHHHHHHC
T ss_pred             ccccccccCCCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHH-hCCCCEEEECCCCCcccHHHHHHHHHHH
Confidence            334445566777888899999999999999999999999999999999999 8999999999999999999999999865


Q ss_pred             HHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHh-cCCCc
Q 042526           98 LEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNR-RKPNK  175 (284)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~-~~~~i  175 (284)
                      ...                    ..+.++|||+|||+||.|+++.+..++...++.+..++|+. ...+...+. ..+++
T Consensus       103 ~~~--------------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  162 (414)
T 3eiq_A          103 ELD--------------------LKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHI  162 (414)
T ss_dssp             CTT--------------------SCSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSE
T ss_pred             hhc--------------------CCceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCE
Confidence            432                    24678999999999999999999999998888887777664 444444444 45677


Q ss_pred             ccccc---------cCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          176 RKRTR---------KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       176 ~v~~~---------~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      ++.+.         ....+.++..+|+|||+.+.+.+|......++...+...+
T Consensus       163 iv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~  216 (414)
T 3eiq_A          163 IVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ  216 (414)
T ss_dssp             EEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCE
T ss_pred             EEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCcHHHHHHHHHhCCCCCe
Confidence            66551         1134566889999999999999999888888776655554

>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=99.91  E-value=6.6e-25  Score=211.11  Aligned_cols=169  Identities=23%  Similarity=0.286  Sum_probs=135.7

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      ++.+|.+++|++.++++|.++||..|||+|.+|||.+ +.|  +|++++||||||||++|++|+++.+...         
T Consensus        90 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~i-l~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~---------  159 (479)
T 3fmp_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLM-LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA---------  159 (479)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHH-TSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT---------
T ss_pred             CcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-HcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc---------
Confidence            4678999999999999999999999999999999999 776  9999999999999999999999766432         


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCcchHHHHHhcCCCcccccc--------
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--------  180 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--------  180 (284)
                                 ..++++|||+|||+||.|++..++.+.... ++.+.+++|+......  ....+++++.+.        
T Consensus       160 -----------~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~Ivv~Tp~~l~~~l~  226 (479)
T 3fmp_B          160 -----------NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG--QKISEQIVIGTPGTVLDWCS  226 (479)
T ss_dssp             -----------SCSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT--CCCCCSEEEECHHHHHHHHT
T ss_pred             -----------CCCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc--ccCCCCEEEECchHHHHHHH
Confidence                       246789999999999999999999998865 6777777766443321  133456665541        


Q ss_pred             --cCCccccccccCCCCCCcccc-cccccchhhhcccCCCCCCCcc
Q 042526          181 --KGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       181 --~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~~~~  223 (284)
                        ....+.++..+|+|||+.|.+ .+|......++...+...+..+
T Consensus       227 ~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~  272 (479)
T 3fmp_B          227 KLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLL  272 (479)
T ss_dssp             TSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEE
T ss_pred             hcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEE
Confidence              233457899999999999887 6788888888777766665443

>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=99.91  E-value=1.1e-24  Score=203.58  Aligned_cols=172  Identities=20%  Similarity=0.278  Sum_probs=137.0

Q ss_pred             ccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHH
Q 042526           28 EISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKM  107 (284)
Q Consensus        28 ~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~  107 (284)
                      ..+....+|++|+|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|++..+...       
T Consensus        15 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i-~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~-------   86 (400)
T 1s2m_A           15 VLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVA-ITGRDILARAKNGTGKTAAFVIPTLEKVKPK-------   86 (400)
T ss_dssp             ------CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-------
T ss_pred             ccccccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hcCCCEEEECCCCcHHHHHHHHHHHHHHhhc-------
Confidence            34556678999999999999999999999999999999999 8999999999999999999999998765331       


Q ss_pred             HhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCc-chHHHHHhcCCCccccc-------
Q 042526          108 LEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPL-LTSEHSNRRKPNKRKRT-------  179 (284)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~-~~q~~~l~~~~~i~v~~-------  179 (284)
                                   ..++++|||+||++||.|+++.++.+....++.+..++|+.. ..+...+...+++++.+       
T Consensus        87 -------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~  153 (400)
T 1s2m_A           87 -------------LNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDL  153 (400)
T ss_dssp             -------------SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHH
T ss_pred             -------------cCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHH
Confidence                         245689999999999999999999999988888888877754 34444555667776655       


Q ss_pred             --ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          180 --RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       180 --~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                        .....+.++..+|+|||+.+.+.+|......++...+...+
T Consensus       154 ~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~i~~~~~~~~~  196 (400)
T 1s2m_A          154 ASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQ  196 (400)
T ss_dssp             HHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCE
T ss_pred             HHhCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCcCce
Confidence              12235677889999999999888887777666665554443

>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=99.90  E-value=8.1e-25  Score=203.25  Aligned_cols=172  Identities=20%  Similarity=0.304  Sum_probs=140.7

Q ss_pred             ccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHH
Q 042526           28 EISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKM  107 (284)
Q Consensus        28 ~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~  107 (284)
                      ....+..+|++++|++.|+++|..+||..|+|+|.++|+.+ +.|+|++++||||||||++|++|++..+...       
T Consensus        15 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i-~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~-------   86 (394)
T 1fuu_A           15 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPI-IEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-------   86 (394)
T ss_dssp             SSCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HHTCCEEECCCSSHHHHHHHHHHHHHHCCTT-------
T ss_pred             hcccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCCEEEECCCCChHHHHHHHHHHHHhhcc-------
Confidence            35567788999999999999999999999999999999999 8999999999999999999999999865432       


Q ss_pred             HhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc-------
Q 042526          108 LEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR-------  180 (284)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~-------  180 (284)
                                   ..++++|||+||++|+.|+++.+..+....++.+..+.|+............+++++.+.       
T Consensus        87 -------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~i~v~T~~~l~~~~  153 (394)
T 1fuu_A           87 -------------VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNI  153 (394)
T ss_dssp             -------------CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHHHCSEEEECHHHHHHHH
T ss_pred             -------------CCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcCCCCEEEECHHHHHHHH
Confidence                         246789999999999999999999999888999988888765544443334667766551       


Q ss_pred             --cCCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          181 --KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 --~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                        ....+.++..+|+|||+.+.+.+|......++...+...+
T Consensus       154 ~~~~~~~~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~~  195 (394)
T 1fuu_A          154 QRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQ  195 (394)
T ss_dssp             HTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCE
T ss_pred             HhCCcchhhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCce
Confidence              1233567889999999999888888877776665544443

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

Probab=99.90  E-value=1.6e-24  Score=213.85  Aligned_cols=164  Identities=21%  Similarity=0.258  Sum_probs=130.1

Q ss_pred             cCcccCC----CCHHHHHHHHHcCCCCCcHHHHHHHHHHHc--CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHH
Q 042526           34 DAWNELR----LHPLLMKSIYKLGFKESTSILKARIPALAH--QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKM  107 (284)
Q Consensus        34 ~~F~~l~----L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~--~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~  107 (284)
                      .+|.+|.    |++.|+++|..+||..|||+|.++||.+ +  .|+|++++||||||||++|++|+++.+....      
T Consensus        17 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i-l~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~------   89 (579)
T 3sqw_A           17 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPI-LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK------   89 (579)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHH-HCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT------
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcc------
Confidence            3455553    9999999999999999999999999999 6  6899999999999999999999999887642      


Q ss_pred             HhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC----CCceeEEEeCC-CcchHHHHHhc-CCCccccccc
Q 042526          108 LEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS----NSLTLAMAAGS-PLLTSEHSNRR-KPNKRKRTRK  181 (284)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~----~~i~v~~~~G~-~~~~q~~~l~~-~~~i~v~~~~  181 (284)
                                .....++++|||+|||+||.|++..+..+...    ..+.+..++|+ ....+...+.. +++|++.+.-
T Consensus        90 ----------~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~  159 (579)
T 3sqw_A           90 ----------FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPG  159 (579)
T ss_dssp             ----------TSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHH
T ss_pred             ----------ccccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHH
Confidence                      22234689999999999999999999998743    23556555555 55555555544 6888776521


Q ss_pred             ----------CCccccccccCCCCCCcccccccccchhhhccc
Q 042526          182 ----------GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNL  214 (284)
Q Consensus       182 ----------~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~  214 (284)
                                ...++.+..+|+|||++|.++||.++...++..
T Consensus       160 ~l~~~l~~~~~~~~~~~~~lViDEah~l~~~gf~~~~~~i~~~  202 (579)
T 3sqw_A          160 RLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGI  202 (579)
T ss_dssp             HHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHH
T ss_pred             HHHHHHHhccccccccCCEEEEEChHHhhcCCCHHHHHHHHHH
Confidence                      124567788999999999999999988666554

>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=99.90  E-value=3.7e-24  Score=199.91  Aligned_cols=168  Identities=23%  Similarity=0.279  Sum_probs=133.6

Q ss_pred             CccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHH
Q 042526           30 STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKM  107 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~  107 (284)
                      +.++.+|++++|++.++++|.++||..|+|+|.++||.+ +.|  +|++++||||||||++|++|+++.+...       
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-------   92 (412)
T 3fht_A           21 LYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLM-LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-------   92 (412)
T ss_dssp             TCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-------
T ss_pred             ccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc-------
Confidence            356788999999999999999999999999999999999 776  9999999999999999999999866432       


Q ss_pred             HhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCcchHHHHHhcCCCcccccc------
Q 042526          108 LEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPLLTSEHSNRRKPNKRKRTR------  180 (284)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~------  180 (284)
                                   ..++++|||+|||+||.|++..+..+.... ++.+....|+......  ....+++++.+.      
T Consensus        93 -------------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ivv~T~~~l~~~  157 (412)
T 3fht_A           93 -------------NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG--QKISEQIVIGTPGTVLDW  157 (412)
T ss_dssp             -------------SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT--CCCCCSEEEECHHHHHHH
T ss_pred             -------------CCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh--hcCCCCEEEECchHHHHH
Confidence                         246789999999999999999999998765 6777777776443321  233456655541      


Q ss_pred             ----cCCccccccccCCCCCCcccc-cccccchhhhcccCCCCCC
Q 042526          181 ----KGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 ----~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~  220 (284)
                          ....+.++..+|+|||+.+.+ .+|......+....+.+.+
T Consensus       158 ~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~  202 (412)
T 3fht_A          158 CSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQ  202 (412)
T ss_dssp             HTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCE
T ss_pred             HHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCce
Confidence                233457889999999999876 6677777666666655554

>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=99.90  E-value=4.2e-24  Score=198.49  Aligned_cols=166  Identities=21%  Similarity=0.269  Sum_probs=133.0

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      .+|++++|++.++++|.++||..|+|+|.++|+.+ +.|+|++++||||||||++|++|++..+...             
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-------------   73 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQA-ILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-------------   73 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHH-TTTCCEEEECSSCSSHHHHHHHHHHHHCCCC-------------
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hcCCcEEEECCCCCcHHHHHHHHHHHhhccc-------------
Confidence            57999999999999999999999999999999999 8999999999999999999999998765321             


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCCCc-chHHHHHhcC-CCcccccc---------c
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGSPL-LTSEHSNRRK-PNKRKRTR---------K  181 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~~~-~~q~~~l~~~-~~i~v~~~---------~  181 (284)
                             ..++++|||+||++|+.|++..+..+.... ++++.++.|+.. ..+...+..+ +++++.+.         .
T Consensus        74 -------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~  146 (391)
T 1xti_A           74 -------TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNK  146 (391)
T ss_dssp             -------TTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTT
T ss_pred             -------CCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcC
Confidence                   235689999999999999999999998876 788888888754 3344444443 67766551         2


Q ss_pred             CCccccccccCCCCCCcccc-cccccchhhhcccCCCCCC
Q 042526          182 GGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~  220 (284)
                      ...+.++..+|+|||+.+.+ .+|......++...+...+
T Consensus       147 ~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~  186 (391)
T 1xti_A          147 SLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ  186 (391)
T ss_dssp             SSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSE
T ss_pred             CccccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCce
Confidence            23467888999999999877 5777777666665554443

>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=99.90  E-value=5.2e-24  Score=197.28  Aligned_cols=165  Identities=23%  Similarity=0.311  Sum_probs=132.7

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      .+.+|++++|++.++++|.++||..|+|+|.++|+.+ +.|  ++++++||||||||++|++|++..+...         
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~-~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~---------   72 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLL-LHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE---------   72 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT---------
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC---------
Confidence            4578999999999999999999999999999999999 777  9999999999999999999999865332         


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc---------c
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT---------R  180 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~---------~  180 (284)
                                 ..++++|||+||++||.|++..++.+....++.+..++|+.....   ....+++++.+         .
T Consensus        73 -----------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~iiv~T~~~l~~~~~~  138 (395)
T 3pey_A           73 -----------DASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKN---KQINAQVIVGTPGTVLDLMRR  138 (395)
T ss_dssp             -----------CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTT---SCBCCSEEEECHHHHHHHHHT
T ss_pred             -----------CCCccEEEECCCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhh---ccCCCCEEEEcHHHHHHHHHc
Confidence                       246789999999999999999999999888888888877754332   12345665554         1


Q ss_pred             cCCccccccccCCCCCCcccc-cccccchhhhcccCCCCCC
Q 042526          181 KGGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 ~~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~  220 (284)
                      ....+.++..+++|||+.+.+ .+|......+....+...+
T Consensus       139 ~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~  179 (395)
T 3pey_A          139 KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQ  179 (395)
T ss_dssp             TCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCE
T ss_pred             CCcccccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcE
Confidence            223467788999999999877 6777777666665555444

>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=99.89  E-value=1e-23  Score=193.40  Aligned_cols=167  Identities=22%  Similarity=0.306  Sum_probs=135.6

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      ...+|++++|++.++++|.++||..|+|+|.++|+.+ +.| ++++++||||||||++|++|++..+..           
T Consensus         4 ~~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~-~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~-----------   71 (367)
T 1hv8_A            4 EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLF-LNDEYNIVAQARTGSGKTASFAIPLIELVNE-----------   71 (367)
T ss_dssp             CCCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HHTCSEEEEECCSSSSHHHHHHHHHHHHSCS-----------
T ss_pred             ccCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCCCEEEECCCCChHHHHHHHHHHHHhcc-----------
Confidence            3468999999999999999999999999999999999 666 799999999999999999999875432           


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------c
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------K  181 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~  181 (284)
                                ..++++|||+||++|+.|+++.+..+....++.+..+.|+............+++++.+.         .
T Consensus        72 ----------~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~  141 (367)
T 1hv8_A           72 ----------NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRG  141 (367)
T ss_dssp             ----------SSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTT
T ss_pred             ----------cCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcCCCCEEEecHHHHHHHHHcC
Confidence                      146789999999999999999999999888888888888765444333334677766551         1


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCCCCC
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      ...+.++..+++|||+.+.+.+|......++...+...+
T Consensus       142 ~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~  180 (367)
T 1hv8_A          142 TLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKR  180 (367)
T ss_dssp             CSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCE
T ss_pred             CcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCce
Confidence            123667888999999999999988888777665544443

>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=99.89  E-value=6.5e-24  Score=207.91  Aligned_cols=164  Identities=21%  Similarity=0.253  Sum_probs=129.2

Q ss_pred             cCcccCC----CCHHHHHHHHHcCCCCCcHHHHHHHHHHHc--CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHH
Q 042526           34 DAWNELR----LHPLLMKSIYKLGFKESTSILKARIPALAH--QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKM  107 (284)
Q Consensus        34 ~~F~~l~----L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~--~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~  107 (284)
                      .+|.++.    |++.++++|..+||..|||+|.+|||.+ +  .|+|++++||||||||++|++|+++.+....      
T Consensus        68 ~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~-l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~------  140 (563)
T 3i5x_A           68 VTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPI-LSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK------  140 (563)
T ss_dssp             CCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHH-HSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT------
T ss_pred             cCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-hcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcc------
Confidence            3455553    9999999999999999999999999999 6  6899999999999999999999999887642      


Q ss_pred             HhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC----CCceeEEEeCC-CcchHHHHH-hcCCCccccccc
Q 042526          108 LEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS----NSLTLAMAAGS-PLLTSEHSN-RRKPNKRKRTRK  181 (284)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~----~~i~v~~~~G~-~~~~q~~~l-~~~~~i~v~~~~  181 (284)
                                .....++++|||+|||+||.|++..++.+...    ..+.+..++|+ ....+...+ ...++|++.+.-
T Consensus       141 ----------~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~  210 (563)
T 3i5x_A          141 ----------FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPG  210 (563)
T ss_dssp             ----------TSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHH
T ss_pred             ----------ccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcH
Confidence                      22234678999999999999999999998653    23456666655 445555555 346888776621


Q ss_pred             ----------CCccccccccCCCCCCcccccccccchhhhccc
Q 042526          182 ----------GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNL  214 (284)
Q Consensus       182 ----------~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~  214 (284)
                                ...++.+..+|+|||++|.++||.+....++..
T Consensus       211 ~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~f~~~~~~i~~~  253 (563)
T 3i5x_A          211 RLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGI  253 (563)
T ss_dssp             HHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHH
T ss_pred             HHHHHHHhccccccccceEEEEeCHHHHhccchHHHHHHHHHh
Confidence                      123567888999999999999998888666543

>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=99.86  E-value=5.4e-22  Score=180.16  Aligned_cols=153  Identities=21%  Similarity=0.245  Sum_probs=125.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      |++.|.++|.++||..|+|+|.++|+.+ +.|++++++||||||||++|++|+++.                        
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i-~~~~~~lv~~~TGsGKT~~~~~~~~~~------------------------   55 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLM-LQGKNVVVRAKTGSGKTAAYAIPILEL------------------------   55 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHH------------------------
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHH-hcCCCEEEEcCCCCcHHHHHHHHHHhh------------------------
Confidence            6899999999999999999999999998 899999999999999999999998752                        


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCcccccccc
Q 042526          121 KGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGEDEKLDSL  191 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~d~l~~l  191 (284)
                        +.++|||+||++|+.|++..+..+....++.+..++|+............+++++.+.         ....+.++..+
T Consensus        56 --~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~i  133 (337)
T 2z0m_A           56 --GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIV  133 (337)
T ss_dssp             --TCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHHTTCSEEEECHHHHHHHHHTTSCCGGGCSEE
T ss_pred             --cCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhcCCCCEEEECHHHHHHHHHcCCcchhhCcEE
Confidence              3569999999999999999999999888888888888765444333344577766551         12346778889


Q ss_pred             CCCCCCcccccccccchhhhcccCCCCCC
Q 042526          192 KWNPLSQPKTTTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       192 v~dEAd~m~~~gflp~~~~~~~~~~r~~~  220 (284)
                      ++|||+.+.+.+|......++...+...+
T Consensus       134 ViDEah~~~~~~~~~~~~~~~~~~~~~~~  162 (337)
T 2z0m_A          134 IIDEADLMFEMGFIDDIKIILAQTSNRKI  162 (337)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHCTTCSE
T ss_pred             EEEChHHhhccccHHHHHHHHhhCCcccE
Confidence            99999999998888777666665544433

>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=99.85  E-value=4.6e-22  Score=201.64  Aligned_cols=138  Identities=15%  Similarity=0.045  Sum_probs=112.5

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      .+|| +|||||..+||.+ +.|+  |+.++||||||+||+||++...+                       .+++++||+
T Consensus        79 ~lG~-~pt~VQ~~~ip~l-l~G~--Iaea~TGeGKTlaf~LP~~l~aL-----------------------~g~~vlVlt  131 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVAL-HDGN--IAEMKTGEGKTLTSTLPVYLNAL-----------------------TGKGVHVVT  131 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHH-HTTS--EEECCTTSCHHHHHHHHHHHHHT-----------------------TSSCEEEEE
T ss_pred             HcCC-CCcHHHHHhhHHH-hCCC--EEEccCCcHHHHHHHHHHHHHHH-----------------------cCCCEEEEe
Confidence            5899 9999999999998 8998  99999999999999999984321                       256799999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc--c--------------CCccccccccCCC
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--K--------------GGEDEKLDSLKWN  194 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--~--------------~~~~d~l~~lv~d  194 (284)
                      |||+||.|++.++..|..+++++|++++|+... +.+.+..+++|++.|.  .              ...+..+.++|+|
T Consensus       132 ptreLA~qd~e~~~~l~~~lgl~v~~i~gg~~~-~~r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlD  210 (844)
T 1tf5_A          132 VNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSK-DEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVID  210 (844)
T ss_dssp             SSHHHHHHHHHHHHHHHHHTTCCEEECCTTSCH-HHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEE
T ss_pred             CCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCH-HHHHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEEC
Confidence            999999999999999999999999999988654 4556667889877662  1              1234677889999


Q ss_pred             CCCccc-cccc---------------ccchhhhcccCC
Q 042526          195 PLSQPK-TTTL---------------LPSSLALMNLTE  216 (284)
Q Consensus       195 EAd~m~-~~gf---------------lp~~~~~~~~~~  216 (284)
                      |||.|+ |+++               ++++..++..++
T Consensus       211 EaD~mLiDea~tplIisg~~~~~~~~~~~i~~iv~~l~  248 (844)
T 1tf5_A          211 EVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLK  248 (844)
T ss_dssp             THHHHHTTTTTCEEEEEEEEECCCHHHHHHHHHHTTCC
T ss_pred             chhhhhhhccccchhhcCCcccchhHHHHHHHHHHhCc
Confidence            999998 8864               455555666665

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

Probab=99.83  E-value=1.6e-21  Score=183.75  Aligned_cols=145  Identities=14%  Similarity=-0.011  Sum_probs=115.6

Q ss_pred             HHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCC
Q 042526           44 LLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKG  122 (284)
Q Consensus        44 ~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~  122 (284)
                      .+.+.+.+ +|| .|||+|.++||.+ +.|+|++++||||||||++|++|++..+.                       .
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i-~~~~~~lv~apTGsGKT~~~l~~~~~~~~-----------------------~   63 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRI-VQGKSFTMVAPTGVGKTTFGMMTALWLAR-----------------------K   63 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHH-TTTCCEECCSCSSSSHHHHHHHHHHHHHT-----------------------T
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHH-hcCCCEEEEeCCCCCHHHHHHHHHHHHhc-----------------------C
Confidence            45556665 577 6999999999999 89999999999999999999999876541                       3


Q ss_pred             CeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcc----hHHHHHhcC-CCccccccc-------CCccccccc
Q 042526          123 HLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLL----TSEHSNRRK-PNKRKRTRK-------GGEDEKLDS  190 (284)
Q Consensus       123 ~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~----~q~~~l~~~-~~i~v~~~~-------~~~~d~l~~  190 (284)
                      ++++|||+|||+||.|++..++.++. .++++..++|+...    .+...+..+ +++++.+.-       ...+.++..
T Consensus        64 ~~~~lil~Pt~~L~~q~~~~~~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~  142 (414)
T 3oiy_A           64 GKKSALVFPTVTLVKQTLERLQKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDF  142 (414)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHHHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSE
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccE
Confidence            67899999999999999999999988 88899888888653    344566665 788766521       123457889


Q ss_pred             cCCCCC----------Ccccc-cccccc-hhhhccc
Q 042526          191 LKWNPL----------SQPKT-TTLLPS-SLALMNL  214 (284)
Q Consensus       191 lv~dEA----------d~m~~-~gflp~-~~~~~~~  214 (284)
                      +|+|||          |+|++ +||.++ ...++..
T Consensus       143 iViDEaH~~~~~~~~~d~~l~~~~~~~~~~~~i~~~  178 (414)
T 3oiy_A          143 VFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFST  178 (414)
T ss_dssp             EEESCHHHHHHCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             EEEeChHhhhhccchhhhHHhhcCCcHHHHHHHHHh
Confidence            999999          78888 999998 4444443

>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=99.81  E-value=6.2e-21  Score=193.09  Aligned_cols=127  Identities=17%  Similarity=0.098  Sum_probs=105.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|||||..++|.+ +.|+  |+.++||||||++|++|++....                       .+++++||+|
T Consensus        71 lg~-~p~~VQ~~~i~~l-l~G~--Iaem~TGsGKTlaf~LP~l~~~l-----------------------~g~~vlVltP  123 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVL-NERC--IAEMRTGEGKTLTATLPAYLNAL-----------------------TGKGVHVVTV  123 (853)
T ss_dssp             HSC-CCCHHHHHHHHHH-HSSE--EEECCTTSCHHHHHHHHHHHHHT-----------------------TSSCCEEEES
T ss_pred             cCC-CCChHHHhhcccc-cCCe--eeeecCCchHHHHHHHHHHHHHH-----------------------cCCcEEEEcC
Confidence            575 8999999999998 8998  99999999999999999986432                       2568999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccC----------------CccccccccCCCC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKG----------------GEDEKLDSLKWNP  195 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~----------------~~~d~l~~lv~dE  195 (284)
                      ||+||.|++..+..|..+++++|++++|+... +.+.+..+++|++.|.--                ..+..+.++|+||
T Consensus       124 TreLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~-~~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDE  202 (853)
T 2fsf_A          124 NDYLAQRDAENNRPLFEFLGLTVGINLPGMPA-PAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDE  202 (853)
T ss_dssp             SHHHHHHHHHHHHHHHHHTTCCEEECCTTCCH-HHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESC
T ss_pred             CHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCH-HHHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECc
Confidence            99999999999999999999999999988654 556677788987766211                2346788899999


Q ss_pred             CCccc-cccccc
Q 042526          196 LSQPK-TTTLLP  206 (284)
Q Consensus       196 Ad~m~-~~gflp  206 (284)
                      ||.|+ ++++.|
T Consensus       203 aD~mLiD~a~tp  214 (853)
T 2fsf_A          203 VDSILIDEARTP  214 (853)
T ss_dssp             HHHHTTTTTTCE
T ss_pred             hHHHHHhcCccc
Confidence            99998 766544

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

Probab=99.79  E-value=5.6e-20  Score=193.59  Aligned_cols=139  Identities=15%  Similarity=-0.001  Sum_probs=113.3

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      .+|| .|||+|.+|||.+ +.|+|++++||||||||++|++|++..+ .                      .++++|||+
T Consensus        74 ~~gf-~pt~iQ~~ai~~i-l~g~dvlv~ApTGSGKTl~~l~~il~~~-~----------------------~~~~~Lil~  128 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRI-VQGKSFTMVAPTGVGKTTFGMMTALWLA-R----------------------KGKKSALVF  128 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHH-TTTCCEEECCSTTCCHHHHHHHHHHHHH-T----------------------TTCCEEEEE
T ss_pred             hcCC-CCCHHHHHHHHHH-HcCCCEEEEeCCCCcHHHHHHHHHHHHH-h----------------------cCCeEEEEe
Confidence            3789 5999999999999 8999999999999999999888887655 1                      367899999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCc----chHHHHHhcC-CCcccccccC-------CccccccccCCCCC--
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPL----LTSEHSNRRK-PNKRKRTRKG-------GEDEKLDSLKWNPL--  196 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~----~~q~~~l~~~-~~i~v~~~~~-------~~~d~l~~lv~dEA--  196 (284)
                      |||+||.|++..++.|+ ..++++++++|+..    ..+...+..+ ++|++.+.-.       ..+.++..+|+|||  
T Consensus       129 PtreLa~Q~~~~l~~l~-~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~lViDEaH~  207 (1104)
T 4ddu_A          129 PTVTLVKQTLERLQKLA-DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDA  207 (1104)
T ss_dssp             SSHHHHHHHHHHHHTTS-CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEEEESCHHH
T ss_pred             chHHHHHHHHHHHHHhh-CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEEEEeCCCc
Confidence            99999999999999988 77889988888854    4455667666 8887766211       12567899999999  


Q ss_pred             --------Ccccc-cccccc-hhhhcccC
Q 042526          197 --------SQPKT-TTLLPS-SLALMNLT  215 (284)
Q Consensus       197 --------d~m~~-~gflp~-~~~~~~~~  215 (284)
                              |+|++ +||.++ +..++..+
T Consensus       208 l~~~~r~~Dr~L~~~gf~~~~i~~il~~l  236 (1104)
T 4ddu_A          208 VLKASRNIDTLLMMVGIPEEIIRKAFSTI  236 (1104)
T ss_dssp             HTTSSHHHHHHHHTSSCCHHHHHHHHHHH
T ss_pred             cccccccchhhhHhcCCCHHHHHHHHHhc
Confidence                    88889 999998 55555433

>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=99.79  E-value=1e-19  Score=191.00  Aligned_cols=148  Identities=16%  Similarity=0.054  Sum_probs=115.6

Q ss_pred             CcccCCCCHHHH-----HHHH-HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHH
Q 042526           35 AWNELRLHPLLM-----KSIY-KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKML  108 (284)
Q Consensus        35 ~F~~l~L~~~Ll-----~~L~-~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~  108 (284)
                      .|..+++++.+.     +.+. .+||. | |+|.++||.+ +.|+|++++||||||||+ |++|++..+..         
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~g~~-p-~iQ~~ai~~i-l~g~dvlv~apTGSGKTl-~~lp~l~~~~~---------   97 (1054)
T 1gku_B           31 AASLCLFPEDFLLKEFVEFFRKCVGEP-R-AIQKMWAKRI-LRKESFAATAPTGVGKTS-FGLAMSLFLAL---------   97 (1054)
T ss_dssp             CCCCSCCTTHHHHHHHHHHHHTTTCSC-C-HHHHHHHHHH-HTTCCEECCCCBTSCSHH-HHHHHHHHHHT---------
T ss_pred             cccccccccccchHHHHHHHHHhcCCC-H-HHHHHHHHHH-HhCCCEEEEcCCCCCHHH-HHHHHHHHHhh---------
Confidence            455555554433     4444 48999 9 9999999999 899999999999999998 99999887643         


Q ss_pred             hhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCc----eeEEEeCCCcchH----HHHHhcCCCcccccc
Q 042526          109 EEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSL----TLAMAAGSPLLTS----EHSNRRKPNKRKRTR  180 (284)
Q Consensus       109 ~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i----~v~~~~G~~~~~q----~~~l~~~~~i~v~~~  180 (284)
                                   .++++|||+|||+||.|++..++.++..+++    ++++++|+.....    ...+.. ++|++.+.
T Consensus        98 -------------~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP  163 (1054)
T 1gku_B           98 -------------KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTT  163 (1054)
T ss_dssp             -------------TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEH
T ss_pred             -------------cCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcH
Confidence                         3678999999999999999999999998888    8888888754433    334445 88877652


Q ss_pred             -----cCCccccccccCCCCCCcccc-----------cccccchh
Q 042526          181 -----KGGEDEKLDSLKWNPLSQPKT-----------TTLLPSSL  209 (284)
Q Consensus       181 -----~~~~~d~l~~lv~dEAd~m~~-----------~gflp~~~  209 (284)
                           .+..+.++..+|+||||+|++           +||..+..
T Consensus       164 ~~L~~~l~~L~~l~~lViDEah~~l~~~~~~~~i~~~lgf~~~~~  208 (1054)
T 1gku_B          164 QFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLK  208 (1054)
T ss_dssp             HHHHHCSTTSCCCSEEEESCHHHHHTSTHHHHHHHHHTTEEEETT
T ss_pred             HHHHHHHHHhccCCEEEEeChhhhhhccccHHHHHHHhCcchhhh
Confidence                 112256788999999999999           77766543

>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=99.79  E-value=1.9e-19  Score=178.56  Aligned_cols=150  Identities=17%  Similarity=0.148  Sum_probs=117.4

Q ss_pred             CccccCcc--cCCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHH
Q 042526           30 STEFDAWN--ELRLHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAK  106 (284)
Q Consensus        30 p~~~~~F~--~l~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~  106 (284)
                      +.....|.  ++++++.+..+|++ +||..|+|+|.++|+.+ +.|+|+++.+|||+|||++|++|++..          
T Consensus        15 ~~~~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~i-l~g~d~lv~~pTGsGKTl~~~lpal~~----------   83 (591)
T 2v1x_A           15 DSSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVT-MAGKEVFLVMPTGGGKSLCYQLPALCS----------   83 (591)
T ss_dssp             -CCGGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHH-HTTCCEEEECCTTSCTTHHHHHHHHTS----------
T ss_pred             CcchhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHH-HcCCCEEEEECCCChHHHHHHHHHHHc----------
Confidence            34445555  47899999999998 79999999999999999 899999999999999999999999741          


Q ss_pred             HHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHH-------hcCCCccccc
Q 042526          107 MLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSN-------RRKPNKRKRT  179 (284)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l-------~~~~~i~v~~  179 (284)
                                      ..++|||+||++|+.|+...+..+    ++.+.++.|+....+....       ....++++.+
T Consensus        84 ----------------~g~~lVisP~~~L~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~T  143 (591)
T 2v1x_A           84 ----------------DGFTLVICPLISLMEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVT  143 (591)
T ss_dssp             ----------------SSEEEEECSCHHHHHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEEC
T ss_pred             ----------------CCcEEEEeCHHHHHHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEC
Confidence                            247999999999999999999887    6778888877654433221       2345665554


Q ss_pred             ccC--------------CccccccccCCCCCCcccccc--cccchhh
Q 042526          180 RKG--------------GEDEKLDSLKWNPLSQPKTTT--LLPSSLA  210 (284)
Q Consensus       180 ~~~--------------~~~d~l~~lv~dEAd~m~~~g--flp~~~~  210 (284)
                      .-.              ..+.++..+++|||+.+.+.|  |-|....
T Consensus       144 pe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~~~~  190 (591)
T 2v1x_A          144 PEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKA  190 (591)
T ss_dssp             HHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGGGGG
T ss_pred             hhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHHHHH
Confidence            310              013367889999999999988  8777643

>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=99.79  E-value=4.2e-20  Score=187.62  Aligned_cols=138  Identities=15%  Similarity=0.043  Sum_probs=113.2

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      .+|+ +||+||..++|.+ +.|+  |+.++||+|||++|+||++...+.                       +.+++||+
T Consensus       107 ~lG~-rP~~VQ~~~ip~L-l~G~--Iaem~TGeGKTLa~~LP~~l~aL~-----------------------g~~v~VvT  159 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAAL-HLGN--VAEMKTGEGKTLTCVLPAYLNALA-----------------------GNGVHIVT  159 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHH-HTTE--EEECCTTSCHHHHTHHHHHHHHTT-----------------------TSCEEEEE
T ss_pred             HcCC-CCCHHHHHHHHhH-hcCC--EEEecCCCccHHHHHHHHHHHHHh-----------------------CCCeEEEe
Confidence            3899 8999999999998 8998  999999999999999999754322                       35799999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccccc----------------CCccccccccCCC
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRK----------------GGEDEKLDSLKWN  194 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~----------------~~~~d~l~~lv~d  194 (284)
                      |||+||.|++.++..|..+++++|++++|+.. .+.+.+..+++|++.+..                ...+..+.++|+|
T Consensus       160 pTreLA~Qdae~m~~l~~~lGLsv~~i~gg~~-~~~r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVD  238 (922)
T 1nkt_A          160 VNDYLAKRDSEWMGRVHRFLGLQVGVILATMT-PDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVD  238 (922)
T ss_dssp             SSHHHHHHHHHHHHHHHHHTTCCEEECCTTCC-HHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEET
T ss_pred             CCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCC-HHHHHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEe
Confidence            99999999999999999999999999998865 355666677888776521                1234578889999


Q ss_pred             CCCccc-c---------------cccccchhhhcccCC
Q 042526          195 PLSQPK-T---------------TTLLPSSLALMNLTE  216 (284)
Q Consensus       195 EAd~m~-~---------------~gflp~~~~~~~~~~  216 (284)
                      |||.|+ |               ++|.+++-.++..++
T Consensus       239 EaDsmLiDeartPLiiSg~~~~~~~~y~~i~~iv~~L~  276 (922)
T 1nkt_A          239 EVDSILIDEARTPLIISGPADGASNWYTEFARLAPLME  276 (922)
T ss_dssp             THHHHHTTGGGSCEEEEEECCCCHHHHHHHHHHHHHSC
T ss_pred             ChHHHHHhcCccceeecCCCCcchhHHHHHHHHHHhCc
Confidence            999998 5               456677777777776

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

Probab=99.79  E-value=3e-19  Score=180.06  Aligned_cols=150  Identities=15%  Similarity=0.104  Sum_probs=121.3

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|++++|++.+.+.|..+||..|+|+|.++|+.++..|++++++||||||||++|.+|+++.+...            
T Consensus         7 ~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~------------   74 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN------------   74 (715)
T ss_dssp             CCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS------------
T ss_pred             cCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC------------
Confidence            35799999999999999999999999999999999448899999999999999999999999876532            


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc--------cC-C
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--------KG-G  183 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--------~~-~  183 (284)
                                +.++||++|||+||.|++..++.+.. .++++..++|+...... . ...+++++.+.        .. .
T Consensus        75 ----------~~~il~i~P~r~La~q~~~~~~~~~~-~g~~v~~~~G~~~~~~~-~-~~~~~Iiv~Tpe~l~~~~~~~~~  141 (715)
T 2va8_A           75 ----------GGKAIYVTPLRALTNEKYLTFKDWEL-IGFKVAMTSGDYDTDDA-W-LKNYDIIITTYEKLDSLWRHRPE  141 (715)
T ss_dssp             ----------CSEEEEECSCHHHHHHHHHHHGGGGG-GTCCEEECCSCSSSCCG-G-GGGCSEEEECHHHHHHHHHHCCG
T ss_pred             ----------CCeEEEEeCcHHHHHHHHHHHHHhhc-CCCEEEEEeCCCCCchh-h-cCCCCEEEEcHHHHHHHHhCChh
Confidence                      46899999999999999999976654 48888888887544332 2 23667766552        11 2


Q ss_pred             ccccccccCCCCCCcccccccccc
Q 042526          184 EDEKLDSLKWNPLSQPKTTTLLPS  207 (284)
Q Consensus       184 ~~d~l~~lv~dEAd~m~~~gflp~  207 (284)
                      .+.++..+|+||+..+.+.++.+.
T Consensus       142 ~l~~~~~vIiDE~H~l~~~~~~~~  165 (715)
T 2va8_A          142 WLNEVNYFVLDELHYLNDPERGPV  165 (715)
T ss_dssp             GGGGEEEEEECSGGGGGCTTTHHH
T ss_pred             HhhccCEEEEechhhcCCcccchH
Confidence            377889999999999876555443

>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=99.78  E-value=2.4e-19  Score=181.04  Aligned_cols=148  Identities=18%  Similarity=0.102  Sum_probs=120.3

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      +|++++|++.+.+.|..+||..|+|+|.++|+.++..|++++++||||||||++|.+|++..+...              
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--------------   67 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--------------   67 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--------------
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--------------
Confidence            699999999999999999999999999999998338899999999999999999999999887642              


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCcc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGED  185 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~  185 (284)
                              +.++||++|||+||.|++..++.+.. .++++..++|+......  ....+++++.+.         ....+
T Consensus        68 --------~~~~l~i~P~raLa~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~--~~~~~~Iiv~Tpe~l~~~~~~~~~~l  136 (720)
T 2zj8_A           68 --------GGKAVYIVPLKALAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE--WLGKYDIIIATAEKFDSLLRHGSSWI  136 (720)
T ss_dssp             --------CSEEEEECSSGGGHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG--GGGGCSEEEECHHHHHHHHHHTCTTG
T ss_pred             --------CCEEEEEcCcHHHHHHHHHHHHHHHh-cCCEEEEecCCCCcccc--ccCCCCEEEECHHHHHHHHHcChhhh
Confidence                    46899999999999999999987765 48889888886433321  234567766552         11236


Q ss_pred             ccccccCCCCCCcccccccccc
Q 042526          186 EKLDSLKWNPLSQPKTTTLLPS  207 (284)
Q Consensus       186 d~l~~lv~dEAd~m~~~gflp~  207 (284)
                      .++..+|+|||..+.+.++-+.
T Consensus       137 ~~~~~vIiDE~H~l~~~~r~~~  158 (720)
T 2zj8_A          137 KDVKILVADEIHLIGSRDRGAT  158 (720)
T ss_dssp             GGEEEEEEETGGGGGCTTTHHH
T ss_pred             hcCCEEEEECCcccCCCcccHH
Confidence            7889999999998876554443

>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=99.77  E-value=4.1e-19  Score=173.73  Aligned_cols=145  Identities=12%  Similarity=0.068  Sum_probs=114.7

Q ss_pred             ccCcccCCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           33 FDAWNELRLHPLLMKSIYK-LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      |.+|++|+|++.+.+.|.+ +||..|+|+|.++|+.+ +.|+|+++.+|||||||++|++|++..               
T Consensus         1 ~~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~i-l~g~d~lv~apTGsGKTl~~~lp~l~~---------------   64 (523)
T 1oyw_A            1 MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTV-LSGRDCLVVMPTGGGKSLCYQIPALLL---------------   64 (523)
T ss_dssp             CCCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHH-HTTCCEEEECSCHHHHHHHHHHHHHHS---------------
T ss_pred             CCChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHH-HcCCCEEEECCCCcHHHHHHHHHHHHh---------------
Confidence            4689999999999999998 89999999999999999 899999999999999999999998731               


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHH----HHh-cCCCccccccc----C
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEH----SNR-RKPNKRKRTRK----G  182 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~----~l~-~~~~i~v~~~~----~  182 (284)
                                 ...+|||+||++|+.|+...+..+    ++.+.++.|+....+..    .+. ..+++++.+.-    .
T Consensus        65 -----------~g~~lvi~P~~aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~  129 (523)
T 1oyw_A           65 -----------NGLTVVVSPLISLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLD  129 (523)
T ss_dssp             -----------SSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTST
T ss_pred             -----------CCCEEEECChHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCh
Confidence                       235899999999999999998865    67777777775544322    222 33566554411    0


Q ss_pred             -----CccccccccCCCCCCcccccc--cccch
Q 042526          183 -----GEDEKLDSLKWNPLSQPKTTT--LLPSS  208 (284)
Q Consensus       183 -----~~~d~l~~lv~dEAd~m~~~g--flp~~  208 (284)
                           ....++..+|+|||+.+.+.|  |-|..
T Consensus       130 ~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~  162 (523)
T 1oyw_A          130 NFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEY  162 (523)
T ss_dssp             THHHHHTTSCEEEEEESSGGGGCTTSSCCCHHH
T ss_pred             HHHHHHhhCCCCEEEEeCccccCcCCCccHHHH
Confidence                 112567789999999999887  65554

>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=99.77  E-value=3.9e-19  Score=172.26  Aligned_cols=137  Identities=11%  Similarity=-0.015  Sum_probs=105.8

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      ++...|+|+|.++|+.+ +.|+|+++++|||||||++|++|+++.+...                  ....++++|||+|
T Consensus         3 ~~~~~~~~~Q~~~i~~~-~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~------------------~~~~~~~~lil~P   63 (556)
T 4a2p_A            3 METKKARSYQIELAQPA-INGKNALICAPTGSGKTFVSILICEHHFQNM------------------PAGRKAKVVFLAT   63 (556)
T ss_dssp             -----CCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC------------------CSSCCCCEEEECS
T ss_pred             CCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCChHHHHHHHHHHHHHHhC------------------cccCCCeEEEEeC
Confidence            45568999999999999 8999999999999999999999999877542                  1123678999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc----------cCCccccccccCCCCCCccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR----------KGGEDEKLDSLKWNPLSQPK  200 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~----------~~~~~d~l~~lv~dEAd~m~  200 (284)
                      |++|+.|++..+..+....++.+..++|+. ...+...+..++++++.+.          ....+..+..+|+|||+++.
T Consensus        64 ~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~  143 (556)
T 4a2p_A           64 KVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTT  143 (556)
T ss_dssp             SHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCS
T ss_pred             CHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccC
Confidence            999999999999999988899998888875 3344555666788876651          11257788999999999998


Q ss_pred             ccccccc
Q 042526          201 TTTLLPS  207 (284)
Q Consensus       201 ~~gflp~  207 (284)
                      +.+++..
T Consensus       144 ~~~~~~~  150 (556)
T 4a2p_A          144 GNHPYNV  150 (556)
T ss_dssp             TTSHHHH
T ss_pred             CcchHHH
Confidence            8775443

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

Probab=99.77  E-value=9.3e-19  Score=175.21  Aligned_cols=137  Identities=10%  Similarity=-0.072  Sum_probs=107.6

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCe
Q 042526           45 LMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHL  124 (284)
Q Consensus        45 Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (284)
                      +..+|..+||..|+|+|.++|+.+ +.|+|+|+++|||||||++|++|+++.+....                  ...+.
T Consensus         2 ~~~~l~~~g~~~lr~~Q~~~i~~~-l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~------------------~~~~~   62 (696)
T 2ykg_A            2 EVSDTNLYSPFKPRNYQLELALPA-MKGKNTIICAPTGCGKTFVSLLICEHHLKKFP------------------QGQKG   62 (696)
T ss_dssp             -----CTTC--CCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHHHHSC------------------TTCCC
T ss_pred             CCCcccccCCCCccHHHHHHHHHH-HcCCCEEEEcCCCchHHHHHHHHHHHHHHhCc------------------cCCCC
Confidence            346788899999999999999998 89999999999999999999999998775421                  11236


Q ss_pred             EEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc----------cCCccccccccCC
Q 042526          125 RALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR----------KGGEDEKLDSLKW  193 (284)
Q Consensus       125 ~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~----------~~~~~d~l~~lv~  193 (284)
                      ++|||+||++|+.|++++++.++...++++..++|+. ...+...+...+++++.+.          ....+.++..+|+
T Consensus        63 ~~lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vVi  142 (696)
T 2ykg_A           63 KVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIF  142 (696)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEE
T ss_pred             eEEEEECCHHHHHHHHHHHHHHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEE
Confidence            7999999999999999999999988889998888874 4455666667788877651          1125778899999


Q ss_pred             CCCCccc
Q 042526          194 NPLSQPK  200 (284)
Q Consensus       194 dEAd~m~  200 (284)
                      |||+++.
T Consensus       143 DEaH~~~  149 (696)
T 2ykg_A          143 DECHNTS  149 (696)
T ss_dssp             ETGGGCS
T ss_pred             eCCCccc
Confidence            9999954

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

Probab=99.76  E-value=9e-19  Score=169.23  Aligned_cols=129  Identities=12%  Similarity=-0.029  Sum_probs=106.4

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+|+|.++|+.+ +.|+|+++++|||||||++|++|+++.+...                  ....+.++|||+||++|
T Consensus         4 ~~~~~Q~~~i~~~-~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~------------------~~~~~~~~lil~P~~~L   64 (555)
T 3tbk_A            4 KPRNYQLELALPA-KKGKNTIICAPTGCGKTFVSLLICEHHLKKF------------------PCGQKGKVVFFANQIPV   64 (555)
T ss_dssp             CCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC------------------CSSCCCCEEEECSSHHH
T ss_pred             CCcHHHHHHHHHH-hCCCCEEEEeCCCChHHHHHHHHHHHHHHhc------------------ccCCCCEEEEEeCCHHH
Confidence            5999999999999 8999999999999999999999999877552                  11236789999999999


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCc-chHHHHHhcCCCcccccc----------cCCccccccccCCCCCCcccccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPL-LTSEHSNRRKPNKRKRTR----------KGGEDEKLDSLKWNPLSQPKTTT  203 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~-~~q~~~l~~~~~i~v~~~----------~~~~~d~l~~lv~dEAd~m~~~g  203 (284)
                      +.|++..+..++...++.+..++|+.. ..+...+..++++++.+.          ....+..+..+|+|||+++...+
T Consensus        65 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~  143 (555)
T 3tbk_A           65 YEQQATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNH  143 (555)
T ss_dssp             HHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTC
T ss_pred             HHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcc
Confidence            999999999999988999988888753 344455666788876651          11257788999999999988775

>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=99.75  E-value=3.7e-19  Score=179.28  Aligned_cols=145  Identities=14%  Similarity=0.092  Sum_probs=115.2

Q ss_pred             CcccCC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           35 AWNELR--LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        35 ~F~~l~--L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      +|++|+  |++.+.++|.++||..|+|+|.++|+.+ ..|++++++||||||||++|.+|++..+..             
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i-~~~~~~lv~apTGsGKT~~~~l~il~~~~~-------------   67 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKV-FSGKNLLLAMPTAAGKTLLAEMAMVREAIK-------------   67 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHH-TTCSCEEEECSSHHHHHHHHHHHHHHHHHT-------------
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHH-hCCCcEEEEcCCccHHHHHHHHHHHHHHHh-------------
Confidence            689998  9999999999999999999999999997 899999999999999999999999986532             


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc--------cC-C
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--------KG-G  183 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--------~~-~  183 (284)
                                +.++||++|||+||.|++..++.+.. .++++..++|+......  ....+++++.+.        .. .
T Consensus        68 ----------~~~~l~i~P~r~La~q~~~~~~~~~~-~g~~v~~~~G~~~~~~~--~~~~~~Iiv~Tpe~l~~~l~~~~~  134 (702)
T 2p6r_A           68 ----------GGKSLYVVPLRALAGEKYESFKKWEK-IGLRIGISTGDYESRDE--HLGDCDIIVTTSEKADSLIRNRAS  134 (702)
T ss_dssp             ----------TCCEEEEESSHHHHHHHHHHHTTTTT-TTCCEEEECSSCBCCSS--CSTTCSEEEEEHHHHHHHHHTTCS
T ss_pred             ----------CCcEEEEeCcHHHHHHHHHHHHHHHh-cCCEEEEEeCCCCcchh--hccCCCEEEECHHHHHHHHHcChh
Confidence                      35799999999999999999976654 58889888887544321  223567766552        11 2


Q ss_pred             ccccccccCCCCCCccccccccc
Q 042526          184 EDEKLDSLKWNPLSQPKTTTLLP  206 (284)
Q Consensus       184 ~~d~l~~lv~dEAd~m~~~gflp  206 (284)
                      .+.++..+|+|||..+.+.++-+
T Consensus       135 ~l~~~~~vIiDE~H~l~~~~r~~  157 (702)
T 2p6r_A          135 WIKAVSCLVVDEIHLLDSEKRGA  157 (702)
T ss_dssp             GGGGCCEEEETTGGGGGCTTTHH
T ss_pred             HHhhcCEEEEeeeeecCCCCccc
Confidence            37789999999999987755433

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.75  E-value=8.6e-19  Score=177.89  Aligned_cols=130  Identities=15%  Similarity=0.086  Sum_probs=107.1

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|| +||+||..+||.+ +.|+  |++++||||||++|++|++...+                       .+.+++||+|
T Consensus        76 lG~-~Pt~VQ~~~ip~L-lqG~--IaeakTGeGKTLvf~Lp~~L~aL-----------------------~G~qv~VvTP  128 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVL-HEGK--IAEMKTGEGKTLVATLAVALNAL-----------------------TGKGVHVVTV  128 (997)
T ss_dssp             TCC-CCCHHHHHHHHHH-HTTS--EEECCSTHHHHHHHHHHHHHHHT-----------------------TCSCCEEEES
T ss_pred             hCC-CCcHHHHhhcccc-cCCc--eeeccCCCchHHHHHHHHHHHHH-----------------------hCCCEEEEeC
Confidence            899 8999999999998 8998  99999999999999999974332                       1457999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccccC----------------Cccc---cccccC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRKG----------------GEDE---KLDSLK  192 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~~----------------~~~d---~l~~lv  192 (284)
                      |++||.|++..+..|..+++++|++++|+.. .+...+..+++|++.|.-.                ..+.   .+..+|
T Consensus       129 TreLA~Qdae~m~~l~~~lGLsv~~i~Gg~~-~~~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lI  207 (997)
T 2ipc_A          129 NDYLARRDAEWMGPVYRGLGLSVGVIQHAST-PAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAI  207 (997)
T ss_dssp             SHHHHHHHHHHHHHHHHTTTCCEEECCTTCC-HHHHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEE
T ss_pred             CHHHHHHHHHHHHHHHHhcCCeEEEEeCCCC-HHHHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEE
Confidence            9999999999999999999999999998865 4556667788887765211                1244   688899


Q ss_pred             CCCCCccc-ccccccchh
Q 042526          193 WNPLSQPK-TTTLLPSSL  209 (284)
Q Consensus       193 ~dEAd~m~-~~gflp~~~  209 (284)
                      +||||.|+ +.+.-|.++
T Consensus       208 IDEaDsmLiDeartPLII  225 (997)
T 2ipc_A          208 IDEVDSILIDEARTPLII  225 (997)
T ss_dssp             ETTHHHHTTSSTTSCEEE
T ss_pred             EechHHHHHhCCCCCeee
Confidence            99999976 666766443

>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=99.74  E-value=4.8e-19  Score=186.57  Aligned_cols=153  Identities=11%  Similarity=0.026  Sum_probs=122.7

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|..+++++.+..++...++..|||+|.+||+.+ +.|+|++++|+||||||++|++|++..+.              
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i-~~g~dvLV~ApTGSGKTlva~l~i~~~l~--------------  225 (1108)
T 3l9o_A          161 PPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCI-DRGESVLVSAHTSAGKTVVAEYAIAQSLK--------------  225 (1108)
T ss_dssp             SSCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHH-TTTCCEEEECCSSSHHHHHHHHHHHHHHH--------------
T ss_pred             CCCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHH-HcCCCEEEECCCCCChHHHHHHHHHHHHh--------------
Confidence            457888899998888887777888999999999998 99999999999999999999999998762              


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCC
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGG  183 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~  183 (284)
                               .+.++||++|||+||.|++..+..+..    .+.+++|+...      ...+++++.|.         ...
T Consensus       226 ---------~g~rvlvl~PtraLa~Q~~~~l~~~~~----~VglltGd~~~------~~~~~IlV~Tpe~L~~~L~~~~~  286 (1108)
T 3l9o_A          226 ---------NKQRVIYTSPIKALSNQKYRELLAEFG----DVGLMTGDITI------NPDAGCLVMTTEILRSMLYRGSE  286 (1108)
T ss_dssp             ---------TTCEEEEEESSHHHHHHHHHHHHHHTS----SEEEECSSCBC------CCSCSEEEEEHHHHHHHHHHCSS
T ss_pred             ---------cCCeEEEEcCcHHHHHHHHHHHHHHhC----CccEEeCcccc------CCCCCEEEeChHHHHHHHHcCcc
Confidence                     256899999999999999999998765    46667776542      23456666551         122


Q ss_pred             ccccccccCCCCCCcccccccccchhhhcccCCCCC
Q 042526          184 EDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKP  219 (284)
Q Consensus       184 ~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~  219 (284)
                      .+.++..+|+|||+.|.+.+|.+....++..++...
T Consensus       287 ~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~  322 (1108)
T 3l9o_A          287 VMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKV  322 (1108)
T ss_dssp             HHHHEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTS
T ss_pred             ccccCCEEEEhhhhhccccchHHHHHHHHHhcCCCc
Confidence            477899999999999999888777666655554443

>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=99.74  E-value=3.6e-18  Score=174.44  Aligned_cols=138  Identities=11%  Similarity=-0.026  Sum_probs=106.9

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      -+|+..|+|+|..+|+.+ +.|+|+|+++|||||||++|++|++..+...                  ....+.++|||+
T Consensus       243 ~~g~~~l~~~Q~~~i~~~-l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~------------------~~~~~~~~Lvl~  303 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPA-INGKNALICAPTGSGKTFVSILICEHHFQNM------------------PAGRKAKVVFLA  303 (797)
T ss_dssp             -----CCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC------------------CSSCCCCEEEEC
T ss_pred             hcCCCCCCHHHHHHHHHH-HhCCCEEEEeCCCChHHHHHHHHHHHHHHhc------------------cccCCCeEEEEe
Confidence            468999999999999999 8999999999999999999999999877542                  112367899999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc----------cCCccccccccCCCCCCcc
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR----------KGGEDEKLDSLKWNPLSQP  199 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~----------~~~~~d~l~~lv~dEAd~m  199 (284)
                      ||++|+.|++..++.+....++++++++|+. ...+...+..++++++.+.          ....+.++..+|+|||+++
T Consensus       304 Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~  383 (797)
T 4a2q_A          304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNT  383 (797)
T ss_dssp             SSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGC
T ss_pred             CCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECcccc
Confidence            9999999999999999988899998888875 3344566667888877651          1125677899999999998


Q ss_pred             cccccccc
Q 042526          200 KTTTLLPS  207 (284)
Q Consensus       200 ~~~gflp~  207 (284)
                      ...+.+..
T Consensus       384 ~~~~~~~~  391 (797)
T 4a2q_A          384 TGNHPYNV  391 (797)
T ss_dssp             STTSHHHH
T ss_pred             CCCccHHH
Confidence            87654333

>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=99.73  E-value=3.3e-18  Score=146.13  Aligned_cols=140  Identities=14%  Similarity=0.036  Sum_probs=99.9

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .....|+|+|.++++.+ +.|+++++.+|||||||++|++|++..+.....                 ...+.++||++|
T Consensus        29 ~~~~~l~~~Q~~~i~~~-~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~-----------------~~~~~~~lil~p   90 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPA-LEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK-----------------ASEPGKVIVLVN   90 (216)
T ss_dssp             SCCCCCCHHHHHHHHHH-HTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH-----------------TTCCCCEEEEES
T ss_pred             cCCCCchHHHHHHHHHH-hcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc-----------------ccCCCcEEEEEC
Confidence            45568999999999998 889999999999999999999999987755421                 123568999999


Q ss_pred             CHHHHHH-HHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc--------c-------CCccccccccCCC
Q 042526          132 TRELALQ-VLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR--------K-------GGEDEKLDSLKWN  194 (284)
Q Consensus       132 TReLa~Q-i~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~--------~-------~~~~d~l~~lv~d  194 (284)
                      |++|+.| +...+..+... ++.+..+.|+. ...+...+...+++++.+.        .       ...+..+..+|+|
T Consensus        91 ~~~L~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiD  169 (216)
T 3b6e_A           91 KVLLVEQLFRKEFQPFLKK-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIID  169 (216)
T ss_dssp             SHHHHHHHHHHTHHHHHTT-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEET
T ss_pred             HHHHHHHHHHHHHHHHhcc-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEE
Confidence            9999999 78888888765 67777777763 3333334445667765541        0       1346788899999


Q ss_pred             CCCcccccccccchhh
Q 042526          195 PLSQPKTTTLLPSSLA  210 (284)
Q Consensus       195 EAd~m~~~gflp~~~~  210 (284)
                      ||+++...+|+..++.
T Consensus       170 Eah~~~~~~~~~~~~~  185 (216)
T 3b6e_A          170 ECHHTNKEAVYNNIMR  185 (216)
T ss_dssp             TC-------CHHHHHH
T ss_pred             CchhhccCCcHHHHHH
Confidence            9999988777777653

>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=99.70  E-value=1.5e-17  Score=181.21  Aligned_cols=139  Identities=19%  Similarity=0.139  Sum_probs=112.7

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      |++..+++|...+|..++|+|.+||+.++..+.|++++||||||||++|.+|++..+...                    
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~--------------------  970 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS--------------------  970 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC--------------------
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC--------------------
Confidence            567888999999999999999999999966788999999999999999999999988653                    


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHhh-hhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc--------c---CCccccc
Q 042526          121 KGHLRALIINPTRELALQVLMVASP-SLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--------K---GGEDEKL  188 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~~~~~-l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--------~---~~~~d~l  188 (284)
                       .+.++||++|||+||.|++..+.. |...++++|..++|+....  ......++|++.|.        .   ...+.+|
T Consensus       971 -~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~--~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v 1047 (1724)
T 4f92_B          971 -SEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTD--LKLLGKGNIIISTPEKWDILSRRWKQRKNVQNI 1047 (1724)
T ss_dssp             -TTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHH--HHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSC
T ss_pred             -CCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcc--hhhcCCCCEEEECHHHHHHHHhCccccccccee
Confidence             245799999999999999999975 6667899999988875432  33445677776651        1   1135678


Q ss_pred             cccCCCCCCccccc
Q 042526          189 DSLKWNPLSQPKTT  202 (284)
Q Consensus       189 ~~lv~dEAd~m~~~  202 (284)
                      ..+|+||++++.+.
T Consensus      1048 ~lvViDE~H~l~d~ 1061 (1724)
T 4f92_B         1048 NLFVVDEVHLIGGE 1061 (1724)
T ss_dssp             SEEEECCGGGGGST
T ss_pred             eEEEeechhhcCCC
Confidence            89999999987653

>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=99.69  E-value=5e-17  Score=165.61  Aligned_cols=132  Identities=17%  Similarity=0.115  Sum_probs=106.5

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHHcCC------CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 042526           43 PLLMKSIYKLGFKESTSILKARIPALAHQR------KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAE  116 (284)
Q Consensus        43 ~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G------~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~  116 (284)
                      +.+...+..++| .||++|.+||+.+ +.+      +|++++|+||||||++|++|++..+..                 
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I-~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~-----------------  416 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEI-RNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA-----------------  416 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHH-HHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH-----------------
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHH-HhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc-----------------
Confidence            344455678999 8999999999998 554      699999999999999999999987632                 


Q ss_pred             hcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHH----HHHhcC-CCcccccccC----Ccccc
Q 042526          117 KYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSE----HSNRRK-PNKRKRTRKG----GEDEK  187 (284)
Q Consensus       117 ~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~----~~l~~~-~~i~v~~~~~----~~~d~  187 (284)
                            +.++|||+||++||.|++..+..+....++++++++|+....+.    ..+..+ +++++.+.-.    ..+.+
T Consensus       417 ------g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~  490 (780)
T 1gm5_A          417 ------GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKN  490 (780)
T ss_dssp             ------TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSC
T ss_pred             ------CCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccC
Confidence                  46899999999999999999999998889999999988655432    334444 7777765321    35678


Q ss_pred             ccccCCCCCCcc
Q 042526          188 LDSLKWNPLSQP  199 (284)
Q Consensus       188 l~~lv~dEAd~m  199 (284)
                      +..+|+||++++
T Consensus       491 l~lVVIDEaHr~  502 (780)
T 1gm5_A          491 LGLVIIDEQHRF  502 (780)
T ss_dssp             CCEEEEESCCCC
T ss_pred             CceEEecccchh
Confidence            889999999985

>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=99.68  E-value=2.5e-17  Score=171.07  Aligned_cols=135  Identities=11%  Similarity=-0.022  Sum_probs=103.9

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      -.|+..|+|+|.++|+.+ +.|+|++++++||||||++|++|++..+...                  ....+.++|||+
T Consensus       243 l~~~~~~r~~Q~~ai~~i-l~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~------------------~~~~~~~vLvl~  303 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPA-INGKNALICAPTGSGKTFVSILICEHHFQNM------------------PAGRKAKVVFLA  303 (936)
T ss_dssp             -----CCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHTTTTTC------------------CSSCCCCEEEEC
T ss_pred             ccCCCCCCHHHHHHHHHH-HcCCCEEEEeCCCchHHHHHHHHHHHHHHhc------------------cccCCCeEEEEe
Confidence            357889999999999999 8999999999999999999999998765432                  112256799999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc----------cCCccccccccCCCCCCcc
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR----------KGGEDEKLDSLKWNPLSQP  199 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~----------~~~~~d~l~~lv~dEAd~m  199 (284)
                      ||++|+.|++..++.+....++++.+++|+. ...+...+..++++++.+.          ....+..+..+|+|||+++
T Consensus       304 Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~  383 (936)
T 4a2w_A          304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNT  383 (936)
T ss_dssp             SSHHHHHHHHHHHHHHHHTTTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGC
T ss_pred             CCHHHHHHHHHHHHHHhcccCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECcccc
Confidence            9999999999999999998899998888875 3344555666788877651          1124677889999999998


Q ss_pred             ccccc
Q 042526          200 KTTTL  204 (284)
Q Consensus       200 ~~~gf  204 (284)
                      ...+.
T Consensus       384 ~~~~~  388 (936)
T 4a2w_A          384 TGNHP  388 (936)
T ss_dssp             STTCH
T ss_pred             CCCcc
Confidence            87653

>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=99.62  E-value=9.1e-18  Score=167.33  Aligned_cols=142  Identities=11%  Similarity=0.059  Sum_probs=95.2

Q ss_pred             ccc-CCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 042526           36 WNE-LRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEE  114 (284)
Q Consensus        36 F~~-l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~  114 (284)
                      |.. +++++.++++|... +..|+|+|+++||.+ +.|+|++++||||||||++|++|+++.+..               
T Consensus       151 ~~~~l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l-~~g~dvlv~a~TGSGKT~~~~lpil~~l~~---------------  213 (618)
T 2whx_A          151 GNGVVTKSGDYVSAITQA-ERIGEPDYEVDEDIF-RKKRLTIMDLHPGAGKTKRILPSIVREALK---------------  213 (618)
T ss_dssp             CC---------CEECBCC-CCCCCCCCCCCGGGG-STTCEEEECCCTTSSTTTTHHHHHHHHHHH---------------
T ss_pred             ccccccchHHHHHHHhhc-cccCCCccccCHHHH-hcCCeEEEEcCCCCCHHHHHHHHHHHHHHh---------------
Confidence            444 66788877777654 589999999999988 999999999999999999999999998754               


Q ss_pred             hhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccc---cc-------ccCCc
Q 042526          115 AEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRK---RT-------RKGGE  184 (284)
Q Consensus       115 ~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v---~~-------~~~~~  184 (284)
                             .++++|||+|||+||.|++..+..      ..+. +.+....     ....+...+   ..       .....
T Consensus       214 -------~~~~vLvl~PtreLa~Qi~~~l~~------~~v~-~~~~~l~-----~~~tp~~~i~~~t~~~l~~~l~~~~~  274 (618)
T 2whx_A          214 -------RRLRTLILAPTRVVAAEMEEALRG------LPIR-YQTPAVK-----SDHTGREIVDLMCHATFTTRLLSSTR  274 (618)
T ss_dssp             -------TTCCEEEEESSHHHHHHHHHHTTT------SCEE-ECCTTSS-----CCCCSSSCEEEEEHHHHHHHHHHCSS
T ss_pred             -------CCCeEEEEcChHHHHHHHHHHhcC------Ccee-Eecccce-----eccCCCceEEEEChHHHHHHHhcccc
Confidence                   257899999999999999998862      2222 1111100     001111111   00       01123


Q ss_pred             cccccccCCCCCCcccccccccchhhhccc
Q 042526          185 DEKLDSLKWNPLSQPKTTTLLPSSLALMNL  214 (284)
Q Consensus       185 ~d~l~~lv~dEAd~m~~~gflp~~~~~~~~  214 (284)
                      ++++..+|+|||++| +++|......++..
T Consensus       275 l~~~~~iViDEah~~-~~~~~~~~~~i~~~  303 (618)
T 2whx_A          275 VPNYNLIVMDEAHFT-DPCSVAARGYISTR  303 (618)
T ss_dssp             CCCCSEEEEESTTCC-SHHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCC-CccHHHHHHHHHHH
Confidence            788999999999999 77777666554443

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

Probab=99.62  E-value=1.1e-15  Score=159.76  Aligned_cols=136  Identities=13%  Similarity=0.102  Sum_probs=105.6

Q ss_pred             HcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEe
Q 042526           51 KLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN  130 (284)
Q Consensus        51 ~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~  130 (284)
                      .++|+ |+|+|.++|+.+ +.|+|++++||||||||++|++|++..+.                       .+.++||++
T Consensus        35 ~~~f~-l~~~Q~~aI~~i-l~g~~vlv~apTGsGKTlv~~~~i~~~~~-----------------------~g~~vlvl~   89 (997)
T 4a4z_A           35 SWPFE-LDTFQKEAVYHL-EQGDSVFVAAHTSAGKTVVAEYAIAMAHR-----------------------NMTKTIYTS   89 (997)
T ss_dssp             CCSSC-CCHHHHHHHHHH-HTTCEEEEECCTTSCSHHHHHHHHHHHHH-----------------------TTCEEEEEE
T ss_pred             hCCCC-CCHHHHHHHHHH-HcCCCEEEEECCCCcHHHHHHHHHHHHHh-----------------------cCCeEEEEe
Confidence            46776 899999999999 89999999999999999999999876431                       256899999


Q ss_pred             cCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc---------ccCCccccccccCCCCCCcccc
Q 042526          131 PTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT---------RKGGEDEKLDSLKWNPLSQPKT  201 (284)
Q Consensus       131 PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~---------~~~~~~d~l~~lv~dEAd~m~~  201 (284)
                      ||++|+.|++..+..+..  ++.+.+++|+....      ...++++.+         .....+.++..+|+|||+.+.+
T Consensus        90 PtraLa~Q~~~~l~~~~~--~~~v~~l~G~~~~~------~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d  161 (997)
T 4a4z_A           90 PIKALSNQKFRDFKETFD--DVNIGLITGDVQIN------PDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVND  161 (997)
T ss_dssp             SCGGGHHHHHHHHHTTC----CCEEEECSSCEEC------TTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCT
T ss_pred             CCHHHHHHHHHHHHHHcC--CCeEEEEeCCCccC------CCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccc
Confidence            999999999999988643  67788888875432      234555544         1223567899999999999999


Q ss_pred             cccccchhhhcccCCCCC
Q 042526          202 TTLLPSSLALMNLTEGKP  219 (284)
Q Consensus       202 ~gflp~~~~~~~~~~r~~  219 (284)
                      .+|-+....++...+...
T Consensus       162 ~~~g~~~e~ii~~l~~~v  179 (997)
T 4a4z_A          162 QDRGVVWEEVIIMLPQHV  179 (997)
T ss_dssp             TCTTCCHHHHHHHSCTTC
T ss_pred             cchHHHHHHHHHhcccCC
Confidence            988887766655554433

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.62  E-value=4.2e-16  Score=156.03  Aligned_cols=134  Identities=14%  Similarity=0.054  Sum_probs=103.5

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+|+|.++|+.+ +.|+|+++++|||||||++|++|++..+.....                 ...+.++|||+||++|
T Consensus         7 ~l~~~Q~~~i~~i-l~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~-----------------~~~~~~vlvl~P~~~L   68 (699)
T 4gl2_A            7 QLRPYQMEVAQPA-LEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK-----------------ASEPGKVIVLVNKVLL   68 (699)
T ss_dssp             CCCHHHHHHHHHH-HSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH-----------------HTCCCCBCCEESCSHH
T ss_pred             CccHHHHHHHHHH-HhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc-----------------cCCCCeEEEEECCHHH
Confidence            5999999999999 889999999999999999999999998876531                 1123579999999999


Q ss_pred             HHHH-HHHHhhhhcCCCceeEEEeCCC-cchHHHHHhcCCCcccccc---------------cCCccccccccCCCCCCc
Q 042526          136 ALQV-LMVASPSLKSNSLTLAMAAGSP-LLTSEHSNRRKPNKRKRTR---------------KGGEDEKLDSLKWNPLSQ  198 (284)
Q Consensus       136 a~Qi-~~~~~~l~~~~~i~v~~~~G~~-~~~q~~~l~~~~~i~v~~~---------------~~~~~d~l~~lv~dEAd~  198 (284)
                      +.|+ +..++.+... ++.+..+.|+. ...+...+....++++.+.               ....+..+..+|+|||++
T Consensus        69 ~~Q~~~~~l~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~  147 (699)
T 4gl2_A           69 VEQLFRKEFQPFLKK-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHH  147 (699)
T ss_dssp             HHHHHHHTHHHHHTT-TSCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGG
T ss_pred             HHHHHHHHHHHHcCc-CceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccc
Confidence            9999 9999998875 47787777774 4444456667788866551               113567888999999999


Q ss_pred             ccccccccch
Q 042526          199 PKTTTLLPSS  208 (284)
Q Consensus       199 m~~~gflp~~  208 (284)
                      +...+++...
T Consensus       148 ~~~~~~~~~i  157 (699)
T 4gl2_A          148 TNKEAVYNNI  157 (699)
T ss_dssp             CBTTBSSCSH
T ss_pred             cCccchHHHH
Confidence            8665555544

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

Probab=99.62  E-value=3.6e-16  Score=163.44  Aligned_cols=125  Identities=13%  Similarity=0.102  Sum_probs=99.3

Q ss_pred             HHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEE
Q 042526           49 IYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALI  128 (284)
Q Consensus        49 L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLI  128 (284)
                      ...++|. |+|+|.+||+.+ ..|++++++||||||||++|++|++..+.                       .+.++||
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l-~~g~~vLV~apTGSGKTlva~lai~~~l~-----------------------~g~rvL~  134 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCI-DRGESVLVSAHTSAGKTVVAEYAIAQSLK-----------------------NKQRVIY  134 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHH-HHTCEEEEECCTTSCHHHHHHHHHHHHHH-----------------------TTCEEEE
T ss_pred             HHhCCCC-CCHHHHHHHHHH-HcCCCEEEECCCCCChHHHHHHHHHHHhc-----------------------cCCeEEE
Confidence            4457886 999999999998 89999999999999999999999987652                       2568999


Q ss_pred             EecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCccccccccCCCCCCcc
Q 042526          129 INPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGEDEKLDSLKWNPLSQP  199 (284)
Q Consensus       129 L~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~d~l~~lv~dEAd~m  199 (284)
                      ++||++||.|++..+..+..    .+.+++|+....      ...++++.+.         ....+.++..+|+|||+.|
T Consensus       135 l~PtkaLa~Q~~~~l~~~~~----~vglltGd~~~~------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l  204 (1010)
T 2xgj_A          135 TSPIKALSNQKYRELLAEFG----DVGLMTGDITIN------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYM  204 (1010)
T ss_dssp             EESSHHHHHHHHHHHHHHHS----CEEEECSSCEEC------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGG
T ss_pred             ECChHHHHHHHHHHHHHHhC----CEEEEeCCCccC------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhh
Confidence            99999999999999998765    567777775432      2345655441         2245778999999999999


Q ss_pred             cccccccch
Q 042526          200 KTTTLLPSS  208 (284)
Q Consensus       200 ~~~gflp~~  208 (284)
                      .+.++-...
T Consensus       205 ~d~~rg~~~  213 (1010)
T 2xgj_A          205 RDKERGVVW  213 (1010)
T ss_dssp             GCTTTHHHH
T ss_pred             cccchhHHH
Confidence            887654433

>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=99.61  E-value=5.7e-16  Score=168.93  Aligned_cols=133  Identities=18%  Similarity=0.187  Sum_probs=103.8

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           53 GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      ||+.++++|++++|.++.++.|++++||||||||++|.+|++..+.+...            ........+.++||++||
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~------------~~~~~~~~~~k~lyiaP~  143 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHIN------------MDGTINVDDFKIIYIAPM  143 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCC------------TTSSCCTTSCEEEEECSS
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhcc------------ccccccCCCCEEEEECCH
Confidence            89999999999999986789999999999999999999999998865310            001223457799999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc--------cCC---ccccccccCCCCCCcc
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR--------KGG---EDEKLDSLKWNPLSQP  199 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~--------~~~---~~d~l~~lv~dEAd~m  199 (284)
                      |+||.|++..+.......|++|..++|+.....  .....++|++.|.        ...   .++.|..+|+||+-++
T Consensus       144 kALa~e~~~~l~~~~~~~gi~V~~~tGd~~~~~--~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l  219 (1724)
T 4f92_B          144 RSLVQEMVGSFGKRLATYGITVAELTGDHQLCK--EEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLL  219 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTTTCCEEECCSSCSSCC--TTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGG
T ss_pred             HHHHHHHHHHHHHHHhhCCCEEEEEECCCCCCc--cccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhc
Confidence            999999999999988889999999988754332  2234577776651        111   2567888999998543

>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=99.58  E-value=1.5e-16  Score=139.57  Aligned_cols=137  Identities=13%  Similarity=0.042  Sum_probs=94.3

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           53 GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      ....++++|.++|+.+ ..|++++++|+||||||++|.++++..+....                  ....+++|+++||
T Consensus        58 ~~~p~~~~q~~~i~~i-~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~------------------~~~~~~~l~~~p~  118 (235)
T 3llm_A           58 ELLPVKKFESEILEAI-SQNSVVIIRGATGCGKTTQVPQFILDDFIQND------------------RAAECNIVVTQPR  118 (235)
T ss_dssp             HTSGGGGGHHHHHHHH-HHCSEEEEECCTTSSHHHHHHHHHHHHHHHTT------------------CGGGCEEEEEESS
T ss_pred             hcCChHHHHHHHHHHH-hcCCEEEEEeCCCCCcHHhHHHHHhcchhhcC------------------CCCceEEEEeccc
Confidence            3445799999999999 99999999999999999999999988665431                  1235689999999


Q ss_pred             HHHHHHHHHHHhhhhc-CCCceeEEEeCCCcchHHHHHhcCCCcccccc------cCCccccccccCCCCCCcc-ccccc
Q 042526          133 RELALQVLMVASPSLK-SNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR------KGGEDEKLDSLKWNPLSQP-KTTTL  204 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~-~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~------~~~~~d~l~~lv~dEAd~m-~~~gf  204 (284)
                      |+||.|++..+..... ..+..+.......    .......+++++.+.      ....++.+..+|+||||.| .+++|
T Consensus       119 ~~la~q~~~~~~~~~~~~~~~~~g~~~~~~----~~~~~~~~~Ivv~Tpg~l~~~l~~~l~~~~~lVlDEah~~~~~~~~  194 (235)
T 3llm_A          119 RISAVSVAERVAFERGEEPGKSCGYSVRFE----SILPRPHASIMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTDF  194 (235)
T ss_dssp             HHHHHHHHHHHHHTTTCCTTSSEEEEETTE----EECCCSSSEEEEEEHHHHHHHHHHCCTTCCEEEECCTTSCCHHHHH
T ss_pred             hHHHHHHHHHHHHHhccccCceEEEeechh----hccCCCCCeEEEECHHHHHHHHHhhhcCCcEEEEECCccCCcchHH
Confidence            9999999887765433 2333332211111    001112344544441      0013678899999999996 89998


Q ss_pred             ccchhhhc
Q 042526          205 LPSSLALM  212 (284)
Q Consensus       205 lp~~~~~~  212 (284)
                      +...+..+
T Consensus       195 ~~~~l~~i  202 (235)
T 3llm_A          195 LLVVLRDV  202 (235)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            86554443

>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=99.58  E-value=2.5e-16  Score=151.14  Aligned_cols=68  Identities=22%  Similarity=0.241  Sum_probs=60.7

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCcE-EEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           53 GFKESTSILKARIPALAHQRKDV-IGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il~~G~dv-iv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      |+..|+|+|+ +||.+ +.|+|+ +++||||||||++|++|++..+..                      .++++|||+|
T Consensus         1 G~~q~~~iq~-~i~~~-l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~----------------------~~~~~lvl~P   56 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDI-FRKKRLTIMDLHPGAGKTKRILPSIVREALL----------------------RRLRTLILAP   56 (451)
T ss_dssp             CCCCCSCCCC-CCGGG-GSTTCEEEECCCTTSSCCTTHHHHHHHHHHH----------------------TTCCEEEEES
T ss_pred             CCCCCCCcHH-HHHHH-HhcCCeEEEECCCCCCHhhHHHHHHHHHHHh----------------------cCCcEEEECC
Confidence            7899999986 79998 788887 999999999999999999987654                      2578999999


Q ss_pred             CHHHHHHHHHHHh
Q 042526          132 TRELALQVLMVAS  144 (284)
Q Consensus       132 TReLa~Qi~~~~~  144 (284)
                      ||+||.|++..+.
T Consensus        57 tr~La~Q~~~~l~   69 (451)
T 2jlq_A           57 TRVVAAEMEEALR   69 (451)
T ss_dssp             SHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHhc
Confidence            9999999999885

>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=99.57  E-value=3.9e-15  Score=133.71  Aligned_cols=121  Identities=14%  Similarity=-0.033  Sum_probs=92.0

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+|+|.++++.+ +.+.+.+++++||||||++|++++...+..                      ...++|||+||++|
T Consensus       113 ~l~~~Q~~ai~~~-l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~----------------------~~~~~lil~Pt~~L  169 (282)
T 1rif_A          113 EPHWYQKDAVFEG-LVNRRRILNLPTSAGRSLIQALLARYYLEN----------------------YEGKILIIVPTTAL  169 (282)
T ss_dssp             CCCHHHHHHHHHH-HHHSEEEECCCTTSCHHHHHHHHHHHHHHH----------------------CSSEEEEECSSHHH
T ss_pred             CccHHHHHHHHHH-HhcCCeEEEcCCCCCcHHHHHHHHHHHHHc----------------------CCCeEEEEECCHHH
Confidence            7999999999998 677888999999999999998887765432                      13379999999999


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc------cCCccccccccCCCCCCcccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR------KGGEDEKLDSLKWNPLSQPKT  201 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~------~~~~~d~l~~lv~dEAd~m~~  201 (284)
                      +.|+++.+..+.......+..++|+.....  ......++++.+.      ....++++..+|+|||+++..
T Consensus       170 ~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~I~v~T~~~l~~~~~~~~~~~~~vIiDEaH~~~~  239 (282)
T 1rif_A          170 TTQMADDFVDYRLFSHAMIKKIGGGASKDD--KYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATG  239 (282)
T ss_dssp             HHHHHHHHHHHTSCCGGGEEECSTTCSSTT--CCCTTCSEEEECHHHHTTSCGGGGGGEEEEEEETGGGCCH
T ss_pred             HHHHHHHHHHhcccccceEEEEeCCCcchh--hhccCCcEEEEchHHHHhhHHHHHhhCCEEEEECCccCCc
Confidence            999999999987766667777777654332  2223455554441      112467888999999999875

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.55  E-value=1.5e-14  Score=153.05  Aligned_cols=136  Identities=15%  Similarity=0.045  Sum_probs=105.4

Q ss_pred             CCCCHHHHHHHH-HcCCCCCcHHHHHHHHHHHcC----CC--cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           39 LRLHPLLMKSIY-KLGFKESTSILKARIPALAHQ----RK--DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        39 l~L~~~Ll~~L~-~~g~~~pT~iQ~~aip~il~~----G~--dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      +++++.+.+.+. .++|+ |||+|..||+.+ +.    |+  |++++++||||||++|+++++..+.             
T Consensus       586 ~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~i-l~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~-------------  650 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPFE-TTPDQAQAINAV-LSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD-------------  650 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHH-HHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT-------------
T ss_pred             CCCCHHHHHHHHHhCCCC-CCHHHHHHHHHH-HHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH-------------
Confidence            456777777764 47887 799999999998 44    66  9999999999999999999876432             


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHH----HHHhc-CCCcccccc----cC
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSE----HSNRR-KPNKRKRTR----KG  182 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~----~~l~~-~~~i~v~~~----~~  182 (284)
                                .+.++|||+||++||.|++..+..+....++.+.++.|.......    ..+.. .+++++.+.    ..
T Consensus       651 ----------~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~  720 (1151)
T 2eyq_A          651 ----------NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSD  720 (1151)
T ss_dssp             ----------TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSC
T ss_pred             ----------hCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCC
Confidence                      256899999999999999999998877778888888876443332    23444 377776652    22


Q ss_pred             CccccccccCCCCCCcc
Q 042526          183 GEDEKLDSLKWNPLSQP  199 (284)
Q Consensus       183 ~~~d~l~~lv~dEAd~m  199 (284)
                      ..+.++..+|+||++++
T Consensus       721 ~~~~~l~lvIiDEaH~~  737 (1151)
T 2eyq_A          721 VKFKDLGLLIVDEEHRF  737 (1151)
T ss_dssp             CCCSSEEEEEEESGGGS
T ss_pred             ccccccceEEEechHhc
Confidence            34678889999999993

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.55  E-value=8.4e-15  Score=137.62  Aligned_cols=123  Identities=13%  Similarity=0.043  Sum_probs=99.4

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+|+|..+++.+ +.+ ++++.++||+|||++|+++++..+..                      .+.++|||+||++|
T Consensus         9 ~l~~~Q~~~i~~~-~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~----------------------~~~~~liv~P~~~L   64 (494)
T 1wp9_A            9 QPRIYQEVIYAKC-KET-NCLIVLPTGLGKTLIAMMIAEYRLTK----------------------YGGKVLMLAPTKPL   64 (494)
T ss_dssp             CCCHHHHHHHHHG-GGS-CEEEECCTTSCHHHHHHHHHHHHHHH----------------------SCSCEEEECSSHHH
T ss_pred             CccHHHHHHHHHH-hhC-CEEEEcCCCCCHHHHHHHHHHHHHhc----------------------CCCeEEEEECCHHH
Confidence            5999999999998 777 99999999999999999999887651                      35679999999999


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc---------cCCccccccccCCCCCCccccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR---------KGGEDEKLDSLKWNPLSQPKTT  202 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~---------~~~~~d~l~~lv~dEAd~m~~~  202 (284)
                      +.|++..+..+.......+.++.|+........+...+++++.+.         ....+.++..+|+|||..+.+.
T Consensus        65 ~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~  140 (494)
T 1wp9_A           65 VLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN  140 (494)
T ss_dssp             HHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTT
T ss_pred             HHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCC
Confidence            999999999887555568888888876665555555677766551         1234667889999999998754

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.55  E-value=6.4e-15  Score=142.31  Aligned_cols=122  Identities=14%  Similarity=-0.035  Sum_probs=96.7

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..|+|+|..||+.+ +.+++++++++||||||++|++|+...+..                      ...++|||+||++
T Consensus       112 ~~l~~~Q~~ai~~~-~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~----------------------~~~~vlvl~P~~~  168 (510)
T 2oca_A          112 IEPHWYQKDAVFEG-LVNRRRILNLPTSAGRSLIQALLARYYLEN----------------------YEGKILIIVPTTA  168 (510)
T ss_dssp             ECCCHHHHHHHHHH-HHHSEEEEECCSTTTHHHHHHHHHHHHHHH----------------------CSSEEEEEESSHH
T ss_pred             CCCCHHHHHHHHHH-HhcCCcEEEeCCCCCHHHHHHHHHHHHHhC----------------------CCCeEEEEECcHH
Confidence            37999999999998 788999999999999999999988876542                      2348999999999


Q ss_pred             HHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc------cCCccccccccCCCCCCcccc
Q 042526          135 LALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR------KGGEDEKLDSLKWNPLSQPKT  201 (284)
Q Consensus       135 La~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~------~~~~~d~l~~lv~dEAd~m~~  201 (284)
                      |+.|++..+..+....++.+..+.|+......  +....++++.+.      ....+.++..+++||+.++..
T Consensus       169 L~~Q~~~~~~~~~~~~~~~v~~~~~~~~~~~~--~~~~~~I~i~T~~~l~~~~~~~~~~~~liIiDE~H~~~~  239 (510)
T 2oca_A          169 LTTQMADDFVDYRLFSHAMIKKIGGGASKDDK--YKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATG  239 (510)
T ss_dssp             HHHHHHHHHHHTTSSCGGGEEECGGGCCTTGG--GCTTCSEEEEEHHHHTTSCGGGGGGEEEEEEETGGGCCH
T ss_pred             HHHHHHHHHHHhhcCCccceEEEecCCccccc--cccCCcEEEEeHHHHhhchhhhhhcCCEEEEECCcCCCc
Confidence            99999999999877767778777776444322  445567766541      113467788999999999765

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

Probab=99.54  E-value=8.8e-17  Score=161.57  Aligned_cols=127  Identities=13%  Similarity=0.137  Sum_probs=88.0

Q ss_pred             HHHHcCCC-----CCcHHHH-----HHHHHHHc------CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           48 SIYKLGFK-----ESTSILK-----ARIPALAH------QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        48 ~L~~~g~~-----~pT~iQ~-----~aip~il~------~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      +|..+||.     .|||||+     ++||.+ +      .|+|++++|+||||||++|++|+++.+..            
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~-l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~------------  268 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEA-YNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ------------  268 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCC-CCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH------------
T ss_pred             EeeeccccccCCCccCceeeccccccchHHH-hhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh------------
Confidence            56778888     9999999     999998 6      89999999999999999999999987654            


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccc---c-------ccc
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRK---R-------TRK  181 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v---~-------~~~  181 (284)
                                .++++|||+|||+||.|++..+..+.    +.  ...+.. .     ....|..++   .       ...
T Consensus       269 ----------~~~~~lilaPTr~La~Q~~~~l~~~~----i~--~~~~~l-~-----~v~tp~~ll~~l~~~~l~~~l~~  326 (673)
T 2wv9_A          269 ----------KRLRTAVLAPTRVVAAEMAEALRGLP----VR--YLTPAV-Q-----REHSGNEIVDVMCHATLTHRLMS  326 (673)
T ss_dssp             ----------TTCCEEEEESSHHHHHHHHHHTTTSC----CE--ECCC---------CCCCSCCCEEEEEHHHHHHHHHS
T ss_pred             ----------CCCcEEEEccHHHHHHHHHHHHhcCC----ee--eecccc-c-----ccCCHHHHHHHHHhhhhHHHHhc
Confidence                      25789999999999999999987552    11  111100 0     001111110   0       001


Q ss_pred             CCccccccccCCCCCCcc-----cccccccchh
Q 042526          182 GGEDEKLDSLKWNPLSQP-----KTTTLLPSSL  209 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m-----~~~gflp~~~  209 (284)
                      ...+.++..+|+|||+++     ..++|+....
T Consensus       327 ~~~l~~l~lvViDEaH~~~~~~~~~~~~l~~~~  359 (673)
T 2wv9_A          327 PLRVPNYNLFVMDEAHFTDPASIAARGYIATRV  359 (673)
T ss_dssp             SSCCCCCSEEEEESTTCCCHHHHHHHHHHHHHH
T ss_pred             ccccccceEEEEeCCcccCccHHHHHHHHHHhc
Confidence            124678999999999998     5666665543

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.50  E-value=2e-15  Score=150.90  Aligned_cols=129  Identities=14%  Similarity=0.103  Sum_probs=95.3

Q ss_pred             CcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHH
Q 042526           57 STSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELA  136 (284)
Q Consensus        57 pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa  136 (284)
                      |...|+.+|+.++..++|++++||||||||++|++|+++                          .+.++|||+|||+||
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~--------------------------~g~~vLVl~PTReLA  270 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA--------------------------QGYKVLVLNPSVAAT  270 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH--------------------------TTCCEEEEESCHHHH
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH--------------------------CCCeEEEEcchHHHH
Confidence            444455555555478999999999999999999999874                          145799999999999


Q ss_pred             HHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc------ccCCccccccccCCCCCCcccccccccchhh
Q 042526          137 LQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT------RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLA  210 (284)
Q Consensus       137 ~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~------~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~  210 (284)
                      .|++..+...   ++..+...+|+..      +..+.++++.+      .....+.++..+|+||| +|++++|.++...
T Consensus       271 ~Qia~~l~~~---~g~~vg~~vG~~~------~~~~~~IlV~TPGrLl~~~~l~l~~l~~lVlDEA-H~l~~~~~~~l~~  340 (666)
T 3o8b_A          271 LGFGAYMSKA---HGIDPNIRTGVRT------ITTGAPVTYSTYGKFLADGGCSGGAYDIIICDEC-HSTDSTTILGIGT  340 (666)
T ss_dssp             HHHHHHHHHH---HSCCCEEECSSCE------ECCCCSEEEEEHHHHHHTTSCCTTSCSEEEETTT-TCCSHHHHHHHHH
T ss_pred             HHHHHHHHHH---hCCCeeEEECcEe------ccCCCCEEEECcHHHHhCCCcccCcccEEEEccc-hhcCccHHHHHHH
Confidence            9998866543   3455666666643      34456665543      23345667999999999 9999999888877


Q ss_pred             hcccCCCCCCC
Q 042526          211 LMNLTEGKPGK  221 (284)
Q Consensus       211 ~~~~~~r~~~~  221 (284)
                      ++...+..++.
T Consensus       341 Il~~l~~~~~~  351 (666)
T 3o8b_A          341 VLDQAETAGAR  351 (666)
T ss_dssp             HHHHTTTTTCS
T ss_pred             HHHhhhhcCCc
Confidence            77777666653

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.48  E-value=7.3e-14  Score=137.21  Aligned_cols=81  Identities=16%  Similarity=0.049  Sum_probs=70.6

Q ss_pred             CCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEE
Q 042526           53 GFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALII  129 (284)
Q Consensus        53 g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL  129 (284)
                      || .|.|.|..++..+   +..|+|++++||||||||++|++|++.    .                      ++++||+
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~----~----------------------~~~v~i~   53 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE----V----------------------KPKVLFV   53 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH----H----------------------CSEEEEE
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh----C----------------------CCeEEEE
Confidence            45 5899999977654   368999999999999999999999987    1                      4689999


Q ss_pred             ecCHHHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          130 NPTRELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       130 ~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      +||++|+.|+.+++..+....+++++++.|.
T Consensus        54 ~pt~~l~~q~~~~~~~l~~~~~~~~~~l~gr   84 (551)
T 3crv_A           54 VRTHNEFYPIYRDLTKIREKRNITFSFLVGK   84 (551)
T ss_dssp             ESSGGGHHHHHHHHTTCCCSSCCCEEECCCH
T ss_pred             cCCHHHHHHHHHHHHHHhhhcCccEEEEccc
Confidence            9999999999999999988888888887774

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.46  E-value=1.1e-13  Score=132.41  Aligned_cols=124  Identities=14%  Similarity=0.013  Sum_probs=95.1

Q ss_pred             HHHHHHHHHcCCC------------------CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHH
Q 042526           43 PLLMKSIYKLGFK------------------ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKA  104 (284)
Q Consensus        43 ~~Ll~~L~~~g~~------------------~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~  104 (284)
                      ..+++.|...|+.                  .|+|+|.++++.+ +.+++++++++||+|||++|++++...        
T Consensus        62 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Q~~ai~~i-~~~~~~ll~~~TGsGKT~~~l~~i~~~--------  132 (472)
T 2fwr_A           62 RDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERW-LVDKRGCIVLPTGSGKTHVAMAAINEL--------  132 (472)
T ss_dssp             HHHHHHHHHTTCCEEEESCCCCCCCCCCCCCCBCHHHHHHHHHH-TTTTEEEEECCTTSCHHHHHHHHHHHH--------
T ss_pred             HHHHHHHHHcCCCcccccccccCcccccCCCCcCHHHHHHHHHH-HhcCCEEEEeCCCCCHHHHHHHHHHHc--------
Confidence            4567777766653                  5899999999998 888899999999999999999987642        


Q ss_pred             HHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCce-eEEEeCCCcchHHHHHhcCCCcccccc---
Q 042526          105 AKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLT-LAMAAGSPLLTSEHSNRRKPNKRKRTR---  180 (284)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~-v~~~~G~~~~~q~~~l~~~~~i~v~~~---  180 (284)
                                        +.++||||||++|+.|++..+..|    ++. +.+++|+...        ..++++.+.   
T Consensus       133 ------------------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v~~~~g~~~~--------~~~Ivv~T~~~l  182 (472)
T 2fwr_A          133 ------------------STPTLIVVPTLALAEQWKERLGIF----GEEYVGEFSGRIKE--------LKPLTVSTYDSA  182 (472)
T ss_dssp             ------------------CSCEEEEESSHHHHHHHHHHGGGG----CGGGEEEBSSSCBC--------CCSEEEEEHHHH
T ss_pred             ------------------CCCEEEEECCHHHHHHHHHHHHhC----CCcceEEECCCcCC--------cCCEEEEEcHHH
Confidence                              346999999999999999999884    677 7787776533        345555442   


Q ss_pred             --cCCc-cccccccCCCCCCcccccccc
Q 042526          181 --KGGE-DEKLDSLKWNPLSQPKTTTLL  205 (284)
Q Consensus       181 --~~~~-~d~l~~lv~dEAd~m~~~gfl  205 (284)
                        .... .+++..+++|||..+.+.+|-
T Consensus       183 ~~~~~~~~~~~~liIvDEaH~~~~~~~~  210 (472)
T 2fwr_A          183 YVNAEKLGNRFMLLIFDEVHHLPAESYV  210 (472)
T ss_dssp             HHTHHHHTTTCSEEEEETGGGTTSTTTH
T ss_pred             HHHHHHhcCCCCEEEEECCcCCCChHHH
Confidence              1111 145788999999998776653

>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=99.44  E-value=1.2e-13  Score=140.86  Aligned_cols=149  Identities=13%  Similarity=0.140  Sum_probs=100.9

Q ss_pred             CccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHh
Q 042526           30 STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLE  109 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~  109 (284)
                      +.++.+|.++++++.+++.|...+ ..|+++|+.+|+.++..|.+++++||||||||+  ++|++.  ....        
T Consensus        68 ~~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll--~~~~--------  134 (773)
T 2xau_A           68 DGKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFV--LFDE--------  134 (773)
T ss_dssp             HSSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHH--HHHH--------
T ss_pred             cCCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHH--HHhc--------
Confidence            456788999999999999999988 789999999999996778899999999999998  677772  2211        


Q ss_pred             hhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc--------cc
Q 042526          110 EKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT--------RK  181 (284)
Q Consensus       110 ~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~--------~~  181 (284)
                              .....+.+++|++|||+||.|++..+...   +++.+...+|...... .......++++.+        ..
T Consensus       135 --------~~~~~g~~ilvl~P~r~La~q~~~~l~~~---~~~~v~~~vG~~i~~~-~~~~~~~~I~v~T~G~l~r~l~~  202 (773)
T 2xau_A          135 --------MPHLENTQVACTQPRRVAAMSVAQRVAEE---MDVKLGEEVGYSIRFE-NKTSNKTILKYMTDGMLLREAME  202 (773)
T ss_dssp             --------CGGGGTCEEEEEESCHHHHHHHHHHHHHH---TTCCBTTTEEEEETTE-EECCTTCSEEEEEHHHHHHHHHH
T ss_pred             --------cccCCCceEEecCchHHHHHHHHHHHHHH---hCCchhheecceeccc-cccCCCCCEEEECHHHHHHHHhh
Confidence                    00112568999999999999998765433   2332221122110000 0011233443322        11


Q ss_pred             CCccccccccCCCCCCc-ccccc
Q 042526          182 GGEDEKLDSLKWNPLSQ-PKTTT  203 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~-m~~~g  203 (284)
                      ...+.++..+++|||+. +++..
T Consensus       203 ~~~l~~~~~lIlDEah~R~ld~d  225 (773)
T 2xau_A          203 DHDLSRYSCIILDEAHERTLATD  225 (773)
T ss_dssp             STTCTTEEEEEECSGGGCCHHHH
T ss_pred             CccccCCCEEEecCccccccchH
Confidence            23477889999999995 77744

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.42  E-value=4.4e-14  Score=135.84  Aligned_cols=119  Identities=13%  Similarity=0.135  Sum_probs=74.2

Q ss_pred             CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           53 GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      |+..+..+|    |.++..|++++++||||||||++|++|+++.+..                      .++++|||+||
T Consensus         6 g~~q~~~~~----~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~----------------------~~~~~lvl~Pt   59 (459)
T 2z83_A            6 GGQQMGRGS----PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ----------------------QRLRTAVLAPT   59 (459)
T ss_dssp             -------------CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH----------------------TTCCEEEEECS
T ss_pred             cHHHHHHHH----HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh----------------------CCCcEEEECch
Confidence            444444444    4444889999999999999999999999988754                      25789999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcc---ccc-------ccCCccccccccCCCCCCc----
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKR---KRT-------RKGGEDEKLDSLKWNPLSQ----  198 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~---v~~-------~~~~~~d~l~~lv~dEAd~----  198 (284)
                      |+||.|++..+..      +.+....+.....      ..+...   +..       .....+.++..+|+|||+.    
T Consensus        60 r~La~Q~~~~l~g------~~v~~~~~~~~~~------~t~~~~i~~~~~~~l~~~l~~~~~l~~~~~iViDEaH~~~~~  127 (459)
T 2z83_A           60 RVVAAEMAEALRG------LPVRYQTSAVQRE------HQGNEIVDVMCHATLTHRLMSPNRVPNYNLFVMDEAHFTDPA  127 (459)
T ss_dssp             HHHHHHHHHHTTT------SCEEECC--------------CCCSEEEEEHHHHHHHHHSCC-CCCCSEEEESSTTCCSHH
T ss_pred             HHHHHHHHHHhcC------ceEeEEecccccC------CCCCcEEEEEchHHHHHHhhccccccCCcEEEEECCccCCch
Confidence            9999999999872      2222111111000      011111   110       1112467899999999999    


Q ss_pred             -ccccccccchh
Q 042526          199 -PKTTTLLPSSL  209 (284)
Q Consensus       199 -m~~~gflp~~~  209 (284)
                       +..++|+....
T Consensus       128 ~~~~~~~~~~~~  139 (459)
T 2z83_A          128 SIAARGYIATKV  139 (459)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHh
Confidence             77788776553

>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=99.40  E-value=1.3e-12  Score=114.90  Aligned_cols=110  Identities=15%  Similarity=-0.017  Sum_probs=83.1

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+++|..++..+ +.+++++++++||+|||++++.++...                          +.++||++||++|
T Consensus        93 ~l~~~Q~~ai~~~-~~~~~~ll~~~tG~GKT~~a~~~~~~~--------------------------~~~~liv~P~~~L  145 (237)
T 2fz4_A           93 SLRDYQEKALERW-LVDKRGCIVLPTGSGKTHVAMAAINEL--------------------------STPTLIVVPTLAL  145 (237)
T ss_dssp             CCCHHHHHHHHHH-TTTSEEEEEESSSTTHHHHHHHHHHHS--------------------------CSCEEEEESSHHH
T ss_pred             CcCHHHHHHHHHH-HhCCCEEEEeCCCCCHHHHHHHHHHHc--------------------------CCCEEEEeCCHHH
Confidence            6899999999998 888899999999999999998776431                          3469999999999


Q ss_pred             HHHHHHHHhhhhcCCCce-eEEEeCCCcchHHHHHhcCCCcccccccC------CccccccccCCCCCCccccccc
Q 042526          136 ALQVLMVASPSLKSNSLT-LAMAAGSPLLTSEHSNRRKPNKRKRTRKG------GEDEKLDSLKWNPLSQPKTTTL  204 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~-v~~~~G~~~~~q~~~l~~~~~i~v~~~~~------~~~d~l~~lv~dEAd~m~~~gf  204 (284)
                      +.|++..+..|    ++. +..+.|+...        ..++++.+.-.      ...+++..+++|||..+.+.+|
T Consensus       146 ~~q~~~~~~~~----~~~~v~~~~g~~~~--------~~~i~v~T~~~l~~~~~~~~~~~~llIiDEaH~l~~~~~  209 (237)
T 2fz4_A          146 AEQWKERLGIF----GEEYVGEFSGRIKE--------LKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESY  209 (237)
T ss_dssp             HHHHHHHHGGG----CGGGEEEESSSCBC--------CCSEEEEEHHHHHHTHHHHTTTCSEEEEECSSCCCTTTH
T ss_pred             HHHHHHHHHhC----CCCeEEEEeCCCCC--------cCCEEEEeHHHHHhhHHHhcccCCEEEEECCccCCChHH
Confidence            99999999884    566 7777776532        33444433100      0113577899999999876554

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.38  E-value=3.1e-14  Score=136.19  Aligned_cols=105  Identities=12%  Similarity=0.069  Sum_probs=72.0

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS  149 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~  149 (284)
                      +.|+|++++||||||||++|++|+++.+..                      .++++|||+|||+||.|++..+..+.  
T Consensus         6 ~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~----------------------~~~~~lil~Ptr~La~Q~~~~l~~~~--   61 (440)
T 1yks_A            6 KKGMTTVLDFHPGAGKTRRFLPQILAECAR----------------------RRLRTLVLAPTRVVLSEMKEAFHGLD--   61 (440)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHH----------------------TTCCEEEEESSHHHHHHHHHHTTTSC--
T ss_pred             hCCCCEEEEcCCCCCHHHHHHHHHHHHHHh----------------------cCCeEEEEcchHHHHHHHHHHHhcCC--
Confidence            789999999999999999999999987754                      25789999999999999999987542  


Q ss_pred             CCceeEEEeCCCcchHHHHHhcCCCccc----------ccccCCccccccccCCCCCCcc-----cccccccch
Q 042526          150 NSLTLAMAAGSPLLTSEHSNRRKPNKRK----------RTRKGGEDEKLDSLKWNPLSQP-----KTTTLLPSS  208 (284)
Q Consensus       150 ~~i~v~~~~G~~~~~q~~~l~~~~~i~v----------~~~~~~~~d~l~~lv~dEAd~m-----~~~gflp~~  208 (284)
                          +...++. ..     ....|..++          .......+.++..+|+|||++|     ..++|+...
T Consensus        62 ----v~~~~~~-~~-----~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~~~~~~~~~~~~~~~  125 (440)
T 1yks_A           62 ----VKFHTQA-FS-----AHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHR  125 (440)
T ss_dssp             ----EEEESSC-CC-----CCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHH
T ss_pred             ----eEEeccc-ce-----eccCCccceeeecccchhHhhhCcccccCccEEEEECccccCcchHHHHHHHHHH
Confidence                2211111 00     001111111          0011123678899999999999     555555443

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

Probab=99.31  E-value=9.2e-13  Score=132.37  Aligned_cols=137  Identities=14%  Similarity=0.080  Sum_probs=90.1

Q ss_pred             CHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCC
Q 042526           42 HPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPK  121 (284)
Q Consensus        42 ~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~  121 (284)
                      ....++++.++++  |.  |.+..... +.|++++++||||||||+    ++++.+...                     
T Consensus       130 ~~d~l~~i~dl~~--p~--~~~p~ar~-l~rk~vlv~apTGSGKT~----~al~~l~~~---------------------  179 (677)
T 3rc3_A          130 CKDDLRKISDLRI--PP--NWYPDARA-MQRKIIFHSGPTNSGKTY----HAIQKYFSA---------------------  179 (677)
T ss_dssp             CHHHHHHHTBCCC--GG--GGCHHHHT-SCCEEEEEECCTTSSHHH----HHHHHHHHS---------------------
T ss_pred             CHHHHHHHhhccC--hh--hhCHHHHh-cCCCEEEEEcCCCCCHHH----HHHHHHHhc---------------------
Confidence            3444555544433  33  33333444 789999999999999997    555554432                     


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCcccccc-cCCccccccccCCCCCCccc
Q 042526          122 GHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTR-KGGEDEKLDSLKWNPLSQPK  200 (284)
Q Consensus       122 ~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~-~~~~~d~l~~lv~dEAd~m~  200 (284)
                        ..++|++|||+||.|++..+..+    ++.+.+++|+....- ..-.+..++++.+. ..+....+..+|+|||++|.
T Consensus       180 --~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv-~TpGr~~~il~~T~e~~~l~~~v~lvVIDEaH~l~  252 (677)
T 3rc3_A          180 --KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTV-QPNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIR  252 (677)
T ss_dssp             --SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECC-STTCCCCSEEEEEGGGCCSSSCEEEEEECSGGGGG
T ss_pred             --CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEe-cCCCcccceeEecHhHhhhcccCCEEEEecceecC
Confidence              23599999999999999998875    677888888754410 00001123333332 34445677999999999999


Q ss_pred             ccccccchhhhcccC
Q 042526          201 TTTLLPSSLALMNLT  215 (284)
Q Consensus       201 ~~gflp~~~~~~~~~  215 (284)
                      +.+|......++...
T Consensus       253 d~~~g~~~~~~l~~l  267 (677)
T 3rc3_A          253 DPARGWAWTRALLGL  267 (677)
T ss_dssp             CTTTHHHHHHHHHHC
T ss_pred             CccchHHHHHHHHcc
Confidence            988877665554444

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.30  E-value=4.8e-12  Score=126.10  Aligned_cols=83  Identities=23%  Similarity=0.112  Sum_probs=70.5

Q ss_pred             CCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      .|.|.|.+.+..+   +..|+++++.||||||||+||++|++..+...                      +.+++|++||
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~----------------------~~kvli~t~T   60 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER----------------------KLKVLYLVRT   60 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH----------------------TCEEEEEESS
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc----------------------CCeEEEECCC
Confidence            4889998887543   27899999999999999999999999987542                      4689999999


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      ++|+.|+.+.+..+....++++++++|+
T Consensus        61 ~~l~~Qi~~el~~l~~~~~~~~~~l~gr   88 (620)
T 4a15_A           61 NSQEEQVIKELRSLSSTMKIRAIPMQGR   88 (620)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCEEECCCH
T ss_pred             HHHHHHHHHHHHHHhhccCeEEEEEECC
Confidence            9999999999999988778888777775

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

Probab=99.27  E-value=2.4e-12  Score=122.68  Aligned_cols=96  Identities=15%  Similarity=0.101  Sum_probs=64.6

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN  150 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~  150 (284)
                      .|+|++++||||||||++|++|+++.+..                      .++++|||+|||+||.|++..+.      
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~----------------------~g~~~lvl~Pt~~La~Q~~~~~~------   52 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK----------------------KRLRTVILAPTRVVASEMYEALR------   52 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH----------------------TTCCEEEEESSHHHHHHHHHHTT------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh----------------------CCCCEEEECcHHHHHHHHHHHhC------
Confidence            37899999999999999999999977654                      25789999999999999998876      


Q ss_pred             CceeEEEeCCCcchHHHHHhcCCCcc-ccc--------ccCCccccccccCCCCCCcc
Q 042526          151 SLTLAMAAGSPLLTSEHSNRRKPNKR-KRT--------RKGGEDEKLDSLKWNPLSQP  199 (284)
Q Consensus       151 ~i~v~~~~G~~~~~q~~~l~~~~~i~-v~~--------~~~~~~d~l~~lv~dEAd~m  199 (284)
                      ++.+.+++|....     ......++ +.+        .....+.++..+|+|||+++
T Consensus        53 ~~~v~~~~~~~~~-----~~~~~~~~~~~~~~~l~~~l~~~~~~~~l~~vViDEaH~~  105 (431)
T 2v6i_A           53 GEPIRYMTPAVQS-----ERTGNEIVDFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFL  105 (431)
T ss_dssp             TSCEEEC--------------CCCSEEEEEHHHHHHHHHHTCCCCCCSEEEEESTTCC
T ss_pred             CCeEEEEecCccc-----cCCCCceEEEEchHHHHHHHhcCccccCCCEEEEeCCccC
Confidence            4455554443111     00000111 000        01123678899999999997

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.17  E-value=3.7e-11  Score=117.70  Aligned_cols=78  Identities=17%  Similarity=0.138  Sum_probs=58.4

Q ss_pred             cCCCCCcHHHHHHHHHH---HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEE
Q 042526           52 LGFKESTSILKARIPAL---AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALI  128 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~i---l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLI  128 (284)
                      +|| .|+|+|.+++..+   +..|+++++.||||||||++|++|++..                          +.++||
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~--------------------------~~~~~~   56 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL--------------------------KKKVLI   56 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH--------------------------TCEEEE
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC--------------------------CCcEEE
Confidence            578 7999999987543   2689999999999999999999998641                          357999


Q ss_pred             EecCHHHHHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          129 INPTRELALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       129 L~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      ++||++|+.|+...+..+    +++++++.|.
T Consensus        57 ~~~t~~l~~q~~~~~~~l----~~~~~~l~gr   84 (540)
T 2vl7_A           57 FTRTHSQLDSIYKNAKLL----GLKTGFLIGK   84 (540)
T ss_dssp             EESCHHHHHHHHHHHGGG----TCCEEEC---
T ss_pred             EcCCHHHHHHHHHHHHhc----CCcEEEecCC
Confidence            999999999999988875    4555555443

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=99.11  E-value=3.8e-11  Score=125.61  Aligned_cols=137  Identities=9%  Similarity=-0.053  Sum_probs=93.0

Q ss_pred             CHHHHHHHHHcC-------CCCCcHHHHHHHHHHHc-------------CCCcEEEEccCCCCchHHhHHHHHHHHHHHH
Q 042526           42 HPLLMKSIYKLG-------FKESTSILKARIPALAH-------------QRKDVIGAAETESGKTRAFGLPALQRLLEER  101 (284)
Q Consensus        42 ~~~Ll~~L~~~g-------~~~pT~iQ~~aip~il~-------------~G~dviv~A~TGSGKTlafllPil~~l~~~~  101 (284)
                      ++.++..|..+-       ...|+|+|..|++.++.             .+++.+++++||||||+++ ++++..+..  
T Consensus       250 ~~~ll~~l~~f~~~~~~~~~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~--  326 (1038)
T 2w00_A          250 KHTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATE--  326 (1038)
T ss_dssp             HHHHHHHHHHSEEECTTCCEEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTT--
T ss_pred             hHHHHHHHHhheeeccccccccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHh--
Confidence            455666676642       23599999999999832             1478999999999999997 677643321  


Q ss_pred             HHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHh-cCCCcccccc
Q 042526          102 EKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNR-RKPNKRKRTR  180 (284)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~-~~~~i~v~~~  180 (284)
                                        .....++|||||+++|+.|+...+..++...     +.+|.+...+...+. ..+++++.+.
T Consensus       327 ------------------~~~~~rvLvlvpr~eL~~Q~~~~f~~f~~~~-----v~~~~s~~~l~~~L~~~~~~IiVtTi  383 (1038)
T 2w00_A          327 ------------------LDFIDKVFFVVDRKDLDYQTMKEYQRFSPDS-----VNGSENTAGLKRNLDKDDNKIIVTTI  383 (1038)
T ss_dssp             ------------------CTTCCEEEEEECGGGCCHHHHHHHHTTSTTC-----SSSSCCCHHHHHHHHCSSCCEEEEEH
T ss_pred             ------------------cCCCceEEEEeCcHHHHHHHHHHHHHhcccc-----cccccCHHHHHHHhcCCCCCEEEEEH
Confidence                              1134689999999999999999999886531     122334444445554 3466655441


Q ss_pred             --------c---CCccccccccCCCCCCccccccc
Q 042526          181 --------K---GGEDEKLDSLKWNPLSQPKTTTL  204 (284)
Q Consensus       181 --------~---~~~~d~l~~lv~dEAd~m~~~gf  204 (284)
                              .   ...++....+++|||+++...++
T Consensus       384 qkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~~~  418 (1038)
T 2w00_A          384 QKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGEA  418 (1038)
T ss_dssp             HHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHHHH
T ss_pred             HHHHHHHhcccchhccccccEEEEEccchhcchHH
Confidence                    0   11345667899999999775443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.10  E-value=2.5e-11  Score=119.55  Aligned_cols=122  Identities=11%  Similarity=0.018  Sum_probs=64.7

Q ss_pred             CCcHHHHHHHHHHHc----CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALAH----QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il~----~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|+|+|..||+.++.    ..++++++++||||||+++ ++++.++.....             .........++|||+|
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~~~~~-------------~~~~~~~~~~vlil~P  243 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLWSARW-------------NRTGDYRKPRILFLAD  243 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHHHTTC-------------CSSCSSSCCCEEEEEC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHHhccc-------------ccccccCCCeEEEEeC
Confidence            699999999998832    2467999999999999995 455555544210             0001124678999999


Q ss_pred             CHHHHHHHH-HHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccccc-------------CCccccccccCCCCCC
Q 042526          132 TRELALQVL-MVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRK-------------GGEDEKLDSLKWNPLS  197 (284)
Q Consensus       132 TReLa~Qi~-~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~-------------~~~~d~l~~lv~dEAd  197 (284)
                      |++|+.|++ +.++.+..    .+..+.++.       .....++++.+.-             ....+.+..+|+|||+
T Consensus       244 ~~~L~~Q~~~~~~~~~~~----~~~~~~~~~-------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH  312 (590)
T 3h1t_A          244 RNVLVDDPKDKTFTPFGD----ARHKIEGGK-------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECH  312 (590)
T ss_dssp             -----------CCTTTCS----SEEECCC---------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC
T ss_pred             CHHHHHHHHHHHHHhcch----hhhhhhccC-------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCc
Confidence            999999999 77776543    233333321       1223444443310             1123456779999999


Q ss_pred             ccccc
Q 042526          198 QPKTT  202 (284)
Q Consensus       198 ~m~~~  202 (284)
                      ++...
T Consensus       313 ~~~~~  317 (590)
T 3h1t_A          313 RGSAR  317 (590)
T ss_dssp             -----
T ss_pred             ccccc
Confidence            98754

>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=98.76  E-value=2.7e-09  Score=105.95  Aligned_cols=73  Identities=21%  Similarity=0.168  Sum_probs=59.9

Q ss_pred             cHHHHHHHHHHHcCCCcEEEEccCCCCch--HHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           58 TSILKARIPALAHQRKDVIGAAETESGKT--RAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        58 T~iQ~~aip~il~~G~dviv~A~TGSGKT--lafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      ++.|..|++.+ +.++++++++++|||||  ++++++.+..+..                     ..+.++++++||+++
T Consensus       151 ~~~Q~~Ai~~~-l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~---------------------~~~~~vll~APTg~A  208 (608)
T 1w36_D          151 INWQKVAAAVA-LTRRISVISGGPGTGKTTTVAKLLAALIQMAD---------------------GERCRIRLAAPTGKA  208 (608)
T ss_dssp             CCHHHHHHHHH-HTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS---------------------SCCCCEEEEBSSHHH
T ss_pred             CHHHHHHHHHH-hcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh---------------------cCCCeEEEEeCChhH
Confidence            78999999998 88999999999999999  7788887764311                     135689999999999


Q ss_pred             HHHHHHHHhhhhcCCCc
Q 042526          136 ALQVLMVASPSLKSNSL  152 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i  152 (284)
                      |.++...+..++..+++
T Consensus       209 A~~L~e~~~~~~~~l~l  225 (608)
T 1w36_D          209 AARLTESLGKALRQLPL  225 (608)
T ss_dssp             HHHHHHHHTHHHHHSSC
T ss_pred             HHHHHHHHHHHHhcCCC
Confidence            99999988876655443

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=98.70  E-value=1.2e-08  Score=97.90  Aligned_cols=121  Identities=11%  Similarity=-0.050  Sum_probs=81.0

Q ss_pred             CCCcHHHHHHHHHHH---cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           55 KESTSILKARIPALA---HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        55 ~~pT~iQ~~aip~il---~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      ..|+|+|.++++.++   ..|+++|++++||+|||+.++ +++..+...                    .....+|||||
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~--------------------~~~~~~LIv~P   94 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKE--------------------NELTPSLVICP   94 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHT--------------------TCCSSEEEEEC
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH-HHHHHHHhc--------------------CCCCCEEEEcc
Confidence            369999999997652   458899999999999999964 444444321                    12346999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccccc--CC----ccccccccCCCCCCcccccc
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRTRK--GG----EDEKLDSLKWNPLSQPKTTT  203 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~~~--~~----~~d~l~~lv~dEAd~m~~~g  203 (284)
                      + .|+.|+.++++++..  ++.+.++.|+...    ......++++.+.-  ..    .......+|+|||.++.+.+
T Consensus        95 ~-~l~~qw~~e~~~~~~--~~~v~~~~g~~~~----~~~~~~~ivi~t~~~l~~~~~l~~~~~~~vIvDEaH~~kn~~  165 (500)
T 1z63_A           95 L-SVLKNWEEELSKFAP--HLRFAVFHEDRSK----IKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQ  165 (500)
T ss_dssp             S-TTHHHHHHHHHHHCT--TSCEEECSSSTTS----CCGGGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGGGGSCTT
T ss_pred             H-HHHHHHHHHHHHHCC--CceEEEEecCchh----ccccCCcEEEeeHHHHhccchhcCCCcCEEEEeCccccCCHh
Confidence            5 589999999998865  4566667666532    11233455544311  01    11245679999999976544

>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=98.57  E-value=1.2e-07  Score=95.35  Aligned_cols=81  Identities=21%  Similarity=0.189  Sum_probs=71.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|....-.+ ..|+  |+.-.||+|||+++.+|++-..+.                       +..+.|++|
T Consensus        72 lg~-r~~dvQligg~~L-~~G~--iaEM~TGEGKTLva~lp~~lnAL~-----------------------G~~vhVvT~  124 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIAL-HEGK--VAEMKTGEGKTLAATMPIYLNALI-----------------------GKGVHLVTV  124 (822)
T ss_dssp             TSC-CCCHHHHHHHHHH-HTTC--EEECCTTSCHHHHTHHHHHHHHTT-----------------------SSCEEEEES
T ss_pred             hCC-CCcHHHHHHHHHH-hCCC--hhhccCCCCccHHHHHHHHHHHhc-----------------------CCceEEEec
Confidence            676 4999999999887 8887  889999999999999999754332                       556999999


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeC
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAG  159 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G  159 (284)
                      |+.||.|-+..+..+...+|++|++++.
T Consensus       125 ndyLA~rdae~m~~l~~~Lglsvg~i~~  152 (822)
T 3jux_A          125 NDYLARRDALWMGPVYLFLGLRVGVINS  152 (822)
T ss_dssp             SHHHHHHHHHHHHHHHHHTTCCEEEEET
T ss_pred             cHHHHHhHHHHHHHHHHHhCCEEEEEcC
Confidence            9999999999999999999999999887

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.41  E-value=7.1e-07  Score=89.03  Aligned_cols=128  Identities=11%  Similarity=-0.042  Sum_probs=80.4

Q ss_pred             CCcHHHHHHHHHHH--------cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           56 ESTSILKARIPALA--------HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        56 ~pT~iQ~~aip~il--------~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      .+.|+|..++..++        ..++..|+..++|+|||+..+..+...+...                .........+|
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~----------------~~~~p~~~~~L  118 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQS----------------PDCKPEIDKVI  118 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCC----------------TTSSCSCSCEE
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhC----------------ccccCCCCcEE
Confidence            58899999998762        3467899999999999988766554432211                11111233589


Q ss_pred             EEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHH---hc------CCCcccccc-------cCCcccccccc
Q 042526          128 IINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSN---RR------KPNKRKRTR-------KGGEDEKLDSL  191 (284)
Q Consensus       128 IL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l---~~------~~~i~v~~~-------~~~~~d~l~~l  191 (284)
                      ||||+ .|+.|+..++.++... .+.+..++|+........+   ..      ..++++.+-       ..........+
T Consensus       119 iV~P~-sll~qW~~E~~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~~l~~~~~~~v  196 (644)
T 1z3i_X          119 VVSPS-SLVRNWYNEVGKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLV  196 (644)
T ss_dssp             EEECH-HHHHHHHHHHHHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTTTTTSCCCEE
T ss_pred             EEecH-HHHHHHHHHHHHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHHHhhcCCccEE
Confidence            99997 8999999999998765 4555566665433222221   11      234444331       11112345679


Q ss_pred             CCCCCCcccc
Q 042526          192 KWNPLSQPKT  201 (284)
Q Consensus       192 v~dEAd~m~~  201 (284)
                      |+|||-++.+
T Consensus       197 I~DEaH~ikn  206 (644)
T 1z3i_X          197 ICDEGHRLKN  206 (644)
T ss_dssp             EETTGGGCCT
T ss_pred             EEECceecCC
Confidence            9999998754

>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=98.40  E-value=1.4e-07  Score=98.37  Aligned_cols=124  Identities=19%  Similarity=0.103  Sum_probs=79.4

Q ss_pred             CCCcHHHHHHHHHHHcC-CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCH
Q 042526           55 KESTSILKARIPALAHQ-RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTR  133 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~-G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTR  133 (284)
                      ..|+|+|..++..++.. +.++|++.+||+|||+.++..+...+...                     ...++|||||+ 
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g---------------------~~~rvLIVvP~-  209 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG---------------------AAERVLIIVPE-  209 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS---------------------SCCCEEEECCT-
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC---------------------CCCeEEEEeCH-
Confidence            36899999999887322 55899999999999999877665443221                     22369999999 


Q ss_pred             HHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHH---hcCCCccccccc-----C-----CccccccccCCCCCCccc
Q 042526          134 ELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSN---RRKPNKRKRTRK-----G-----GEDEKLDSLKWNPLSQPK  200 (284)
Q Consensus       134 eLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l---~~~~~i~v~~~~-----~-----~~~d~l~~lv~dEAd~m~  200 (284)
                      .|+.|+...+....   ++.+.++.|..........   ....++++.+.-     .     .....+..+|+|||-++.
T Consensus       210 sLl~Qw~~E~~~~f---~l~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~k  286 (968)
T 3dmq_A          210 TLQHQWLVEMLRRF---NLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLV  286 (968)
T ss_dssp             TTHHHHHHHHHHHS---CCCCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCC
T ss_pred             HHHHHHHHHHHHHh---CCCEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhc
Confidence            99999999886543   5666666554322211111   112344443310     0     112246679999999976


Q ss_pred             ccc
Q 042526          201 TTT  203 (284)
Q Consensus       201 ~~g  203 (284)
                      ..+
T Consensus       287 n~~  289 (968)
T 3dmq_A          287 WSE  289 (968)
T ss_dssp             CBT
T ss_pred             CCC
Confidence            543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.15  E-value=3e-06  Score=86.48  Aligned_cols=123  Identities=16%  Similarity=-0.022  Sum_probs=79.0

Q ss_pred             CCcHHHHHHHHHHH---cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPALA---HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      .+.|+|..++..++   ..|++.|++.++|+|||+..+..+...+....                    ..-.+||||| 
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~--------------------~~~~~LIV~P-  294 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARR--------------------QNGPHIIVVP-  294 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHS--------------------CCSCEEEECC-
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcC--------------------CCCCEEEEEC-
Confidence            57789999997551   47899999999999999887655443332221                    1224799999 


Q ss_pred             HHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH-H------------hcCCCcccccccCC--c-----cccccccC
Q 042526          133 RELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS-N------------RRKPNKRKRTRKGG--E-----DEKLDSLK  192 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~-l------------~~~~~i~v~~~~~~--~-----~d~l~~lv  192 (284)
                      ..|+.|....+.+++.  ++.+.+++|......... .            ....++++.+--..  .     .-....+|
T Consensus       295 ~sll~qW~~E~~~~~p--~~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~l~~~~w~~vI  372 (800)
T 3mwy_W          295 LSTMPAWLDTFEKWAP--DLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMA  372 (800)
T ss_dssp             TTTHHHHHHHHHHHST--TCCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHHHHTSEEEEEE
T ss_pred             chHHHHHHHHHHHHCC--CceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHHHhcCCcceee
Confidence            7788999999988864  566777777654332211 1            11234444331100  0     11356699


Q ss_pred             CCCCCcccc
Q 042526          193 WNPLSQPKT  201 (284)
Q Consensus       193 ~dEAd~m~~  201 (284)
                      +|||.++.+
T Consensus       373 vDEaH~lkn  381 (800)
T 3mwy_W          373 VDEAHRLKN  381 (800)
T ss_dssp             ETTGGGGCC
T ss_pred             hhhhhhhcC
Confidence            999998744

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.01  E-value=0.0022  Score=65.49  Aligned_cols=69  Identities=14%  Similarity=0.054  Sum_probs=53.2

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..+++-|..|+-.+ +.+.-++++||+|||||.+. .-++..+...                     .+.++||++||..
T Consensus       359 ~~Ln~~Q~~Av~~~-l~~~~~lI~GppGTGKT~~i-~~~i~~l~~~---------------------~~~~ILv~a~tn~  415 (802)
T 2xzl_A          359 AQLNSSQSNAVSHV-LQRPLSLIQGPPGTGKTVTS-ATIVYHLSKI---------------------HKDRILVCAPSNV  415 (802)
T ss_dssp             CCCCHHHHHHHHHH-TTCSEEEEECSTTSSHHHHH-HHHHHHHHHH---------------------HCCCEEEEESSHH
T ss_pred             ccCCHHHHHHHHHH-hcCCCEEEECCCCCCHHHHH-HHHHHHHHhC---------------------CCCeEEEEcCcHH
Confidence            35679999999988 77777899999999999654 3344444332                     1357999999999


Q ss_pred             HHHHHHHHHhhh
Q 042526          135 LALQVLMVASPS  146 (284)
Q Consensus       135 La~Qi~~~~~~l  146 (284)
                      -|.++...+..+
T Consensus       416 A~d~l~~rL~~~  427 (802)
T 2xzl_A          416 AVDHLAAKLRDL  427 (802)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhh
Confidence            999998887754

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.99  E-value=0.0018  Score=64.32  Aligned_cols=66  Identities=14%  Similarity=0.085  Sum_probs=48.9

Q ss_pred             CCcHHHHHHHHHHHcCCCc-EEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           56 ESTSILKARIPALAHQRKD-VIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~d-viv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      .+.+-|.+|+-.+ +..++ .+|++|+|||||.+.+ -+|..+..                      .+.++||++||..
T Consensus       189 ~LN~~Q~~AV~~a-l~~~~~~lI~GPPGTGKT~ti~-~~I~~l~~----------------------~~~~ILv~a~TN~  244 (646)
T 4b3f_X          189 CLDTSQKEAVLFA-LSQKELAIIHGPPGTGKTTTVV-EIILQAVK----------------------QGLKVLCCAPSNI  244 (646)
T ss_dssp             TCCHHHHHHHHHH-HHCSSEEEEECCTTSCHHHHHH-HHHHHHHH----------------------TTCCEEEEESSHH
T ss_pred             CCCHHHHHHHHHH-hcCCCceEEECCCCCCHHHHHH-HHHHHHHh----------------------CCCeEEEEcCchH
Confidence            4578999999988 55554 6899999999997643 33333332                      2457999999999


Q ss_pred             HHHHHHHHHhh
Q 042526          135 LALQVLMVASP  145 (284)
Q Consensus       135 La~Qi~~~~~~  145 (284)
                      -|.++...+..
T Consensus       245 AvD~i~erL~~  255 (646)
T 4b3f_X          245 AVDNLVERLAL  255 (646)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99888777654

>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=96.98  E-value=0.0016  Score=64.47  Aligned_cols=69  Identities=14%  Similarity=0.095  Sum_probs=52.4

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..+++-|..|+-.+ +.+.-++++||+|||||.+.. .++..+...                     .+.++||++||..
T Consensus       179 ~~ln~~Q~~av~~~-l~~~~~li~GppGTGKT~~~~-~~i~~l~~~---------------------~~~~ilv~a~tn~  235 (624)
T 2gk6_A          179 PDLNHSQVYAVKTV-LQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ---------------------GNGPVLVCAPSNI  235 (624)
T ss_dssp             CCCCHHHHHHHHHH-HTCSEEEEECCTTSCHHHHHH-HHHHHHHTS---------------------SSCCEEEEESSHH
T ss_pred             CCCCHHHHHHHHHH-hcCCCeEEECCCCCCHHHHHH-HHHHHHHHc---------------------CCCeEEEEeCcHH
Confidence            35689999999988 677788999999999996543 333333221                     2457999999999


Q ss_pred             HHHHHHHHHhhh
Q 042526          135 LALQVLMVASPS  146 (284)
Q Consensus       135 La~Qi~~~~~~l  146 (284)
                      .|.++...+...
T Consensus       236 A~~~l~~~l~~~  247 (624)
T 2gk6_A          236 AVDQLTEKIHQT  247 (624)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhc
Confidence            999998887654

>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=96.90  E-value=0.00073  Score=67.57  Aligned_cols=69  Identities=23%  Similarity=0.250  Sum_probs=51.8

Q ss_pred             CCCCCcHHHHHHHHHHH---cCCC-cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEE
Q 042526           53 GFKESTSILKARIPALA---HQRK-DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALI  128 (284)
Q Consensus        53 g~~~pT~iQ~~aip~il---~~G~-dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLI  128 (284)
                      +| .|++.|..+|..++   ..|. ..++.+.||||||+++.- ++..+                        .. .+||
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~------------------------~~-~~lv   58 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL------------------------GR-PALV   58 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH------------------------TC-CEEE
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh------------------------CC-CEEE
Confidence            56 79999999988662   3343 567889999999976642 22211                        12 2899


Q ss_pred             EecCHHHHHHHHHHHhhhhc
Q 042526          129 INPTRELALQVLMVASPSLK  148 (284)
Q Consensus       129 L~PTReLa~Qi~~~~~~l~~  148 (284)
                      |+|+..+|.|+++.++.|..
T Consensus        59 v~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A           59 LAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             EESSHHHHHHHHHHHHHHCT
T ss_pred             EecCHHHHHHHHHHHHHHCC
Confidence            99999999999999999964

>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=96.82  E-value=0.0031  Score=59.94  Aligned_cols=72  Identities=14%  Similarity=0.184  Sum_probs=50.2

Q ss_pred             HHcCCCCCcHHHHHHHHHHHcC----CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeE
Q 042526           50 YKLGFKESTSILKARIPALAHQ----RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLR  125 (284)
Q Consensus        50 ~~~g~~~pT~iQ~~aip~il~~----G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (284)
                      .-+.|..+++-|..|+-.++..    ...+++.|+.|||||. .+..++..+...                     ....
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~-ll~~~~~~l~~~---------------------~~~~   76 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATT-LTKFIIEALIST---------------------GETG   76 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHH-HHHHHHHHHHHT---------------------TCCC
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHH-HHHHHHHHHHhc---------------------CCce
Confidence            3467889999999999876222    2399999999999994 333444444332                     1136


Q ss_pred             EEEEecCHHHHHHHHHHH
Q 042526          126 ALIINPTRELALQVLMVA  143 (284)
Q Consensus       126 aLIL~PTReLa~Qi~~~~  143 (284)
                      +++++||...|..+...+
T Consensus        77 il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           77 IILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             EEEEESSHHHHHHHHHHH
T ss_pred             EEEecCcHHHHHHHHhhh
Confidence            899999998887766544

>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=96.75  E-value=0.0033  Score=64.19  Aligned_cols=68  Identities=15%  Similarity=0.091  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+++-|..|+-.+ +.+.-++++||+|||||.+. .-++..+...                     .+.++|+++||..-
T Consensus       356 ~Ln~~Q~~Av~~~-l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~---------------------~~~~ilv~a~tn~A  412 (800)
T 2wjy_A          356 DLNHSQVYAVKTV-LQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ---------------------GNGPVLVCAPSNIA  412 (800)
T ss_dssp             CCCHHHHHHHHHH-HTSSEEEEECCTTSCHHHHH-HHHHHHHHTT---------------------CSSCEEEEESSHHH
T ss_pred             CCCHHHHHHHHHh-ccCCeEEEEcCCCCCHHHHH-HHHHHHHHHc---------------------CCCcEEEEcCcHHH
Confidence            4688999999988 67777899999999999653 3333333221                     24579999999999


Q ss_pred             HHHHHHHHhhh
Q 042526          136 ALQVLMVASPS  146 (284)
Q Consensus       136 a~Qi~~~~~~l  146 (284)
                      |.++...+...
T Consensus       413 ~~~l~~~l~~~  423 (800)
T 2wjy_A          413 VDQLTEKIHQT  423 (800)
T ss_dssp             HHHHHHHHHTT
T ss_pred             HHHHHHHHHHh
Confidence            99988877653

>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=96.71  E-value=0.0036  Score=61.57  Aligned_cols=72  Identities=15%  Similarity=0.123  Sum_probs=52.2

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..+++-|.+|+-.   ....++|.|+.|||||.+.+--+. ++...                  .....-+.|+|++|+.
T Consensus         8 ~~Ln~~Q~~av~~---~~~~~lV~a~aGsGKT~~l~~ri~-~l~~~------------------~~~~~~~iL~ltft~~   65 (647)
T 3lfu_A            8 DSLNDKQREAVAA---PRSNLLVLAGAGSGKTRVLVHRIA-WLMSV------------------ENCSPYSIMAVTFTNK   65 (647)
T ss_dssp             TTCCHHHHHHHTC---CSSCEEEEECTTSCHHHHHHHHHH-HHHHT------------------SCCCGGGEEEEESSHH
T ss_pred             hcCCHHHHHHHhC---CCCCEEEEECCCCCHHHHHHHHHH-HHHHh------------------CCCChhhEEEEeccHH
Confidence            4689999999963   356899999999999965543332 23221                  0112236999999999


Q ss_pred             HHHHHHHHHhhhhc
Q 042526          135 LALQVLMVASPSLK  148 (284)
Q Consensus       135 La~Qi~~~~~~l~~  148 (284)
                      .|.++...+..+..
T Consensus        66 aa~e~~~rl~~~~~   79 (647)
T 3lfu_A           66 AAAEMRHRIGQLMG   79 (647)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999887754

>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=96.52  E-value=0.0072  Score=59.36  Aligned_cols=64  Identities=14%  Similarity=0.040  Sum_probs=48.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+++-|..|+..+ +.++.+++.+++|||||... ..++..+..                      .+..+++++||...
T Consensus       189 ~L~~~Q~~Av~~~-~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~----------------------~g~~Vl~~ApT~~A  244 (574)
T 3e1s_A          189 GLSEEQASVLDQL-AGHRLVVLTGGPGTGKSTTT-KAVADLAES----------------------LGLEVGLCAPTGKA  244 (574)
T ss_dssp             TCCHHHHHHHHHH-TTCSEEEEECCTTSCHHHHH-HHHHHHHHH----------------------TTCCEEEEESSHHH
T ss_pred             CCCHHHHHHHHHH-HhCCEEEEEcCCCCCHHHHH-HHHHHHHHh----------------------cCCeEEEecCcHHH
Confidence            4789999999998 78899999999999999542 233332222                      24578999999999


Q ss_pred             HHHHHHHH
Q 042526          136 ALQVLMVA  143 (284)
Q Consensus       136 a~Qi~~~~  143 (284)
                      |..+...+
T Consensus       245 a~~L~e~~  252 (574)
T 3e1s_A          245 ARRLGEVT  252 (574)
T ss_dssp             HHHHHHHH
T ss_pred             HHHhHhhh
Confidence            98876543

>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=96.39  E-value=0.0049  Score=61.30  Aligned_cols=71  Identities=14%  Similarity=0.022  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+|+-|.+|+-.   .+..++|.|..|||||.+..-=+.. +....                  ....-..|+|+.|+..
T Consensus         2 ~L~~~Q~~av~~---~~~~~lV~AgaGSGKT~~l~~ri~~-ll~~~------------------~~~~~~IL~lTfT~~A   59 (673)
T 1uaa_A            2 RLNPGQQQAVEF---VTGPCLVLAGAGSGKTRVITNKIAH-LIRGC------------------GYQARHIAAVTFTNKA   59 (673)
T ss_dssp             CCCHHHHHHHHC---CSSEEEECCCTTSCHHHHHHHHHHH-HHHHH------------------CCCGGGEEEEESSHHH
T ss_pred             CCCHHHHHHHhC---CCCCEEEEeCCCCChHHHHHHHHHH-HHHhc------------------CCCHHHeEEEeccHHH
Confidence            478999999864   3678999999999999655433333 22221                  0123468999999999


Q ss_pred             HHHHHHHHhhhhc
Q 042526          136 ALQVLMVASPSLK  148 (284)
Q Consensus       136 a~Qi~~~~~~l~~  148 (284)
                      |.++...+..+..
T Consensus        60 a~em~~Rl~~~l~   72 (673)
T 1uaa_A           60 AREMKERVGQTLG   72 (673)
T ss_dssp             HHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHcC
Confidence            9999998887654

>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=95.76  E-value=0.016  Score=58.23  Aligned_cols=72  Identities=18%  Similarity=0.104  Sum_probs=51.0

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      ..++|-|.+|+-.   .+..++|.|..|||||.+..--+.. +...                  .....-+.|+|+.|+.
T Consensus        10 ~~Ln~~Q~~av~~---~~g~~lV~AgAGSGKT~vL~~ri~~-ll~~------------------~~~~p~~IL~vTFTnk   67 (724)
T 1pjr_A           10 AHLNKEQQEAVRT---TEGPLLIMAGAGSGKTRVLTHRIAY-LMAE------------------KHVAPWNILAITFTNK   67 (724)
T ss_dssp             TTSCHHHHHHHHC---CSSCEEEEECTTSCHHHHHHHHHHH-HHHT------------------TCCCGGGEEEEESSHH
T ss_pred             hhCCHHHHHHHhC---CCCCEEEEEcCCCCHHHHHHHHHHH-HHHh------------------cCCCHHHeEEEeccHH
Confidence            4689999999864   3568999999999999665433332 2221                  0112236899999999


Q ss_pred             HHHHHHHHHhhhhc
Q 042526          135 LALQVLMVASPSLK  148 (284)
Q Consensus       135 La~Qi~~~~~~l~~  148 (284)
                      .|..+...+..+..
T Consensus        68 AA~Em~~Rl~~~l~   81 (724)
T 1pjr_A           68 AAREMRERVQSLLG   81 (724)
T ss_dssp             HHHHHHHHHHHHHG
T ss_pred             HHHHHHHHHHHHhc
Confidence            99998888776643

>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=95.74  E-value=0.016  Score=61.74  Aligned_cols=70  Identities=21%  Similarity=0.151  Sum_probs=50.9

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+|+-|..+|-   ..+.+++|.|..|||||.+.+--++..+...                 ......-+.|+|++|+..
T Consensus        10 ~~t~eQ~~~i~---~~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~-----------------~~~~~~~~il~~Tft~~a   69 (1232)
T 3u4q_A           10 TWTDDQWNAIV---STGQDILVAAAAGSGKTAVLVERMIRKITAE-----------------ENPIDVDRLLVVTFTNAS   69 (1232)
T ss_dssp             CCCHHHHHHHH---CCSSCEEEEECTTCCHHHHHHHHHHHHHSCS-----------------SSCCCGGGEEEECSSHHH
T ss_pred             CCCHHHHHHHh---CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC-----------------CCCCCccceEEEeccHHH
Confidence            57999999995   4588999999999999966554444333221                 011123368999999999


Q ss_pred             HHHHHHHHhh
Q 042526          136 ALQVLMVASP  145 (284)
Q Consensus       136 a~Qi~~~~~~  145 (284)
                      |..+...+..
T Consensus        70 a~e~~~ri~~   79 (1232)
T 3u4q_A           70 AAEMKHRIAE   79 (1232)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9998887766

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=94.59  E-value=0.094  Score=51.43  Aligned_cols=73  Identities=8%  Similarity=0.062  Sum_probs=56.0

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|+|.|...+-.+ ...+-+++..+.|+|||.+...-++-.+...                     .+..++++.||++.
T Consensus       163 ~l~p~Q~~i~~~l-~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~---------------------~~~~i~~va~t~~q  220 (592)
T 3cpe_A          163 QLRDYQRDMLKIM-SSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN---------------------KDKAVGILAHKGSM  220 (592)
T ss_dssp             CCCHHHHHHHHHH-HHCSEEEEEECSSSCHHHHHHHHHHHHHHTS---------------------SSCEEEEEESSHHH
T ss_pred             cCCHHHHHHHHhh-ccccEEEEEEcCccChHHHHHHHHHHHHHhC---------------------CCCeEEEEECCHHH
Confidence            4799999998876 5678899999999999987665444333221                     35579999999999


Q ss_pred             HHHHHHHHhhhhcCC
Q 042526          136 ALQVLMVASPSLKSN  150 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~  150 (284)
                      |..+...++.+....
T Consensus       221 A~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          221 SAEVLDRTKQAIELL  235 (592)
T ss_dssp             HHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHhC
Confidence            999988888776544

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=94.44  E-value=0.042  Score=54.76  Aligned_cols=67  Identities=18%  Similarity=0.148  Sum_probs=48.7

Q ss_pred             CCcHHHHHHHHHHH---cCCC-cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           56 ESTSILKARIPALA---HQRK-DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G~-dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      .|+.-|..+|..++   ..|. ..++.+-||||||++..- ++..+                        .. ..|||+|
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~------------------------~~-~~lvv~~   65 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV------------------------NK-PTLVIAH   65 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH------------------------CC-CEEEECS
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh------------------------CC-CEEEEEC
Confidence            58888888887552   3343 467889999999965532 22111                        12 2899999


Q ss_pred             CHHHHHHHHHHHhhhhc
Q 042526          132 TRELALQVLMVASPSLK  148 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~  148 (284)
                      +..+|.|++..++.|..
T Consensus        66 ~~~~A~~l~~el~~~~~   82 (661)
T 2d7d_A           66 NKTLAGQLYSEFKEFFP   82 (661)
T ss_dssp             SHHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHHcC
Confidence            99999999999999964

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=94.11  E-value=0.12  Score=48.10  Aligned_cols=71  Identities=8%  Similarity=0.087  Sum_probs=53.9

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .++|.|...+-.+ ...+-+++..+-+.|||.+.+.-++-.+..                     ..+..+++++||++.
T Consensus       163 ~L~p~Qk~il~~l-~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~---------------------~~g~~v~~vA~t~~q  220 (385)
T 2o0j_A          163 QLRDYQRDMLKIM-SSKRMTVCNLSRQLGKTTVVAIFLAHFVCF---------------------NKDKAVGILAHKGSM  220 (385)
T ss_dssp             CCCHHHHHHHHHH-HHSSEEEEEECSSSCHHHHHHHHHHHHHHS---------------------SSSCEEEEEESSHHH
T ss_pred             CCCHHHHHHHHhh-ccCcEEEEEEcCcCChhHHHHHHHHHHHHh---------------------CCCCeEEEEeCCHHH
Confidence            6899999998876 455778999999999998766544432221                     135679999999999


Q ss_pred             HHHHHHHHhhhhc
Q 042526          136 ALQVLMVASPSLK  148 (284)
Q Consensus       136 a~Qi~~~~~~l~~  148 (284)
                      |..+...+..+..
T Consensus       221 A~~vf~~i~~mi~  233 (385)
T 2o0j_A          221 SAEVLDRTKQAIE  233 (385)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9988887777654

>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=93.06  E-value=0.2  Score=40.60  Aligned_cols=19  Identities=21%  Similarity=0.198  Sum_probs=16.3

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|+.+++.+|+|+|||..
T Consensus        36 ~~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           36 EEGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             GGCCEEEECCSSSSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3588999999999999943

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.29  E-value=0.046  Score=51.85  Aligned_cols=55  Identities=11%  Similarity=0.117  Sum_probs=38.3

Q ss_pred             CccccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           30 STEFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      ..|-.+|++++-.+...+.|.+.   -+.+|--++..-++    .-+.+++.+|+|||||+.
T Consensus       174 ~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~----~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          174 EKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIR----APKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCC----CCCEEEEESCTTSSHHHH
T ss_pred             CCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC----CCCeeEEECcCCCCHHHH
Confidence            35667899998778888777653   23344444443332    357899999999999954

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=90.19  E-value=0.13  Score=45.60  Aligned_cols=57  Identities=12%  Similarity=0.038  Sum_probs=33.3

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|.+++-...+.+.|.+.- ..|..........-+..++.+++.+|+|||||+.
T Consensus         9 ~~~~~~~di~G~~~~~~~l~~~v-~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~l   65 (301)
T 3cf0_A            9 VPQVTWEDIGGLEDVKRELQELV-QYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLL   65 (301)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHH-HHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHH-HHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHH
Confidence            34567999977777777776531 0010000000110114578899999999999954

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=89.58  E-value=0.29  Score=38.38  Aligned_cols=19  Identities=16%  Similarity=0.053  Sum_probs=16.7

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..+.+|++.+++|||||+.
T Consensus        25 ~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHH
T ss_pred             CCCCcEEEECCCCccHHHH
Confidence            6678999999999999953

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=89.20  E-value=0.18  Score=43.83  Aligned_cols=53  Identities=15%  Similarity=0.147  Sum_probs=33.1

Q ss_pred             cccCcccCCCCHHHHHHHHHcC---CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLG---FKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g---~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      |-.+|.++.-.+..++.|..+=   +..|-.++.  + .+ ..++.+++.+|+|+|||..
T Consensus        12 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~--~-~~-~~~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           12 PNVRYEDIGGLEKQMQEIREVVELPLKHPELFEK--V-GI-EPPKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHH--H-CC-CCCSEEEEESSSSSSHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHh--c-CC-CCCCeEEEECCCCCcHHHH
Confidence            4467999977777777776531   111111111  1 12 4577899999999999953

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=88.73  E-value=0.33  Score=45.24  Aligned_cols=45  Identities=16%  Similarity=0.145  Sum_probs=32.6

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELAL  137 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~  137 (284)
                      ....++++.|+||||||.+ +-+++..+..                      .+..++|+=|..|+..
T Consensus        51 ~~~~h~~i~G~tGsGKs~~-~~~li~~~~~----------------------~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           51 AEPRHLLVNGATGTGKSVL-LRELAYTGLL----------------------RGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGGCEEEEECTTSSHHHH-HHHHHHHHHH----------------------TTCEEEEEEETTHHHH
T ss_pred             cCcceEEEECCCCCCHHHH-HHHHHHHHHH----------------------CCCcEEEEeCCCchhH
Confidence            3467999999999999976 3445544433                      2456888889988864

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=88.55  E-value=0.22  Score=47.35  Aligned_cols=45  Identities=24%  Similarity=0.238  Sum_probs=32.3

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhh
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASP  145 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~  145 (284)
                      +=.++.|+.|||||..+. -++    .                       .-..+||+||++++..+.+.+..
T Consensus       162 ~v~~I~G~aGsGKTt~I~-~~~----~-----------------------~~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL-SRV----N-----------------------FEEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH-HHC----C-----------------------TTTCEEEESCHHHHHHHHHHHTT
T ss_pred             cEEEEEcCCCCCHHHHHH-HHh----c-----------------------cCCeEEEeCCHHHHHHHHHHhhh
Confidence            345789999999996542 111    0                       01359999999999999888864

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.54  E-value=0.13  Score=48.25  Aligned_cols=54  Identities=20%  Similarity=0.109  Sum_probs=35.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|++++=-....+.|.+.   -+.+|--++..-+    ..-+.+++.+|+|||||+.
T Consensus       142 ~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi----~~prGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          142 VPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI----AQPKGVILYGPPGTGKTLL  198 (405)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC----CCCCCEEEESCSSSSHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC----CCCCceEEeCCCCCCHHHH
Confidence            3457899997556666666653   1233333333322    2357899999999999954

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=88.47  E-value=0.73  Score=42.29  Aligned_cols=19  Identities=32%  Similarity=0.291  Sum_probs=15.6

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|.-+++.+|||||||..
T Consensus       121 ~~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4566899999999999943

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=88.42  E-value=0.35  Score=37.90  Aligned_cols=20  Identities=10%  Similarity=0.014  Sum_probs=17.2

Q ss_pred             cCCCcEEEEccCCCCchHHh
Q 042526           70 HQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlaf   89 (284)
                      ..+.+|++.+++|||||+..
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            56889999999999999543

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.27  E-value=0.12  Score=48.98  Aligned_cols=54  Identities=13%  Similarity=0.113  Sum_probs=34.6

Q ss_pred             ccccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|++++=-+...+.|.+.   -+.+|--++..-+    ..-+.+++.+|+|||||+.
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~----~~prGvLL~GPPGtGKTll  231 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGI----KPPKGVLLYGPPGTGKTLL  231 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCC----CCCCEEEEESCTTSSHHHH
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCC----CCCCeEEEECCCCCcHHHH
Confidence            4557899997666666666552   1223333332222    2357899999999999954

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=87.52  E-value=0.65  Score=38.94  Aligned_cols=19  Identities=26%  Similarity=0.251  Sum_probs=16.3

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|.-+++.+++|+|||..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl   39 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIF   39 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHH
T ss_pred             CCCcEEEEECCCCCCHHHH
Confidence            5688899999999999943

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.35  E-value=0.25  Score=47.16  Aligned_cols=54  Identities=9%  Similarity=0.059  Sum_probs=35.7

Q ss_pred             ccccCcccCCCCHHHHHHHHHcC---CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLG---FKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g---~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|++++=-..+.+.|.+.=   +.+|--++..-+    ..-+.|++.+|+|||||+.
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi----~pprGILLyGPPGTGKTlL  259 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGI----DPPKGILLYGPPGTGKTLC  259 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTC----CCCSEEEECSCTTSSHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCC----CCCCceEeeCCCCCcHHHH
Confidence            34578999987777777777631   223332322222    3457999999999999954

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=87.17  E-value=0.39  Score=42.01  Aligned_cols=40  Identities=18%  Similarity=0.250  Sum_probs=25.2

Q ss_pred             CccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           30 STEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        30 p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      |..+.++++|++++ +   |..             +. + ..|.-+++.+|||||||..
T Consensus         2 ~~~~~~l~~l~~~~-v---l~~-------------i~-i-~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A            2 PAEIPEFKKLGLPD-K---VLE-------------LC-H-RKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             ----CCGGGSSCCT-H---HHH-------------GG-G-CSSEEEEEECSTTCSHHHH
T ss_pred             CCCCCChHHCCCHH-H---HHH-------------Hh-h-CCCCEEEEECCCCccHHHH
Confidence            55566778887762 1   211             11 3 6788899999999999954

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=87.08  E-value=0.62  Score=43.77  Aligned_cols=19  Identities=21%  Similarity=0.263  Sum_probs=15.2

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      ..|.-+++.+|||||||..
T Consensus       165 ~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          165 RPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             SSSEEEEEECSTTSCHHHH
T ss_pred             hcCCeEEEECCCCCCHHHH
Confidence            3456789999999999943

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=86.62  E-value=0.62  Score=39.11  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=18.1

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPAL   94 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil   94 (284)
                      ..|.-+++.|++|+||| +|++-++
T Consensus        28 ~~G~l~~i~G~pG~GKT-~l~l~~~   51 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKT-TFAAQFI   51 (251)
T ss_dssp             ETTCEEEEECCTTSSHH-HHHHHHH
T ss_pred             CCCeEEEEEeCCCCCHH-HHHHHHH
Confidence            45778999999999999 4444433

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=86.48  E-value=0.83  Score=40.96  Aligned_cols=51  Identities=12%  Similarity=0.154  Sum_probs=32.1

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHH----cCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALA----HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il----~~G~dviv~A~TGSGKTla   88 (284)
                      |-.+|++++-...+.+.|.++=.   .|+   ..|.++    ...+.+++.+|+|+|||+.
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~---~p~---~~~~~~~~~~~~~~~iLL~GppGtGKT~l   61 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVI---LPI---KFPHLFTGKRTPWRGILLFGPPGTGKSYL   61 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHH---HHH---HCGGGSCTTCCCCSEEEEESSSSSCHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHH---HHH---hCHHHHhCCCCCCceEEEECCCCccHHHH
Confidence            44689999777777777765210   011   112220    2247899999999999954

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.09  E-value=0.28  Score=46.42  Aligned_cols=54  Identities=15%  Similarity=0.116  Sum_probs=34.9

Q ss_pred             ccccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|++++=-+...+.|.+.   -+.+|--++..-++    .-+.+++.+|+|||||+.
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~----~prGvLLyGPPGTGKTlL  232 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIK----PPKGVILYGAPGTGKTLL  232 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCC----CCSEEEEESSTTTTHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCC----CCCCCceECCCCchHHHH
Confidence            4557899996445555555542   23344444443332    347899999999999954

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=86.01  E-value=0.38  Score=40.94  Aligned_cols=51  Identities=12%  Similarity=0.063  Sum_probs=29.9

Q ss_pred             cCcccCCCCHHHHHHHHHcC--CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           34 DAWNELRLHPLLMKSIYKLG--FKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g--~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .+|+++.-.+.+.+.|.++-  +..|..+....   + ...+.+++.+|+|+|||..
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g---~-~~~~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQLG---A-KVPKGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC---------C-CCCCEEEEESCTTSSHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcC---C-CCCceEEEECCCCCCHHHH
Confidence            56888866666777765420  12222221111   1 3457899999999999954

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=85.21  E-value=0.85  Score=38.95  Aligned_cols=52  Identities=15%  Similarity=0.107  Sum_probs=30.3

Q ss_pred             ccCcccCCCCHHHHHHHHHcC--CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           33 FDAWNELRLHPLLMKSIYKLG--FKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g--~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      -.+|+++.-.+.+.+.|..+-  +..|..++...+    ...+.+++.+|+|||||..
T Consensus         8 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~----~~~~~vll~G~~GtGKT~l   61 (257)
T 1lv7_A            8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGG----KIPKGVLMVGPPGTGKTLL   61 (257)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC---------CCCCEEEEECCTTSCHHHH
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCC----CCCCeEEEECcCCCCHHHH
Confidence            457999977777777765420  111111111111    2245799999999999944

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.67  E-value=0.26  Score=46.57  Aligned_cols=54  Identities=11%  Similarity=0.054  Sum_probs=33.0

Q ss_pred             ccccCcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|+++|=-..+.+.|.+.   -+.+|--++..-+    ...+.+++.+|+|||||+.
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~----~~prGiLL~GPPGtGKT~l  222 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGI----DPPRGVLLYGPPGTGKTML  222 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCC----CCCCEEEEESCTTTTHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCC----CCCceEEEECCCCCCHHHH
Confidence            3446899997556666666542   1222222222221    3357899999999999954

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=84.55  E-value=0.79  Score=44.16  Aligned_cols=41  Identities=24%  Similarity=0.142  Sum_probs=26.7

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           46 MKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        46 l~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      +..|.++|.  +++.+..-+...+..|..+++.+|||||||..
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHH
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            444556663  23333344433337899999999999999944

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=84.15  E-value=1.4  Score=35.88  Aligned_cols=16  Identities=25%  Similarity=0.110  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCchHH
Q 042526           73 KDVIGAAETESGKTRA   88 (284)
Q Consensus        73 ~dviv~A~TGSGKTla   88 (284)
                      +.+++.+++|+|||..
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999954

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=84.13  E-value=0.3  Score=41.79  Aligned_cols=53  Identities=15%  Similarity=0.159  Sum_probs=31.4

Q ss_pred             ccccCcccCCCCHHHHHHHHHcC--CCCCcHHHHHHHHHH-HcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLG--FKESTSILKARIPAL-AHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g--~~~pT~iQ~~aip~i-l~~G~dviv~A~TGSGKTla   88 (284)
                      .|-.+|+++.-.+.....+...-  |..+     .++..+ +.-.+.+++.+|+|+|||..
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~~~~~~-----~~~~~~~~~~~~g~ll~G~~G~GKTtl   65 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVEFLKNP-----SRFHEMGARIPKGVLLVGPPGVGKTHL   65 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHHHHCH-----HHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHHHCH-----HHHHHcCCCCCCeEEEECCCCCCHHHH
Confidence            34568999977777766665531  2111     122211 01134499999999999943

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=84.07  E-value=2  Score=37.86  Aligned_cols=44  Identities=16%  Similarity=0.133  Sum_probs=31.7

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHH-HHHHHcCCC-----cEEEEccCCCCchHHhH
Q 042526           43 PLLMKSIYKLGFKESTSILKAR-IPALAHQRK-----DVIGAAETESGKTRAFG   90 (284)
Q Consensus        43 ~~Ll~~L~~~g~~~pT~iQ~~a-ip~il~~G~-----dviv~A~TGSGKTlafl   90 (284)
                      ..+.+-|+-.||.   |++... +-.+ +.|+     .+++.+|+|||||+.+.
T Consensus        73 n~i~~~l~~qg~~---~~~~~~~l~~~-l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKILELNGYD---PQYAASVFLGW-ATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHHHHTTCC---HHHHHHHHHHH-HTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHcCCC---HHHHHHHHHHH-HhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            4788889888887   666443 3333 4443     59999999999996654

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=83.85  E-value=1.3  Score=39.33  Aligned_cols=51  Identities=10%  Similarity=0.128  Sum_probs=33.1

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHH----cCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALA----HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il----~~G~dviv~A~TGSGKTla   88 (284)
                      |-.+|.++.-...+.+.|..+=.   .|   ...|.++    ...+.+++.+|+|+|||+.
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~---~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~l   67 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVI---LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYL   67 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTH---HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHH
T ss_pred             CCCCHHHhcChHHHHHHHHHHHH---HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHH
Confidence            44679999878888888776411   11   1112221    2245799999999999954

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=83.52  E-value=1  Score=40.39  Aligned_cols=49  Identities=14%  Similarity=0.009  Sum_probs=28.7

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      .|..+|+++--.+....++..+        ...+-... ..++.+++.+|+|+|||..
T Consensus        38 ~p~~~~~~ivG~~~~~~~l~~l--------~~~~~~~~-~~~~~vLl~GppGtGKT~l   86 (368)
T 3uk6_A           38 EPRQASQGMVGQLAARRAAGVV--------LEMIREGK-IAGRAVLIAGQPGTGKTAI   86 (368)
T ss_dssp             CBCSEETTEESCHHHHHHHHHH--------HHHHHTTC-CTTCEEEEEESTTSSHHHH
T ss_pred             CcCcchhhccChHHHHHHHHHH--------HHHHHcCC-CCCCEEEEECCCCCCHHHH
Confidence            4445577775555555554321        11111111 3356899999999999954

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=83.28  E-value=0.26  Score=43.37  Aligned_cols=54  Identities=15%  Similarity=0.138  Sum_probs=27.1

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHH-HHHHHH-HcCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILK-ARIPAL-AHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~-~aip~i-l~~G~dviv~A~TGSGKTla   88 (284)
                      |-.+|.+++-.+.+.+.|.+.=.   .|+.. .++..+ +.-.+.+++.+|+|+|||+.
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~---~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtL   60 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAIL---APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLL   60 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHT---HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHH
Confidence            44689999877888887775311   11111 111111 01234499999999999954

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=83.09  E-value=1.5  Score=37.31  Aligned_cols=50  Identities=6%  Similarity=0.130  Sum_probs=29.8

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHHcCC----CcEEEEccCCCCchHHhHHHHHHHH
Q 042526           44 LLMKSIYKLGFKESTSILKARIPALAHQR----KDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        44 ~Ll~~L~~~g~~~pT~iQ~~aip~il~~G----~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      .|.+-|+=.|+. |..+ ..++..+ ..+    +.+++.+|+|||||.. +..++..+
T Consensus        29 ~I~~~l~yq~~~-~~~f-~~~l~~~-~~~iPkkn~ili~GPPGtGKTt~-a~ala~~l   82 (212)
T 1tue_A           29 PIVQFLRYQQIE-FITF-LGALKSF-LKGTPKKNCLVFCGPANTGKSYF-GMSFIHFI   82 (212)
T ss_dssp             HHHHHHHHTTCC-HHHH-HHHHHHH-HHTCTTCSEEEEESCGGGCHHHH-HHHHHHHH
T ss_pred             HHHHHHHHcCcC-HHHH-HHHHHHH-HhcCCcccEEEEECCCCCCHHHH-HHHHHHHh
Confidence            566666644543 3333 3344444 333    3599999999999943 34555443

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=82.93  E-value=1.1  Score=35.49  Aligned_cols=17  Identities=18%  Similarity=0.176  Sum_probs=15.2

Q ss_pred             CCCcEEEEccCCCCchH
Q 042526           71 QRKDVIGAAETESGKTR   87 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTl   87 (284)
                      .|..+++.+|+|+|||.
T Consensus        35 ~g~~~~l~G~~G~GKTt   51 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSH   51 (149)
T ss_dssp             CCSEEEEESSSTTTTCH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57889999999999994

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=82.04  E-value=1.8  Score=39.05  Aligned_cols=18  Identities=28%  Similarity=0.326  Sum_probs=15.7

Q ss_pred             CCCcEEEEccCCCCchHH
Q 042526           71 QRKDVIGAAETESGKTRA   88 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTla   88 (284)
                      .+..+++.+|+|||||..
T Consensus        50 ~~~~vll~GppGtGKT~l   67 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLL   67 (363)
T ss_dssp             CCCCEEEECCTTSSHHHH
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            467899999999999964

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=81.50  E-value=2.2  Score=36.96  Aligned_cols=51  Identities=14%  Similarity=0.176  Sum_probs=32.0

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHH----HHcCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPA----LAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~----il~~G~dviv~A~TGSGKTla   88 (284)
                      +-.+|.++.=.....+.|..+=.   .|.   ..|.    +...++.+++.+|+|+|||+.
T Consensus        16 ~~~~~~~i~G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vll~Gp~GtGKT~l   70 (297)
T 3b9p_A           16 AKVEWTDIAGQDVAKQALQEMVI---LPS---VRPELFTGLRAPAKGLLLFGPPGNGKTLL   70 (297)
T ss_dssp             SCCCGGGSCCCHHHHHHHHHHTH---HHH---HCGGGSCGGGCCCSEEEEESSSSSCHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHH---hhh---hCHHHHhcCCCCCCeEEEECcCCCCHHHH
Confidence            44679998767777777765310   000   0011    112467999999999999954

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=80.89  E-value=0.46  Score=41.34  Aligned_cols=52  Identities=15%  Similarity=0.158  Sum_probs=31.7

Q ss_pred             cccCcccCCCCHHHHHHHHHcC--CCCCcHHHHHHHHHH-HcCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLG--FKESTSILKARIPAL-AHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g--~~~pT~iQ~~aip~i-l~~G~dviv~A~TGSGKTla   88 (284)
                      +-.+|+++.-.+.+...+..+-  |..+     .++..+ +.-.+.+++.+|+|||||..
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~~~~~-----~~l~~~~~~~~~gvll~Gp~GtGKTtl   89 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEFLKNP-----SRFHEMGARIPKGVLLVGPPGVGKTHL   89 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHHHHCH-----HHHHHTTCCCCCEEEEECCTTSSHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHHCH-----HHHHHcCCCCCCeEEEECCCcChHHHH
Confidence            4567999987777777776532  1111     122211 01133499999999999944

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=80.47  E-value=1.7  Score=35.76  Aligned_cols=18  Identities=28%  Similarity=0.115  Sum_probs=15.6

Q ss_pred             cCCCcEEEEccCCCCchH
Q 042526           70 HQRKDVIGAAETESGKTR   87 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTl   87 (284)
                      ..|.-+++.+++|+|||.
T Consensus        21 ~~G~~~~i~G~~GsGKTt   38 (235)
T 2w0m_A           21 PQGFFIALTGEPGTGKTI   38 (235)
T ss_dssp             ETTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEEcCCCCCHHH
Confidence            457889999999999994

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=80.32  E-value=3.3  Score=36.81  Aligned_cols=25  Identities=40%  Similarity=0.462  Sum_probs=19.4

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQ   95 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~   95 (284)
                      ..|.=+++.|++|+||| +|++-++.
T Consensus        66 ~~G~l~li~G~pG~GKT-tl~l~ia~   90 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKT-AFALKQAK   90 (315)
T ss_dssp             CTTCEEEEECCTTSSHH-HHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHH-HHHHHHHH
Confidence            66888999999999999 45554443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=80.28  E-value=0.75  Score=36.31  Aligned_cols=17  Identities=24%  Similarity=0.298  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCCCchHH
Q 042526           72 RKDVIGAAETESGKTRA   88 (284)
Q Consensus        72 G~dviv~A~TGSGKTla   88 (284)
                      ++.+++.+++|+|||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            46899999999999943

---

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	284
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	1e-12
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-08
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-08
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	4e-08
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	5e-08
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	6e-08
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-08
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	9e-08
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	5e-07
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-06
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-04
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	6e-04
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	0.002

>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 = 63.8 bits (154), Expect = 1e-12
 Identities = 35/135 (25%), Positives = 66/135 (48%), Gaps = 12/135 (8%)

Query: 25  NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESG 84
            +   +   + ++EL+L P +  +I    ++  T I K  IPA+  + +D++  A+T SG
Sbjct: 12  PDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAIL-EHRDIMACAQTGSG 70

Query: 85  KTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVAS 144
           KT AF +P +  L+ +               ++Y+   + + LI+ PTRELA+Q+L  + 
Sbjct: 71  KTAAFLIPIINHLVCQDLN-----------QQRYSKTAYPKCLILAPTRELAIQILSESQ 119

Query: 145 PSLKSNSLTLAMAAG 159
               +  L   +  G
Sbjct: 120 KFSLNTPLRSCVVYG 134

>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 = 52.0 bits (124), Expect = 1e-08
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGL 91
          E+  +NEL L   ++ +I   GF++ T I    IP   +   +++  A T SGKT +F +
Sbjct: 2  EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAI 61

Query: 92 P 92
          P
Sbjct: 62 P 62

>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 = 51.1 bits (121), Expect = 4e-08
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 22/69 (31%)

Query: 71  QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIIN 130
           +++  I      +GKT+ +    ++  +                      K  LR LI+ 
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAI----------------------KRGLRTLILA 45

Query: 131 PTRELALQV 139
           PTR +A ++
Sbjct: 46  PTRVVAAEM 54

>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 = 50.2 bits (119), Expect = 4e-08
 Identities = 31/119 (26%), Positives = 58/119 (48%), Gaps = 21/119 (17%)

Query: 24  VNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETES 83
           V E+  +   D+++++ L   L++ IY  GF++ ++I +  I     +  DVI  A++ +
Sbjct: 2   VIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPC-IKGYDVIAQAQSGT 60

Query: 84  GKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMV 142
           GKT  F +  LQ++  + +                      +AL++ PTRELA Q+  V
Sbjct: 61  GKTATFAISILQQIELDLK--------------------ATQALVLAPTRELAQQIQKV 99

>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 = 50.1 bits (118), Expect = 5e-08
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFG 90
          T+F         P ++++I  L F + T I +  IP    + + ++G ++T +GKT A+ 
Sbjct: 1  TQFT---RFPFQPFIIEAIKTLRFYKPTEIQERIIPGA-LRGESMVGQSQTGTGKTHAYL 56

Query: 91 LP 92
          LP
Sbjct: 57 LP 58

>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 = 49.8 bits (118), Expect = 6e-08
 Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 4/79 (5%)

Query: 18 DAQEELVNEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIG 77
            + E   E +++  FD    + L   L++ IY  GF++ ++I +  I  +  + +DVI 
Sbjct: 4  KVEFETSEEVDVTPTFD---TMGLREDLLRGIYAYGFEKPSAIQQRAIKQI-IKGRDVIA 59

Query: 78 AAETESGKTRAFGLPALQR 96
           +++ +GKT  F +  LQ 
Sbjct: 60 QSQSGTGKTATFSISVLQC 78

>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 = 49.4 bits (117), Expect = 7e-08
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 4/79 (5%)

Query: 25  NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESG 84
           N  ++  +FD   ++ L   L++ ++  GF+E ++I +  I  +  +  DV+  A++ +G
Sbjct: 4   NYDKVVYKFD---DMELDENLLRGVFGYGFEEPSAIQQRAIMPI-IEGHDVLAQAQSGTG 59

Query: 85  KTRAFGLPALQRLLEEREK 103
           KT  F + ALQR+    + 
Sbjct: 60  KTGTFSIAALQRIDTSVKA 78

>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 = 49.2 bits (116), Expect = 9e-08
 Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 31  TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFG 90
            EF+   +  L   L+  I+++G+++ + I +  IP      +D++  A+  +GK+ A+ 
Sbjct: 3   NEFE---DYCLKRELLMGIFEMGWEKPSPIQEESIPIAL-SGRDILARAKNGTGKSGAYL 58

Query: 91  LPALQRLLEER 101
           +P L+RL  ++
Sbjct: 59  IPLLERLDLKK 69

>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 = 46.9 bits (110), Expect = 5e-07
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLP 92
          + + +  L   L+  I++ GF++ + I +  IP      +D++  A+  +GKT AF +P
Sbjct: 1  NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAI-TGRDILARAKNGTGKTAAFVIP 58

>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 = 46.0 bits (108), Expect = 1e-06
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPAL 94
           + +  L P L+++I   GF+  + +    IP       DV+  A++  GKT  F L  L
Sbjct: 2  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQA-ILGMDVLCQAKSGMGKTAVFVLATL 60

Query: 95 Q 95
          Q
Sbjct: 61 Q 61

>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 = 39.2 bits (90), Expect = 2e-04
 Identities = 9/65 (13%), Positives = 24/65 (36%), Gaps = 2/65 (3%)

Query: 33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLP 92
           +   E  +    +  + + G +E        +  +    K+++ A  T +GKT    + 
Sbjct: 3  VEELAE-SISSYAVGILKEEGIEELFPPQAEAVEKV-FSGKNLLLAMPTAAGKTLLAEMA 60

Query: 93 ALQRL 97
           ++  
Sbjct: 61 MVREA 65

>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 = 38.0 bits (87), Expect = 6e-04
 Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 6/92 (6%)

Query: 47  KSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEER----- 101
              ++    E  +I K     +  +++     A T  GKT      +L   L+ +     
Sbjct: 34  VEFFRKCVGEPRAIQKMWAKRIL-RKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVI 92

Query: 102 EKAAKMLEEKGEEAEKYAPKGHLRALIINPTR 133
              + ++ +  E   KYA K  +    +    
Sbjct: 93  FPTSLLVIQAAETIRKYAEKAGVGTENLIGYY 124

>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 = 36.5 bits (83), Expect = 0.002
 Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 38 ELRLHPLLMKSIYKL-GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQR 96
           L L     + + +  G+++     +  I  +    +D +    T  GK+  + +PAL  
Sbjct: 6  VLNLESGAKQVLQETFGYQQFRPGQEEIIDTVL-SGRDCLVVMPTGGGKSLCYQIPALLL 64

Query: 97 L 97
           
Sbjct: 65 N 65

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	284
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.98
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.97
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.96
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.87
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.78
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.77
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.6
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.41
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.21
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.2
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.07
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.93
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.77
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.67
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.62
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.22
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.1
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.71
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.3
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.23
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	96.19
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	95.76
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.37
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.65
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	92.01
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	91.6
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	91.55
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	90.57
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.51
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	90.36
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	89.14
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	88.81
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	88.2
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	88.18
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	88.07
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	87.94
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	87.5
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	87.45
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	86.91
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	86.54
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	86.22
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	86.16
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	84.66
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	84.66
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	84.22
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	83.43
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	82.48
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	82.34
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	82.33
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	81.45
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	81.4
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	81.34
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	81.14
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	81.07
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	80.19
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	80.09

>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=100.00  E-value=4.4e-39  Score=281.16  Aligned_cols=172  Identities=19%  Similarity=0.224  Sum_probs=153.4

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      ....+|++|+|++.|+++|.++||+.|||||++|||.+ +.|+|++++|+||||||+||++|+++++...          
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~i-l~g~dvi~~a~TGSGKTlayllPil~~l~~~----------   82 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQI-IKGRDVIAQSQSGTGKTATFSISVLQCLDIQ----------   82 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHTCCTT----------
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HCCCCeEEEcCcchhhhhhhccccccccccc----------
Confidence            45568999999999999999999999999999999999 8999999999999999999999999877543          


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc---------c
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT---------R  180 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~---------~  180 (284)
                                ...+++||++||||||.|+++++..++++.++++.+++|+ ....+...+..+++|++.+         .
T Consensus        83 ----------~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~  152 (222)
T d2j0sa1          83 ----------VRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR  152 (222)
T ss_dssp             ----------SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHT
T ss_pred             ----------ccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccc
Confidence                      2578999999999999999999999999999999777766 5566677788889998766         2


Q ss_pred             cCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          181 KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       181 ~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ....++++.++|+||||+|+++||.+++..++..+++.+|..+
T Consensus       153 ~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~il  195 (222)
T d2j0sa1         153 RSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVL  195 (222)
T ss_dssp             TSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEE
T ss_pred             cccccccceeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEEE
Confidence            3346789999999999999999999999999999999888766

>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=100.00  E-value=2e-37  Score=269.81  Aligned_cols=178  Identities=20%  Similarity=0.253  Sum_probs=152.9

Q ss_pred             cccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHH
Q 042526           25 NEAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKA  104 (284)
Q Consensus        25 ~~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~  104 (284)
                      -+++.|.++.+|++|+|++.|+++|.++||++|||||++|||.+ +.|+|++++|+||||||+||++|+++++...    
T Consensus         3 ~~~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~i-l~g~dvl~~a~TGsGKTlayllp~l~~i~~~----   77 (218)
T d2g9na1           3 IESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPC-IKGYDVIAQAQSGTGKTATFAISILQQIELD----   77 (218)
T ss_dssp             CCCCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HHTCCEEEECCTTSSHHHHHHHHHHHHCCTT----
T ss_pred             CCCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCEEEEcccchhhhhhhhhhhhheeccc----
Confidence            35667899999999999999999999999999999999999999 8999999999999999999999999887432    


Q ss_pred             HHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHH-hcCCCccccc---
Q 042526          105 AKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSN-RRKPNKRKRT---  179 (284)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l-~~~~~i~v~~---  179 (284)
                                      ..++++||++||||||.|++.++..+....++.+.+++|+ ....+.... ...+++++.+   
T Consensus        78 ----------------~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~r  141 (218)
T d2g9na1          78 ----------------LKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGR  141 (218)
T ss_dssp             ----------------CCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHH
T ss_pred             ----------------ccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChh
Confidence                            3688999999999999999999999999998887666665 344333333 3457776665   


Q ss_pred             ------ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          180 ------RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       180 ------~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                            .....++++.++|+||||+|++.||..++..++..+++++|..+
T Consensus       142 l~~~l~~~~~~~~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il  191 (218)
T d2g9na1         142 VFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVL  191 (218)
T ss_dssp             HHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEE
T ss_pred             HHHHHhcCCcccccceEEEeeecchhhcCchHHHHHHHHHhCCCCCeEEE
Confidence                  23457889999999999999999999999999999999888665

>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=100.00  E-value=1.2e-36  Score=262.52  Aligned_cols=170  Identities=19%  Similarity=0.275  Sum_probs=146.6

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..+|++|+|++.|+++|.++||++|||||++|||.+ ++|+|++++||||||||+||++|+++++...            
T Consensus         2 ~~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~i-l~g~dvl~~a~TGsGKTlayllP~l~~~~~~------------   68 (206)
T d1veca_           2 GNEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIA-LSGRDILARAKNGTGKSGAYLIPLLERLDLK------------   68 (206)
T ss_dssp             CSSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHH-HTTCCEEEECCSSSTTHHHHHHHHHHHCCTT------------
T ss_pred             CCChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCEEeeccCccccccccccchhhccccc------------
Confidence            368999999999999999999999999999999999 8999999999999999999999999876443            


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCC-CceeEEEeCC-CcchHHHHHhcCCCccccc---------cc
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSN-SLTLAMAAGS-PLLTSEHSNRRKPNKRKRT---------RK  181 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~-~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~---------~~  181 (284)
                              ..++++|||+||||||.|++.++..+.... ++.+..++|+ ....+...+..++++++.+         ..
T Consensus        69 --------~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~  140 (206)
T d1veca_          69 --------KDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKG  140 (206)
T ss_dssp             --------SCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTT
T ss_pred             --------ccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccch
Confidence                    357899999999999999999999988765 4566666665 4555556667788887765         22


Q ss_pred             CCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          182 GGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ...+++|.++|+||||.|++.||..++..++..+++..|..+
T Consensus       141 ~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~~l  182 (206)
T d1veca_         141 VAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILL  182 (206)
T ss_dssp             CSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCEEEE
T ss_pred             hccccccceEEEeccccccccchHHHHHHHHHhCCCCCEEEE
Confidence            346789999999999999999999999999999988887665

>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=100.00  E-value=1.4e-36  Score=263.29  Aligned_cols=177  Identities=20%  Similarity=0.311  Sum_probs=150.0

Q ss_pred             ccccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHH
Q 042526           26 EAEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAA  105 (284)
Q Consensus        26 ~~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~  105 (284)
                      +.|.|.++.+|++|+|++.|+++|.++||++|||||++|||.+ +.|+|++++||||||||+||++|+++++...     
T Consensus         2 ~~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~i-l~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~-----   75 (212)
T d1qdea_           2 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPI-IEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----   75 (212)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----
T ss_pred             CCCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCEEeecccccchhhhhHhhhHhhhhcc-----
Confidence            5678999999999999999999999999999999999999999 9999999999999999999999999987432     


Q ss_pred             HHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc------
Q 042526          106 KMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT------  179 (284)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~------  179 (284)
                                     ..+|++|||+||||||.|++.++..+.....+.+..++|+....+.....+++++++.+      
T Consensus        76 ---------------~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~  140 (212)
T d1qdea_          76 ---------------VKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFD  140 (212)
T ss_dssp             ---------------CCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHH
T ss_pred             ---------------CCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhcCCcEEEECCCcccc
Confidence                           35799999999999999999999999998888887777765554445555678887765      


Q ss_pred             ---ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          180 ---RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       180 ---~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                         .....+.++.++|+||||.|+++||..++..++..+++..|..+
T Consensus       141 ~~~~~~~~l~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl  187 (212)
T d1qdea_         141 NIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVL  187 (212)
T ss_dssp             HHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEE
T ss_pred             ccccCceecCcceEEeehhhhhhcccchHHHHHHHHHhCCCCCeEEE
Confidence               23346889999999999999999999999999999988877554

>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=100.00  E-value=1.6e-35  Score=255.54  Aligned_cols=169  Identities=21%  Similarity=0.267  Sum_probs=143.5

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      ++|++|+|++.|+++|.++||++|||||++|||.+ ++|+|++++||||||||+||++|+++++..              
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~i-l~g~dvl~~A~TGsGKTla~~lp~l~~~~~--------------   65 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQA-ILGMDVLCQAKSGMGKTAVFVLATLQQLEP--------------   65 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHH-HTTCCEEEECCTTSCHHHHHHHHHHHHCCC--------------
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCeEEEeccccccccccccceeeeecc--------------
Confidence            47999999999999999999999999999999999 999999999999999999999999986543              


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCC-ceeEEEeCC-CcchHHHHHh-cCCCcccccc---------c
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNS-LTLAMAAGS-PLLTSEHSNR-RKPNKRKRTR---------K  181 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~-i~v~~~~G~-~~~~q~~~l~-~~~~i~v~~~---------~  181 (284)
                            ...+++++|++||||||.|+++.++.++.+.+ +++++++|+ ....+...+. ..+++++.+.         .
T Consensus        66 ------~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~  139 (207)
T d1t6na_          66 ------VTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNK  139 (207)
T ss_dssp             ------CTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTT
T ss_pred             ------cCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCC
Confidence                  23578999999999999999999999998874 566666666 4455555554 4678877652         2


Q ss_pred             CCccccccccCCCCCCcccc-cccccchhhhcccCCCCCCCcc
Q 042526          182 GGEDEKLDSLKWNPLSQPKT-TTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       182 ~~~~d~l~~lv~dEAd~m~~-~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ...+++|.++|+||||+|++ +||..++..++..+++.+|..+
T Consensus       140 ~~~l~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il  182 (207)
T d1t6na_         140 SLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMM  182 (207)
T ss_dssp             SSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEE
T ss_pred             ceeccccceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEE
Confidence            34688999999999999997 6899999999999988887655

>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=100.00  E-value=5.5e-36  Score=263.81  Aligned_cols=178  Identities=21%  Similarity=0.298  Sum_probs=150.8

Q ss_pred             cccCccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHH
Q 042526           27 AEISTEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAK  106 (284)
Q Consensus        27 ~~~p~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~  106 (284)
                      .+.|.++.+|++|+|++.|+++|.++||++|||||++|||.+ +.|+|++++||||||||+||++|+|+++......   
T Consensus        14 ~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~i-l~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~---   89 (238)
T d1wrba1          14 YSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAI-LEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLN---   89 (238)
T ss_dssp             SSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHH-HTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhh-hCCCCEEEECCCCCCcceeeHHHHHHHHHhcccc---
Confidence            345788999999999999999999999999999999999999 8999999999999999999999999998753210   


Q ss_pred             HHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCcccccc-----
Q 042526          107 MLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRTR-----  180 (284)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~~-----  180 (284)
                              ........+|+||||+||||||.|++.++..++...++++.+++|+ ....+...+..++++++.+.     
T Consensus        90 --------~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~  161 (238)
T d1wrba1          90 --------QQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVD  161 (238)
T ss_dssp             -------------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHH
T ss_pred             --------cccccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHh
Confidence                    0123345689999999999999999999999999999999888776 45556667777889877662     


Q ss_pred             ----cCCccccccccCCCCCCcccccccccchhhhcccCC
Q 042526          181 ----KGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTE  216 (284)
Q Consensus       181 ----~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~  216 (284)
                          ....+.++.++|+||||.|++.||.+++..++..+.
T Consensus       162 ~~~~~~~~l~~v~~lViDEaD~ll~~~f~~~i~~Il~~~~  201 (238)
T d1wrba1         162 FIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESN  201 (238)
T ss_dssp             HHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSC
T ss_pred             HHccCceeccccceeeeehhhhhhhhccHHHHHHHHHHhc
Confidence                234588999999999999999999999999887553

>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=99.98  E-value=2.5e-33  Score=241.65  Aligned_cols=169  Identities=22%  Similarity=0.306  Sum_probs=147.3

Q ss_pred             ccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhh
Q 042526           33 FDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEK  111 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~  111 (284)
                      +.+|++|+|++.|+++|.++||..|||+|++|||.+ ++| +|++++||||||||++|++|++++...            
T Consensus         3 ~msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~-l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~------------   69 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLF-LNDEYNIVAQARTGSGKTASFAIPLIELVNE------------   69 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHH-HHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------------
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCCeeeechhcccccceeeccccccccc------------
Confidence            579999999999999999999999999999999998 666 599999999999999999999875432            


Q ss_pred             hhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc---------ccC
Q 042526          112 GEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT---------RKG  182 (284)
Q Consensus       112 ~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~---------~~~  182 (284)
                               ..++++|||+||++||.|++.++..+....++++.+++|+..........+++++++.|         ...
T Consensus        70 ---------~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~IlV~TP~~l~~~l~~~~  140 (208)
T d1hv8a1          70 ---------NNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGT  140 (208)
T ss_dssp             ---------SSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTC
T ss_pred             ---------ccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcCCCCEEEEChHHHHHHHHcCC
Confidence                     36889999999999999999999999999999998888886555544555688998876         223


Q ss_pred             CccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          183 GEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       183 ~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      ..+++|.++|+||||+|++.+|.+++..++..+++..|..+
T Consensus       141 ~~~~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~  181 (208)
T d1hv8a1         141 LNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILL  181 (208)
T ss_dssp             SCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEE
T ss_pred             CCcccCcEEEEEChHHhhcCCChHHHHHHHHhCCCCCeEEE
Confidence            46889999999999999999999999999999888777554

>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=99.97  E-value=5.2e-33  Score=239.04  Aligned_cols=169  Identities=21%  Similarity=0.298  Sum_probs=150.1

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      .||++|+|++.|+++|.++||.+|||+|++|||.+ +.|+|++++||||||||+||++|+++++...             
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~i-l~g~dvi~~a~tGsGKTlay~lp~i~~~~~~-------------   66 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVA-ITGRDILARAKNGTGKTAAFVIPTLEKVKPK-------------   66 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-------------
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHH-HcCCCEEEecCCcchhhhhhccccccccccc-------------
Confidence            38999999999999999999999999999999999 9999999999999999999999999876443             


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCC-CcchHHHHHhcCCCccccc---------ccCC
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGS-PLLTSEHSNRRKPNKRKRT---------RKGG  183 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~-~~~~q~~~l~~~~~i~v~~---------~~~~  183 (284)
                             ...+++++++|+++++.|+..++..+....++++.+++|+ ....+...+..++++++.+         ....
T Consensus        67 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~  139 (206)
T d1s2ma1          67 -------LNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVA  139 (206)
T ss_dssp             -------SCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCS
T ss_pred             -------cccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCccccccccccee
Confidence                   3578899999999999999999999999999999888776 5666666777888887766         2234


Q ss_pred             ccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          184 EDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       184 ~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      .+++|.++|+||||.|++.||.+++..++..+++..|..+
T Consensus       140 ~l~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il  179 (206)
T d1s2ma1         140 DLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLL  179 (206)
T ss_dssp             CCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEE
T ss_pred             ecccceEEEeechhhhhhhhhHHHHHHHHHhCCCCCEEEE
Confidence            6889999999999999999999999999999998887655

>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=99.96  E-value=1.1e-30  Score=223.94  Aligned_cols=169  Identities=18%  Similarity=0.246  Sum_probs=142.1

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      ++|++|+|++.|+++|+++||++|||+|++|||.+ +.|+|++++||||||||+||++|+++.+...             
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~-l~G~dvii~a~TGSGKTlayllp~l~~~~~~-------------   66 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGA-LRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-------------   66 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHH-HHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-------------
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHH-HCCCCeEeecccccccceeeeeeeccccccc-------------
Confidence            47999999999999999999999999999999999 9999999999999999999999999876543             


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCC----ceeEEEeCCC-cchHHHHHhcCCCccccc---------
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNS----LTLAMAAGSP-LLTSEHSNRRKPNKRKRT---------  179 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~----i~v~~~~G~~-~~~q~~~l~~~~~i~v~~---------  179 (284)
                             ...+..++++|+++++.|.+..+........    ..+.++.|+. ...+...+..++++++.+         
T Consensus        67 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~  139 (209)
T d1q0ua_          67 -------RAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIR  139 (209)
T ss_dssp             -------SCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHH
T ss_pred             -------cccccccccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhh
Confidence                   3567899999999999999999887766543    3455555554 444445566778887765         


Q ss_pred             ccCCccccccccCCCCCCcccccccccchhhhcccCCCCCCCcc
Q 042526          180 RKGGEDEKLDSLKWNPLSQPKTTTLLPSSLALMNLTEGKPGKKL  223 (284)
Q Consensus       180 ~~~~~~d~l~~lv~dEAd~m~~~gflp~~~~~~~~~~r~~~~~~  223 (284)
                      .....+++|.++|+||||.|++.||.+++..++..+++..|..+
T Consensus       140 ~~~~~~~~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q~il  183 (209)
T d1q0ua_         140 EQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLV  183 (209)
T ss_dssp             TTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEE
T ss_pred             hhccccccceEEEEeecccccccccHHHHHHHHHHCCCCCEEEE
Confidence            23457889999999999999999999999999999988887655

>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=99.87  E-value=6.4e-23  Score=178.44  Aligned_cols=165  Identities=15%  Similarity=0.022  Sum_probs=117.6

Q ss_pred             ccccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhh
Q 042526           31 TEFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEE  110 (284)
Q Consensus        31 ~~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~  110 (284)
                      ..+..|.+.++.+.+ .++.+.+|..|+++|..+||.+ +.|+|++++||||||||++|++|++..+.            
T Consensus        19 ~~~~~~~~~~~~~~~-~~~~~~~~~~p~~~Q~~~i~~~-l~g~~~~i~apTGsGKT~~~~~~~~~~~~------------   84 (237)
T d1gkub1          19 ASLCLFPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRI-LRKESFAATAPTGVGKTSFGLAMSLFLAL------------   84 (237)
T ss_dssp             CCCSCCTTHHHHHHH-HHHHHTTTCSCCHHHHHHHHHH-HTTCCEECCCCBTSCSHHHHHHHHHHHHT------------
T ss_pred             cccccCccchhHHHH-HHHHHhccCCCCHHHHHHHHHH-HCCCCEEEEecCCChHHHHHHHHHHHHHH------------
Confidence            344556665555554 4556678999999999999999 99999999999999999999999875432            


Q ss_pred             hhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCcee----EEEeCCCcch-HHHHHh--cCCCcccccc---
Q 042526          111 KGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTL----AMAAGSPLLT-SEHSNR--RKPNKRKRTR---  180 (284)
Q Consensus       111 ~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v----~~~~G~~~~~-q~~~l~--~~~~i~v~~~---  180 (284)
                                 .+.++|||+||++|+.|+++.++.+....++.+    ..+.+..... +...+.  ..++|++.+.   
T Consensus        85 -----------~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l  153 (237)
T d1gkub1          85 -----------KGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFL  153 (237)
T ss_dssp             -----------TSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHH
T ss_pred             -----------hcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHH
Confidence                       245899999999999999999999998876543    3333443333 222222  3366666542   


Q ss_pred             --cCCccccccccCCCCCCcccc-----------cccccchhhhcccCCCCCC
Q 042526          181 --KGGEDEKLDSLKWNPLSQPKT-----------TTLLPSSLALMNLTEGKPG  220 (284)
Q Consensus       181 --~~~~~d~l~~lv~dEAd~m~~-----------~gflp~~~~~~~~~~r~~~  220 (284)
                        ..+.+.++..+|+||+|.|++           +||...+.......+...|
T Consensus       154 ~~~~~~~~~~~~vVvDE~d~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~  206 (237)
T d1gkub1         154 SKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGC  206 (237)
T ss_dssp             HHCSTTSCCCSEEEESCHHHHHTSTHHHHHHHHHTTEEEETTTTEEEECCSSE
T ss_pred             HHhhhhcCCCCEEEEEChhhhhhcccchhHHHHhcCChHHHHHHHhhCCCCCe
Confidence              224566788899999998765           5666666555444444433

>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=99.78  E-value=2.3e-20  Score=158.48  Aligned_cols=141  Identities=11%  Similarity=-0.010  Sum_probs=103.8

Q ss_pred             cCcccCCCCHHHHHHHHHc-CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhh
Q 042526           34 DAWNELRLHPLLMKSIYKL-GFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKG  112 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~-g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~  112 (284)
                      ..++.++|++.+.+.|+++ ||+.++|+|.+||+++ +.|+|++++||||||||++|.+|++.                 
T Consensus         2 ~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~-l~g~~vlv~apTGsGKT~~~~~~~~~-----------------   63 (206)
T d1oywa2           2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTV-LSGRDCLVVMPTGGGKSLCYQIPALL-----------------   63 (206)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHH-HTTCCEEEECSCHHHHHHHHHHHHHH-----------------
T ss_pred             CchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCCCCcchhhhhhhh-----------------
Confidence            3467789999999999986 9999999999999999 89999999999999999999999864                 


Q ss_pred             hhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcch----H-HHHHhcCCCcccccc-------
Q 042526          113 EEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLT----S-EHSNRRKPNKRKRTR-------  180 (284)
Q Consensus       113 ~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~----q-~~~l~~~~~i~v~~~-------  180 (284)
                               ...+++|++||++|+.|+...++.+...    .....+.....    . .........+++.+.       
T Consensus        64 ---------~~~~~~~v~P~~~L~~q~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~  130 (206)
T d1oywa2          64 ---------LNGLTVVVSPLISLMKDQVDQLQANGVA----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDN  130 (206)
T ss_dssp             ---------SSSEEEEECSCHHHHHHHHHHHHHTTCC----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTT
T ss_pred             ---------ccCceEEeccchhhhhhHHHHHHhhccc----ccccccccccccchhHHHHHhcCCceEEEEechhhhchh
Confidence                     1346999999999999999999877443    22332222111    1 112222344433321       


Q ss_pred             --cCCccccccccCCCCCCcccccccc
Q 042526          181 --KGGEDEKLDSLKWNPLSQPKTTTLL  205 (284)
Q Consensus       181 --~~~~~d~l~~lv~dEAd~m~~~gfl  205 (284)
                        .......+..+++|||+.+.+.|+.
T Consensus       131 ~~~~~~~~~v~~lviDEaH~~~~~~~~  157 (206)
T d1oywa2         131 FLEHLAHWNPVLLAVDEAHCISQWGHD  157 (206)
T ss_dssp             HHHHHTTSCEEEEEESSGGGGCTTSSC
T ss_pred             hcccchhheeeeeeeeeeeeeeccccc
Confidence              1123446888999999998887743

>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=99.77  E-value=7.4e-20  Score=155.10  Aligned_cols=137  Identities=13%  Similarity=0.099  Sum_probs=102.6

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCC
Q 042526           41 LHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAP  120 (284)
Q Consensus        41 L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~  120 (284)
                      +++.++..|.+.||..|+|+|.+||+.+ ++|+|++++||||||||++|+++++..+..                     
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l-~~~~~~il~apTGsGKT~~a~l~i~~~~~~---------------------   67 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKV-FSGKNLLLAMPTAAGKTLLAEMAMVREAIK---------------------   67 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHH-TTCSCEEEECSSHHHHHHHHHHHHHHHHHT---------------------
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHH-HcCCCEEEEcCCCCchhHHHHHHHHHHhhc---------------------
Confidence            7889999999999999999999999999 899999999999999999999999876533                     


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc---------ccCCcccccccc
Q 042526          121 KGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT---------RKGGEDEKLDSL  191 (284)
Q Consensus       121 ~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~---------~~~~~~d~l~~l  191 (284)
                        ..++|||+||++|+.|++..++.+.... ..+..++|.....  ......+++++.+         .....+..+..+
T Consensus        68 --~~~vl~l~P~~~L~~q~~~~~~~~~~~~-~~v~~~~~~~~~~--~~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~i  142 (202)
T d2p6ra3          68 --GGKSLYVVPLRALAGEKYESFKKWEKIG-LRIGISTGDYESR--DEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCL  142 (202)
T ss_dssp             --TCCEEEEESSHHHHHHHHHHHTTTTTTT-CCEEEECSSCBCC--SSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEE
T ss_pred             --cCcceeecccHHHHHHHHHHHHHHhhcc-ccceeeccCcccc--cccccccceeeeccHHHHHHHhccchhhhhhhhc
Confidence              3479999999999999999999887644 3455555543322  1222334443322         223457788889


Q ss_pred             CCCCCCccccccc
Q 042526          192 KWNPLSQPKTTTL  204 (284)
Q Consensus       192 v~dEAd~m~~~gf  204 (284)
                      ++||++.+.+.++
T Consensus       143 i~DE~h~~~~~~r  155 (202)
T d2p6ra3         143 VVDEIHLLDSEKR  155 (202)
T ss_dssp             EETTGGGGGCTTT
T ss_pred             cccHHHHhccccc
Confidence            9999998776553

>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=99.60  E-value=1.6e-15  Score=127.01  Aligned_cols=125  Identities=13%  Similarity=0.029  Sum_probs=94.5

Q ss_pred             CCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHH
Q 042526           55 KESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRE  134 (284)
Q Consensus        55 ~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTRe  134 (284)
                      -.|.++|..++..+ . ++|+|+++|||||||++|++++...+..                      .+-++||++||++
T Consensus         8 ~~pr~~Q~~~~~~~-~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~----------------------~~~~il~i~P~~~   63 (200)
T d1wp9a1           8 IQPRIYQEVIYAKC-K-ETNCLIVLPTGLGKTLIAMMIAEYRLTK----------------------YGGKVLMLAPTKP   63 (200)
T ss_dssp             HCCCHHHHHHHHHG-G-GSCEEEECCTTSCHHHHHHHHHHHHHHH----------------------SCSCEEEECSSHH
T ss_pred             CCCCHHHHHHHHHH-h-cCCeEEEeCCCCcHHHHHHHHHHHHHHh----------------------cCCcEEEEcCchH
Confidence            36999999999876 4 6689999999999999999887665433                      1346999999999


Q ss_pred             HHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc---------ccCCccccccccCCCCCCcccccc
Q 042526          135 LALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT---------RKGGEDEKLDSLKWNPLSQPKTTT  203 (284)
Q Consensus       135 La~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~---------~~~~~~d~l~~lv~dEAd~m~~~g  203 (284)
                      |+.|.++.+..+....+..+..+.++....+.........+++.+         .....++++..+++|||.++..-.
T Consensus        64 L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~  141 (200)
T d1wp9a1          64 LVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNY  141 (200)
T ss_dssp             HHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTC
T ss_pred             HHHHHHHHHHHhhcccccceeeeecccchhHHHHhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcch
Confidence            999999999999888888888777776665555544444554433         111245677889999998865433

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.41  E-value=6.6e-14  Score=123.61  Aligned_cols=103  Identities=12%  Similarity=0.082  Sum_probs=68.5

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcC
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLKS  149 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~  149 (284)
                      ..|+++++.||||||||++|++|++......                      +.++|||+|||+||.|+++.++.+...
T Consensus         7 ~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~----------------------~~~~lvi~Ptr~La~q~~~~l~~~~~~   64 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTKRYLPAIVREAIKR----------------------GLRTLILAPTRVVAAEMEEALRGLPIR   64 (305)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHH----------------------TCCEEEEESSHHHHHHHHHHTTTSCCB
T ss_pred             hcCCcEEEEECCCCCHHHHHHHHHHHHHHhc----------------------CCEEEEEccHHHHHHHHHHHHhcCCcc
Confidence            7899999999999999999998988765543                      467999999999999999988766432


Q ss_pred             CCceeEEEeCCCcchHHHHHhcCCCccccc--------ccCCccccccccCCCCCCccccccc
Q 042526          150 NSLTLAMAAGSPLLTSEHSNRRKPNKRKRT--------RKGGEDEKLDSLKWNPLSQPKTTTL  204 (284)
Q Consensus       150 ~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~--------~~~~~~d~l~~lv~dEAd~m~~~gf  204 (284)
                      ...  ....+...        ....+++.+        .....+.++..+|+||++++...++
T Consensus        65 ~~~--~~~~~~~~--------~~~~i~~~t~~~l~~~~~~~~~~~~~~~vViDE~H~~~~~~~  117 (305)
T d2bmfa2          65 YQT--PAIRAEHT--------GREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASI  117 (305)
T ss_dssp             CCC------------------CCCSEEEEEHHHHHHHHTSSSCCCCCSEEEEESTTCCSHHHH
T ss_pred             eee--eEEeeccc--------CccccccCCcHHHHHHHhcCccccceeEEEeeeeeecchhhH
Confidence            211  11111000        011111111        1223456788899999999876553

>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=99.21  E-value=4.2e-11  Score=103.31  Aligned_cols=134  Identities=17%  Similarity=0.055  Sum_probs=101.2

Q ss_pred             CCCHHHHHHHHH-cCCCCCcHHHHHHHHHHH---cCC--CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhh
Q 042526           40 RLHPLLMKSIYK-LGFKESTSILKARIPALA---HQR--KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGE  113 (284)
Q Consensus        40 ~L~~~Ll~~L~~-~g~~~pT~iQ~~aip~il---~~G--~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~  113 (284)
                      ..+....+.+.+ +.| .+|+-|..|+..+.   .++  .+.++++.||||||..|+..+...+.               
T Consensus        39 ~~~~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~---------------  102 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD---------------  102 (233)
T ss_dssp             CCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT---------------
T ss_pred             CCCHHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH---------------
Confidence            345666666655 555 49999999998772   333  47899999999999999998876553               


Q ss_pred             hhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH----Hhc-CCCcccccccCC----c
Q 042526          114 EAEKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS----NRR-KPNKRKRTRKGG----E  184 (284)
Q Consensus       114 ~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~----l~~-~~~i~v~~~~~~----~  184 (284)
                              .+-++++|+||..||.|.+..++.+...+++.+++++|.....+...    +.. ..++++.+....    .
T Consensus       103 --------~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~  174 (233)
T d2eyqa3         103 --------NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVK  174 (233)
T ss_dssp             --------TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCC
T ss_pred             --------cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCc
Confidence                    36689999999999999999999998889999999998866554322    333 367777664332    4


Q ss_pred             cccccccCCCCCC
Q 042526          185 DEKLDSLKWNPLS  197 (284)
Q Consensus       185 ~d~l~~lv~dEAd  197 (284)
                      +.+|--+|.||--
T Consensus       175 f~~LgLiIiDEeH  187 (233)
T d2eyqa3         175 FKDLGLLIVDEEH  187 (233)
T ss_dssp             CSSEEEEEEESGG
T ss_pred             cccccceeeechh
Confidence            5677778888844

>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=99.20  E-value=3.8e-11  Score=105.44  Aligned_cols=132  Identities=18%  Similarity=0.125  Sum_probs=100.0

Q ss_pred             CHHHHHH-HHHcCCCCCcHHHHHHHHHHH---cC--CCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 042526           42 HPLLMKS-IYKLGFKESTSILKARIPALA---HQ--RKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEA  115 (284)
Q Consensus        42 ~~~Ll~~-L~~~g~~~pT~iQ~~aip~il---~~--G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~  115 (284)
                      ...+.+. +..+.|+ +|+-|..|+..|.   .+  ..+.++++.||||||..|+..++..+..                
T Consensus        69 ~~~l~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~----------------  131 (264)
T d1gm5a3          69 EGKLAEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA----------------  131 (264)
T ss_dssp             CTHHHHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH----------------
T ss_pred             ChHHHHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc----------------
Confidence            3344444 4567785 9999999999882   22  3477999999999999999999876644                


Q ss_pred             hhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH----Hhc-CCCcccccccCC----ccc
Q 042526          116 EKYAPKGHLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS----NRR-KPNKRKRTRKGG----EDE  186 (284)
Q Consensus       116 ~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~----l~~-~~~i~v~~~~~~----~~d  186 (284)
                             +-++++|+||..||.|.+..+..+....++.++++.|+....+...    +.. ..+++|.+....    .+.
T Consensus       132 -------g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~  204 (264)
T d1gm5a3         132 -------GFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFK  204 (264)
T ss_dssp             -------TSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCS
T ss_pred             -------ccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCcc
Confidence                   4589999999999999999999999989999999998876655332    333 367777765433    345


Q ss_pred             cccccCCCCCC
Q 042526          187 KLDSLKWNPLS  197 (284)
Q Consensus       187 ~l~~lv~dEAd  197 (284)
                      +|--+|.||.-
T Consensus       205 ~LglviiDEqH  215 (264)
T d1gm5a3         205 NLGLVIIDEQH  215 (264)
T ss_dssp             CCCEEEEESCC
T ss_pred             ccceeeecccc
Confidence            67777888843

>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=99.07  E-value=1.2e-10  Score=103.18  Aligned_cols=120  Identities=14%  Similarity=0.008  Sum_probs=80.2

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|.+.|..|+..+ +..+..++.+|||+|||+..+. ++..+...                     ..-++||||||++|
T Consensus       113 ~~rdyQ~~av~~~-l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~---------------------~~~k~Liivp~~~L  169 (282)
T d1rifa_         113 EPHWYQKDAVFEG-LVNRRRILNLPTSAGRSLIQAL-LARYYLEN---------------------YEGKILIIVPTTAL  169 (282)
T ss_dssp             CCCHHHHHHHHHH-HHHSEEEECCCTTSCHHHHHHH-HHHHHHHH---------------------CSSEEEEECSSHHH
T ss_pred             ccchHHHHHHHHH-HhcCCceeEEEcccCccHHHHH-HHHHhhhc---------------------ccceEEEEEcCchh
Confidence            5899999999998 6677789999999999987543 33333222                     23479999999999


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCCCcchHHHHHhcCCCccccc------ccCCccccccccCCCCCCccc
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHSNRRKPNKRKRT------RKGGEDEKLDSLKWNPLSQPK  200 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~l~~~~~i~v~~------~~~~~~d~l~~lv~dEAd~m~  200 (284)
                      +.|.++.+..+.......+..++++......  ......+.+.+      .....++....+++|||=+..
T Consensus       170 v~Q~~~~f~~~~~~~~~~~~~~~~g~~~~~~--~~~~~~i~i~t~qs~~~~~~~~~~~f~~VIvDEaH~~~  238 (282)
T d1rifa_         170 TTQMADDFVDYRLFSHAMIKKIGGGASKDDK--YKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLAT  238 (282)
T ss_dssp             HHHHHHHHHHHTSCCGGGEEECSTTCSSTTC--CCTTCSEEEECHHHHTTSCGGGGGGEEEEEEETGGGCC
T ss_pred             HHHHHHHHHHhhccccccceeecceeccccc--ccccceEEEEeeehhhhhcccccCCCCEEEEECCCCCC
Confidence            9999999998876555555566665433211  11112222222      112245567889999987743

>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=98.93  E-value=3.5e-11  Score=93.19  Aligned_cols=56  Identities=21%  Similarity=0.216  Sum_probs=45.8

Q ss_pred             HcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhh
Q 042526           69 AHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPS  146 (284)
Q Consensus        69 l~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l  146 (284)
                      +..|+++++.+|||||||+.++..++..+..                      .+.++||++|+++|+.|.++.+..+
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~----------------------~~~~vli~~p~~~l~~q~~~~~~~~   59 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR----------------------RRLRTLVLAPTRVVLSEMKEAFHGL   59 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH----------------------TTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh----------------------cCceeeeeecchhHHHHHHHHhhhh
Confidence            3679999999999999999887666665533                      2567999999999999999887543

>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=98.77  E-value=8.2e-09  Score=86.53  Aligned_cols=75  Identities=19%  Similarity=-0.001  Sum_probs=57.2

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .|.+.|.+++..+ ..+...++.+|||+|||+..+..+ ..                         ...++|||||++.|
T Consensus        70 ~Lr~yQ~eav~~~-~~~~~~ll~~~tG~GKT~~a~~~~-~~-------------------------~~~~~Liv~p~~~L  122 (206)
T d2fz4a1          70 SLRDYQEKALERW-LVDKRGCIVLPTGSGKTHVAMAAI-NE-------------------------LSTPTLIVVPTLAL  122 (206)
T ss_dssp             CCCHHHHHHHHHH-TTTSEEEEEESSSTTHHHHHHHHH-HH-------------------------SCSCEEEEESSHHH
T ss_pred             CcCHHHHHHHHHH-HhCCCcEEEeCCCCCceehHHhHH-HH-------------------------hcCceeEEEcccch
Confidence            5889999999998 777788899999999998754322 11                         12358999999999


Q ss_pred             HHHHHHHHhhhhcCCCceeEEEeCC
Q 042526          136 ALQVLMVASPSLKSNSLTLAMAAGS  160 (284)
Q Consensus       136 a~Qi~~~~~~l~~~~~i~v~~~~G~  160 (284)
                      +.|..+.+..+...   .+..+.|.
T Consensus       123 ~~q~~~~~~~~~~~---~~~~~~~~  144 (206)
T d2fz4a1         123 AEQWKERLGIFGEE---YVGEFSGR  144 (206)
T ss_dssp             HHHHHHHHGGGCGG---GEEEESSS
T ss_pred             HHHHHHHHHhhccc---chhhcccc
Confidence            99999999877543   34444454

>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=98.67  E-value=2e-09  Score=84.03  Aligned_cols=52  Identities=23%  Similarity=0.188  Sum_probs=39.2

Q ss_pred             CCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHHHHHHHHhhhhc
Q 042526           71 QRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELALQVLMVASPSLK  148 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~Qi~~~~~~l~~  148 (284)
                      ..+..++.||||||||+.+  +.+  +..                      .+.++||++||++|+.|+...+.....
T Consensus         7 ~~~~~ll~apTGsGKT~~~--~~~--~~~----------------------~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKV--PAA--YAA----------------------QGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHH--HHH--HHT----------------------TTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCCEEEEEeCCCCCHHHHH--HHH--HHH----------------------cCCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            4567799999999999643  221  111                      245799999999999999999887644

>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=97.62  E-value=4.6e-05  Score=65.43  Aligned_cols=71  Identities=14%  Similarity=0.026  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      +++|-|.+|+-.   ....++|.|+.|||||.+.+--+ .++....               .   ...-++|||++|+.+
T Consensus         1 ~L~~eQ~~av~~---~~~~~lI~g~aGTGKTt~l~~rv-~~ll~~~---------------~---~~~~~ILvlt~tn~a   58 (306)
T d1uaaa1           1 RLNPGQQQAVEF---VTGPCLVLAGAGSGKTRVITNKI-AHLIRGC---------------G---YQARHIAAVTFTNKA   58 (306)
T ss_dssp             CCCHHHHHHHHC---CSSEEEECCCTTSCHHHHHHHHH-HHHHHHH---------------C---CCGGGEEEEESSHHH
T ss_pred             CcCHHHHHHHhC---CCCCEEEEeeCCccHHHHHHHHH-HHHHHhc---------------C---CChhHEEEEeCcHHH
Confidence            468999999953   34579999999999997654333 3333321               0   122368999999999


Q ss_pred             HHHHHHHHhhhhc
Q 042526          136 ALQVLMVASPSLK  148 (284)
Q Consensus       136 a~Qi~~~~~~l~~  148 (284)
                      |..+...+..+..
T Consensus        59 ~~~i~~~~~~~~~   71 (306)
T d1uaaa1          59 AREMKERVGQTLG   71 (306)
T ss_dssp             HHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHhcC
Confidence            9999888877654

>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=97.22  E-value=0.00034  Score=60.37  Aligned_cols=71  Identities=17%  Similarity=0.074  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      .+++=|..+|-..   +..++|.|+.|||||.+.+--+...+...                   ....-++|++++|+..
T Consensus        11 ~L~~eQ~~~v~~~---~g~~lV~g~aGSGKTt~l~~ri~~ll~~~-------------------~~~p~~il~lt~t~~a   68 (318)
T d1pjra1          11 HLNKEQQEAVRTT---EGPLLIMAGAGSGKTRVLTHRIAYLMAEK-------------------HVAPWNILAITFTNKA   68 (318)
T ss_dssp             TSCHHHHHHHHCC---SSCEEEEECTTSCHHHHHHHHHHHHHHTT-------------------CCCGGGEEEEESSHHH
T ss_pred             hCCHHHHHHHhCC---CCCEEEEecCCccHHHHHHHHHHHHHHcC-------------------CCCHHHeEeEeccHHH
Confidence            4789999999643   45799999999999976654333322111                   1112368999999999


Q ss_pred             HHHHHHHHhhhhc
Q 042526          136 ALQVLMVASPSLK  148 (284)
Q Consensus       136 a~Qi~~~~~~l~~  148 (284)
                      |..+...+.....
T Consensus        69 a~~~~~~~~~~~~   81 (318)
T d1pjra1          69 AREMRERVQSLLG   81 (318)
T ss_dssp             HHHHHHHHHHHHG
T ss_pred             HHHHHHHHHhhcc
Confidence            9999998876544

>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=97.10  E-value=0.00057  Score=61.19  Aligned_cols=72  Identities=18%  Similarity=0.171  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHH
Q 042526           56 ESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTREL  135 (284)
Q Consensus        56 ~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReL  135 (284)
                      ..+.-|..|+-.+ +.++-+++++++|||||... .-++..+...                  ....+.++++++||.--
T Consensus       148 ~~~~~Q~~A~~~a-l~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~------------------~~~~~~~I~l~ApTgkA  207 (359)
T d1w36d1         148 DEINWQKVAAAVA-LTRRISVISGGPGTGKTTTV-AKLLAALIQM------------------ADGERCRIRLAAPTGKA  207 (359)
T ss_dssp             TSCCHHHHHHHHH-HTBSEEEEECCTTSTHHHHH-HHHHHHHHHT------------------CSSCCCCEEEEBSSHHH
T ss_pred             ccccHHHHHHHHH-HcCCeEEEEcCCCCCceehH-HHHHHHHHHH------------------HhccCCeEEEecCcHHH
Confidence            4567899999988 78889999999999999663 2333333321                  12346679999999888


Q ss_pred             HHHHHHHHhhhh
Q 042526          136 ALQVLMVASPSL  147 (284)
Q Consensus       136 a~Qi~~~~~~l~  147 (284)
                      |..+...+....
T Consensus       208 A~~L~e~~~~~~  219 (359)
T d1w36d1         208 AARLTESLGKAL  219 (359)
T ss_dssp             HHHHHHHHTHHH
T ss_pred             HHHHHHHHHHHH
Confidence            888777665443

>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=96.71  E-value=0.0015  Score=56.25  Aligned_cols=89  Identities=15%  Similarity=0.078  Sum_probs=57.1

Q ss_pred             CCcHHHHHHHHHHH--------cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           56 ESTSILKARIPALA--------HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        56 ~pT~iQ~~aip~il--------~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      .+.|+|..++.-++        ..+...|+.-..|.|||+..+ .++..+....               .........+|
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qai-a~l~~l~~~~---------------~~~~~~~~~~L  118 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCI-TLIWTLLKQS---------------PDCKPEIDKVI  118 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHH-HHHHHHHHCC---------------TTSSCSCSCEE
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHH-HHHHHHHHhc---------------ccccCCCCcEE
Confidence            46799999986331        245678888899999997543 3444443321               11111233589


Q ss_pred             EEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCc
Q 042526          128 IINPTRELALQVLMVASPSLKSNSLTLAMAAGSPL  162 (284)
Q Consensus       128 IL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~  162 (284)
                      ||||.. |..|..+++.++.... +.+..++|+..
T Consensus       119 IV~P~s-l~~qW~~Ei~k~~~~~-~~~v~~~~~~~  151 (298)
T d1z3ix2         119 VVSPSS-LVRNWYNEVGKWLGGR-VQPVAIDGGSK  151 (298)
T ss_dssp             EEECHH-HHHHHHHHHHHHHGGG-CCEEEECSSCH
T ss_pred             EEccch-hhHHHHHHHHhhcCCc-eeEEEEeCchH
Confidence            999986 8889999999887643 33445555543

>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=96.23  E-value=0.0057  Score=50.31  Aligned_cols=72  Identities=13%  Similarity=-0.040  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHHHHH---cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           56 ESTSILKARIPALA---HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        56 ~pT~iQ~~aip~il---~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      .+.|+|..++.-++   ..+..+|+.-.+|.|||+..+ .++..+....                    ....+||||| 
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~~--------------------~~~~~LIv~p-   69 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKEN--------------------ELTPSLVICP-   69 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTT--------------------CCSSEEEEEC-
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHH-Hhhhhhhhcc--------------------cccccceecc-
Confidence            46799999986431   346678999999999998753 4444433321                    2235899998 


Q ss_pred             HHHHHHHHHHHhhhhcC
Q 042526          133 RELALQVLMVASPSLKS  149 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~  149 (284)
                      ..+..|..+++..+...
T Consensus        70 ~~l~~~W~~e~~~~~~~   86 (230)
T d1z63a1          70 LSVLKNWEEELSKFAPH   86 (230)
T ss_dssp             STTHHHHHHHHHHHCTT
T ss_pred             hhhhhHHHHHHHhhccc
Confidence            66778888888877653

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=96.19  E-value=0.011  Score=50.43  Aligned_cols=86  Identities=20%  Similarity=0.114  Sum_probs=69.5

Q ss_pred             cCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEec
Q 042526           52 LGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINP  131 (284)
Q Consensus        52 ~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~P  131 (284)
                      +|. +|+++|...-=.+ ..|+  |+.-.||-|||++..+|+.-..+.                       +-.+=|++.
T Consensus        77 lG~-RhyDVQLiGgi~L-~~G~--iaem~TGEGKTL~a~l~a~l~al~-----------------------g~~vhvvTv  129 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVAL-HDGN--IAEMKTGEGKTLTSTLPVYLNALT-----------------------GKGVHVVTV  129 (273)
T ss_dssp             HSC-CCCHHHHHHHHHH-HTTS--EEECCTTSCHHHHHHHHHHHHHTT-----------------------SSCEEEEES
T ss_pred             hce-EEehhHHHHHHHH-Hhhh--heeecCCCcchhHHHHHHHHHHhc-----------------------CCCceEEec
Confidence            566 6999998887766 7774  889999999999999998754433                       334778899


Q ss_pred             CHHHHHHHHHHHhhhhcCCCceeEEEeCCCcch
Q 042526          132 TRELALQVLMVASPSLKSNSLTLAMAAGSPLLT  164 (284)
Q Consensus       132 TReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~  164 (284)
                      +--||..=..++..+...+|++|.++.......
T Consensus       130 NdyLA~RDae~m~~iy~~lGlsvg~~~~~~~~~  162 (273)
T d1tf5a3         130 NEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKD  162 (273)
T ss_dssp             SHHHHHHHHHHHHHHHHHTTCCEEECCTTSCHH
T ss_pred             CccccchhhhHHhHHHHHcCCCccccccccCHH
Confidence            999999999999999999999998887664443

>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=95.76  E-value=0.0038  Score=56.70  Aligned_cols=67  Identities=18%  Similarity=0.158  Sum_probs=46.5

Q ss_pred             CcHHHHHHHHHHH---cCC-CcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecC
Q 042526           57 STSILKARIPALA---HQR-KDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPT  132 (284)
Q Consensus        57 pT~iQ~~aip~il---~~G-~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PT  132 (284)
                      |+-=|=+||..++   ..| ++.++.+-||||||+...  .   +....                    .. .+|||+|+
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA--~---l~~~~--------------------~r-p~LVVt~n   65 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS--N---VIAQV--------------------NK-PTLVIAHN   65 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH--H---HHHHH--------------------TC-CEEEECSS
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH--H---HHHHh--------------------CC-CEEEEeCC
Confidence            5555655555441   345 678999999999995432  2   22221                    12 27999999


Q ss_pred             HHHHHHHHHHHhhhhcC
Q 042526          133 RELALQVLMVASPSLKS  149 (284)
Q Consensus       133 ReLa~Qi~~~~~~l~~~  149 (284)
                      ..+|.|+++.++.|...
T Consensus        66 ~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          66 KTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             HHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHHcCC
Confidence            99999999999988753

>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=94.65  E-value=0.012  Score=51.40  Aligned_cols=48  Identities=23%  Similarity=0.166  Sum_probs=31.5

Q ss_pred             HHHHHHcCCCC---CcHHHHHHHHHHHcCCCcEEEEccCCCCchHHhHHHHH
Q 042526           46 MKSIYKLGFKE---STSILKARIPALAHQRKDVIGAAETESGKTRAFGLPAL   94 (284)
Q Consensus        46 l~~L~~~g~~~---pT~iQ~~aip~il~~G~dviv~A~TGSGKTlafllPil   94 (284)
                      +..|...|+-.   +.+-+...+..++..+++++++++||||||. ++-.++
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT-~l~al~  187 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTT-YIKSIM  187 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHH-HHHHHG
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchH-HHHHHh
Confidence            34455555433   3455555565555789999999999999994 444444

>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=92.01  E-value=0.092  Score=46.84  Aligned_cols=49  Identities=18%  Similarity=0.170  Sum_probs=30.3

Q ss_pred             cccCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHc-CCCcEEEEccCCCCchHHhHHHHHHHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAH-QRKDVIGAAETESGKTRAFGLPALQRL   97 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~-~G~dviv~A~TGSGKTlafllPil~~l   97 (284)
                      +..+|.+||+++..+..|.                .++. .+-=+|+.+|||||||.+. ..++..+
T Consensus       133 ~~~~l~~LG~~~~~~~~l~----------------~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~  182 (401)
T d1p9ra_         133 TRLDLHSLGMTAHNHDNFR----------------RLIKRPHGIILVTGPTGSGKSTTL-YAGLQEL  182 (401)
T ss_dssp             TCCCGGGSCCCHHHHHHHH----------------HHHTSSSEEEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             cchhhhhhcccHHHHHHHH----------------HHHhhhhceEEEEcCCCCCccHHH-HHHhhhh
Confidence            3455667777666555544                3312 2335788999999999554 4456554

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=91.60  E-value=0.083  Score=47.40  Aligned_cols=70  Identities=21%  Similarity=0.264  Sum_probs=46.2

Q ss_pred             CCCCcH--HHHHHHHHH---HcCCC-cEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEE
Q 042526           54 FKESTS--ILKARIPAL---AHQRK-DVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRAL  127 (284)
Q Consensus        54 ~~~pT~--iQ~~aip~i---l~~G~-dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL  127 (284)
                      |..|||  =|-.||..+   +..|. .+.+.+-+||+||+.  +..+   ....                    ..| .|
T Consensus         4 ~~~~~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~--~A~l---~~~~--------------------~rp-~L   57 (408)
T d1c4oa1           4 YRGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVT--MAKV---IEAL--------------------GRP-AL   57 (408)
T ss_dssp             CCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHH--HHHH---HHHH--------------------TCC-EE
T ss_pred             ccCCCCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHH--HHHH---HHHh--------------------CCC-EE
Confidence            444544  344455543   25565 578899999999843  3322   2221                    122 78


Q ss_pred             EEecCHHHHHHHHHHHhhhhcC
Q 042526          128 IINPTRELALQVLMVASPSLKS  149 (284)
Q Consensus       128 IL~PTReLa~Qi~~~~~~l~~~  149 (284)
                      ||||+.+.|.|+++.+..+...
T Consensus        58 vVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1          58 VLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             EEESSHHHHHHHHHHHHHHCTT
T ss_pred             EEeCCHHHHHHHHHHHHHhcCc
Confidence            9999999999999999988653

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {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: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.55  E-value=0.085  Score=39.96  Aligned_cols=25  Identities=24%  Similarity=0.149  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCCchHHhHHHHHHHHH
Q 042526           73 KDVIGAAETESGKTRAFGLPALQRLL   98 (284)
Q Consensus        73 ~dviv~A~TGSGKTlafllPil~~l~   98 (284)
                      |.|++.+|+|||||. ++--++..+.
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHH
Confidence            689999999999995 4445554443

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {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: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.57  E-value=0.15  Score=40.87  Aligned_cols=39  Identities=15%  Similarity=0.267  Sum_probs=28.1

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCC--cEEEEccCCCCchHH
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRK--DVIGAAETESGKTRA   88 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~--dviv~A~TGSGKTla   88 (284)
                      .+|.++-.++.+.+.|..+               + ..++  .+++.+|+|+|||.+
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i-~~~~~~~lLl~Gp~G~GKttl   51 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------V-DEGKLPHLLFYGPPGTGKTST   51 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------H-HTTCCCCEEEECSSSSSHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------H-HcCCCCeEEEECCCCCChhHH
Confidence            4688887788888877653               1 2222  589999999999943

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {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: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=90.51  E-value=0.11  Score=45.82  Aligned_cols=45  Identities=16%  Similarity=0.145  Sum_probs=32.3

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCCeEEEEEecCHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQRLLEEREKAAKMLEEKGEEAEKYAPKGHLRALIINPTRELAL  137 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~aLIL~PTReLa~  137 (284)
                      ...+++++.|+||||||.+ +..++..+..                      .+..++|+=|..|++.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~-l~~li~~~~~----------------------~g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVL-LRELAYTGLL----------------------RGDRMVIVDPNGDMLS   92 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHH-HHHHHHHHHH----------------------TTCEEEEEEETTHHHH
T ss_pred             cccceEEEEeCCCCcHHHH-HHHHHHHHHh----------------------CCCCEEEEeCChhHHH
Confidence            4567899999999999965 4455554443                      2446888889988754

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=90.36  E-value=0.038  Score=46.17  Aligned_cols=53  Identities=11%  Similarity=0.097  Sum_probs=31.7

Q ss_pred             cccCcccCCCCHHHHHHHHHc-C-CCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           32 EFDAWNELRLHPLLMKSIYKL-G-FKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        32 ~~~~F~~l~L~~~Ll~~L~~~-g-~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      |-.+|.+++-.+...+.|.+. . +..|..+|..-+    ..-+.+++.+|+|||||+.
T Consensus         4 p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~----~~~~giLl~GppGtGKT~l   58 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGA----RIPKGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTC----CCCSEEEEECCTTSSHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCC----CCCceEEEecCCCCChhHH
Confidence            447899997677766666542 0 112222221111    2235799999999999954

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {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: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=89.14  E-value=0.2  Score=40.38  Aligned_cols=47  Identities=15%  Similarity=-0.012  Sum_probs=29.8

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      .+|+++--.+.+.+.|..+       ++. +.-.- .....+++.+|+|+|||.+.
T Consensus         6 ~~~~divGqe~~~~~l~~~-------i~~-~~~~~-~~~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLA-------LEA-AKMRG-EVLDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-------HHH-HHHHT-CCCCCEEEESSTTSSHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHH-------HHH-HHhcC-CCCCeEEEECCCCCcHHHHH
Confidence            3788887778877776642       111 00000 12357999999999999654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=88.81  E-value=0.27  Score=39.55  Aligned_cols=43  Identities=14%  Similarity=0.050  Sum_probs=28.3

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHc---CCCcEEEEccCCCCchHHh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAH---QRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~---~G~dviv~A~TGSGKTlaf   89 (284)
                      +|+++--.+.+.+.|..+            +.....   .-.++++.+|+|+|||.+.
T Consensus         7 ~~ddivGq~~~~~~L~~~------------i~~~~~~~~~~~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2           7 TLDEYIGQERLKQKLRVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             SGGGSCSCHHHHHHHHHH------------HHHHTTSSSCCCCEEEECCTTSCHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHH------------HHHHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            688876667777776543            111101   1257999999999999554

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=88.20  E-value=0.054  Score=45.44  Aligned_cols=52  Identities=15%  Similarity=0.103  Sum_probs=31.4

Q ss_pred             ccCcccCCCCHHHHHHHHHc--CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           33 FDAWNELRLHPLLMKSIYKL--GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        33 ~~~F~~l~L~~~Ll~~L~~~--g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      -.+|.+++-.+...+.|.+.  -+.+|..+|..-+    ...+.+++.+|+|||||+.
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~----~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGG----KIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC---------CCCCEEEEECCTTSCHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCC----CCCCeEEeeCCCCCCccHH
Confidence            36899998777777766542  0222222222211    2347899999999999954

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {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: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.18  E-value=0.22  Score=40.16  Aligned_cols=42  Identities=14%  Similarity=0.138  Sum_probs=29.9

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      +|+++-.++.+.+.|..+= ..           - .....+++.+|+|+|||...
T Consensus         9 ~~~diig~~~~~~~L~~~~-~~-----------~-~~~~~lll~Gp~G~GKTt~~   50 (252)
T d1sxje2           9 SLNALSHNEELTNFLKSLS-DQ-----------P-RDLPHLLLYGPNGTGKKTRC   50 (252)
T ss_dssp             SGGGCCSCHHHHHHHHTTT-TC-----------T-TCCCCEEEECSTTSSHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHH-Hc-----------C-CCCCeEEEECCCCCCHHHHH
Confidence            6889988999999887531 10           0 12235899999999999543

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon 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: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=88.07  E-value=0.22  Score=39.89  Aligned_cols=41  Identities=15%  Similarity=0.148  Sum_probs=29.4

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHHh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTlaf   89 (284)
                      +|.++-.++.+.+.|..+            +- - ..-.++++.+|+|+|||.+.
T Consensus        22 ~~~diig~~~~~~~l~~~------------i~-~-~~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHY------------VK-T-GSMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             STTTCCSCHHHHHHHHHH------------HH-H-TCCCEEEEESCTTSSHHHHH
T ss_pred             CHHHccCcHHHHHHHHHH------------HH-c-CCCCeEEEECCCCCcHHHHH
Confidence            688888888888877653            11 1 12346999999999998543

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {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: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.94  E-value=0.02  Score=46.97  Aligned_cols=53  Identities=9%  Similarity=-0.111  Sum_probs=31.0

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHH-HHHHH----HcCCCcEEEEccCCCCchHHh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKA-RIPAL----AHQRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~-aip~i----l~~G~dviv~A~TGSGKTlaf   89 (284)
                      +|.++..++..++.|..+=-  -...... .++..    ....+.+++.||+|+|||.+.
T Consensus        12 ~~~dlig~~~~~~~L~~~l~--~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLA--NWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHH--THHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHHHH--hhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            69999999998888765200  0000000 00000    012357999999999999543

>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=87.50  E-value=0.094  Score=47.51  Aligned_cols=17  Identities=29%  Similarity=0.368  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCchHH
Q 042526           72 RKDVIGAAETESGKTRA   88 (284)
Q Consensus        72 G~dviv~A~TGSGKTla   88 (284)
                      -+||++.+|||||||+-
T Consensus        49 ksNILliGPTGvGKTlL   65 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEI   65 (443)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             cccEEEECCCCCCHHHH
Confidence            56999999999999953

>d1ofha_ 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=87.45  E-value=0.25  Score=42.11  Aligned_cols=19  Identities=26%  Similarity=0.289  Sum_probs=16.2

Q ss_pred             CCCcEEEEccCCCCchHHh
Q 042526           71 QRKDVIGAAETESGKTRAF   89 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTlaf   89 (284)
                      ..+.+++.+|||+|||+..
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4689999999999999544

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.91  E-value=0.041  Score=46.05  Aligned_cols=50  Identities=8%  Similarity=0.151  Sum_probs=27.7

Q ss_pred             CcccCCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           35 AWNELRLHPLLMKSIYKL---GFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~---g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      +|.+++=.+...+.|.+.   -+.+|--++..-+    ..-+.+++.+|+|||||+.
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~----~~~~giLL~GppGtGKT~l   54 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGV----KPPRGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCC----CCCCEEEEECCTTSSHHHH
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCC----CCCceeEEecCCCCCchHH
Confidence            688885444555555442   1122222221111    2246799999999999953

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=86.54  E-value=1.4  Score=34.26  Aligned_cols=93  Identities=8%  Similarity=-0.077  Sum_probs=54.2

Q ss_pred             CeEEEEEecCHHHHHHHHHHHhhhhcCCCceeEEEeCCCcchHHHH----HhcC-CCcccccc---cCCccccccccCCC
Q 042526          123 HLRALIINPTRELALQVLMVASPSLKSNSLTLAMAAGSPLLTSEHS----NRRK-PNKRKRTR---KGGEDEKLDSLKWN  194 (284)
Q Consensus       123 ~~~aLIL~PTReLa~Qi~~~~~~l~~~~~i~v~~~~G~~~~~q~~~----l~~~-~~i~v~~~---~~~~~d~l~~lv~d  194 (284)
                      +-++||.|+|+..|..+...|..    .|+.+..+.|+....+...    ++.+ .++++.+.   .+.+...+..+++=
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~----~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~  106 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVE----HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAIL  106 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHH----TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEET
T ss_pred             CCcEEEEEcchhHHHHHHHHHHh----cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEe
Confidence            55799999999999999988876    4889999999866555433    3333 44455443   22334444444433


Q ss_pred             CCCcccccccccchhhhcccCCCCC
Q 042526          195 PLSQPKTTTLLPSSLALMNLTEGKP  219 (284)
Q Consensus       195 EAd~m~~~gflp~~~~~~~~~~r~~  219 (284)
                      .++...-..-..+.++.+++.-|..
T Consensus       107 ~~~~~~~~~~~~~~iq~~GR~gR~~  131 (174)
T d1c4oa2         107 DADKEGFLRSERSLIQTIGRAARNA  131 (174)
T ss_dssp             TTTSCSGGGSHHHHHHHHGGGTTST
T ss_pred             ccccccccchhHHHHHHhhhhhhcC
Confidence            3332111111122356666665544

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=86.22  E-value=0.33  Score=36.19  Aligned_cols=24  Identities=25%  Similarity=0.135  Sum_probs=17.0

Q ss_pred             EEEEccCCCCchHHhHHHHHHHHHH
Q 042526           75 VIGAAETESGKTRAFGLPALQRLLE   99 (284)
Q Consensus        75 viv~A~TGSGKTlafllPil~~l~~   99 (284)
                      +.+.++.||||| +++--++.++..
T Consensus         5 i~itG~~GSGKT-TL~~~L~~~l~~   28 (170)
T d1np6a_           5 LAFAAWSGTGKT-TLLKKLIPALCA   28 (170)
T ss_dssp             EEEECCTTSCHH-HHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHH-HHHHHHHHHHHH
Confidence            578899999999 555555554443

>d1um8a_ c.37.1.20 (A:) ClpX {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: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=86.16  E-value=0.32  Score=42.64  Aligned_cols=16  Identities=31%  Similarity=0.341  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCchHH
Q 042526           73 KDVIGAAETESGKTRA   88 (284)
Q Consensus        73 ~dviv~A~TGSGKTla   88 (284)
                      .+++..+|||+|||..
T Consensus        69 ~niLfiGPTGvGKTEl   84 (364)
T d1um8a_          69 SNILLIGPTGSGKTLM   84 (364)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             cceeeeCCCCccHHHH
Confidence            5799999999999944

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {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: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.66  E-value=0.44  Score=37.90  Aligned_cols=39  Identities=10%  Similarity=0.128  Sum_probs=27.1

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC--CcEEEEccCCCCchHHh
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR--KDVIGAAETESGKTRAF   89 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G--~dviv~A~TGSGKTlaf   89 (284)
                      +|.++=.++.+++.|..+               + ..+  .++++.+|+|+|||.+.
T Consensus        13 ~~~d~ig~~~~~~~L~~~---------------~-~~~~~~~~ll~Gp~G~GKTt~a   53 (224)
T d1sxjb2          13 VLSDIVGNKETIDRLQQI---------------A-KDGNMPHMIISGMPGIGKTTSV   53 (224)
T ss_dssp             SGGGCCSCTHHHHHHHHH---------------H-HSCCCCCEEEECSTTSSHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHH---------------H-HcCCCCeEEEECCCCCCchhhH
Confidence            577776677777776542               1 233  26899999999999554

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

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: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=84.66  E-value=0.23  Score=40.04  Aligned_cols=17  Identities=18%  Similarity=0.077  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCCchHH
Q 042526           72 RKDVIGAAETESGKTRA   88 (284)
Q Consensus        72 G~dviv~A~TGSGKTla   88 (284)
                      ...+++.+|+|+|||.+
T Consensus        43 ~~~lll~GppGtGKT~l   59 (276)
T d1fnna2          43 YPRATLLGRPGTGKTVT   59 (276)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            36899999999999954

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

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: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=84.22  E-value=0.66  Score=37.91  Aligned_cols=24  Identities=13%  Similarity=0.158  Sum_probs=18.4

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPAL   94 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil   94 (284)
                      ..|.=+++.|+||+||| +|++-++
T Consensus        33 ~~G~l~vi~G~~G~GKT-~~~~~la   56 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKS-TFVRQQA   56 (277)
T ss_dssp             CTTCEEEEECSTTSSHH-HHHHHHH
T ss_pred             CCCeEEEEEeCCCCCHH-HHHHHHH
Confidence            56888899999999999 4444443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=83.43  E-value=0.9  Score=36.60  Aligned_cols=40  Identities=10%  Similarity=0.094  Sum_probs=29.3

Q ss_pred             cCcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCC---CcEEEEccCCCCchHHh
Q 042526           34 DAWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQR---KDVIGAAETESGKTRAF   89 (284)
Q Consensus        34 ~~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G---~dviv~A~TGSGKTlaf   89 (284)
                      .+|.++-.+..+.+.|...               + .++   +.+++.+|+|+|||.+.
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i-~~~~~~~~~Ll~Gp~G~GKtt~a   51 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------L-SLGRIHHAYLFSGTRGVGKTSIA   51 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------H-HTTCCCSEEEEECSTTSSHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------H-HcCCCCeeEEEECCCCCcHHHHH
Confidence            4788888888888877642               1 222   34899999999999653

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=82.48  E-value=0.26  Score=36.17  Aligned_cols=16  Identities=13%  Similarity=0.380  Sum_probs=14.1

Q ss_pred             CCcEEEEccCCCCchH
Q 042526           72 RKDVIGAAETESGKTR   87 (284)
Q Consensus        72 G~dviv~A~TGSGKTl   87 (284)
                      -++|++.+++|||||.
T Consensus         2 ~k~I~l~G~~GsGKST   17 (169)
T d1kaga_           2 KRNIFLVGPMGAGKST   17 (169)
T ss_dssp             CCCEEEECCTTSCHHH
T ss_pred             CCeEEEECCCCCCHHH
Confidence            3689999999999994

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=82.34  E-value=0.23  Score=37.40  Aligned_cols=19  Identities=16%  Similarity=0.127  Sum_probs=16.2

Q ss_pred             cCCCcEEEEccCCCCchHH
Q 042526           70 HQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTla   88 (284)
                      +.|+-|++.+++|||||..
T Consensus         2 ~~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           2 LGGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             CTTEEEEEEECTTSCHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4688899999999999953

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=82.33  E-value=0.27  Score=36.92  Aligned_cols=18  Identities=17%  Similarity=0.283  Sum_probs=15.2

Q ss_pred             CCCcEEEEccCCCCchHH
Q 042526           71 QRKDVIGAAETESGKTRA   88 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTla   88 (284)
                      .+.++++.+++|||||..
T Consensus         4 k~~~I~i~G~~GsGKTT~   21 (174)
T d1y63a_           4 KGINILITGTPGTGKTSM   21 (174)
T ss_dssp             SSCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEEeCCCCCHHHH
Confidence            366899999999999953

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.45  E-value=0.42  Score=36.47  Aligned_cols=18  Identities=22%  Similarity=0.091  Sum_probs=15.7

Q ss_pred             cCCCcEEEEccCCCCchH
Q 042526           70 HQRKDVIGAAETESGKTR   87 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTl   87 (284)
                      ..|+-+++.+++|||||.
T Consensus        21 ~~G~v~~i~G~~GsGKT~   38 (242)
T d1n0wa_          21 ETGSITEMFGEFRTGKTQ   38 (242)
T ss_dssp             ETTSEEEEECCTTSSHHH
T ss_pred             cCCEEEEEEeCCCCCHHH
Confidence            457889999999999994

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

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: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=81.40  E-value=0.75  Score=36.56  Aligned_cols=25  Identities=16%  Similarity=0.203  Sum_probs=18.2

Q ss_pred             cCCCcEEEEccCCCCchHHhHHHHHH
Q 042526           70 HQRKDVIGAAETESGKTRAFGLPALQ   95 (284)
Q Consensus        70 ~~G~dviv~A~TGSGKTlafllPil~   95 (284)
                      -.|.-+++.+++|+|||. |++-++.
T Consensus        24 ~~gsl~li~G~pGsGKT~-l~~qia~   48 (242)
T d1tf7a2          24 FKDSIILATGATGTGKTL-LVSRFVE   48 (242)
T ss_dssp             ESSCEEEEEECTTSSHHH-HHHHHHH
T ss_pred             cCCeEEEEEeCCCCCHHH-HHHHHHH
Confidence            357789999999999994 4433333

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.34  E-value=0.065  Score=45.00  Aligned_cols=18  Identities=28%  Similarity=0.187  Sum_probs=15.2

Q ss_pred             CCCcEEEEccCCCCchHH
Q 042526           71 QRKDVIGAAETESGKTRA   88 (284)
Q Consensus        71 ~G~dviv~A~TGSGKTla   88 (284)
                      ..+.+++.+|+|||||+.
T Consensus        40 ~~~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHH
T ss_pred             CCCeEEEECCCCCcchhH
Confidence            357899999999999954

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {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: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.14  E-value=0.56  Score=37.20  Aligned_cols=40  Identities=15%  Similarity=0.163  Sum_probs=24.5

Q ss_pred             CcccCCCCHHHHHHHHHcCCCCCcHHHHHHHHHHHcCCCcEEEEccCCCCchHH
Q 042526           35 AWNELRLHPLLMKSIYKLGFKESTSILKARIPALAHQRKDVIGAAETESGKTRA   88 (284)
Q Consensus        35 ~F~~l~L~~~Ll~~L~~~g~~~pT~iQ~~aip~il~~G~dviv~A~TGSGKTla   88 (284)
                      +|.++-.++.+.+.|..+ +..             ..-.++++.+|+|+|||..
T Consensus        10 ~~~diig~~~~~~~l~~~-i~~-------------~~~~~lll~Gp~G~GKTtl   49 (237)
T d1sxjd2          10 NLDEVTAQDHAVTVLKKT-LKS-------------ANLPHMLFYGPPGTGKTST   49 (237)
T ss_dssp             STTTCCSCCTTHHHHHHH-TTC-------------TTCCCEEEECSTTSSHHHH
T ss_pred             CHHHccCcHHHHHHHHHH-HHc-------------CCCCeEEEECCCCCChHHH
Confidence            566765566666655432 110             1113589999999999843

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {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: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=81.07  E-value=0.28  Score=36.20  Aligned_cols=13  Identities=23%  Similarity=0.363  Sum_probs=11.7

Q ss_pred             EEEEccCCCCchH
Q 042526           75 VIGAAETESGKTR   87 (284)
Q Consensus        75 viv~A~TGSGKTl   87 (284)
                      |++.+++|||||.
T Consensus         5 Iii~G~pGsGKTT   17 (152)
T d1ly1a_           5 ILTIGCPGSGKST   17 (152)
T ss_dssp             EEEECCTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            6789999999985

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal 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: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.19  E-value=1.4  Score=38.37  Aligned_cols=22  Identities=23%  Similarity=0.212  Sum_probs=16.6

Q ss_pred             cEEEEccCCCCchHHhHHHHHH
Q 042526           74 DVIGAAETESGKTRAFGLPALQ   95 (284)
Q Consensus        74 dviv~A~TGSGKTlafllPil~   95 (284)
                      .+||.|.-|||||.+..-=++.
T Consensus        18 ~~lv~A~AGsGKT~~l~~r~~~   39 (485)
T d1w36b1          18 ERLIEASAGTGKTFTIAALYLR   39 (485)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             CeEEEEcCchHHHHHHHHHHHH
Confidence            5889999999999665544443

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

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: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=80.09  E-value=0.54  Score=35.42  Aligned_cols=14  Identities=36%  Similarity=0.434  Sum_probs=12.4

Q ss_pred             cEEEEccCCCCchH
Q 042526           74 DVIGAAETESGKTR   87 (284)
Q Consensus        74 dviv~A~TGSGKTl   87 (284)
                      -|++.+|+|+|||.
T Consensus         2 ki~I~G~~G~GKST   15 (178)
T d1ye8a1           2 KIIITGEPGVGKTT   15 (178)
T ss_dssp             EEEEECCTTSSHHH
T ss_pred             EEEEECCCCcHHHH
Confidence            47899999999995