Psyllid ID: psy17587

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-
Protein Sequence
MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAREL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHccccccccEEEEEccccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHcccccEEEEEEccccccccccccEEEEccccccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccEEEEHHHHHccccccccEEEEEEcccccHHHHEEEcccccccccccEEEEEEccccHHHHHHHHHHHHHHcccccHHHHHHHHHccccccccccccccccEEcccccccccccccHHHHHcccccccHHHccEEEEcccHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mkagypclslhggidqydrdstivdfkngKVRLLVCAIVKELMKagypclslhggidqydrdstivdfkngKVRLLIATSVAargldvkhlnlvvnydcpnhyedyvhrcgrtgragnkgfAYTFITLEQERHAGEIIRALeasgvpipedldkMWAEDLIVRTFCfragnkgfAYTFITLEQERHAGEIIRALeasgvpipeDLDKILAEGLVWLRDYKQRVDQRIAREL
Flexible Loop (DISEMBL)
mkagypclslhggidqydRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSvaargldvkhlNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALeasgvpipeDLDKILAEGLVWLRDYKQRVDQRIAREL
Low Complexity Region (SEG)
MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAREL
Disordered region (IsUnstruct)
****YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQR*********
Disordered Region (DISOPRED)
***GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDK*****************************************************************************
Disordered Region (DISEMBL)
MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAREL
Disordered Region (DISPRO)
MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCF****KGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAREL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAREL
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	231	2.2.26 [Sep-21-2011]
Q569Z5	1032	Probable ATP-dependent RN	yes	N/A	0.597	0.133	0.659	2e-52
Q62780	1032	Probable ATP-dependent RN	yes	N/A	0.597	0.133	0.659	2e-52
Q7L014	1031	Probable ATP-dependent RN	yes	N/A	0.597	0.133	0.659	3e-52
Q5R6D8	1032	Probable ATP-dependent RN	yes	N/A	0.597	0.133	0.659	3e-52
Q4TVV3	1018	Probable ATP-dependent RN	yes	N/A	0.597	0.135	0.639	2e-50
Q4IP34	1207	Pre-mRNA-processing ATP-d	yes	N/A	0.510	0.097	0.694	3e-43
A1CQA9	1192	Pre-mRNA-processing ATP-d	N/A	N/A	0.658	0.127	0.584	7e-43
A1D373	1193	Pre-mRNA-processing ATP-d	N/A	N/A	0.662	0.128	0.574	2e-42
Q5BDW4	1173	Pre-mRNA-processing ATP-d	yes	N/A	0.662	0.130	0.567	2e-42
Q2U2J6	1186	Pre-mRNA-processing ATP-d	yes	N/A	0.662	0.129	0.567	3e-42

>sp|Q569Z5|DDX46_MOUSE Probable ATP-dependent RNA helicase DDX46 OS=Mus musculus GN=Ddx46 PE=1 SV=2

 Score =  205 bits (522), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 97/147 (65%), Positives = 116/147 (78%), Gaps = 9/147 (6%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct: 635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW- 156
            CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W 
Sbjct: 695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query: 157 -------AEDLIVRTFCFRAGNKGFAY 176
                  AE  I++     +G KGF +
Sbjct: 755 DFKDQQKAEGKIIKKSSGFSG-KGFKF 780

Plays an essential role in splicing, either prior to, or during A complex formation.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q62780|DDX46_RAT Probable ATP-dependent RNA helicase DDX46 OS=Rattus norvegicus GN=Ddx46 PE=1 SV=1

 Score =  205 bits (521), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 97/147 (65%), Positives = 116/147 (78%), Gaps = 9/147 (6%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct: 635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW- 156
            CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W 
Sbjct: 695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query: 157 -------AEDLIVRTFCFRAGNKGFAY 176
                  AE  I++     +G KGF +
Sbjct: 755 DFKDQQKAEGKIIKKSSGFSG-KGFKF 780

Plays an essential role in splicing, either prior to, or during A complex formation.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7L014|DDX46_HUMAN Probable ATP-dependent RNA helicase DDX46 OS=Homo sapiens GN=DDX46 PE=1 SV=2

 Score =  204 bits (520), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 97/147 (65%), Positives = 116/147 (78%), Gaps = 9/147 (6%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct: 635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW- 156
            CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W 
Sbjct: 695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query: 157 -------AEDLIVRTFCFRAGNKGFAY 176
                  AE  I++     +G KGF +
Sbjct: 755 DFKDQQKAEGKIIKKSSGFSG-KGFKF 780

Plays an essential role in splicing, either prior to, or during splicing A complex formation.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R6D8|DDX46_PONAB Probable ATP-dependent RNA helicase DDX46 OS=Pongo abelii GN=DDX46 PE=2 SV=1

 Score =  204 bits (520), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 97/147 (65%), Positives = 116/147 (78%), Gaps = 9/147 (6%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct: 635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW- 156
            CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W 
Sbjct: 695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query: 157 -------AEDLIVRTFCFRAGNKGFAY 176
                  AE  I++     +G KGF +
Sbjct: 755 DFKDQQKAEGKIIKKSSGFSG-KGFKF 780

Plays an essential role in splicing, either prior to, or during A complex formation.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4TVV3|DDX46_DANRE Probable ATP-dependent RNA helicase DDX46 OS=Danio rerio GN=ddx46 PE=2 SV=1

 Score =  198 bits (504), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/147 (63%), Positives = 115/147 (78%), Gaps = 9/147 (6%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LMKA YPC+SLHGGIDQYDRDS I DFKNG  RLL+ATSVAARGLDVK L LVVNY
Sbjct: 603 LLKDLMKASYPCMSLHGGIDQYDRDSIINDFKNGACRLLVATSVAARGLDVKQLILVVNY 662

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW- 156
            CPNHYEDYVHR GRTGRAGNKG+AYTFIT  Q R++G+I++ALE SG  +P +L+++W 
Sbjct: 663 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEGQARYSGDILKALELSGSSVPAELEQLWT 722

Query: 157 -------AEDLIVRTFCFRAGNKGFAY 176
                  AE  I+++    +G KGF +
Sbjct: 723 NFKEQQKAEGKIIKSSSGFSG-KGFKF 748

Plays an essential role in splicing, either prior to, or during A complex formation.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4IP34|PRP5_GIBZE Pre-mRNA-processing ATP-dependent RNA helicase PRP5 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=PRP5 PE=3 SV=2

 Score =  175 bits (443), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 82/118 (69%), Positives = 93/118 (78%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++KELM  GYPC+S+HGG DQ DRDSTI DFK G V +LIATSVAARGLDVK L LV+NY
Sbjct: 843 LLKELMMKGYPCMSIHGGKDQIDRDSTISDFKKGVVPILIATSVAARGLDVKQLKLVINY 902

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKM 155
           D PNH EDYVHR GRTGRAGN G A TF+T EQE  A  I +ALE SG PIP+ L++M
Sbjct: 903 DAPNHLEDYVHRAGRTGRAGNTGVAVTFVTPEQENCAPGIAKALEQSGQPIPDRLNEM 960

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1CQA9|PRP5_ASPCL Pre-mRNA-processing ATP-dependent RNA helicase prp5 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=prp5 PE=3 SV=1

 Score =  174 bits (440), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 90/154 (58%), Positives = 109/154 (70%), Gaps = 2/154 (1%)

Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN 96
           A+++ELM+ GYPC+S+HGG DQ DRDSTI DFK G   +LIATSVAARGLDVK L LVVN
Sbjct: 824 ALLRELMRKGYPCMSIHGGKDQIDRDSTIEDFKAGIFPVLIATSVAARGLDVKQLKLVVN 883

Query: 97  YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           YD PNH EDYVHR GRTGRAGN G A TF+T EQER++ +I +AL+ SG  +PE + KM 
Sbjct: 884 YDAPNHLEDYVHRAGRTGRAGNTGTAVTFLTEEQERYSVDIAKALKQSGQQVPEPVQKMV 943

Query: 157 AEDL-IVRTFCFRAGNKGFAYTFIT-LEQERHAG 188
              L  V+    +A   GF    +  L+QER A 
Sbjct: 944 DSFLEKVKAGKEKASASGFGGKGLERLDQERDAA 977

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) (taxid: 344612)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1D373|PRP5_NEOFI Pre-mRNA-processing ATP-dependent RNA helicase prp5 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=prp5 PE=3 SV=1

 Score =  172 bits (436), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 89/155 (57%), Positives = 108/155 (69%), Gaps = 2/155 (1%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +++ELM+ GYPC+S+HGG DQ DRDSTI DFK G   +LIATSVAARGLDVK L LVVNY
Sbjct: 825 LLRELMRKGYPCMSIHGGKDQIDRDSTIEDFKAGIFPILIATSVAARGLDVKQLKLVVNY 884

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
           D PNH EDYVHR GRTGRAGN G A TF+T EQER++ +I +AL  SG  +PE + KM  
Sbjct: 885 DAPNHLEDYVHRAGRTGRAGNTGTAVTFLTEEQERYSVDIAKALRQSGQKVPEPVQKMVD 944

Query: 158 EDL-IVRTFCFRAGNKGFAYTFIT-LEQERHAGEI 190
             L  V+    +A   GF    +  L+QER A  +
Sbjct: 945 SFLEKVKAGKEKASASGFGGKGLERLDQERDAARM 979

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) (taxid: 331117)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5BDW4|PRP5_EMENI Pre-mRNA-processing ATP-dependent RNA helicase prp5 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=prp5 PE=3 SV=1

 Score =  172 bits (436), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 88/155 (56%), Positives = 110/155 (70%), Gaps = 2/155 (1%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +++ELM+ GYPC+S+HGG DQ DRDSTI DFK G   +LIATSVAARGLDVK L LVVNY
Sbjct: 809 LLRELMRKGYPCMSIHGGKDQIDRDSTIEDFKAGIFPVLIATSVAARGLDVKQLKLVVNY 868

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
           D PNH EDYVHR GRTGRAGN G A TF+T +QER++ +I +AL+ SG  +PE + K+  
Sbjct: 869 DAPNHLEDYVHRAGRTGRAGNTGTAVTFLTEDQERYSVDIAKALKQSGQEVPEAVQKLVD 928

Query: 158 EDL-IVRTFCFRAGNKGFAYTFIT-LEQERHAGEI 190
             L  V+    +A N GF    +  L+QER A  +
Sbjct: 929 SFLEKVKAGKEKASNSGFGGKGLERLDQERDAARM 963

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2U2J6|PRP5_ASPOR Pre-mRNA-processing ATP-dependent RNA helicase prp5 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=prp5 PE=3 SV=1

 Score =  171 bits (434), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 88/155 (56%), Positives = 109/155 (70%), Gaps = 2/155 (1%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +++ELM+ GYPC+S+HGG DQ DRDSTI DFK G   +LIATSVAARGLDVK L LVVNY
Sbjct: 822 LLRELMRKGYPCMSIHGGKDQIDRDSTIEDFKAGIFPVLIATSVAARGLDVKQLKLVVNY 881

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
           D PNH EDYVHR GRTGRAGN G A TF+T +QER++ +I +AL+ SG  +PE + KM  
Sbjct: 882 DAPNHLEDYVHRAGRTGRAGNTGTAVTFLTEDQERYSVDIAKALKQSGQSVPEPVQKMVD 941

Query: 158 EDL-IVRTFCFRAGNKGFAYTFIT-LEQERHAGEI 190
             L  V+    +A   GF    +  L+QER A  +
Sbjct: 942 SFLEKVKAGKEKASASGFGGKGLERLDQERDAARM 976

ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. Catalyzes an ATP-dependent conformational change of U2 snRNP. Bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

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	231
189240548	984	PREDICTED: similar to DEAD box ATP-depen	0.515	0.120	0.815	3e-53
270011364	1007	hypothetical protein TcasGA2_TC005373 [T	0.515	0.118	0.815	3e-53
405962641	913	Putative ATP-dependent RNA helicase DDX4	0.515	0.130	0.798	5e-53
242009038	1014	DEAD box ATP-dependent RNA helicase, put	0.515	0.117	0.815	5e-53
427795059	1123	Putative atp-dependent rna helicase, par	0.632	0.130	0.648	3e-52
195397525	1244	GJ17053 [Drosophila virilis] gi|19414714	0.515	0.095	0.781	4e-52
427793119	1147	Putative atp-dependent rna helicase, par	0.632	0.127	0.648	4e-52
321456211	797	hypothetical protein DAPPUDRAFT_302036 [	0.515	0.149	0.756	6e-52
195130219	1229	GI15175 [Drosophila mojavensis] gi|19390	0.515	0.096	0.781	7e-52
363739175	1028	PREDICTED: probable ATP-dependent RNA he	0.593	0.133	0.675	8e-52

>gi|189240548|ref|XP_973126.2| PREDICTED: similar to DEAD box ATP-dependent RNA helicase [Tribolium castaneum]

 Score =  214 bits (544), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 97/119 (81%), Positives = 108/119 (90%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++KELMKA Y CLSLHGGIDQ+DRDSTI+DFK+GKV+LLIATSVAARGLDVKHL LVVNY
Sbjct: 588 LLKELMKAAYNCLSLHGGIDQFDRDSTIIDFKSGKVKLLIATSVAARGLDVKHLILVVNY 647

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           DCPNHYEDYVHRCGRTGRAGNKGFAYTFIT EQ R+AG+IIRA E + VPIP+ L  +W
Sbjct: 648 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITPEQSRYAGDIIRAFELASVPIPDPLRALW 706

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270011364|gb|EFA07812.1| hypothetical protein TcasGA2_TC005373 [Tribolium castaneum]

 Score =  214 bits (544), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 97/119 (81%), Positives = 108/119 (90%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++KELMKA Y CLSLHGGIDQ+DRDSTI+DFK+GKV+LLIATSVAARGLDVKHL LVVNY
Sbjct: 611 LLKELMKAAYNCLSLHGGIDQFDRDSTIIDFKSGKVKLLIATSVAARGLDVKHLILVVNY 670

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           DCPNHYEDYVHRCGRTGRAGNKGFAYTFIT EQ R+AG+IIRA E + VPIP+ L  +W
Sbjct: 671 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITPEQSRYAGDIIRAFELASVPIPDPLRALW 729

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405962641|gb|EKC28298.1| Putative ATP-dependent RNA helicase DDX46 [Crassostrea gigas]

 Score =  213 bits (542), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 95/119 (79%), Positives = 108/119 (90%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++KELM   YPC+SLHGGIDQYDRDSTIVDFKNG V+LL+ATSVAARGLDVKHL LVVNY
Sbjct: 513 LMKELMTHSYPCMSLHGGIDQYDRDSTIVDFKNGNVKLLVATSVAARGLDVKHLILVVNY 572

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           DCPNHYEDYVHRCGRTGRAGNKG+A+TFIT EQER+AG+II+ALE SG  +  DL+K+W
Sbjct: 573 DCPNHYEDYVHRCGRTGRAGNKGYAFTFITPEQERYAGDIIKALELSGATVNADLEKLW 631

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|242009038|ref|XP_002425300.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis] gi|212509065|gb|EEB12562.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis]

 Score =  213 bits (542), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 97/119 (81%), Positives = 107/119 (89%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++KELMKA YP +SLHGGIDQ+DRDSTI+DFK+GKV+LLIATSVAARGLDVK L LVVNY
Sbjct: 611 LLKELMKASYPSMSLHGGIDQFDRDSTIIDFKSGKVKLLIATSVAARGLDVKQLILVVNY 670

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           DCPNHYEDYVHRCGRTGRAGNKG AYTFIT EQER+AGEIIRALE S V +PE L  +W
Sbjct: 671 DCPNHYEDYVHRCGRTGRAGNKGVAYTFITPEQERYAGEIIRALELSSVAVPESLRNLW 729

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427795059|gb|JAA62981.1| Putative atp-dependent rna helicase, partial [Rhipicephalus pulchellus]

 Score =  210 bits (535), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 105/162 (64%), Positives = 123/162 (75%), Gaps = 16/162 (9%)

Query: 1   MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID--- 57
           MKA +  ++LHGGIDQ+DRDSTIVDFK GKV +L+   V               G+D   
Sbjct: 661 MKASHNAMALHGGIDQFDRDSTIVDFKAGKVGVLIATSVAAR------------GLDVKH 708

Query: 58  -QYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRA 116
             +DRDSTIVDFK GKV +LIATSVAARGLDVKHL LVVN+DCPNHYEDYVHRCGRTGRA
Sbjct: 709 LXFDRDSTIVDFKAGKVGVLIATSVAARGLDVKHLILVVNFDCPNHYEDYVHRCGRTGRA 768

Query: 117 GNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAE 158
           GNKG+AYTFIT +Q R+  ++I+ALE SG PIPEDL K++ E
Sbjct: 769 GNKGYAYTFITEDQGRYTADVIKALELSGNPIPEDLQKLFDE 810

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195397525|ref|XP_002057379.1| GJ17053 [Drosophila virilis] gi|194147146|gb|EDW62865.1| GJ17053 [Drosophila virilis]

 Score =  210 bits (534), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 93/119 (78%), Positives = 107/119 (89%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++++LMKA YPC+SLHGGIDQ+DRDSTI+DFK+GKVRLLIATSVAARGLDVK L LVVNY
Sbjct: 800 LLRDLMKASYPCMSLHGGIDQFDRDSTIIDFKSGKVRLLIATSVAARGLDVKDLILVVNY 859

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           D PNHYEDYVHRCGRTGRAGNKG AYTFIT EQ R+AG++IRAL+ SG P+P DL  +W
Sbjct: 860 DVPNHYEDYVHRCGRTGRAGNKGSAYTFITPEQSRYAGDVIRALDLSGTPVPPDLQTLW 918

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427793119|gb|JAA62011.1| Putative atp-dependent rna helicase, partial [Rhipicephalus pulchellus]

 Score =  210 bits (534), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 105/162 (64%), Positives = 123/162 (75%), Gaps = 16/162 (9%)

Query: 1   MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID--- 57
           MKA +  ++LHGGIDQ+DRDSTIVDFK GKV +L+   V               G+D   
Sbjct: 685 MKASHNAMALHGGIDQFDRDSTIVDFKAGKVGVLIATSV------------AARGLDVKH 732

Query: 58  -QYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRA 116
             +DRDSTIVDFK GKV +LIATSVAARGLDVKHL LVVN+DCPNHYEDYVHRCGRTGRA
Sbjct: 733 LXFDRDSTIVDFKAGKVGVLIATSVAARGLDVKHLILVVNFDCPNHYEDYVHRCGRTGRA 792

Query: 117 GNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAE 158
           GNKG+AYTFIT +Q R+  ++I+ALE SG PIPEDL K++ E
Sbjct: 793 GNKGYAYTFITEDQGRYTADVIKALELSGNPIPEDLQKLFDE 834

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321456211|gb|EFX67324.1| hypothetical protein DAPPUDRAFT_302036 [Daphnia pulex]

 Score =  209 bits (532), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 90/119 (75%), Positives = 108/119 (90%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LMKAGY C+SLHGGIDQYDRDS +VDFKNGK++L+IATSVAARGLDVKHL LVVNY
Sbjct: 395 LLKDLMKAGYDCISLHGGIDQYDRDSAVVDFKNGKIKLMIATSVAARGLDVKHLILVVNY 454

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           DCPNH+EDY+HRCGRTGRAGNKGFAYTFIT +Q+R AG+II+A+E S  P+P +L  +W
Sbjct: 455 DCPNHHEDYIHRCGRTGRAGNKGFAYTFITPDQQRAAGDIIKAMEQSETPVPVELQTLW 513

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195130219|ref|XP_002009550.1| GI15175 [Drosophila mojavensis] gi|193908000|gb|EDW06867.1| GI15175 [Drosophila mojavensis]

 Score =  209 bits (532), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 93/119 (78%), Positives = 107/119 (89%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++++LMKA YPC+SLHGGIDQ+DRDSTI+DFK+GKVRLLIATSVAARGLDVK L LVVNY
Sbjct: 796 LLRDLMKASYPCMSLHGGIDQFDRDSTIIDFKSGKVRLLIATSVAARGLDVKDLILVVNY 855

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           D PNHYEDYVHRCGRTGRAGNKG A+TFIT EQ R+AG++IRALE SG P+P DL  +W
Sbjct: 856 DVPNHYEDYVHRCGRTGRAGNKGCAFTFITPEQSRYAGDVIRALELSGTPVPPDLQTLW 914

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|363739175|ref|XP_414629.3| PREDICTED: probable ATP-dependent RNA helicase DDX46 [Gallus gallus]

 Score =  209 bits (531), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 100/148 (67%), Positives = 116/148 (78%), Gaps = 11/148 (7%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           ++K+LM+A YPCLSLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVK L LVVNY
Sbjct: 632 LLKDLMRASYPCLSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKQLMLVVNY 691

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
            CPNHYEDYVHR GRTGRAGNKGFAYTFIT +Q R+AG+II+ALE SG PIP DL+K+WA
Sbjct: 692 SCPNHYEDYVHRAGRTGRAGNKGFAYTFITEDQARYAGDIIKALELSGNPIPADLEKLWA 751

Query: 158 E---------DLIVRTFCFRAGNKGFAY 176
           +          LI ++  F    KGF +
Sbjct: 752 DFKEQQKAEGKLIKKSSGF--SGKGFKF 777

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	231
UNIPROTKB|E1BSC0	1031	DDX46 "Uncharacterized protein	0.523	0.117	0.776	4.1e-48
UNIPROTKB|Q7L014	1031	DDX46 "Probable ATP-dependent	0.523	0.117	0.743	2.3e-47
UNIPROTKB|F1MX40	1032	DDX46 "Uncharacterized protein	0.523	0.117	0.743	2.4e-47
UNIPROTKB|F1PK90	1032	DDX46 "Uncharacterized protein	0.523	0.117	0.743	2.4e-47
UNIPROTKB|I3LR20	1032	DDX46 "Uncharacterized protein	0.523	0.117	0.743	2.4e-47
MGI|MGI:1920895	1032	Ddx46 "DEAD (Asp-Glu-Ala-Asp)	0.523	0.117	0.743	2.4e-47
RGD|708480	1032	Ddx46 "DEAD (Asp-Glu-Ala-Asp)	0.523	0.117	0.743	2.4e-47
UNIPROTKB|Q62780	1032	Ddx46 "Probable ATP-dependent	0.523	0.117	0.743	2.4e-47
FB|FBgn0030631	1224	CG6227 [Drosophila melanogaste	0.774	0.146	0.548	4.7e-47
ZFIN|ZDB-GENE-030131-667	1035	ddx46 "DEAD (Asp-Glu-Ala-Asp)	0.636	0.142	0.620	5.5e-45

UNIPROTKB|E1BSC0 DDX46 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 512 (185.3 bits), Expect = 4.1e-48, P = 4.1e-48
 Identities = 94/121 (77%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPCLSLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVK L LVVNY
Sbjct:   634 LLKDLMRASYPCLSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKQLMLVVNY 693

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKGFAYTFIT +Q R+AG+II+ALE SG PIP DL+K+WA
Sbjct:   694 SCPNHYEDYVHRAGRTGRAGNKGFAYTFITEDQARYAGDIIKALELSGNPIPADLEKLWA 753

Query:   158 E 158
             +
Sbjct:   754 D 754

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|Q7L014 DDX46 "Probable ATP-dependent RNA helicase DDX46" [Homo sapiens (taxid:9606)]

 Score = 505 (182.8 bits), Expect = 2.3e-47, P = 2.3e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1MX40 DDX46 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 505 (182.8 bits), Expect = 2.4e-47, P = 2.4e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1PK90 DDX46 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 505 (182.8 bits), Expect = 2.4e-47, P = 2.4e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|I3LR20 DDX46 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 505 (182.8 bits), Expect = 2.4e-47, P = 2.4e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

GO:0005730 "nucleolus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1920895 Ddx46 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 46" [Mus musculus (taxid:10090)]

 Score = 505 (182.8 bits), Expect = 2.4e-47, P = 2.4e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

RGD|708480 Ddx46 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 46" [Rattus norvegicus (taxid:10116)]

 Score = 505 (182.8 bits), Expect = 2.4e-47, P = 2.4e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|Q62780 Ddx46 "Probable ATP-dependent RNA helicase DDX46" [Rattus norvegicus (taxid:10116)]

 Score = 505 (182.8 bits), Expect = 2.4e-47, P = 2.4e-47
 Identities = 90/121 (74%), Positives = 107/121 (88%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LM+A YPC+SLHGGIDQYDRDS I DFKNG  +LL+ATSVAARGLDVKHL LVVNY
Sbjct:   635 LLKDLMRASYPCMSLHGGIDQYDRDSIINDFKNGTCKLLVATSVAARGLDVKHLILVVNY 694

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT +Q R+AG+II+ALE SG  +P DL+K+W+
Sbjct:   695 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEDQARYAGDIIKALELSGTAVPPDLEKLWS 754

Query:   158 E 158
             +
Sbjct:   755 D 755

GO:0005524 "ATP binding" evidence=IEA

FB|FBgn0030631 CG6227 [Drosophila melanogaster (taxid:7227)]

 Score = 504 (182.5 bits), Expect = 4.7e-47, P = 4.7e-47
 Identities = 107/195 (54%), Positives = 136/195 (69%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++++LMKA YPC+SLHGGIDQ+DRDSTI+DFK+GKVRLLIATSVAARGLDVK L LVVNY
Sbjct:   773 LLRDLMKASYPCMSLHGGIDQFDRDSTIIDFKSGKVRLLIATSVAARGLDVKDLILVVNY 832

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
             D PNHYEDYVHRCGRTGRAG KG AYTFIT EQ R+AG+IIRA++ SG  IP +L  +W 
Sbjct:   833 DVPNHYEDYVHRCGRTGRAGKKGSAYTFITPEQSRYAGDIIRAMDLSGTLIPAELQALWT 892

Query:   158 EDLIV-----RTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEG 212
             E   +     +T     G  G  + F   EQE +A +  + L+ + + + +  D+     
Sbjct:   893 EYKALQEAEGKTVHTGGGFSGKGFKFD--EQEFNAAKESKKLQKAALGLADSDDE----- 945

Query:   213 LVWLRDYKQRVDQRI 227
                  D +Q +DQ+I
Sbjct:   946 ----EDIEQDIDQQI 956

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0005634 "nucleus" evidence=IC

ZFIN|ZDB-GENE-030131-667 ddx46 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 46" [Danio rerio (taxid:7955)]

 Score = 483 (175.1 bits), Expect = 5.5e-45, P = 5.5e-45
 Identities = 98/158 (62%), Positives = 119/158 (75%)

Query:    38 IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
             ++K+LMKA YPC+SLHGGIDQYDRDS I DFKNG  RLL+ATSVAARGLDVK L LVVNY
Sbjct:   620 LLKDLMKASYPCMSLHGGIDQYDRDSIINDFKNGACRLLVATSVAARGLDVKQLILVVNY 679

Query:    98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW- 156
              CPNHYEDYVHR GRTGRAGNKG+AYTFIT  Q R++G+I++ALE SG  +P +L+++W 
Sbjct:   680 SCPNHYEDYVHRAGRTGRAGNKGYAYTFITEGQARYSGDILKALELSGSSVPAELEQLWT 739

Query:   157 -------AEDLIVRTFCFRAGNKGFAY--TFITLEQER 185
                    AE  I+++    +G KGF +  T   L  ER
Sbjct:   740 NFKEQQKAEGKIIKSSSGFSG-KGFKFDETEHALANER 776

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:0000398 "mRNA splicing, via spliceosome" evidence=IMP

GO:0031017 "exocrine pancreas development" evidence=IMP

GO:0007420 "brain development" evidence=IMP

GO:0048546 "digestive tract morphogenesis" evidence=IMP

GO:0072576 "liver morphogenesis" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0015030 "Cajal body" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9P7C7	PRP11_SCHPO	3, ., 6, ., 4, ., 1, 3	0.6147	0.5281	0.1203	yes	N/A
Q4TVV3	DDX46_DANRE	3, ., 6, ., 4, ., 1, 3	0.6394	0.5974	0.1355	yes	N/A
Q4WT99	PRP5_ASPFU	3, ., 6, ., 4, ., 1, 3	0.5741	0.6623	0.1263	yes	N/A
Q5BDW4	PRP5_EMENI	3, ., 6, ., 4, ., 1, 3	0.5677	0.6623	0.1304	yes	N/A
Q62780	DDX46_RAT	3, ., 6, ., 4, ., 1, 3	0.6598	0.5974	0.1337	yes	N/A
Q6BML1	PRP5_DEBHA	3, ., 6, ., 4, ., 1, 3	0.5315	0.4718	0.1193	yes	N/A
Q8H0U8	RH42_ARATH	3, ., 6, ., 4, ., 1, 3	0.6141	0.5454	0.1080	yes	N/A
P0CQ98	PRP5_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.5899	0.5974	0.1287	yes	N/A
A2QQA8	PRP5_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5641	0.6666	0.1305	yes	N/A
Q84UQ1	RH42_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6315	0.5497	0.1210	yes	N/A
Q553B1	DDX46_DICDI	3, ., 6, ., 4, ., 1, 3	0.6101	0.5108	0.1025	yes	N/A
Q5R6D8	DDX46_PONAB	3, ., 6, ., 4, ., 1, 3	0.6598	0.5974	0.1337	yes	N/A
Q4IP34	PRP5_GIBZE	3, ., 6, ., 4, ., 1, 3	0.6949	0.5108	0.0977	yes	N/A
Q569Z5	DDX46_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6598	0.5974	0.1337	yes	N/A
A3LQ55	PRP5_PICST	3, ., 6, ., 4, ., 1, 3	0.5603	0.4848	0.128	yes	N/A
Q7L014	DDX46_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6598	0.5974	0.1338	yes	N/A
Q6CCZ1	PRP5_YARLI	3, ., 6, ., 4, ., 1, 3	0.6302	0.5151	0.1221	yes	N/A
Q2U2J6	PRP5_ASPOR	3, ., 6, ., 4, ., 1, 3	0.5677	0.6623	0.1290	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	231
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	4e-37
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-35
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-32
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-28
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	2e-27
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	7e-26
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-23
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	6e-23
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-22
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-22
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-19
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-18
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	5e-18
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-17
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	4e-08
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	8e-06
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	1e-05
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-04
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	3e-04

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

 Score =  136 bits (343), Expect = 4e-37
 Identities = 56/118 (47%), Positives = 81/118 (68%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + KEL   G+P L +HG   Q +R   + +FK GK  ++IAT VA+RGLDVK +  V+N+
Sbjct: 393 LTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINF 452

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKM 155
           D PN  EDYVHR GRTGRAG KG +YTF+T ++ R A ++++ L  +  P+P +L+K+
Sbjct: 453 DFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKL 510

Length = 545

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

 Score =  130 bits (329), Expect = 3e-35
 Identities = 56/139 (40%), Positives = 79/139 (56%), Gaps = 3/139 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +   D    IV F   K  +    + + L K G+   +LHG + Q +RD  +  FK+G++
Sbjct: 268 LKDEDEGRVIV-FVRTKRLVE--ELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGEL 324

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+L+AT VAARGLD+  ++ V+NYD P   EDYVHR GRTGRAG KG A +F+T E+E  
Sbjct: 325 RVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVK 384

Query: 134 AGEIIRALEASGVPIPEDL 152
             + I       +P    L
Sbjct: 385 KLKRIEKRLERKLPSAVLL 403

Length = 513

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

 Score =  122 bits (308), Expect = 2e-32
 Identities = 50/122 (40%), Positives = 70/122 (57%), Gaps = 3/122 (2%)

Query: 16  QYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRL 75
            +  +S +V F N K       +   L   G+  L+LHG ++Q DRD  +V F N    +
Sbjct: 239 HHQPESCVV-FCNTKKE--CQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSV 295

Query: 76  LIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAG 135
           L+AT VAARGLD+K L  V+NY+     E +VHR GRTGRAG+KG A + +  E+ + A 
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRAN 355

Query: 136 EI 137
            I
Sbjct: 356 AI 357

Length = 460

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

 Score =  102 bits (257), Expect = 1e-28
 Identities = 38/78 (48%), Positives = 52/78 (66%)

Query: 40  KELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDC 99
           K L K G     LHGG+ Q +R+  + DF+NGK ++L+AT VA RG+D+  +NLV+NYD 
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 100 PNHYEDYVHRCGRTGRAG 117
           P +   Y+ R GR GRAG
Sbjct: 61  PWNPASYIQRIGRAGRAG 78

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score =  101 bits (254), Expect = 2e-27
 Identities = 35/88 (39%), Positives = 54/88 (61%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + + L K G    +LHG   Q +R+  + DF+ G++ +L+AT V ARG+D+ ++++V+NY
Sbjct: 44  LAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINY 103

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTF 125
           D P     Y+ R GR GRAG KG A   
Sbjct: 104 DLPWSPSSYLQRIGRAGRAGQKGTAILL 131

Length = 131

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 95.7 bits (239), Expect = 7e-26
 Identities = 34/80 (42%), Positives = 50/80 (62%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + + L + G     LHGG+ Q +R+  +  F NGK+++L+AT VA RGLD+  ++LV+ Y
Sbjct: 3   LAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIY 62

Query: 98  DCPNHYEDYVHRCGRTGRAG 117
           D P     Y+ R GR GRAG
Sbjct: 63  DLPWSPASYIQRIGRAGRAG 82

Length = 82

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

 Score = 97.6 bits (243), Expect = 2e-23
 Identities = 50/113 (44%), Positives = 71/113 (62%), Gaps = 3/113 (2%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + + L + GY   +L+G ++Q  R+ T+   K+G++ +LIAT VAARGLDV+ ++LVVNY
Sbjct: 261 VAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNY 320

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPE 150
           D P   E YVHR GRTGRAG  G A  F+   + R    I R ++ +   IPE
Sbjct: 321 DIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLT---IPE 370

Length = 629

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

 Score = 95.3 bits (237), Expect = 6e-23
 Identities = 44/108 (40%), Positives = 67/108 (62%)

Query: 32  RLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHL 91
           R  V  + K++ +  +    +HG +DQ DRD  + +F++G  R+LI T + ARG+DV+ +
Sbjct: 277 RRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQV 336

Query: 92  NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIR 139
           +LV+NYD P   E+Y+HR GR+GR G KG A  F+T +      EI R
Sbjct: 337 SLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384

Length = 401

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

 Score = 94.2 bits (235), Expect = 2e-22
 Identities = 44/113 (38%), Positives = 64/113 (56%)

Query: 30  KVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK 89
           + R  V  +   L KAG  C  L G + Q  R+  I    +G+V +L+AT VAARG+D+ 
Sbjct: 253 RTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDID 312

Query: 90  HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
            ++ V+N+D P   + Y+HR GRTGRAG KG A + +        G+I R +E
Sbjct: 313 DVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIE 365

Length = 434

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

 Score = 94.1 bits (234), Expect = 3e-22
 Identities = 44/105 (41%), Positives = 67/105 (63%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + ++L K G    ++HG   Q  R   + DFK+G +R+L+AT +AARGLD++ L  VVNY
Sbjct: 261 LAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNY 320

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
           + PN  EDYVHR GRTGRA   G A + + +++ +   +I + L+
Sbjct: 321 ELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLK 365

Length = 456

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

 Score = 85.0 bits (211), Expect = 3e-19
 Identities = 36/77 (46%), Positives = 45/77 (58%), Gaps = 6/77 (7%)

Query: 52  LHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL---DVKHLNLVVNYDCPNHYEDYVH 108
           L G + Q  R   + +F  G + +L+AT VAARGL    V H   V NYD P+  EDYVH
Sbjct: 285 LTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTH---VFNYDLPDDCEDYVH 341

Query: 109 RCGRTGRAGNKGFAYTF 125
           R GRTGRAG  G + + 
Sbjct: 342 RIGRTGRAGASGHSISL 358

Length = 423

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

 Score = 83.0 bits (205), Expect = 2e-18
 Identities = 37/88 (42%), Positives = 55/88 (62%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           I + L+K G     L G + Q+ R  T+  F+ GK+R+L+AT VA RG+ +  ++ V+N+
Sbjct: 351 IEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINF 410

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTF 125
             P   +DYVHR GRTGRAG  G + +F
Sbjct: 411 TLPEDPDDYVHRIGRTGRAGASGVSISF 438

Length = 475

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

 Score = 81.9 bits (202), Expect = 5e-18
 Identities = 45/109 (41%), Positives = 61/109 (55%), Gaps = 5/109 (4%)

Query: 26  FKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG 85
           F N K    V  + + L + GY    L G + Q  R+S +  F+ G++ +L+AT VAARG
Sbjct: 263 FVNTKA--FVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARG 320

Query: 86  LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHA 134
           L +  +  V NYD P   EDYVHR GRT R G +G A +F     ER+A
Sbjct: 321 LHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC---ERYA 366

Length = 572

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

 Score = 80.6 bits (199), Expect = 1e-17
 Identities = 37/107 (34%), Positives = 59/107 (55%)

Query: 46  GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
           G   LS+HG     +R   +  F  G+V +++AT V  RG+D+  +  V+ +D PN  ++
Sbjct: 392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKE 451

Query: 106 YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDL 152
           Y+H+ GR  R G KG A  F+  E      E++  L++SG  IP +L
Sbjct: 452 YIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPREL 498

Length = 518

>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 52.7 bits (127), Expect = 4e-08
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 55  GIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTG 114
           G+ Q ++   I  F+ G+  +L+ATSV   GLD+  ++LV+ Y+        + R GRTG
Sbjct: 408 GMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTG 467

Query: 115 RAGNKGFAYTFIT 127
           R   KG     +T
Sbjct: 468 R-KRKGRVVVLVT 479

Length = 542

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 46.0 bits (110), Expect = 8e-06
 Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 26/98 (26%)

Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDS-----------TIVDFKNGKVRLLIATSVAARG 85
            IV  L K G   +   G   Q  +D             +  F+ G+  +L++TSVA  G
Sbjct: 380 KIVDLLEKEGIKAVRFVG---QASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEG 436

Query: 86  LDVKHLNLVVNYDCPNHYED------YVHRCGRTGRAG 117
           LD+  ++LV+       YE        + R GRTGR  
Sbjct: 437 LDIPSVDLVI------FYEPVPSEIRSIQRKGRTGRQE 468

Length = 773

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

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 24/88 (27%), Positives = 41/88 (46%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + + L K G    + H G+   +R+     F N ++++++AT+    G+D   +  V++Y
Sbjct: 246 LAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHY 305

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTF 125
           D P   E Y    GR GR G    A   
Sbjct: 306 DLPGSIESYYQETGRAGRDGLPAEAILL 333

Length = 590

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

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 24/80 (30%), Positives = 37/80 (46%)

Query: 46  GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
           G   L+ H G+    R     DF    V++++AT+    G+D  ++  V++YD P + E 
Sbjct: 248 GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLES 307

Query: 106 YVHRCGRTGRAGNKGFAYTF 125
           Y    GR GR G    A   
Sbjct: 308 YYQEAGRAGRDGLPAEAILL 327

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

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

 Score = 40.9 bits (96), Expect = 3e-04
 Identities = 20/77 (25%), Positives = 35/77 (45%)

Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
            L   G    + H G++   RD     F+  ++++++AT     G++   +  V++Y  P
Sbjct: 245 SLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLP 304

Query: 101 NHYEDYVHRCGRTGRAG 117
              E Y    GR GR G
Sbjct: 305 KSMESYYQESGRAGRDG 321

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	231
KOG0345|consensus	567		100.0
KOG0331|consensus	519		100.0
KOG0328|consensus	400		99.97
KOG0342|consensus	543		99.97
KOG0333|consensus	673		99.97
KOG0330|consensus	476		99.97
PTZ00110	545	helicase; Provisional	99.97
KOG0341|consensus	610		99.97
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.96
KOG0336|consensus	629		99.96
KOG0348|consensus	708		99.96
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.96
KOG0340|consensus	442		99.96
KOG0335|consensus	482		99.96
KOG0326|consensus	459		99.95
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.95
KOG0343|consensus	758		99.95
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.94
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.94
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.94
KOG0332|consensus	477		99.94
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.94
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.94
KOG0334|consensus	997		99.94
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.93
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.93
PTZ00424	401	helicase 45; Provisional	99.93
KOG0338|consensus	691		99.93
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.93
KOG0344|consensus	593		99.93
KOG0347|consensus	731		99.92
KOG0339|consensus	731		99.92
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.92
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.91
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.91
KOG0327|consensus	397		99.9
PRK04914	956	ATP-dependent helicase HepA; Validated	99.89
KOG0350|consensus	620		99.88
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.86
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.86
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.85
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.85
KOG0346|consensus	569		99.85
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.84
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.84
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.84
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.84
PRK05298	652	excinuclease ABC subunit B; Provisional	99.84
PRK13767	876	ATP-dependent helicase; Provisional	99.84
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.83
KOG4284|consensus	980		99.83
PRK02362	737	ski2-like helicase; Provisional	99.82
PHA02653	675	RNA helicase NPH-II; Provisional	99.82
KOG0351|consensus	941		99.82
PRK10689	1147	transcription-repair coupling factor; Provisional	99.82
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.81
PRK13766	773	Hef nuclease; Provisional	99.81
KOG0349|consensus	725		99.8
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.8
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.8
KOG0337|consensus	529		99.8
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.8
PRK00254	720	ski2-like helicase; Provisional	99.77
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.77
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.77
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.76
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.76
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.75
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.74
PRK01172	674	ski2-like helicase; Provisional	99.73
KOG0352|consensus	641		99.73
PHA02558	501	uvsW UvsW helicase; Provisional	99.73
KOG0354|consensus	746		99.73
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.71
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.7
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.66
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.66
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.65
COG1202	830	Superfamily II helicase, archaea-specific [General	99.65
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.61
KOG0353|consensus	695		99.59
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.59
PRK14701	1638	reverse gyrase; Provisional	99.55
PRK09694	878	helicase Cas3; Provisional	99.55
COG1204	766	Superfamily II helicase [General function predicti	99.55
PRK09401	1176	reverse gyrase; Reviewed	99.54
KOG0329|consensus	387		99.5
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.45
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.42
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.42
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.41
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.38
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.36
PRK05580	679	primosome assembly protein PriA; Validated	99.35
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.33
KOG0950|consensus	1008		99.32
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.32
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.29
KOG0384|consensus	1373		99.26
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.25
KOG0953|consensus	700		99.19
COG1205	851	Distinct helicase family with a unique C-terminal	99.13
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.07
KOG4150|consensus	1034		99.05
KOG0947|consensus	1248		99.04
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.03
KOG0385|consensus	971		99.03
KOG0922|consensus	674		98.96
KOG0951|consensus	1674		98.93
KOG0390|consensus	776		98.92
KOG0387|consensus	923		98.87
KOG0948|consensus	1041		98.87
KOG0952|consensus	1230		98.86
KOG0920|consensus	924		98.86
KOG0923|consensus	902		98.83
KOG0392|consensus	1549		98.78
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.7
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.7
KOG0924|consensus	1042		98.67
KOG0388|consensus	1185		98.63
KOG0389|consensus	941		98.6
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.59
KOG0391|consensus	1958		98.52
KOG1002|consensus	791		98.51
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.47
KOG0926|consensus	1172		98.44
KOG0949|consensus	1330		98.39
KOG1000|consensus	689		98.37
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.34
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.31
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.28
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.26
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.21
KOG1015|consensus	1567		98.14
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.07
KOG1123|consensus	776		97.99
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.95
KOG0386|consensus	1157		97.95
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.94
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.93
KOG4439|consensus	901		97.83
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	97.72
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.69
COG4889	1518	Predicted helicase [General function prediction on	97.63
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.61
PF13959	65	DUF4217: Domain of unknown function (DUF4217)	97.57
PF13871	278	Helicase_C_4: Helicase_C-like	97.57
COG4096	875	HsdR Type I site-specific restriction-modification	97.52
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.49
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.44
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.42
KOG0925|consensus	699		97.42
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	97.32
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.29
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.19
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	97.14
KOG1016|consensus	1387		97.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	96.96
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	96.7
PRK05580	679	primosome assembly protein PriA; Validated	96.56
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	96.55
TIGR00595	505	priA primosomal protein N'. All proteins in this f	96.46
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	96.37
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.17
KOG0701|consensus	1606		96.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.91
KOG1001|consensus	674		95.8
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	95.68
PF10593	239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	95.46
PRK14873	665	primosome assembly protein PriA; Provisional	95.23
KOG0921|consensus	1282		95.16
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.98
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.95
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	94.77
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.7
KOG1513|consensus	1300		94.69
PRK10689	1147	transcription-repair coupling factor; Provisional	94.66
PRK14873	665	primosome assembly protein PriA; Provisional	94.25
PRK14701	1638	reverse gyrase; Provisional	94.06
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	93.78
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	93.53
KOG0951|consensus	1674		93.46
KOG0339|consensus	731		93.31
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	93.3
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	92.68
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	92.6
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	91.86
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	91.21
KOG0331|consensus	519		90.4
KOG2340|consensus	698		90.27
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	90.17
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	89.9
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	88.76
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	88.53
KOG0347|consensus	731		88.23
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	87.61
KOG0298|consensus	1394		87.23
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	86.59
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	85.83
KOG0389|consensus	941		85.25
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	84.92
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	84.27
PRK09401	1176	reverse gyrase; Reviewed	83.8
PTZ00110	545	helicase; Provisional	83.72
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	83.3
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	83.28
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	82.02
PRK13766	773	Hef nuclease; Provisional	81.95
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	81.12
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	81.09
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	80.5
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	80.24

>KOG0345|consensus

Probab=100.00  E-value=2.3e-35  Score=257.16  Aligned_cols=192  Identities=28%  Similarity=0.348  Sum_probs=158.1

Q ss_pred             CCCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHH--CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec
Q psy17587          2 KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK--AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT   79 (231)
Q Consensus         2 ~~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~--~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT   79 (231)
                      ++.+|+.+|+++|..+...+.+|+|..+   ..++.....|..  .+.++..+||.|.+..|.++++.|++..-.+|+||
T Consensus       238 ~a~eK~~~lv~~L~~~~~kK~iVFF~TC---asVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~T  314 (567)
T KOG0345|consen  238 EADEKLSQLVHLLNNNKDKKCIVFFPTC---ASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCT  314 (567)
T ss_pred             cHHHHHHHHHHHHhccccccEEEEecCc---chHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEee
Confidence            5678999999999987656666655443   336777666654  36889999999999999999999999888999999


Q ss_pred             CccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhhc
Q psy17587         80 SVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAED  159 (231)
Q Consensus        80 ~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~  159 (231)
                      |+++||||||+|++||+||+|.+++.|+||+|||||.|+.|.+++|+.+.+..    +++++...+.+..+.+...   .
T Consensus       315 DVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~gr~G~Aivfl~p~E~a----YveFl~i~~~v~le~~~~e---~  387 (567)
T KOG0345|consen  315 DVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARAGREGNAIVFLNPREEA----YVEFLRIKGKVELERIDTE---K  387 (567)
T ss_pred             hhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhccCccceEEEecccHHH----HHHHHHhcCccchhhhccc---c
Confidence            99999999999999999999999999999999999999999999999997664    7888876654322222100   0


Q ss_pred             hhhhhccccCCCCCcccchhhHHhhhcHHHHHHHHHhcCCCCcHHHHHHHHhhHHHHHhHHHHHHHHHHh
Q psy17587        160 LIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAR  229 (231)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~s~~r~y~~~~~~~i~~  229 (231)
                                                ....+...+..+..++++.+++..++||||+|+|++|.+|+|||
T Consensus       388 --------------------------~~~~~~~~ir~~~~~DR~~~dkG~kAFVS~VraY~~H~cs~Ifr  431 (567)
T KOG0345|consen  388 --------------------------ASLSVYQDIRSIISKDRAVLDKGLKAFVSHVRAYKKHHCSYIFR  431 (567)
T ss_pred             --------------------------cchhHHHHHHHHhcccHHHHhhhHHHHHHHHHHHhhcceeEEEe
Confidence                                      00014566778888899999999999999999999999999997

>KOG0331|consensus

Probab=100.00  E-value=2.8e-33  Score=251.03  Aligned_cols=151  Identities=40%  Similarity=0.654  Sum_probs=139.3

Q ss_pred             chhhhhcccccc--CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          6 PCLSLHGGIDQY--DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         6 k~~~L~~~L~~~--~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      |...|..+|..+  +++.++||||+++  ..|+.|+..|...++++.++||+.++.+|..+++.|++|+..||||||+++
T Consensus       325 K~~~l~~lL~~~~~~~~~KvIIFc~tk--r~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAa  402 (519)
T KOG0331|consen  325 KLRKLGKLLEDISSDSEGKVIIFCETK--RTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAA  402 (519)
T ss_pred             HHHHHHHHHHHHhccCCCcEEEEecch--hhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEccccc
Confidence            344555555555  3577999999999  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhh
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAE  158 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~  158 (231)
                      ||||+|+|++|||||+|.++++|+||+|||||+|+.|.+++|++..+......+.+.+...++.+|+.+..+...
T Consensus       403 RGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~~~l~e~~q~v~~~l~~~~~~  477 (519)
T KOG0331|consen  403 RGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELIKVLREAGQTVPPDLLEYARV  477 (519)
T ss_pred             ccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHHHHHHHccCCCChHHHHHHhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999998887653

>KOG0328|consensus

Probab=99.97  E-value=6e-32  Score=223.27  Aligned_cols=148  Identities=34%  Similarity=0.532  Sum_probs=132.6

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      .+||-.+|-++-.... -...|||||++  ..++.|.+.++..++.+.++||+|+++||.+++.+||+|+.+||++||+.
T Consensus       250 EewKfdtLcdLYd~Lt-ItQavIFcnTk--~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVw  326 (400)
T KOG0328|consen  250 EEWKFDTLCDLYDTLT-ITQAVIFCNTK--RKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVW  326 (400)
T ss_pred             hhhhHhHHHHHhhhhe-hheEEEEeccc--chhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEechh
Confidence            3456555555443332 45566699998  67999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHH
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLD  153 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~  153 (231)
                      +||+|+|.|++|||||+|.+.+.|+||+||.||-|++|.++.|+...+...++++++++.....++|..+.
T Consensus       327 aRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq~yst~i~emp~nva  397 (400)
T KOG0328|consen  327 ARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYSTQIDEMPMNVA  397 (400)
T ss_pred             hccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHHHHhhhcccccchhh
Confidence            99999999999999999999999999999999999999999999999999999999999988888887643

>KOG0342|consensus

Probab=99.97  E-value=3.2e-31  Score=232.35  Aligned_cols=130  Identities=30%  Similarity=0.399  Sum_probs=121.7

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      ...|+++|+++....+|+|||++.  ..+..+++.|....++|.-+||++++..|..+..+|++.+.-|||||||++||+
T Consensus       317 f~ll~~~LKk~~~~~KiiVF~sT~--~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaARGl  394 (543)
T KOG0342|consen  317 FSLLYTFLKKNIKRYKIIVFFSTC--MSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAARGL  394 (543)
T ss_pred             HHHHHHHHHHhcCCceEEEEechh--hHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhhccC
Confidence            678899999998889999999987  669999999998899999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHH
Q psy17587         87 DVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEII  138 (231)
Q Consensus        87 dip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~  138 (231)
                      |+|+|++||+||+|.++.+|+||+||+||.|..|.+++++.|.+..+++.+.
T Consensus       395 D~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK  446 (543)
T KOG0342|consen  395 DIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLK  446 (543)
T ss_pred             CCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999988655443

>KOG0333|consensus

Probab=99.97  E-value=6.7e-31  Score=231.83  Aligned_cols=146  Identities=38%  Similarity=0.560  Sum_probs=131.7

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|...|.+.|..+ ....+|||+|.+  +.|+.|++.|.+.|+++..+||+-++++|..+++.|++|..+||||||+++
T Consensus       502 d~k~kkL~eil~~~-~~ppiIIFvN~k--k~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAg  578 (673)
T KOG0333|consen  502 DEKRKKLIEILESN-FDPPIIIFVNTK--KGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAG  578 (673)
T ss_pred             hHHHHHHHHHHHhC-CCCCEEEEEech--hhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccc
Confidence            44567788888777 567788899998  889999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHH-hCCCCCchhH
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE-ASGVPIPEDL  152 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~-~~~~~~~~~l  152 (231)
                      ||||+|+|++|||||++.+.++|.||+||+||+|+.|.+++|+++.+...+.++.+.+. ......|..+
T Consensus       579 RGIDIpnVSlVinydmaksieDYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~l~es~~s~~P~El  648 (673)
T KOG0333|consen  579 RGIDIPNVSLVINYDMAKSIEDYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQALRESVKSHCPPEL  648 (673)
T ss_pred             cCCCCCccceeeecchhhhHHHHHHHhccccccccCceeEEEeccchhHHHHHHHHHHHHhhhccCChhh
Confidence            99999999999999999999999999999999999999999999999998888888665 3444455543

>KOG0330|consensus

Probab=99.97  E-value=1.4e-30  Score=222.84  Aligned_cols=142  Identities=32%  Similarity=0.460  Sum_probs=131.6

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      .+||-..|+.+|++.. +..+||||++.  .+++.++-.|+..|+.+..+||.|++..|..+++.|++|..+||||||++
T Consensus       284 ~k~K~~yLV~ll~e~~-g~s~iVF~~t~--~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVa  360 (476)
T KOG0330|consen  284 GKDKDTYLVYLLNELA-GNSVIVFCNTC--NTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVA  360 (476)
T ss_pred             ccccchhHHHHHHhhc-CCcEEEEEecc--chHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchh
Confidence            4678888888888665 47788899988  66999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCC
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVP  147 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~  147 (231)
                      +||+|+|.|++|||||+|.+..+|+||+||+||+|..|.+|+|++..|.+....++..+.++...
T Consensus       361 SRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~~gkkl~~  425 (476)
T KOG0330|consen  361 SRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHALGKKLPE  425 (476)
T ss_pred             cccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHHHHhcCCCc
Confidence            99999999999999999999999999999999999999999999999999999998888776644

>PTZ00110 helicase; Provisional

Probab=99.97  E-value=8.3e-30  Score=235.58  Aligned_cols=153  Identities=40%  Similarity=0.627  Sum_probs=141.3

Q ss_pred             chhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          6 PCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         6 k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      |...|.++|.... .+.++||||+++  ..++.|+..|...++.+..+||+|++++|..++++|++|+.+|||||++++|
T Consensus       362 k~~~L~~ll~~~~~~~~k~LIF~~t~--~~a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~r  439 (545)
T PTZ00110        362 KRGKLKMLLQRIMRDGDKILIFVETK--KGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASR  439 (545)
T ss_pred             HHHHHHHHHHHhcccCCeEEEEecCh--HHHHHHHHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhc
Confidence            4555666665544 567899999998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhhch
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDL  160 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~  160 (231)
                      |||+|+|++|||||+|.++++|+||+||+||.|+.|.|++|+++.+...+.++.+.+...++++|+++.++.....
T Consensus       440 GIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~~~~~~~~l~~~l~~~~q~vp~~l~~~~~~~~  515 (545)
T PTZ00110        440 GLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERS  515 (545)
T ss_pred             CCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcchHHHHHHHHHHHHHccCCCCHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999876544

>KOG0341|consensus

Probab=99.97  E-value=5.3e-30  Score=219.59  Aligned_cols=176  Identities=31%  Similarity=0.449  Sum_probs=154.4

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      -+.|+..|+++|++..  ..++|||..+  .-++.++++|.-+|..++.+|||-++++|...++.|+.|+.+||||||++
T Consensus       406 qEaKiVylLeCLQKT~--PpVLIFaEkK--~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVA  481 (610)
T KOG0341|consen  406 QEAKIVYLLECLQKTS--PPVLIFAEKK--ADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVA  481 (610)
T ss_pred             hhhhhhhHHHHhccCC--CceEEEeccc--cChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecch
Confidence            4678999999999874  6788899988  56999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhCCCCCchhHHHHHhhchh
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEASGVPIPEDLDKMWAEDLI  161 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~  161 (231)
                      +.|+|+|++.+|||||+|..+++|+||+||+||.|+.|.+.+|++.. +...+.++..++...++.+|+.+..+......
T Consensus       482 SKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRsg~~GiATTfINK~~~esvLlDLK~LL~EakQ~vP~~L~~L~~~~E~  561 (610)
T KOG0341|consen  482 SKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRSGKTGIATTFINKNQEESVLLDLKHLLQEAKQEVPPVLAELAGPMEE  561 (610)
T ss_pred             hccCCCccchhhccCCChHHHHHHHHHhcccCCCCCcceeeeeecccchHHHHHHHHHHHHHhhccCCHHHHHhCCCccc
Confidence            99999999999999999999999999999999999999999999977 56777888889999999999999988764331


Q ss_pred             --h-----hhccccCCCCCcccchhhHH
Q psy17587        162 --V-----RTFCFRAGNKGFAYTFITLE  182 (231)
Q Consensus       162 --~-----~~~~~~~~~~~~~~~~~~~~  182 (231)
                        .     ..+|--.+|.|+.+++-...
T Consensus       562 ~~~a~~~~~kGCayCgGLGHRItdCPKl  589 (610)
T KOG0341|consen  562 ETIADAGGEKGCAYCGGLGHRITDCPKL  589 (610)
T ss_pred             cccccCCCccccccccCCCcccccCchh
Confidence              1     11233457888888874443

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

Probab=99.96  E-value=1.2e-29  Score=232.79  Aligned_cols=137  Identities=41%  Similarity=0.626  Sum_probs=125.7

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|+..|..+++..... ++||||+++  ..++.|+..|...|+++..+||+|++++|.++++.|++|+.+||||||+++|
T Consensus       259 ~k~~~L~~ll~~~~~~-~~IVF~~tk--~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaR  335 (513)
T COG0513         259 EKLELLLKLLKDEDEG-RVIVFVRTK--RLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAAR  335 (513)
T ss_pred             HHHHHHHHHHhcCCCC-eEEEEeCcH--HHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhc
Confidence            3777888888777655 577799998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhC
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEAS  144 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~  144 (231)
                      |||+|+|++|||||+|.++++|+||+||+||+|..|.+++|+++. +...+..+.+.+...
T Consensus       336 GiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~~~e~~~l~~ie~~~~~~  396 (513)
T COG0513         336 GLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERK  396 (513)
T ss_pred             cCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCcHHHHHHHHHHHHHHhcc
Confidence            999999999999999999999999999999999999999999986 777777787776554

>KOG0336|consensus

Probab=99.96  E-value=9.1e-30  Score=219.35  Aligned_cols=153  Identities=35%  Similarity=0.560  Sum_probs=142.4

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |....-.++....+..++||||.++  ..++.|+..|...|+.+.++||+-++.+|+.++++|++|+++||||||+++||
T Consensus       451 k~~~~~~f~~~ms~ndKvIiFv~~K--~~AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRG  528 (629)
T KOG0336|consen  451 KLEIVQFFVANMSSNDKVIIFVSRK--VMADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRG  528 (629)
T ss_pred             HHHHHHHHHHhcCCCceEEEEEech--hhhhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcC
Confidence            3444455567777889999999999  55999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhhch
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDL  160 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~  160 (231)
                      +|+|++.+|+|||+|.++++|+||+||+||+|+.|.+++|++.++...+.++++.|...++++|++|..++..-+
T Consensus       529 lDv~DiTHV~NyDFP~nIeeYVHRvGrtGRaGr~G~sis~lt~~D~~~a~eLI~ILe~aeQevPdeL~~mAeryk  603 (629)
T KOG0336|consen  529 LDVPDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGTSISFLTRNDWSMAEELIQILERAEQEVPDELVRMAERYK  603 (629)
T ss_pred             CCchhcceeeccCCCccHHHHHHHhcccccCCCCcceEEEEehhhHHHHHHHHHHHHHhhhhCcHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999998877544

>KOG0348|consensus

Probab=99.96  E-value=1.7e-28  Score=217.11  Aligned_cols=205  Identities=26%  Similarity=0.359  Sum_probs=150.3

Q ss_pred             hhhhhccc---cccCCCCeEEEEcCChhHHHHHHHHHHHHHC----------------------CCCeeeccCCCCHHHH
Q psy17587          7 CLSLHGGI---DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----------------------GYPCLSLHGGIDQYDR   61 (231)
Q Consensus         7 ~~~L~~~L---~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----------------------~~~~~~lhg~~~~~~R   61 (231)
                      +.+|..+|   -+....+++|||..+.  +.+++=+..|...                      +.++.-+||+|++++|
T Consensus       409 LV~Laa~L~~~~k~~~~qk~iVF~S~~--d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeR  486 (708)
T KOG0348|consen  409 LVALAALLLNKVKFEEKQKMIVFFSCS--DSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEER  486 (708)
T ss_pred             HHHHHHHHHHHhhhhhhceeEEEEech--hHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHH
Confidence            34444444   2333466777787765  6677766665321                      4668899999999999


Q ss_pred             HHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHH
Q psy17587         62 DSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRAL  141 (231)
Q Consensus        62 ~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l  141 (231)
                      ..+++.|+...-.||+||||++||+|+|+|.+||+||+|.++.+|+||+||++|.|..|.+++|+.|.+.++    .+.+
T Consensus       487 ts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARaG~kG~alLfL~P~Eaey----~~~l  562 (708)
T KOG0348|consen  487 TSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARAGEKGEALLFLLPSEAEY----VNYL  562 (708)
T ss_pred             HHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhccCCCceEEEecccHHHH----HHHH
Confidence            999999999988999999999999999999999999999999999999999999999999999999999873    4444


Q ss_pred             HhCCCCCchhHHHHHhhchhhhhccccCCCCCcccchhhHHhhhcHHHHHHHHHhcCCCCcHHHHHHHHhhHHHHHhHHH
Q psy17587        142 EASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQ  221 (231)
Q Consensus       142 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~s~~r~y~~  221 (231)
                      +.....+.+.     +....+..++...+.      ....+....+...+..++.+...+++....+.++|+||+|+|+-
T Consensus       563 ~~~~~~l~q~-----~~~~~l~~~~~~~~k------~~~~e~~~~at~~q~~~e~~~~~~~~~~~~a~kaf~S~vr~Yat  631 (708)
T KOG0348|consen  563 KKHHIMLLQF-----DMEILLPAFKPRKDK------AKTKEWQERATTLQLNLERLVVGDEAMKNLAKKAFVSWVRAYAT  631 (708)
T ss_pred             Hhhcchhhcc-----chhhhhhhcCccccc------ccchhhhhhHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHhh
Confidence            3322221111     001112222211111      11123455677889999999999988888888888999999998


Q ss_pred             HHH--HHHH
Q psy17587        222 RVD--QRIA  228 (231)
Q Consensus       222 ~~~--~~i~  228 (231)
                      |..  ..||
T Consensus       632 h~~elk~iF  640 (708)
T KOG0348|consen  632 HPSELKSIF  640 (708)
T ss_pred             Chhhhccce
Confidence            864  4555

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

Probab=99.96  E-value=2e-28  Score=225.36  Aligned_cols=149  Identities=28%  Similarity=0.471  Sum_probs=134.2

Q ss_pred             chhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHHH-CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          6 PCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELMK-AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         6 k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~~-~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      |...|.+.|..... ..++||||+++  ..++.+++.|.. .++.+..+||+|++.+|..+++.|++|+++|||||++++
T Consensus       352 k~~~l~~~l~~~~~~~~~~iVFv~s~--~~a~~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~  429 (518)
T PLN00206        352 KKQKLFDILKSKQHFKPPAVVFVSSR--LGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLG  429 (518)
T ss_pred             HHHHHHHHHHhhcccCCCEEEEcCCc--hhHHHHHHHHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhh
Confidence            44556666654432 45788899998  779999999975 589999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHH
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW  156 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~  156 (231)
                      ||+|+|+|++|||||+|.++.+|+||+||+||.|..|.+++|+++++...+.++.+.++..++.+|+++.+..
T Consensus       430 rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~~~~~~~~~l~~~l~~~~~~vp~~l~~~~  502 (518)
T PLN00206        430 RGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAIPRELANSR  502 (518)
T ss_pred             ccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEchhHHHHHHHHHHHHHHcCCCCCHHHHhCh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999877543

>KOG0340|consensus

Probab=99.96  E-value=1.2e-28  Score=208.93  Aligned_cols=140  Identities=31%  Similarity=0.441  Sum_probs=128.9

Q ss_pred             hhhhccccccCC--CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          8 LSLHGGIDQYDR--DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         8 ~~L~~~L~~~~~--~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      ..|+.+|..+..  ++.++||+|+.  ..|..|+..|...++.+.++||.|++.+|...+.+|+++..+||||||+++||
T Consensus       240 aYLv~~Lr~~~~~~~~simIFvntt--r~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTDVAsRG  317 (442)
T KOG0340|consen  240 AYLVHLLRDFENKENGSIMIFVNTT--RECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATDVASRG  317 (442)
T ss_pred             HHHHHHHhhhhhccCceEEEEeehh--HHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEechhhcC
Confidence            456777776665  78899999987  67999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCc
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIP  149 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~  149 (231)
                      +|||.|+.|||||+|.+|.+|+||+||++|+|+.|.+++|++..|.+.+..+++...++..+.+
T Consensus       318 LDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~~igkKl~e~~  381 (442)
T KOG0340|consen  318 LDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEEEIGKKLTEYN  381 (442)
T ss_pred             CCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHHHHhccccccc
Confidence            9999999999999999999999999999999999999999999999988888888877665544

>KOG0335|consensus

Probab=99.96  E-value=1.6e-28  Score=217.46  Aligned_cols=152  Identities=36%  Similarity=0.561  Sum_probs=140.0

Q ss_pred             CchhhhhccccccC---CCC-----eEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEE
Q psy17587          5 YPCLSLHGGIDQYD---RDS-----TIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLL   76 (231)
Q Consensus         5 ~k~~~L~~~L~~~~---~~~-----~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vL   76 (231)
                      +|...|+++|....   ...     +++|||.++  +.+++++..|...++++..+||.-++.+|.+++..|++|++.+|
T Consensus       314 ~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~--~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~pvl  391 (482)
T KOG0335|consen  314 EKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETK--RGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKAPVL  391 (482)
T ss_pred             hhHHHHHHHhhcccCCcccCCcccceEEEEeecc--chhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCcceE
Confidence            56667777776444   333     788899998  77999999999999999999999999999999999999999999


Q ss_pred             EecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHH
Q psy17587         77 IATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW  156 (231)
Q Consensus        77 vaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~  156 (231)
                      |||++++||+|+|+|.+|||||+|.+..+|+||+|||||.|+.|.++.|+...+....+.+.+.+...++.+|+++.++.
T Consensus       392 VaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~Gn~G~atsf~n~~~~~i~~~L~~~l~ea~q~vP~wl~~~~  471 (482)
T KOG0335|consen  392 VATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRVGNGGRATSFFNEKNQNIAKALVEILTEANQEVPQWLSELS  471 (482)
T ss_pred             EEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccCCCCceeEEEeccccchhHHHHHHHHHHhcccCcHHHHhhh
Confidence            99999999999999999999999999999999999999999999999999988999999999999999999999999855


Q ss_pred             hh
Q psy17587        157 AE  158 (231)
Q Consensus       157 ~~  158 (231)
                      .+
T Consensus       472 ~~  473 (482)
T KOG0335|consen  472 RE  473 (482)
T ss_pred             hh
Confidence            43

>KOG0326|consensus

Probab=99.95  E-value=7.7e-29  Score=207.89  Aligned_cols=148  Identities=32%  Similarity=0.574  Sum_probs=137.1

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ..+|+.+|-.+..+..-++.|| |||+.  ..++.|++.+...|+++.++|+.|.++.|..++.+|++|.++.|||||.+
T Consensus       306 e~qKvhCLntLfskLqINQsII-FCNS~--~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~  382 (459)
T KOG0326|consen  306 ERQKVHCLNTLFSKLQINQSII-FCNST--NRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLF  382 (459)
T ss_pred             hhhhhhhHHHHHHHhcccceEE-Eeccc--hHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhh
Confidence            4678888888877776666666 99998  44999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHH
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLD  153 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~  153 (231)
                      -||+|+++|++|||||+|.+.++|+||+||.||-|-.|.+|.+++-+|...+..+++.+.....++|..++
T Consensus       383 TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLGtEI~pip~~iD  453 (459)
T KOG0326|consen  383 TRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELGTEIKPIPSNID  453 (459)
T ss_pred             hcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhccccccCCCcCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999987644

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=4.6e-28  Score=218.01  Aligned_cols=138  Identities=33%  Similarity=0.406  Sum_probs=123.7

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|...|..++... ...++||||+++  ..++.+++.|...|+++..+||+|++.+|..++++|++|+++||||||+++|
T Consensus       241 ~k~~~l~~ll~~~-~~~~~lVF~~t~--~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~r  317 (423)
T PRK04837        241 EKMRLLQTLIEEE-WPDRAIIFANTK--HRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAAR  317 (423)
T ss_pred             HHHHHHHHHHHhc-CCCeEEEEECCH--HHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhc
Confidence            3555666666544 356788899998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      |+|+|+|++|||||+|.++.+|+||+||+||.|+.|.|++|+++.+...+..+.+.+....
T Consensus       318 GiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~~~~~~~~~i~~~~~~~~  378 (423)
T PRK04837        318 GLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSI  378 (423)
T ss_pred             CCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCHHHHHHHHHHHHHhCCCC
Confidence            9999999999999999999999999999999999999999999998888877777665443

>KOG0343|consensus

Probab=99.95  E-value=1.1e-27  Score=212.77  Aligned_cols=192  Identities=28%  Similarity=0.379  Sum_probs=152.1

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHH--HCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELM--KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~--~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      -+.|+..|..+|+.+...+.|| |.++.  .++..+++.+.  ..|+++.++||+|++..|..++.+|-...--||+|||
T Consensus       297 l~~Ki~~L~sFI~shlk~K~iV-F~Ssc--Kqvkf~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~~~F~~~~~~vLF~TD  373 (758)
T KOG0343|consen  297 LEDKIDMLWSFIKSHLKKKSIV-FLSSC--KQVKFLYEAFCRLRPGIPLLALHGTMSQKKRIEVYKKFVRKRAVVLFCTD  373 (758)
T ss_pred             hhhHHHHHHHHHHhccccceEE-EEehh--hHHHHHHHHHHhcCCCCceeeeccchhHHHHHHHHHHHHHhcceEEEeeh
Confidence            3578899999999876666666 55544  46788887775  4589999999999999999999999999999999999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhhch
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDL  160 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~  160 (231)
                      +++||+|+|.|+|||++|+|.++++|+||+||++|.+..|.++++++|.+++.   ++..+.....++.+.  .+     
T Consensus       374 v~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~~~G~sll~L~psEeE~---~l~~Lq~k~I~i~~i--~i-----  443 (758)
T KOG0343|consen  374 VAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYKERGESLLMLTPSEEEA---MLKKLQKKKIPIKEI--KI-----  443 (758)
T ss_pred             hhhccCCCcccceEEEecCchhHHHHHHHhhhhhcccCCCceEEEEcchhHHH---HHHHHHHcCCCHHhh--cc-----
Confidence            99999999999999999999999999999999999999999999999998653   445554444322221  00     


Q ss_pred             hhhhccccCCCCCcccchhhHHhhhcHHHHHHHHHhcCCCCcHHHHHHHHhhHHHHHhHHHHHHHHHHh
Q psy17587        161 IVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKILAEGLVWLRDYKQRVDQRIAR  229 (231)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~s~~r~y~~~~~~~i~~  229 (231)
                                            ......++...|....+++++.-....+++++|+|+--....+++|.
T Consensus       444 ----------------------~~~k~~~i~~~l~~ll~~~~eLk~~aqka~isY~rsi~~~rdK~~f~  490 (758)
T KOG0343|consen  444 ----------------------DPEKLTSIRNKLEALLAKDPELKEYAQKAFISYLRSIYLMRDKRVFD  490 (758)
T ss_pred             ----------------------CHHHhhhHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHhhccchhhc
Confidence                                  01112345566777777888888888888899999877766666664

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.94  E-value=7.2e-27  Score=212.14  Aligned_cols=126  Identities=37%  Similarity=0.584  Sum_probs=117.6

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      .....++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+++|||||+++++|+|+|+|++|||
T Consensus       242 ~~~~~~~lVF~~t~--~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~VI~  319 (456)
T PRK10590        242 KGNWQQVLVFTRTK--HGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVN  319 (456)
T ss_pred             cCCCCcEEEEcCcH--HHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEEEE
Confidence            34456788899998  7799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhC
Q psy17587         97 YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEAS  144 (231)
Q Consensus        97 ~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~  144 (231)
                      ||+|.++.+|+||+||+||.|..|.+++|++..+...++.+++.+...
T Consensus       320 ~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~~d~~~~~~ie~~l~~~  367 (456)
T PRK10590        320 YELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKE  367 (456)
T ss_pred             eCCCCCHHHhhhhccccccCCCCeeEEEEecHHHHHHHHHHHHHhcCC
Confidence            999999999999999999999999999999999988888888776544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.94  E-value=8.1e-27  Score=212.00  Aligned_cols=135  Identities=38%  Similarity=0.538  Sum_probs=122.4

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |...|..+|.... ..++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++|
T Consensus       229 k~~~l~~ll~~~~-~~~~lVF~~t~--~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rG  305 (460)
T PRK11776        229 RLPALQRLLLHHQ-PESCVVFCNTK--KECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARG  305 (460)
T ss_pred             HHHHHHHHHHhcC-CCceEEEECCH--HHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccc
Confidence            5556666665544 45677799998  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHh
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                      +|+|++++|||||+|.++++|+||+||+||.|..|.|++|+.+.+...+..+.+.+..
T Consensus       306 iDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~e~~~~~~i~~~~~~  363 (460)
T PRK11776        306 LDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGR  363 (460)
T ss_pred             cchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchhHHHHHHHHHHHhCC
Confidence            9999999999999999999999999999999999999999999988877777776654

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.94  E-value=1.5e-26  Score=210.70  Aligned_cols=132  Identities=17%  Similarity=0.275  Sum_probs=119.2

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      .+..+..+|....++++.||||+++  ..++.++..|...|+.+..+||+|++++|..+++.|++|+++|||||+++++|
T Consensus       212 ~~~~l~~~l~~~~~~~~~IIF~~s~--~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~G  289 (470)
T TIGR00614       212 ILEDLLRFIRKEFKGKSGIIYCPSR--KKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG  289 (470)
T ss_pred             HHHHHHHHHHHhcCCCceEEEECcH--HHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhcc
Confidence            3445666666555677778899988  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHH
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIR  139 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~  139 (231)
                      +|+|+|++||||++|.++++|+||+||+||.|..|.|++|+++.+...++.++.
T Consensus       290 ID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~~~d~~~~~~~~~  343 (470)
T TIGR00614       290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAPADINRLRRLLM  343 (470)
T ss_pred             CCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEechhHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999988776555543

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

>KOG0332|consensus

Probab=99.94  E-value=1.8e-26  Score=196.97  Aligned_cols=139  Identities=32%  Similarity=0.492  Sum_probs=119.7

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      +..|...|.++--...-++.|| ||.++  .++..|+..|...|+.|.++||.|+-.+|..++.+|+.|+..|||+|+++
T Consensus       314 ~~~K~~~l~~lyg~~tigqsiI-Fc~tk--~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~  390 (477)
T KOG0332|consen  314 RDDKYQALVNLYGLLTIGQSII-FCHTK--ATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVC  390 (477)
T ss_pred             hhhHHHHHHHHHhhhhhhheEE-EEeeh--hhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceEEEEechh
Confidence            4566666666333333345555 99998  78999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCC------CHhHHHHHhcccCCCCCceeEEEEecccc-hHHHHHHHHHHHhC
Q psy17587         83 ARGLDVKHLNLVVNYDCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQ-ERHAGEIIRALEAS  144 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~------~~~~y~qr~GR~gR~g~~g~~i~~~~~~~-~~~~~~~~~~l~~~  144 (231)
                      +||+|++.|++|||||+|.      +++.|+||+||+||-|+.|.++.|+..++ ...+..+.+++...
T Consensus       391 ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~  459 (477)
T KOG0332|consen  391 ARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMK  459 (477)
T ss_pred             hcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhc
Confidence            9999999999999999996      69999999999999999999999998774 55666777777543

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.94  E-value=2.8e-26  Score=207.04  Aligned_cols=135  Identities=34%  Similarity=0.523  Sum_probs=121.2

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |...|..+++. ....++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+++|||||+++++|
T Consensus       232 k~~~l~~l~~~-~~~~~~lVF~~s~--~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~G  308 (434)
T PRK11192        232 KTALLCHLLKQ-PEVTRSIVFVRTR--ERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARG  308 (434)
T ss_pred             HHHHHHHHHhc-CCCCeEEEEeCCh--HHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccC
Confidence            44455555543 3457788899988  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHh
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                      +|+|+|++|||||+|.+...|+||+||+||.|..|.+++|+...+...+..+.+++..
T Consensus       309 iDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~~d~~~~~~i~~~~~~  366 (434)
T PRK11192        309 IDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEE  366 (434)
T ss_pred             ccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999888888777766643

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=1.7e-26  Score=214.47  Aligned_cols=137  Identities=34%  Similarity=0.484  Sum_probs=122.8

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|+..|..++... .+.++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+++|||||+++++
T Consensus       243 ~k~~~L~~ll~~~-~~~k~LVF~nt~--~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~ar  319 (572)
T PRK04537        243 EKQTLLLGLLSRS-EGARTMVFVNTK--AFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAAR  319 (572)
T ss_pred             HHHHHHHHHHhcc-cCCcEEEEeCCH--HHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhc
Confidence            3455566666543 456778899998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhC
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEAS  144 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~  144 (231)
                      |||+|+|++|||||+|.++++|+||+||+||.|..|.|++|+++.+...+.++.+.+..+
T Consensus       320 GIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~~~~~l~~i~~~~~~~  379 (572)
T PRK04537        320 GLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQK  379 (572)
T ss_pred             CCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999999998888778887776543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.94  E-value=3.7e-26  Score=213.83  Aligned_cols=138  Identities=37%  Similarity=0.538  Sum_probs=123.8

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      +|...|..+|.... ...+||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+++|||||+++++
T Consensus       231 ~k~~~L~~~L~~~~-~~~~IVF~~tk--~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~ar  307 (629)
T PRK11634        231 RKNEALVRFLEAED-FDAAIIFVRTK--NATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAAR  307 (629)
T ss_pred             hHHHHHHHHHHhcC-CCCEEEEeccH--HHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhc
Confidence            46667777776554 45677799998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      |||+|+|++|||||+|.++++|+||+|||||.|+.|.+++|+.+.+...++.+.+.+....
T Consensus       308 GIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~~e~~~l~~ie~~~~~~i  368 (629)
T PRK11634        308 GLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTI  368 (629)
T ss_pred             CCCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEechHHHHHHHHHHHHhCCCc
Confidence            9999999999999999999999999999999999999999999988887777777665443

>KOG0334|consensus

Probab=99.94  E-value=4.7e-26  Score=214.49  Aligned_cols=174  Identities=49%  Similarity=0.684  Sum_probs=155.0

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|...|+++|..+..+.++||||.+.  ..|+.+.+.|++.|+.+..+||+.++.+|..+++.|+++.+++||||++++
T Consensus       597 ~eKf~kL~eLl~e~~e~~~tiiFv~~q--e~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvva  674 (997)
T KOG0334|consen  597 NEKFLKLLELLGERYEDGKTIIFVDKQ--EKADALLRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVA  674 (997)
T ss_pred             hHHHHHHHHHHHHHhhcCCEEEEEcCc--hHHHHHHHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhh
Confidence            356788888888777788888899988  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhh-----
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAE-----  158 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~-----  158 (231)
                      ||+|++++.+|||||+|.+..+|+||+||+||+|+.|.|++|+.+.+....-++.+.+...++++|..+..++..     
T Consensus       675 rGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtFi~p~q~~~a~dl~~al~~~~~~~P~~l~~l~~~f~~~~  754 (997)
T KOG0334|consen  675 RGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTFITPDQLKYAGDLCKALELSKQPVPKLLQALSERFKAKQ  754 (997)
T ss_pred             cccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEEeChHHhhhHHHHHHHHHhccCCCchHHHHHHHHHHhhh
Confidence            999999999999999999999999999999999999999999999988899999999999999999888877652     


Q ss_pred             --chhhhhccccCCCCCcccchh
Q psy17587        159 --DLIVRTFCFRAGNKGFAYTFI  179 (231)
Q Consensus       159 --~~~~~~~~~~~~~~~~~~~~~  179 (231)
                        +.......++++|+|+++.+.
T Consensus       755 ~~~~s~~~~~Gg~~G~g~~~~~~  777 (997)
T KOG0334|consen  755 KAGGSQVHGGGGFGGKGLKFDEV  777 (997)
T ss_pred             hcccccccccCcccCCcccccHH
Confidence              112222233688999998764

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.93  E-value=9.3e-26  Score=205.86  Aligned_cols=137  Identities=34%  Similarity=0.485  Sum_probs=122.7

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |...|..++.. ....++||||+++  ..++.+++.|...++.+..+||+|++++|.++++.|++|+++|||||+++++|
T Consensus       322 k~~~l~~ll~~-~~~~~~IVF~~s~--~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~G  398 (475)
T PRK01297        322 KYKLLYNLVTQ-NPWERVMVFANRK--DEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRG  398 (475)
T ss_pred             HHHHHHHHHHh-cCCCeEEEEeCCH--HHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccC
Confidence            33445555543 3456788899988  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      +|+|++++||+||+|.+..+|+||+||+||.|+.|.+++|+...|...+..+.+.+..+.
T Consensus       399 IDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~d~~~~~~~~~~~~~~~  458 (475)
T PRK01297        399 IHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKI  458 (475)
T ss_pred             CcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHHHHHHHHHHHHHhCCCC
Confidence            999999999999999999999999999999999999999999988888888888776654

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

Probab=99.93  E-value=4.7e-26  Score=218.96  Aligned_cols=129  Identities=17%  Similarity=0.306  Sum_probs=115.1

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLD   87 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gld   87 (231)
                      ..+..++.....+...||||+++  ..++.+++.|...|+++..+||+|++++|..++++|.+|+++|||||+++++|||
T Consensus       668 e~L~~~I~~~~~~esgIIYC~SR--ke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdAFGMGID  745 (1195)
T PLN03137        668 EDIDKFIKENHFDECGIIYCLSR--MDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGIN  745 (1195)
T ss_pred             HHHHHHHHhcccCCCceeEeCch--hHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEechhhcCCC
Confidence            44555665544456677799988  7799999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHH
Q psy17587         88 VKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEII  138 (231)
Q Consensus        88 ip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~  138 (231)
                      +|+|++|||||+|.+++.|+||+|||||.|..|.|++|+...|....+.++
T Consensus       746 kPDVR~VIHydlPkSiEsYyQriGRAGRDG~~g~cILlys~~D~~~~~~lI  796 (1195)
T PLN03137        746 KPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMI  796 (1195)
T ss_pred             ccCCcEEEEcCCCCCHHHHHhhhcccCCCCCCceEEEEecHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999887765444443

>PTZ00424 helicase 45; Provisional

Probab=99.93  E-value=7.2e-26  Score=202.05  Aligned_cols=142  Identities=32%  Similarity=0.538  Sum_probs=124.0

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      +...+...+... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+++|||||+++++|
T Consensus       254 ~~~~l~~~~~~~-~~~~~ivF~~t~--~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~G  330 (401)
T PTZ00424        254 KFDTLCDLYETL-TITQAIIYCNTR--RKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG  330 (401)
T ss_pred             HHHHHHHHHHhc-CCCeEEEEecCc--HHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCC
Confidence            444444444433 345678899998  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCch
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPE  150 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~  150 (231)
                      +|+|++++||+||+|.+..+|+||+||+||.|+.|.|++|+++.+...+..+.+.+.....+.++
T Consensus       331 iDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~~~~~~~~~e~~~~~~~~~~~~  395 (401)
T PTZ00424        331 IDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPM  395 (401)
T ss_pred             cCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHHHHHHHHHHHHHHCCcccccCc
Confidence            99999999999999999999999999999999999999999999888888887777655554443

>KOG0338|consensus

Probab=99.93  E-value=1.1e-25  Score=198.53  Aligned_cols=131  Identities=32%  Similarity=0.449  Sum_probs=117.4

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLD   87 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gld   87 (231)
                      ..|..++.+.. ..+++||+.++  .++..|.=.|-..|+++.-+||.|+|++|...++.|++++++||||||+++||||
T Consensus       415 a~l~~l~~rtf-~~~~ivFv~tK--k~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAsRGLD  491 (691)
T KOG0338|consen  415 AMLASLITRTF-QDRTIVFVRTK--KQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVASRGLD  491 (691)
T ss_pred             HHHHHHHHHhc-ccceEEEEehH--HHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhhccCC
Confidence            34555556555 45556699988  7788887777778999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHH
Q psy17587         88 VKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRAL  141 (231)
Q Consensus        88 ip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l  141 (231)
                      |+.|.+||||++|.+...|+||+||++|+|+.|.+++|+...+...++.+++..
T Consensus       492 I~gV~tVINy~mP~t~e~Y~HRVGRTARAGRaGrsVtlvgE~dRkllK~iik~~  545 (691)
T KOG0338|consen  492 IEGVQTVINYAMPKTIEHYLHRVGRTARAGRAGRSVTLVGESDRKLLKEIIKSS  545 (691)
T ss_pred             ccceeEEEeccCchhHHHHHHHhhhhhhcccCcceEEEeccccHHHHHHHHhhh
Confidence            999999999999999999999999999999999999999999999888888764

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.93  E-value=3.7e-25  Score=207.06  Aligned_cols=128  Identities=21%  Similarity=0.322  Sum_probs=114.5

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      +..|...+... .+++.||||+++  ..++.+++.|...|+++..+||+|++++|..+++.|++|+++|||||+++++|+
T Consensus       224 ~~~l~~~l~~~-~~~~~IIFc~tr--~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GI  300 (607)
T PRK11057        224 LDQLMRYVQEQ-RGKSGIIYCNSR--AKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGI  300 (607)
T ss_pred             HHHHHHHHHhc-CCCCEEEEECcH--HHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccC
Confidence            34455555443 456777799988  779999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHH
Q psy17587         87 DVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEI  137 (231)
Q Consensus        87 dip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~  137 (231)
                      |+|+|++|||||+|.+.++|+||+||+||.|..|.|++|+.+.+...++.+
T Consensus       301 Dip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G~~~~~ill~~~~d~~~~~~~  351 (607)
T PRK11057        301 NKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRC  351 (607)
T ss_pred             CCCCcCEEEEeCCCCCHHHHHHHhhhccCCCCCceEEEEeCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999998876554433

>KOG0344|consensus

Probab=99.93  E-value=3.8e-25  Score=197.85  Aligned_cols=152  Identities=34%  Similarity=0.472  Sum_probs=139.0

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHH-HHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKEL-MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L-~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      .+.|++++.+.+..- -...++||+.++  +.+.+|...| .-.++.+.++||..++.+|..++++|+.|+++||+||++
T Consensus       371 e~~K~lA~rq~v~~g-~~PP~lIfVQs~--eRak~L~~~L~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdl  447 (593)
T KOG0344|consen  371 EKGKLLALRQLVASG-FKPPVLIFVQSK--ERAKQLFEELEIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDL  447 (593)
T ss_pred             chhHHHHHHHHHhcc-CCCCeEEEEecH--HHHHHHHHHhhhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhh
Confidence            355777787777654 467778899998  6699999999 677899999999999999999999999999999999999


Q ss_pred             cccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHh
Q psy17587         82 AARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA  157 (231)
Q Consensus        82 ~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~  157 (231)
                      ++||+|+.+|++|||||+|.+..+|+||+||+||+|+.|.||+|++..+....+.+.+.+...+.++|+++..+..
T Consensus       448 l~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~Aitfytd~d~~~ir~iae~~~~sG~evpe~~m~~~k  523 (593)
T KOG0344|consen  448 LARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGKAITFYTDQDMPRIRSIAEVMEQSGCEVPEKIMGIKK  523 (593)
T ss_pred             hhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcceEEEeccccchhhhhHHHHHHHcCCcchHHHHhhhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999998776643

>KOG0347|consensus

Probab=99.92  E-value=6.3e-25  Score=195.10  Aligned_cols=133  Identities=30%  Similarity=0.392  Sum_probs=121.0

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDV   88 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldi   88 (231)
                      .|+=+|.+|  .++.+||||++  +-+..|+-.|...++....+|+.|.+.+|.+++++|++....||+||||++||+||
T Consensus       454 ylyYfl~ry--PGrTlVF~NsI--d~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDI  529 (731)
T KOG0347|consen  454 YLYYFLTRY--PGRTLVFCNSI--DCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDI  529 (731)
T ss_pred             eEEEEEeec--CCceEEEechH--HHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCC
Confidence            344455555  35555699998  66999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         89 KHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        89 p~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      |.|.+||||.+|.+.+-|+||.||++|++..|..++++.|.+...++++.+.|+...
T Consensus       530 p~V~HVIHYqVPrtseiYVHRSGRTARA~~~Gvsvml~~P~e~~~~~KL~ktL~k~~  586 (731)
T KOG0347|consen  530 PGVQHVIHYQVPRTSEIYVHRSGRTARANSEGVSVMLCGPQEVGPLKKLCKTLKKKE  586 (731)
T ss_pred             CCcceEEEeecCCccceeEecccccccccCCCeEEEEeChHHhHHHHHHHHHHhhcc
Confidence            999999999999999999999999999999999999999999988888888887654

>KOG0339|consensus

Probab=99.92  E-value=5.8e-25  Score=193.84  Aligned_cols=158  Identities=33%  Similarity=0.517  Sum_probs=147.2

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|+.-|+..|.......++|+|+..+  ..++.++..|...++++..+||+|.+.+|.+++.+|+.+...|||+||+++
T Consensus       452 ~~Kl~wl~~~L~~f~S~gkvlifVTKk--~~~e~i~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaa  529 (731)
T KOG0339|consen  452 EKKLNWLLRHLVEFSSEGKVLIFVTKK--ADAEEIAANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAA  529 (731)
T ss_pred             HHHHHHHHHHhhhhccCCcEEEEEecc--CCHHHHHHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhh
Confidence            457778888888888888999999988  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHhhchhhh
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVR  163 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~  163 (231)
                      ||+|+|++..|||||+..+++.|.||+||+||.|..|.+++++++.+....-.+++.|+..++.+|..|.++.-....++
T Consensus       530 rgldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeKDa~fAG~LVnnLe~agQnVP~~l~dlamk~s~fr  609 (731)
T KOG0339|consen  530 RGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEKDAEFAGHLVNNLEGAGQNVPDELMDLAMKSSWFR  609 (731)
T ss_pred             cCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechhhHHHhhHHHHHHhhccccCChHHHHHHhhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999988876544443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.92  E-value=2.2e-24  Score=201.61  Aligned_cols=128  Identities=21%  Similarity=0.331  Sum_probs=115.0

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      +...+.+.|.... +.+.||||+++  ..++.+++.|...|+++..+||+|++++|..+++.|.+|+++|||||+++++|
T Consensus       211 ~~~~l~~~l~~~~-~~~~IIf~~sr--~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~G  287 (591)
T TIGR01389       211 KQKFLLDYLKKHR-GQSGIIYASSR--KKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG  287 (591)
T ss_pred             HHHHHHHHHHhcC-CCCEEEEECcH--HHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhcc
Confidence            4455667776544 56677799988  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHH
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGE  136 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~  136 (231)
                      +|+|+|++||+|++|.++++|+|++||+||.|..+.|++++.+.+....+.
T Consensus       288 ID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G~~~~~il~~~~~d~~~~~~  338 (591)
T TIGR01389       288 IDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKR  338 (591)
T ss_pred             CcCCCCCEEEEcCCCCCHHHHhhhhccccCCCCCceEEEecCHHHHHHHHH
Confidence            999999999999999999999999999999999999999998877654443

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.

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

Probab=99.91  E-value=7.8e-24  Score=193.34  Aligned_cols=122  Identities=23%  Similarity=0.359  Sum_probs=112.0

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      ....+.-||||.++  ..++.+++.|...|+++..+||||+.++|..+.++|..+++.|+|||.++++|||.|+|++|||
T Consensus       227 ~~~~~~GIIYc~sR--k~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH  304 (590)
T COG0514         227 PQLSKSGIIYCLTR--KKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIH  304 (590)
T ss_pred             cccCCCeEEEEeeH--HhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEE
Confidence            33455566699988  7899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHH
Q psy17587         97 YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRA  140 (231)
Q Consensus        97 ~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~  140 (231)
                      ||+|.++++|+|.+|||||.|.+..|++|+.+.|....+.+++.
T Consensus       305 ~~lP~s~EsYyQE~GRAGRDG~~a~aill~~~~D~~~~~~~i~~  348 (590)
T COG0514         305 YDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLIEQ  348 (590)
T ss_pred             ecCCCCHHHHHHHHhhccCCCCcceEEEeeccccHHHHHHHHHh
Confidence            99999999999999999999999999999999997755555443

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

Probab=99.91  E-value=6.5e-24  Score=202.14  Aligned_cols=123  Identities=14%  Similarity=0.147  Sum_probs=108.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC--------CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA--------GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHL   91 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~--------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v   91 (231)
                      +.++||||+++  ..++.++..|...        +.++..+||+|++++|.+++++|++|++++|||||++++|||+|++
T Consensus       271 ~~~~IVF~~sr--~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~v  348 (742)
T TIGR03817       271 GARTLTFVRSR--RGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGL  348 (742)
T ss_pred             CCCEEEEcCCH--HHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECchHhccCCcccc
Confidence            46788899988  7799999988653        5688999999999999999999999999999999999999999999


Q ss_pred             cEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecc--cchHHHHHHHHHHHhC
Q psy17587         92 NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITL--EQERHAGEIIRALEAS  144 (231)
Q Consensus        92 ~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~--~~~~~~~~~~~~l~~~  144 (231)
                      ++|||||+|.+.++|+||+||+||.|+.|.++++...  .|...+....+.++.+
T Consensus       349 d~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~~~~~~~~  403 (742)
T TIGR03817       349 DAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHPEALFDRP  403 (742)
T ss_pred             cEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCHHHHhcCC
Confidence            9999999999999999999999999999999999873  4555555555555443

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

>KOG0327|consensus

Probab=99.90  E-value=6.6e-24  Score=181.86  Aligned_cols=144  Identities=34%  Similarity=0.563  Sum_probs=130.5

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|+.+|.++.+   .....++|||++  ..++.+...|...++.+.++||.|.+.+|..++..|++|..+|||+|+.++|
T Consensus       251 ~k~~~l~dl~~---~~~q~~if~nt~--r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~ar  325 (397)
T KOG0327|consen  251 EKLDTLCDLYR---RVTQAVIFCNTR--RKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLAR  325 (397)
T ss_pred             ccccHHHHHHH---hhhcceEEecch--hhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeecccccc
Confidence            46667776666   345556699988  6799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHH
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLD  153 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~  153 (231)
                      |+|+.+++.|||||+|.+.++|+||+||+||.|.+|.++.|++..+...++++++++.....++|....
T Consensus       326 gidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~~~i~e~p~~~~  394 (397)
T KOG0327|consen  326 GIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYNTPIEELPSNFA  394 (397)
T ss_pred             ccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHhcCCcceecccchh
Confidence            999999999999999999999999999999999999999999999999999999988777777776543

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.89  E-value=1.3e-22  Score=195.57  Aligned_cols=137  Identities=15%  Similarity=0.202  Sum_probs=115.9

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHH-HCCCCeeeccCCCCHHHHHHHHHHHhCC--CccEEEecC
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELM-KAGYPCLSLHGGIDQYDRDSTIVDFKNG--KVRLLIATS   80 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~-~~~~~~~~lhg~~~~~~R~~~~~~F~~g--~~~vLvaT~   80 (231)
                      +-|+..|.++|+... +.++||||+++  .+++.|.+.|+ ..|+++..+||+|++.+|.++++.|+++  ..+|||||+
T Consensus       478 d~Ki~~L~~~L~~~~-~~KvLVF~~~~--~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTd  554 (956)
T PRK04914        478 DPRVEWLIDFLKSHR-SEKVLVICAKA--ATALQLEQALREREGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSE  554 (956)
T ss_pred             CHHHHHHHHHHHhcC-CCeEEEEeCcH--HHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEech
Confidence            346777888887654 67888899988  77999999994 6699999999999999999999999974  699999999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHh
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                      ++++|+|++.+++|||||+||+++.|.||+||++|.|+++.+.+++...+......+.+.+..
T Consensus       555 vgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i~~~~~~  617 (956)
T PRK04914        555 IGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERLFRWYHE  617 (956)
T ss_pred             hhccCCCcccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHHHHHHhh
Confidence            999999999999999999999999999999999999998887666654444444444444443

>KOG0350|consensus

Probab=99.88  E-value=8.6e-23  Score=179.86  Aligned_cols=137  Identities=26%  Similarity=0.448  Sum_probs=120.5

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHH----HCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEe
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELM----KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIA   78 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~----~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLva   78 (231)
                      -+.|...++.+|..+. ..++|+|+++.  +.+..++.-|.    ..++++..+.|+++...|.+.+.+|..|+++||||
T Consensus       413 ~~~kpl~~~~lI~~~k-~~r~lcf~~S~--~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIc  489 (620)
T KOG0350|consen  413 PKFKPLAVYALITSNK-LNRTLCFVNSV--SSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLIC  489 (620)
T ss_pred             cccchHhHHHHHHHhh-cceEEEEecch--HHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEe
Confidence            3567788888887765 55666699987  66888888775    45788889999999999999999999999999999


Q ss_pred             cCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHH
Q psy17587         79 TSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE  142 (231)
Q Consensus        79 T~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~  142 (231)
                      ||+++||+|+-+|+.|||||+|.+...|+||+||++|+|+.|.|++++...+...+.++++...
T Consensus       490 SD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~G~a~tll~~~~~r~F~klL~~~~  553 (620)
T KOG0350|consen  490 SDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQDGYAITLLDKHEKRLFSKLLKKTN  553 (620)
T ss_pred             hhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCCceEEEeeccccchHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999999999999998887766666443

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.86  E-value=2.6e-20  Score=176.46  Aligned_cols=126  Identities=19%  Similarity=0.251  Sum_probs=102.7

Q ss_pred             CCCCeEEEEcCChh------HHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCC
Q psy17587         18 DRDSTIVDFKNGKV------RLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK   89 (231)
Q Consensus        18 ~~~~~iiiF~~~~~------~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip   89 (231)
                      ..+.+++|||+...      ...++.+++.|...  ++++..+||+|++++|..++++|++|+++|||||+++++|+|+|
T Consensus       469 ~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip  548 (681)
T PRK10917        469 AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP  548 (681)
T ss_pred             HcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccC
Confidence            45678888998531      13456777777654  57899999999999999999999999999999999999999999


Q ss_pred             CCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHh
Q psy17587         90 HLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus        90 ~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                      ++++||++++|. ..+.|.||+||+||.|..|.|+++..........+..+.+..
T Consensus       549 ~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~rl~~~~~  603 (681)
T PRK10917        549 NATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRE  603 (681)
T ss_pred             CCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHHHHHHHH
Confidence            999999999997 578889999999999999999999964432223334444443

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

Probab=99.86  E-value=3.8e-21  Score=170.19  Aligned_cols=122  Identities=28%  Similarity=0.368  Sum_probs=106.9

Q ss_pred             chhhhhccccccC---CCCeEEEEcCChhHHHHHHHHHHHHHCCCCee-ecc--------CCCCHHHHHHHHHHHhCCCc
Q psy17587          6 PCLSLHGGIDQYD---RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCL-SLH--------GGIDQYDRDSTIVDFKNGKV   73 (231)
Q Consensus         6 k~~~L~~~L~~~~---~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~-~lh--------g~~~~~~R~~~~~~F~~g~~   73 (231)
                      |+..+.+++++..   ++.++|||++-+  ++++.+.++|.+.+..+. .+-        .||+|.++.+++++|++|++
T Consensus       349 Kl~~l~eilke~~~k~~~~RvIVFT~yR--dTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~  426 (542)
T COG1111         349 KLEKLREILKEQLEKNGDSRVIVFTEYR--DTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEY  426 (542)
T ss_pred             cHHHHHHHHHHHHhcCCCceEEEEehhH--hHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhcCCc
Confidence            4666666665443   468999999966  889999999999887774 222        47999999999999999999


Q ss_pred             cEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         74 RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        74 ~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      +|||||+++++|||+|+|++||.|++-.+...++||.|||||. +.|.++++++.+.
T Consensus       427 nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~-r~Grv~vLvt~gt  482 (542)
T COG1111         427 NVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRK-RKGRVVVLVTEGT  482 (542)
T ss_pred             eEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccC-CCCeEEEEEecCc
Confidence            9999999999999999999999999999999999999999996 7899999998873

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=99.85  E-value=2.6e-21  Score=133.93  Aligned_cols=78  Identities=37%  Similarity=0.664  Sum_probs=75.5

Q ss_pred             HHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCC
Q psy17587         40 KELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAG  117 (231)
Q Consensus        40 ~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g  117 (231)
                      +.|...++.+..+||++++.+|..+++.|++++.+|||||+++++|+|+|.+++||++++|+++..|.|++||++|.|
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~g   78 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRIG   78 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCCC
Confidence            467889999999999999999999999999999999999999999999999999999999999999999999999986

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

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

Probab=99.85  E-value=5.7e-21  Score=143.75  Aligned_cols=119  Identities=32%  Similarity=0.520  Sum_probs=107.8

Q ss_pred             CchhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...+...+.+.. .++++||||++.  ..++.+.+.|...+..+..+||++++.+|..+++.|.++...+|++|++++
T Consensus        12 ~k~~~i~~~i~~~~~~~~~~lvf~~~~--~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~   89 (131)
T cd00079          12 EKLEALLELLKEHLKKGGKVLIFCPSK--KMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIA   89 (131)
T ss_pred             HHHHHHHHHHHhcccCCCcEEEEeCcH--HHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhh
Confidence            45666777776554 577889999988  779999999998889999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEE
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTF  125 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~  125 (231)
                      +|+|+|.+++||.+++|++..+|.|++||++|.|+.|.++++
T Consensus        90 ~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~~  131 (131)
T cd00079          90 RGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL  131 (131)
T ss_pred             cCcChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEeC
Confidence            999999999999999999999999999999999988887653

>KOG0346|consensus

Probab=99.85  E-value=2.5e-21  Score=168.46  Aligned_cols=137  Identities=26%  Similarity=0.334  Sum_probs=119.4

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC---
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS---   80 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~---   80 (231)
                      ..|.+-++-+++-.--.+++|||+|+.  +.|..|--.|...|++.+.+.|.||..-|..++++|..|-++++||||   
T Consensus       252 ~DKflllyallKL~LI~gKsliFVNtI--dr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~  329 (569)
T KOG0346|consen  252 EDKFLLLYALLKLRLIRGKSLIFVNTI--DRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSA  329 (569)
T ss_pred             chhHHHHHHHHHHHHhcCceEEEEech--hhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCcc
Confidence            345556666665555567888899998  559999999999999999999999999999999999999999999998   


Q ss_pred             --------------------------------ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecc
Q psy17587         81 --------------------------------VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITL  128 (231)
Q Consensus        81 --------------------------------~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~  128 (231)
                                                      -++||||+.+|..|+|||+|.++.+|+||+||++|++++|.+++|+.|
T Consensus       330 ~~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~n~GtalSfv~P  409 (569)
T KOG0346|consen  330 DGDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGNNKGTALSFVSP  409 (569)
T ss_pred             chhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCCCCCceEEEecc
Confidence                                            257999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHH
Q psy17587        129 EQERHAGEIIRALE  142 (231)
Q Consensus       129 ~~~~~~~~~~~~l~  142 (231)
                      .+......++..+.
T Consensus       410 ~e~~g~~~le~~~~  423 (569)
T KOG0346|consen  410 KEEFGKESLESILK  423 (569)
T ss_pred             hHHhhhhHHHHHHh
Confidence            98775555555444

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.84  E-value=5.9e-21  Score=177.25  Aligned_cols=123  Identities=20%  Similarity=0.259  Sum_probs=105.4

Q ss_pred             CchhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...|.+.+.... .++.+||||+++  ..++.+++.|...|+++..+||++++.+  ..+..|+.++..|+||||+++
T Consensus       457 ~K~~aL~~~i~~~~~~~~pvLIft~t~--~~se~L~~~L~~~gi~~~~Lhg~~~~rE--~~ii~~ag~~g~VlVATdmAg  532 (656)
T PRK12898        457 AKWAAVAARVRELHAQGRPVLVGTRSV--AASERLSALLREAGLPHQVLNAKQDAEE--AAIVARAGQRGRITVATNMAG  532 (656)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcH--HHHHHHHHHHHHCCCCEEEeeCCcHHHH--HHHHHHcCCCCcEEEEccchh
Confidence            46677777776643 357799999998  7799999999999999999999976544  455556666667999999999


Q ss_pred             cccCCC---CCc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         84 RGLDVK---HLN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        84 ~Gldip---~v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||+||+   +|.     +||+||+|.+...|.||+||+||.|.+|.+++|++.+|.
T Consensus       533 RGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~G~s~~~is~eD~  588 (656)
T PRK12898        533 RGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQGDPGSYEAILSLEDD  588 (656)
T ss_pred             cccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCCCCeEEEEEechhHH
Confidence            999999   676     999999999999999999999999999999999998654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.84  E-value=1.8e-20  Score=181.11  Aligned_cols=111  Identities=17%  Similarity=0.328  Sum_probs=101.9

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEE
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLV   94 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~V   94 (231)
                      ...+.+++||||+.  +.++.+++.|...  ++++..+||+|++.+|.+++++|++|+++|||||+++++|+|+|++++|
T Consensus       657 l~~g~qv~if~n~i--~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~V  734 (926)
T TIGR00580       657 LLRGGQVFYVHNRI--ESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTI  734 (926)
T ss_pred             HHcCCeEEEEECCc--HHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEE
Confidence            33567888899988  7799999999874  7899999999999999999999999999999999999999999999999


Q ss_pred             EEecCCC-CHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         95 VNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        95 I~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      |+++.|. +..+|+||+||+||.|+.|.|++++.+.
T Consensus       735 Ii~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~  770 (926)
T TIGR00580       735 IIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQ  770 (926)
T ss_pred             EEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCc
Confidence            9999975 6789999999999999999999998654

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.84  E-value=6.4e-21  Score=180.31  Aligned_cols=124  Identities=19%  Similarity=0.227  Sum_probs=111.5

Q ss_pred             CCchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          4 GYPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         4 ~~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      +.|...|.+.+... ..++.+||||+++  ..++.++..|...|+++..+||+++++++..+...++.|  +|+|||+++
T Consensus       411 ~~K~~al~~~i~~~~~~~~pvLIf~~t~--~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmA  486 (790)
T PRK09200        411 DEKYKAVIEEVKERHETGRPVLIGTGSI--EQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMA  486 (790)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEeCcH--HHHHHHHHHHHHCCCCEEEecCCccHHHHHHHHHcCCCC--eEEEEccch
Confidence            45677788877653 4578899999998  779999999999999999999999999988888888766  799999999


Q ss_pred             ccccCC---CCCc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         83 ARGLDV---KHLN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        83 ~~Gldi---p~v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +||+|+   |+|.     +||+||+|.+...|.||+||+||.|.+|.+++|++.+|.
T Consensus       487 gRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~G~s~~~is~eD~  543 (790)
T PRK09200        487 GRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDPGSSQFFISLEDD  543 (790)
T ss_pred             hcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCCCCeeEEEEEcchHH
Confidence            999999   7998     999999999999999999999999999999999987654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.84  E-value=4.1e-20  Score=173.86  Aligned_cols=135  Identities=19%  Similarity=0.271  Sum_probs=105.8

Q ss_pred             hhhcccccc-CCCCeEEEEcCChh------HHHHHHHHHHHHH--CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec
Q psy17587          9 SLHGGIDQY-DRDSTIVDFKNGKV------RLLVCAIVKELMK--AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT   79 (231)
Q Consensus         9 ~L~~~L~~~-~~~~~iiiF~~~~~------~~~~~~l~~~L~~--~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT   79 (231)
                      .+++.+.+. ..+..++|||+...      ...++.+++.|..  .++.+..+||+|++++|..++++|++|+.+|||||
T Consensus       436 ~~~~~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT  515 (630)
T TIGR00643       436 IVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVAT  515 (630)
T ss_pred             HHHHHHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEC
Confidence            344444332 45677888997531      1346677777764  37889999999999999999999999999999999


Q ss_pred             CccccccCCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHh
Q psy17587         80 SVAARGLDVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus        80 ~~~~~Gldip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                      +++++|+|+|++++||+++.|. +.+.|.||+||+||.|..|.|+++..........+..+.+..
T Consensus       516 ~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~il~~~~~~~~~~~~rl~~~~~  580 (630)
T TIGR00643       516 TVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPKSESAKKRLRVMAD  580 (630)
T ss_pred             ceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccCCCCcEEEEEECCCCCHHHHHHHHHHHh
Confidence            9999999999999999999997 678889999999999999999999843333333333444443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.84  E-value=3.4e-20  Score=174.60  Aligned_cols=146  Identities=20%  Similarity=0.271  Sum_probs=126.0

Q ss_pred             chhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          6 PCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         6 k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      ++..|++.|.... .+.++||||+++  ..++.|++.|...|+++..+||++++.+|..++..|+.|++.|+|||+++++
T Consensus       431 q~~~L~~~L~~~~~~g~~viIf~~t~--~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~r  508 (652)
T PRK05298        431 QVDDLLSEIRKRVAKGERVLVTTLTK--RMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE  508 (652)
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEeCCH--HHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhC
Confidence            4556667775543 478899999988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecC-----CCCHhHHHHHhcccCCCCCceeEEEEecc---------cchHHHHHHHHHHHhCCCCCch
Q psy17587         85 GLDVKHLNLVVNYDC-----PNHYEDYVHRCGRTGRAGNKGFAYTFITL---------EQERHAGEIIRALEASGVPIPE  150 (231)
Q Consensus        85 Gldip~v~~VI~~d~-----P~~~~~y~qr~GR~gR~g~~g~~i~~~~~---------~~~~~~~~~~~~l~~~~~~~~~  150 (231)
                      |+|+|++++||++|.     |.+..+|+||+||+||. ..|.+++|+..         .+....+++...++.+...+|.
T Consensus       509 Gfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~-~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  587 (652)
T PRK05298        509 GLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPK  587 (652)
T ss_pred             CccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC-CCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCCh
Confidence            999999999999885     78999999999999996 68999999984         3555666677777777777887


Q ss_pred             hHHH
Q psy17587        151 DLDK  154 (231)
Q Consensus       151 ~l~~  154 (231)
                      .+.+
T Consensus       588 ~~~~  591 (652)
T PRK05298        588 TIKK  591 (652)
T ss_pred             hHHH
Confidence            6543

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.84  E-value=1.9e-20  Score=181.40  Aligned_cols=107  Identities=18%  Similarity=0.240  Sum_probs=94.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC------CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA------GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNL   93 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~   93 (231)
                      .+++|||||++  ..++.++..|...      +..+.++||+|++++|..+++.|++|+++|||||+++++|||+|++++
T Consensus       284 ~~~~LVF~nTr--~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~  361 (876)
T PRK13767        284 HRTTLIFTNTR--SGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDL  361 (876)
T ss_pred             CCCEEEEeCCH--HHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcE
Confidence            56788899988  7799999999762      467999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCCCHhHHHHHhcccCCCC-CceeEEEEecc
Q psy17587         94 VVNYDCPNHYEDYVHRCGRTGRAG-NKGFAYTFITL  128 (231)
Q Consensus        94 VI~~d~P~~~~~y~qr~GR~gR~g-~~g~~i~~~~~  128 (231)
                      ||+++.|.++.+|+||+||+||.+ ..+.++++...
T Consensus       362 VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~~~  397 (876)
T PRK13767        362 VVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIVVD  397 (876)
T ss_pred             EEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEEcC
Confidence            999999999999999999999864 33444444443

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.83  E-value=4.2e-20  Score=173.40  Aligned_cols=128  Identities=20%  Similarity=0.259  Sum_probs=113.9

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .++..|++.|+.. ..+.+++|||+++  ..++.|++.|...|+++..+||++++.+|.+++..|+.|++.|||||++++
T Consensus       426 ~qi~~Ll~eI~~~~~~g~~vLIf~~tk--~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~  503 (655)
T TIGR00631       426 GQVDDLLSEIRQRVARNERVLVTTLTK--KMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLR  503 (655)
T ss_pred             chHHHHHHHHHHHHcCCCEEEEEECCH--HHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhc
Confidence            3556677777654 4478899999998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEec-----CCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHH
Q psy17587         84 RGLDVKHLNLVVNYD-----CPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAG  135 (231)
Q Consensus        84 ~Gldip~v~~VI~~d-----~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~  135 (231)
                      +|+|+|++++||++|     .|.+..+|+||+||+||. ..|.+++++...+.....
T Consensus       504 rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~-~~G~vi~~~~~~~~~~~~  559 (655)
T TIGR00631       504 EGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVIMYADKITDSMQK  559 (655)
T ss_pred             CCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC-CCCEEEEEEcCCCHHHHH
Confidence            999999999999998     799999999999999998 579999999876544333

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

>KOG4284|consensus

Probab=99.83  E-value=1.5e-20  Score=170.12  Aligned_cols=123  Identities=33%  Similarity=0.479  Sum_probs=112.4

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |+..|-+.+++..-.+.+| ||+..++  |+.++..|...|+.|.++.|.|++.+|..+++.++.=.++|||+||+.+||
T Consensus       259 klq~L~~vf~~ipy~QAlV-F~~~~sr--a~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~rILVsTDLtaRG  335 (980)
T KOG4284|consen  259 KLQKLTHVFKSIPYVQALV-FCDQISR--AEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRVRILVSTDLTARG  335 (980)
T ss_pred             HHHHHHHHHhhCchHHHHh-hhhhhhh--hhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceEEEEEecchhhcc
Confidence            5566666666665566666 9998856  999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||-|+|++|||.|+|.+-.+|.||+|||||-|..|.+++|+..+.+
T Consensus       336 IDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG~~G~aVT~~~~~~e  381 (980)
T KOG4284|consen  336 IDADNVNLVVNIDAPADEETYFHRIGRAGRFGAHGAAVTLLEDERE  381 (980)
T ss_pred             CCccccceEEecCCCcchHHHHHHhhhcccccccceeEEEeccchh
Confidence            9999999999999999999999999999999999999999988754

>PRK02362 ski2-like helicase; Provisional

Probab=99.82  E-value=2e-19  Score=172.02  Aligned_cols=110  Identities=20%  Similarity=0.296  Sum_probs=96.3

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC------------------------------------CCCeeeccCCCCHHHHH
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA------------------------------------GYPCLSLHGGIDQYDRD   62 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~------------------------------------~~~~~~lhg~~~~~~R~   62 (231)
                      .++++||||+++  ..++.++..|...                                    ...+.++||+|++.+|.
T Consensus       242 ~~~~~LVF~~sr--~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~  319 (737)
T PRK02362        242 EGGQCLVFVSSR--RNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRE  319 (737)
T ss_pred             cCCCeEEEEeCH--HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHH
Confidence            567888899988  6788888777532                                    13688999999999999


Q ss_pred             HHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ec-----CCCCHhHHHHHhcccCCCCC--ceeEEEEecccc
Q psy17587         63 STIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YD-----CPNHYEDYVHRCGRTGRAGN--KGFAYTFITLEQ  130 (231)
Q Consensus        63 ~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d-----~P~~~~~y~qr~GR~gR~g~--~g~~i~~~~~~~  130 (231)
                      .+++.|++|.++|||||+++++|+|+|++++||+    ||     .|.+..+|.||+|||||.|.  .|.++++..+.+
T Consensus       320 ~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d~~G~~ii~~~~~~  398 (737)
T PRK02362        320 LVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYD  398 (737)
T ss_pred             HHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCCCCceEEEEecCch
Confidence            9999999999999999999999999999999997    77     68899999999999999986  499999887653

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.82  E-value=2e-19  Score=168.75  Aligned_cols=107  Identities=20%  Similarity=0.239  Sum_probs=95.9

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHH-hCCCccEEEecCccccccCCCCCcEEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDF-KNGKVRLLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F-~~g~~~vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      ++.+||||+++  ..++.+.+.|...  ++.+..+||+|++.  .+.+++| ++|+.+||||||++++|||+|+|++||+
T Consensus       395 ~g~iLVFlpg~--~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID  470 (675)
T PHA02653        395 GSSGIVFVASV--SQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYD  470 (675)
T ss_pred             CCcEEEEECcH--HHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccccCeeEEEE
Confidence            46788999998  6799999999876  79999999999975  4667787 7899999999999999999999999999


Q ss_pred             ec---CCC---------CHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         97 YD---CPN---------HYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        97 ~d---~P~---------~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ++   .|.         +.++|.||+|||||. ++|.|+.|++..+.
T Consensus       471 ~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~-~~G~c~rLyt~~~~  516 (675)
T PHA02653        471 TGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV-SPGTYVYFYDLDLL  516 (675)
T ss_pred             CCCccCCCcccCcccccCHHHHHHhccCcCCC-CCCeEEEEECHHHh
Confidence            98   665         788999999999999 78999999988764

>KOG0351|consensus

Probab=99.82  E-value=3.8e-20  Score=177.57  Aligned_cols=128  Identities=18%  Similarity=0.296  Sum_probs=119.1

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      +..++..++.+.+....||||.++  ..|+.++..|+..|+++..||+||++.+|..+..+|..++++|+|||=++++||
T Consensus       472 ~~~~~~~~~~~~~~~s~IIYC~sr--~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMGI  549 (941)
T KOG0351|consen  472 LLDILEESKLRHPDQSGIIYCLSR--KECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMGI  549 (941)
T ss_pred             hHHHHHHhhhcCCCCCeEEEeCCc--chHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCCC
Confidence            456677778888999999999988  779999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHH
Q psy17587         87 DVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGE  136 (231)
Q Consensus        87 dip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~  136 (231)
                      |.|+|+.||||.+|.+.+.|+|.+|||||.|....|++|+...+...++.
T Consensus       550 dK~DVR~ViH~~lPks~E~YYQE~GRAGRDG~~s~C~l~y~~~D~~~l~~  599 (941)
T KOG0351|consen  550 DKPDVRFVIHYSLPKSFEGYYQEAGRAGRDGLPSSCVLLYGYADISELRR  599 (941)
T ss_pred             CCCceeEEEECCCchhHHHHHHhccccCcCCCcceeEEecchhHHHHHHH
Confidence            99999999999999999999999999999999999999999886654433

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.82  E-value=1.1e-19  Score=178.90  Aligned_cols=112  Identities=15%  Similarity=0.245  Sum_probs=98.7

Q ss_pred             ccCCCCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcE
Q psy17587         16 QYDRDSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNL   93 (231)
Q Consensus        16 ~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~   93 (231)
                      ....+..++||||+.  ..++.+++.|...  +..+.++||+|++.+|.+++.+|++|+++|||||+++++|+|+|++++
T Consensus       805 el~r~gqv~vf~n~i--~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~  882 (1147)
T PRK10689        805 EILRGGQVYYLYNDV--ENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT  882 (1147)
T ss_pred             HHhcCCeEEEEECCH--HHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCE
Confidence            333467788899987  7799999999876  789999999999999999999999999999999999999999999999


Q ss_pred             EEEecCC-CCHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         94 VVNYDCP-NHYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        94 VI~~d~P-~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      ||..+.. .+...|+||+||+||.|..|.|+++..+.
T Consensus       883 VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~  919 (1147)
T PRK10689        883 IIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  919 (1147)
T ss_pred             EEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCC
Confidence            9965443 35678999999999999999999887543

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.81  E-value=1.4e-19  Score=159.39  Aligned_cols=118  Identities=19%  Similarity=0.251  Sum_probs=97.5

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCC--CeeeccCCCCHHHHHHH----HHHHhCCCccEEEecC
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGY--PCLSLHGGIDQYDRDST----IVDFKNGKVRLLIATS   80 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~--~~~~lhg~~~~~~R~~~----~~~F~~g~~~vLvaT~   80 (231)
                      ...+..+++....+++++|||+++  ..++.+++.|...+.  .+..+||+|++.+|...    ++.|++|+.+|||||+
T Consensus       209 ~~~l~~l~~~~~~~~~~lVf~~t~--~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~  286 (358)
T TIGR01587       209 ISSLERLLEFIKKGGKIAIIVNTV--DRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ  286 (358)
T ss_pred             HHHHHHHHHHhhCCCeEEEEECCH--HHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc
Confidence            344444555555678899999998  779999999987765  59999999999999764    8899999999999999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc----eeEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK----GFAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~----g~~i~~~~~~  129 (231)
                      ++++|+|+| +++||+++.|  +++|+||+||+||.|+.    |..+++....
T Consensus       287 ~~~~GiDi~-~~~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~  336 (358)
T TIGR01587       287 VIEASLDIS-ADVMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP  336 (358)
T ss_pred             chhceeccC-CCEEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence            999999996 7899999887  78999999999998863    3566665433

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.81  E-value=1.5e-19  Score=173.79  Aligned_cols=122  Identities=27%  Similarity=0.368  Sum_probs=109.2

Q ss_pred             Cchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCC--------CCHHHHHHHHHHHhCCCc
Q psy17587          5 YPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGG--------IDQYDRDSTIVDFKNGKV   73 (231)
Q Consensus         5 ~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~--------~~~~~R~~~~~~F~~g~~   73 (231)
                      .|+..|.+.|+..   ..+.++||||+.+  .+++.|.+.|...|+.+..+||.        |++.+|..++++|++|+.
T Consensus       347 pK~~~L~~il~~~~~~~~~~kvlIF~~~~--~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~  424 (773)
T PRK13766        347 PKLEKLREIVKEQLGKNPDSRIIVFTQYR--DTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEF  424 (773)
T ss_pred             hHHHHHHHHHHHHHhcCCCCeEEEEeCcH--HHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCCC
Confidence            3566677777553   4678999999988  78999999999999999999986        999999999999999999


Q ss_pred             cEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         74 RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        74 ~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      +|||||+++++|+|+|++++||+||+|+++..|+||+||+||.+. |.++.++..+
T Consensus       425 ~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~-~~v~~l~~~~  479 (773)
T PRK13766        425 NVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEE-GRVVVLIAKG  479 (773)
T ss_pred             CEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCcCCC-CEEEEEEeCC
Confidence            999999999999999999999999999999999999999999865 7888887654

>KOG0349|consensus

Probab=99.80  E-value=9.2e-20  Score=158.79  Aligned_cols=115  Identities=32%  Similarity=0.530  Sum_probs=102.9

Q ss_pred             ccccCCCCeEEEEcCChhHHHHHHHHHHHHHC---CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCC
Q psy17587         14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA---GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKH   90 (231)
Q Consensus        14 L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~   90 (231)
                      +++..- .+.||||.++  ..|+.|-+++.+.   .++++++||+..+.||...++.|+.++++.|||||+++||+||..
T Consensus       500 i~~h~m-dkaiifcrtk--~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g  576 (725)
T KOG0349|consen  500 IRRHAM-DKAIIFCRTK--QDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITG  576 (725)
T ss_pred             hhhhcc-CceEEEEecc--ccchHHHHHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccC
Confidence            344433 4555599998  6699999999876   489999999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         91 LNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        91 v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +.++||..+|.+...|+||+||+||+.+-|.+|+++....+
T Consensus       577 ~p~~invtlpd~k~nyvhrigrvgraermglaislvat~~e  617 (725)
T KOG0349|consen  577 LPFMINVTLPDDKTNYVHRIGRVGRAERMGLAISLVATVPE  617 (725)
T ss_pred             CceEEEEecCcccchhhhhhhccchhhhcceeEEEeeccch
Confidence            99999999999999999999999999999999999865543

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.80  E-value=1.5e-19  Score=169.96  Aligned_cols=123  Identities=21%  Similarity=0.312  Sum_probs=109.4

Q ss_pred             CCchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          4 GYPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         4 ~~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ..|...+.+.+.+. ..++.+||||+++  ..++.++..|...|+++..+||.++++++..+...|+.|  .|+||||++
T Consensus       407 ~~K~~ai~~~i~~~~~~~~pvLIft~s~--~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmA  482 (762)
T TIGR03714       407 PEKLMATLEDVKEYHETGQPVLLITGSV--EMSEIYSELLLREGIPHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMA  482 (762)
T ss_pred             HHHHHHHHHHHHHHhhCCCCEEEEECcH--HHHHHHHHHHHHCCCCEEEecCCChHHHHHHHHHcCCCC--eEEEEcccc
Confidence            35677777777654 4578899999998  779999999999999999999999999988887777777  799999999


Q ss_pred             ccccCCC---------CCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         83 ARGLDVK---------HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        83 ~~Gldip---------~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +||+|+|         ++.+|++|++|....+ .||+||+||.|.+|.+++|++.+|.
T Consensus       483 gRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG~~G~s~~~is~eD~  539 (762)
T TIGR03714       483 GRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQGDPGSSQFFVSLEDD  539 (762)
T ss_pred             ccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCCCceeEEEEEccchh
Confidence            9999999         9999999999998777 9999999999999999999987664

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.80  E-value=2.6e-19  Score=178.18  Aligned_cols=107  Identities=25%  Similarity=0.371  Sum_probs=92.1

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCC---------------------------------CCeeeccCCCCHHHHHHHH
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAG---------------------------------YPCLSLHGGIDQYDRDSTI   65 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~---------------------------------~~~~~lhg~~~~~~R~~~~   65 (231)
                      ..+++|||||++  ..++.++..|....                                 +.+.++||+|++++|..++
T Consensus       243 ~~~stLVFvNSR--~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE  320 (1490)
T PRK09751        243 RHRSTIVFTNSR--GLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITE  320 (1490)
T ss_pred             cCCCEEEECCCH--HHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHH
Confidence            456778899988  77999999886531                                 1256899999999999999


Q ss_pred             HHHhCCCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCC-CCceeEEEEec
Q psy17587         66 VDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRA-GNKGFAYTFIT  127 (231)
Q Consensus        66 ~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~-g~~g~~i~~~~  127 (231)
                      +.|++|++++||||+.+++|||+|+|++|||++.|.++.+|+||+||+||. |..+.++++..
T Consensus       321 ~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~~gg~s~gli~p~  383 (1490)
T PRK09751        321 QALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQVGGVSKGLFFPR  383 (1490)
T ss_pred             HHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCCCCCccEEEEEeC
Confidence            999999999999999999999999999999999999999999999999996 33455554443

>KOG0337|consensus

Probab=99.80  E-value=5.3e-20  Score=159.52  Aligned_cols=139  Identities=29%  Similarity=0.350  Sum_probs=128.0

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .+|...|+..+.....+++.++||.++  -.++.+...|...|+.+..++|.|++..|...+.+|+.++..+||.||+++
T Consensus       245 a~K~aaLl~il~~~~~~~~t~vf~~tk--~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaa  322 (529)
T KOG0337|consen  245 AEKEAALLSILGGRIKDKQTIVFVATK--HHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAA  322 (529)
T ss_pred             HHHHHHHHHHHhccccccceeEEeccc--chHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhh
Confidence            467888888888888777888899998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhC
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEAS  144 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~  144 (231)
                      ||+|+|-.+.|||||+|.+..-|+||+||++|+|+.|.+|.++.+.+...+-++..++..+
T Consensus       323 RG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~~~~yl~DL~lflgr~  383 (529)
T KOG0337|consen  323 RGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVASTDDPYLLDLQLFLGRP  383 (529)
T ss_pred             ccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecccchhhhhhhhhcCCc
Confidence            9999999999999999999999999999999999999999999999887776666666443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.80  E-value=2.1e-19  Score=172.13  Aligned_cols=110  Identities=21%  Similarity=0.363  Sum_probs=99.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH---CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK---AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      ...+||||++.  ..++.+++.|..   .++.+..+||+|++++|.++++.|++|+.+|+||||++++|||||+|++||+
T Consensus       209 ~g~iLVFlpg~--~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID  286 (819)
T TIGR01970       209 TGSILVFLPGQ--AEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVID  286 (819)
T ss_pred             CCcEEEEECCH--HHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEE
Confidence            46788899998  679999999976   4789999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC------------------HhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587         97 YDCPNH------------------YEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus        97 ~d~P~~------------------~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                      +++|..                  ..+|.||+||+||. .+|.||.+++..+..
T Consensus       287 ~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~-~~G~cyrL~t~~~~~  339 (819)
T TIGR01970       287 SGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL-EPGVCYRLWSEEQHQ  339 (819)
T ss_pred             cCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC-CCCEEEEeCCHHHHH
Confidence            998853                  34699999999998 799999999876543

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.

>PRK00254 ski2-like helicase; Provisional

Probab=99.77  E-value=2.1e-18  Score=164.72  Aligned_cols=110  Identities=19%  Similarity=0.273  Sum_probs=91.8

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH---------------------------------CCCCeeeccCCCCHHHHHHHH
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK---------------------------------AGYPCLSLHGGIDQYDRDSTI   65 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~---------------------------------~~~~~~~lhg~~~~~~R~~~~   65 (231)
                      .++++||||+++  ..++.++..|..                                 ....+.++||+|++++|..++
T Consensus       237 ~~~~vLVF~~sr--~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve  314 (720)
T PRK00254        237 KGKGALVFVNTR--RSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIE  314 (720)
T ss_pred             hCCCEEEEEcCh--HHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHH
Confidence            357888899987  667776655531                                 123588999999999999999


Q ss_pred             HHHhCCCccEEEecCccccccCCCCCcEEEE-------ecCCC-CHhHHHHHhcccCCCC--CceeEEEEecccc
Q psy17587         66 VDFKNGKVRLLIATSVAARGLDVKHLNLVVN-------YDCPN-HYEDYVHRCGRTGRAG--NKGFAYTFITLEQ  130 (231)
Q Consensus        66 ~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~-------~d~P~-~~~~y~qr~GR~gR~g--~~g~~i~~~~~~~  130 (231)
                      +.|++|.++|||||+++++|+|+|.+++||.       ++.|. +..+|.||+|||||.|  ..|.++++..+.+
T Consensus       315 ~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~~d~~G~~ii~~~~~~  389 (720)
T PRK00254        315 DAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEE  389 (720)
T ss_pred             HHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCCcCCCceEEEEecCcc
Confidence            9999999999999999999999999999994       55544 5779999999999976  5799999987654

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.77  E-value=8.1e-19  Score=168.19  Aligned_cols=109  Identities=20%  Similarity=0.342  Sum_probs=98.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH---CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK---AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      ...++|||++.  ..++.+++.|..   .++.+..+||+|++.+|.+++..|++|+.+|+||||++++|||+|+|++||+
T Consensus       212 ~g~iLVFlpg~--~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID  289 (812)
T PRK11664        212 SGSLLLFLPGV--GEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVD  289 (812)
T ss_pred             CCCEEEEcCCH--HHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEE
Confidence            57788899998  779999999986   5788999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCC------------------HhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         97 YDCPNH------------------YEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        97 ~d~P~~------------------~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +++|..                  ..+|.||+||+||. .+|.||.+++..+.
T Consensus       290 ~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~~G~cyrL~t~~~~  341 (812)
T PRK11664        290 SGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-EPGICLHLYSKEQA  341 (812)
T ss_pred             CCCcccccccccCCcceeEEEeechhhhhhhccccCCC-CCcEEEEecCHHHH
Confidence            877653                  35899999999998 69999999986643

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.77  E-value=2e-18  Score=161.64  Aligned_cols=122  Identities=21%  Similarity=0.251  Sum_probs=109.9

Q ss_pred             chhhhhccc-cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          6 PCLSLHGGI-DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         6 k~~~L~~~L-~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      |..++.+.+ ..+..++.+||||++.  ..++.+++.|...|+++..+||+  +.+|...+..|+.+...|+|||++++|
T Consensus       390 k~~ai~~~i~~~~~~grpvLV~t~si--~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgR  465 (745)
T TIGR00963       390 KWKAVVDEIKERHAKGQPVLVGTTSV--EKSELLSNLLKERGIPHNVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGR  465 (745)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCcH--HHHHHHHHHHHHcCCCeEEeeCC--hHHHHHHHHHhcCCCceEEEEeccccC
Confidence            455565555 3345689999999988  77999999999999999999998  789999999999999999999999999


Q ss_pred             ccCCCC-------CcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         85 GLDVKH-------LNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        85 Gldip~-------v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      |+||+.       ..+||+++.|.+...|.|+.||+||.|.+|.+..|++..|.
T Consensus       466 GtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG~~G~s~~~ls~eD~  519 (745)
T TIGR00963       466 GTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQGDPGSSRFFLSLEDN  519 (745)
T ss_pred             CcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCCCCcceEEEEeccHH
Confidence            999998       45999999999999999999999999999999999988764

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.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.76  E-value=3.8e-18  Score=117.93  Aligned_cols=81  Identities=42%  Similarity=0.758  Sum_probs=77.1

Q ss_pred             HHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCC
Q psy17587         37 AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRA  116 (231)
Q Consensus        37 ~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~  116 (231)
                      .+.+.|...++.+..+||+|++.+|..+++.|+++...||++|+++++|+|+|+++.||.+++|++...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            46677888899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy17587        117 G  117 (231)
Q Consensus       117 g  117 (231)
                      |
T Consensus        82 g   82 (82)
T smart00490       82 G   82 (82)
T ss_pred             C
Confidence            5

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.76  E-value=7.2e-18  Score=158.43  Aligned_cols=134  Identities=18%  Similarity=0.206  Sum_probs=107.5

Q ss_pred             CchhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccEEEecCcc
Q psy17587          5 YPCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRLLIATSVA   82 (231)
Q Consensus         5 ~k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLvaT~~~   82 (231)
                      +|+..+..++..+. .+.++||||+..  ..++.++..|     .+..+||++++.+|.+++++|+.| .+++||+|+++
T Consensus       480 ~K~~~~~~Li~~he~~g~kiLVF~~~~--~~l~~~a~~L-----~~~~I~G~ts~~ER~~il~~Fr~~~~i~vLv~SkVg  552 (732)
T TIGR00603       480 NKFRACQFLIRFHEQRGDKIIVFSDNV--FALKEYAIKL-----GKPFIYGPTSQQERMQILQNFQHNPKVNTIFLSKVG  552 (732)
T ss_pred             HHHHHHHHHHHHHhhcCCeEEEEeCCH--HHHHHHHHHc-----CCceEECCCCHHHHHHHHHHHHhCCCccEEEEeccc
Confidence            45555555665443 678999999987  6788888877     246799999999999999999965 88999999999


Q ss_pred             ccccCCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeE-------EEEecccc--hHHHHHHHHHHHhCC
Q psy17587         83 ARGLDVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFA-------YTFITLEQ--ERHAGEIIRALEASG  145 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~-------i~~~~~~~--~~~~~~~~~~l~~~~  145 (231)
                      .+|+|+|++++||+++.|. +...|+||+||++|.+..|.+       +.+++++.  ......-.++|...+
T Consensus       553 deGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~~s~~Rq~fl~~qG  625 (732)
T TIGR00603       553 DTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMYYSTKRQRFLVDQG  625 (732)
T ss_pred             ccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHHHHHHHHHHHHHCC
Confidence            9999999999999999985 999999999999999876654       78888764  444445555554433

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).

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.75  E-value=4.1e-18  Score=160.67  Aligned_cols=123  Identities=20%  Similarity=0.228  Sum_probs=110.0

Q ss_pred             Cchhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...|.+.+.. ...++.+||||+++  ..++.+++.|.+.|+++..+||++..+++..+.+.++.|.  |+|||++++
T Consensus       424 ~K~~al~~~i~~~~~~g~pvLI~t~si--~~se~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAG  499 (796)
T PRK12906        424 SKFNAVVKEIKERHAKGQPVLVGTVAI--ESSERLSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAG  499 (796)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEEeCcH--HHHHHHHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEecccc
Confidence            355667777743 34689999999998  7799999999999999999999999888888888888777  999999999


Q ss_pred             cccCCC---CCc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         84 RGLDVK---HLN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        84 ~Gldip---~v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||+||+   +|.     +||+++.|.+...|.|+.||+||.|.+|.+..|++.+|.
T Consensus       500 RGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG~~G~s~~~~sleD~  555 (796)
T PRK12906        500 RGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQGDPGSSRFYLSLEDD  555 (796)
T ss_pred             CCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCCCCcceEEEEeccch
Confidence            999995   899     999999999999999999999999999999999987754

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

Probab=99.74  E-value=1.2e-17  Score=158.71  Aligned_cols=103  Identities=23%  Similarity=0.341  Sum_probs=89.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHH-----HHHHHHhC----CC-------ccEEEecCcc
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRD-----STIVDFKN----GK-------VRLLIATSVA   82 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~-----~~~~~F~~----g~-------~~vLvaT~~~   82 (231)
                      .++++|||||++  ..++.+++.|...++  ..+||+|++.+|.     .++++|++    |+       ..|||||+++
T Consensus       271 ~g~~vLVF~NTv--~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVa  346 (844)
T TIGR02621       271 SGGAILVFCRTV--KHVRKVFAKLPKEKF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAG  346 (844)
T ss_pred             CCCcEEEEECCH--HHHHHHHHHHHhcCC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccchh
Confidence            457888899998  779999999998876  8999999999999     88999987    54       6899999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc-eeEEEEecc
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK-GFAYTFITL  128 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~-g~~i~~~~~  128 (231)
                      ++|||++. ++||++..|  .++|+||+||+||.|.. +..+.++..
T Consensus       347 erGLDId~-d~VI~d~aP--~esyIQRiGRtgR~G~~~~~~i~vv~~  390 (844)
T TIGR02621       347 EVGVNISA-DHLVCDLAP--FESMQQRFGRVNRFGELQACQIAVVHL  390 (844)
T ss_pred             hhcccCCc-ceEEECCCC--HHHHHHHhcccCCCCCCCCceEEEEee
Confidence            99999987 899998877  69999999999999985 444666543

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.

>PRK01172 ski2-like helicase; Provisional

Probab=99.73  E-value=3.7e-17  Score=155.22  Aligned_cols=110  Identities=18%  Similarity=0.266  Sum_probs=91.0

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHC-------------------------CCCeeeccCCCCHHHHHHHHHHHhCCC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKA-------------------------GYPCLSLHGGIDQYDRDSTIVDFKNGK   72 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~-------------------------~~~~~~lhg~~~~~~R~~~~~~F~~g~   72 (231)
                      ..++.++|||+++  ..++.++..|...                         ...+.++||+|++++|..+++.|++|.
T Consensus       234 ~~~~~vLVF~~sr--~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~  311 (674)
T PRK01172        234 NDGGQVLVFVSSR--KNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRY  311 (674)
T ss_pred             hCCCcEEEEeccH--HHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCC
Confidence            3467888899988  6799888887542                         124778999999999999999999999


Q ss_pred             ccEEEecCccccccCCCCCcEEEEecC---------CCCHhHHHHHhcccCCCCC--ceeEEEEecccc
Q psy17587         73 VRLLIATSVAARGLDVKHLNLVVNYDC---------PNHYEDYVHRCGRTGRAGN--KGFAYTFITLEQ  130 (231)
Q Consensus        73 ~~vLvaT~~~~~Gldip~v~~VI~~d~---------P~~~~~y~qr~GR~gR~g~--~g~~i~~~~~~~  130 (231)
                      ++|||||+++++|+|+|+..+|| +|.         |.+..+|.||+|||||.|.  .|.+++++...+
T Consensus       312 i~VLvaT~~la~Gvnipa~~VII-~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~d~~g~~~i~~~~~~  379 (674)
T PRK01172        312 IKVIVATPTLAAGVNLPARLVIV-RDITRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPA  379 (674)
T ss_pred             CeEEEecchhhccCCCcceEEEE-cCceEeCCCCceeCCHHHHHHHhhcCCCCCCCCcceEEEEecCcc
Confidence            99999999999999999865544 443         5578899999999999984  677888876543

>KOG0352|consensus

Probab=99.73  E-value=1.3e-17  Score=145.20  Aligned_cols=110  Identities=17%  Similarity=0.372  Sum_probs=104.1

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCC
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP  100 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P  100 (231)
                      ..-||||.++  +.|++++=.|...|+.+..+|+|+...||..+.++|.++++.|++||..+++|+|-|+|++|||+|+|
T Consensus       256 GCGIVYCRTR--~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~  333 (641)
T KOG0352|consen  256 GCGIVYCRTR--NECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPS  333 (641)
T ss_pred             cceEEEeccH--HHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCch
Confidence            4556699987  88999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587        101 NHYEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus       101 ~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                      .++..|.|..||+||.|..+.|-+++...|..
T Consensus       334 qn~AgYYQESGRAGRDGk~SyCRLYYsR~D~~  365 (641)
T KOG0352|consen  334 QNLAGYYQESGRAGRDGKRSYCRLYYSRQDKN  365 (641)
T ss_pred             hhhHHHHHhccccccCCCccceeeeecccchH
Confidence            99999999999999999999999999877654

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.73  E-value=2.5e-17  Score=151.34  Aligned_cols=99  Identities=17%  Similarity=0.128  Sum_probs=90.9

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec-CccccccCCCCCcEEEEe
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT-SVAARGLDVKHLNLVVNY   97 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT-~~~~~Gldip~v~~VI~~   97 (231)
                      .+.+++|||++.  ++++.|++.|...+.++..+||+|++++|..+++.|++|+..||||| +++++|+|+|++++||++
T Consensus       343 ~~~~~lV~~~~~--~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~eG~Dip~ld~vIl~  420 (501)
T PHA02558        343 KGENTFVMFKYV--EHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVIFA  420 (501)
T ss_pred             cCCCEEEEEEEH--HHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceeccccccccccEEEEe
Confidence            345666677766  68999999999999999999999999999999999999999999998 899999999999999999


Q ss_pred             cCCCCHhHHHHHhcccCCCCCc
Q psy17587         98 DCPNHYEDYVHRCGRTGRAGNK  119 (231)
Q Consensus        98 d~P~~~~~y~qr~GR~gR~g~~  119 (231)
                      ++|.+...|+||+||++|.+..
T Consensus       421 ~p~~s~~~~~QriGR~~R~~~~  442 (501)
T PHA02558        421 HPSKSKIIVLQSIGRVLRKHGS  442 (501)
T ss_pred             cCCcchhhhhhhhhccccCCCC
Confidence            9999999999999999998754

>KOG0354|consensus

Probab=99.73  E-value=3.9e-17  Score=151.68  Aligned_cols=121  Identities=29%  Similarity=0.395  Sum_probs=99.8

Q ss_pred             chhhhhccccc---cCCCCeEEEEcCChhHHHHHHHHHHHHH---CCCCeeeccC--------CCCHHHHHHHHHHHhCC
Q psy17587          6 PCLSLHGGIDQ---YDRDSTIVDFKNGKVRLLVCAIVKELMK---AGYPCLSLHG--------GIDQYDRDSTIVDFKNG   71 (231)
Q Consensus         6 k~~~L~~~L~~---~~~~~~iiiF~~~~~~~~~~~l~~~L~~---~~~~~~~lhg--------~~~~~~R~~~~~~F~~g   71 (231)
                      |+..|.+.|.+   ..++.++||||..+  ..++.|..+|..   .+++...+-|        +|++.++..++++|++|
T Consensus       396 kle~l~~~l~e~f~~~~dsR~IIFve~R--~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G  473 (746)
T KOG0354|consen  396 KLEKLVEILVEQFEQNPDSRTIIFVETR--ESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDG  473 (746)
T ss_pred             hHHHHHHHHHHHhhcCCCccEEEEEehH--HHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCC
Confidence            45555555532   34578999999977  789999999872   2344444433        79999999999999999


Q ss_pred             CccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         72 KVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        72 ~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      +++|||||+++++|||+|+|++||-||.-.++...+||.|| ||.. .|.++++++..+
T Consensus       474 ~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~-ns~~vll~t~~~  530 (746)
T KOG0354|consen  474 EINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQRRGR-GRAR-NSKCVLLTTGSE  530 (746)
T ss_pred             CccEEEEecchhccCCcccccEEEEecCCccHHHHHHHhcc-cccc-CCeEEEEEcchh
Confidence            99999999999999999999999999999999999999999 9975 578888887433

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.71  E-value=1.9e-17  Score=157.64  Aligned_cols=124  Identities=20%  Similarity=0.248  Sum_probs=110.8

Q ss_pred             CCchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          4 GYPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         4 ~~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ..|..+|.+.+... ..++.+||||+++  +.++.|+..|...|+++..+|+  .+.+|...+..|+.+...|+|||+++
T Consensus       581 ~eK~~Ali~~I~~~~~~grpVLIft~Sv--e~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~g~VtIATNMA  656 (1025)
T PRK12900        581 REKYNAIVLKVEELQKKGQPVLVGTASV--EVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQKGAVTIATNMA  656 (1025)
T ss_pred             HHHHHHHHHHHHHHhhCCCCEEEEeCcH--HHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCCCeEEEeccCc
Confidence            35677888888544 4578999999998  7799999999999999999997  58899999999999999999999999


Q ss_pred             ccccCCC---CCc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         83 ARGLDVK---HLN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        83 ~~Gldip---~v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +||+||+   +|.     +||+++.|.+...|.|+.||+||.|.+|.+++|++.+|.
T Consensus       657 GRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqGdpGsS~ffvSleD~  713 (1025)
T PRK12900        657 GRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQGDPGESVFYVSLEDE  713 (1025)
T ss_pred             CCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCCCCcceEEEechhHH
Confidence            9999999   554     459999999999999999999999999999999988764

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.70  E-value=4.7e-17  Score=159.97  Aligned_cols=108  Identities=20%  Similarity=0.297  Sum_probs=94.5

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCC---eeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEE
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYP---CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV   95 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~---~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI   95 (231)
                      ..+.+||||++.  ..++.+++.|...++.   +..+||+|++.+|.++++.  .|..+|+||||++++|||+|+|++||
T Consensus       285 ~~GdILVFLpg~--~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVI  360 (1294)
T PRK11131        285 GPGDILIFMSGE--REIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVI  360 (1294)
T ss_pred             CCCCEEEEcCCH--HHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEE
Confidence            457789999998  6799999999887764   6789999999999999886  47889999999999999999999999


Q ss_pred             Eec---------------CCC---CHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         96 NYD---------------CPN---HYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        96 ~~d---------------~P~---~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +++               +|.   +.++|.||.|||||. .+|.||.+++..+.
T Consensus       361 D~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~-~~G~c~rLyte~d~  413 (1294)
T PRK11131        361 DPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV-SEGICIRLYSEDDF  413 (1294)
T ss_pred             ECCCccccccccccCcccCCeeecCHhhHhhhccccCCC-CCcEEEEeCCHHHH
Confidence            985               443   458999999999999 68999999987653

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

Probab=99.66  E-value=3.4e-15  Score=137.24  Aligned_cols=170  Identities=16%  Similarity=0.194  Sum_probs=121.3

Q ss_pred             hhhccc-cccCCCCeEEEEcCChhH------HHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec
Q psy17587          9 SLHGGI-DQYDRDSTIVDFKNGKVR------LLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT   79 (231)
Q Consensus         9 ~L~~~L-~~~~~~~~iiiF~~~~~~------~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT   79 (231)
                      .+++.+ .+...++.+-+.|+-...      ..++.+++.|...  ++.+..+||.|++.+++.+|++|++|+++|||||
T Consensus       461 ~v~e~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaT  540 (677)
T COG1200         461 EVYERIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVAT  540 (677)
T ss_pred             HHHHHHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEe
Confidence            334444 233356677767765322      2466777777643  6779999999999999999999999999999999


Q ss_pred             CccccccCCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCC--CchhHHHHH
Q psy17587         80 SVAARGLDVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVP--IPEDLDKMW  156 (231)
Q Consensus        80 ~~~~~Gldip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~--~~~~l~~~~  156 (231)
                      .|.+.|+|+|+.+++|.+|.-. ..++..|-.||+||.+..+.|+++..+...+..+.-.+.+.....-  +.+.-.++.
T Consensus       541 TVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG~~qSyC~Ll~~~~~~~~a~~RL~im~~t~DGF~IAE~DLklR  620 (677)
T COG1200         541 TVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGDLQSYCVLLYKPPLSEVAKQRLKIMRETTDGFVIAEEDLKLR  620 (677)
T ss_pred             eEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCCCcceEEEEEeCCCCChhHHHHHHHHHhcCCcceehhhhHhcc
Confidence            9999999999999999988765 6888999999999999999999999988756555566666554433  223212222


Q ss_pred             hhchhhhhccccCCCCCcccchhh
Q psy17587        157 AEDLIVRTFCFRAGNKGFAYTFIT  180 (231)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~  180 (231)
                      ..+..+  +....|..+|.+.+..
T Consensus       621 GpGe~l--G~rQSG~~~f~~Adl~  642 (677)
T COG1200         621 GPGELL--GTRQSGLPEFRVADLV  642 (677)
T ss_pred             CCcccc--CCcccCCcceEEeeHH
Confidence            222221  1223456667766643

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

Probab=99.66  E-value=1.1e-15  Score=144.71  Aligned_cols=117  Identities=21%  Similarity=0.280  Sum_probs=102.5

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCC-CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAG-YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~-~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      +..+.++++++   +.++||+|++  .+++.++..|.+.+ ..+..+||+++.+.|..+.++|++|+.+++|||+.++-|
T Consensus       243 ~~~i~~~v~~~---~ttLIF~NTR--~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLELG  317 (814)
T COG1201         243 YERIAELVKKH---RTTLIFTNTR--SGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLELG  317 (814)
T ss_pred             HHHHHHHHhhc---CcEEEEEeCh--HHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhhc
Confidence            34455555544   4788899988  77999999998876 899999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCC-CCCceeEEEEecc
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGR-AGNKGFAYTFITL  128 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR-~g~~g~~i~~~~~  128 (231)
                      ||+.+++.||++..|.+++..+||+||+|+ .+....++.+...
T Consensus       318 IDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~  361 (814)
T COG1201         318 IDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAED  361 (814)
T ss_pred             cccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecC
Confidence            999999999999999999999999999995 4555677777665

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.65  E-value=5e-16  Score=153.13  Aligned_cols=108  Identities=20%  Similarity=0.260  Sum_probs=92.7

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCC---CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEE
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAG---YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV   95 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~---~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI   95 (231)
                      ..+.|+||+++.  ..++.+++.|...+   +.+..+||+|++++|.+++..+  +..+|+|||+++++|||+|+|.+||
T Consensus       278 ~~GdILVFLpg~--~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVI  353 (1283)
T TIGR01967       278 GPGDILIFLPGE--REIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVI  353 (1283)
T ss_pred             CCCCEEEeCCCH--HHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEE
Confidence            357889999998  67999999998764   4588999999999999986654  2468999999999999999999999


Q ss_pred             EecCCC------------------CHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         96 NYDCPN------------------HYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        96 ~~d~P~------------------~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +++++.                  +.++|.||.||+||.+ +|.||.+++..+.
T Consensus       354 DsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~-~G~cyRLyte~~~  406 (1283)
T TIGR01967       354 DTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA-PGICIRLYSEEDF  406 (1283)
T ss_pred             eCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC-CceEEEecCHHHH
Confidence            988543                  5679999999999998 8999999986643

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.

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

Probab=99.65  E-value=6.7e-16  Score=138.78  Aligned_cols=109  Identities=17%  Similarity=0.305  Sum_probs=94.9

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE---
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN---   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~---   96 (231)
                      ....|||++++  ..|..|+..|..+|+++.++|+||+..+|..+...|.++++.++|+|-+++.|+|+|.-.+|+.   
T Consensus       440 rGQtIVFT~SR--rr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAAL~AGVDFPASQVIFEsLa  517 (830)
T COG1202         440 RGQTIVFTYSR--RRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLA  517 (830)
T ss_pred             CCceEEEecch--hhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhhhhcCCCCchHHHHHHHHH
Confidence            45566699988  6699999999999999999999999999999999999999999999999999999998544331   


Q ss_pred             ecCCC-CHhHHHHHhcccCCCCC--ceeEEEEecccc
Q psy17587         97 YDCPN-HYEDYVHRCGRTGRAGN--KGFAYTFITLEQ  130 (231)
Q Consensus        97 ~d~P~-~~~~y~qr~GR~gR~g~--~g~~i~~~~~~~  130 (231)
                      ...-| ++.+|.||+|||||++.  .|.+++++.++.
T Consensus       518 MG~~WLs~~EF~QM~GRAGRp~yHdrGkVyllvepg~  554 (830)
T COG1202         518 MGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGK  554 (830)
T ss_pred             cccccCCHHHHHHHhcccCCCCcccCceEEEEecCCh
Confidence            33344 79999999999999985  699999998764

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.61  E-value=1.7e-15  Score=133.64  Aligned_cols=85  Identities=19%  Similarity=0.219  Sum_probs=73.7

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCC--CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAG--YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~--~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      .+.+++||||++  ..++.+++.|...+  +.+..+||.+++.+|.++      ++.+|||||++++||+|+|.+ +|| 
T Consensus       271 ~~~k~LIf~nt~--~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-  340 (357)
T TIGR03158       271 PGERGAIILDSL--DEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-  340 (357)
T ss_pred             CCCeEEEEECCH--HHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-
Confidence            467888899998  77999999998754  578899999999998754      478999999999999999986 555 


Q ss_pred             ecCCCCHhHHHHHhcccC
Q psy17587         97 YDCPNHYEDYVHRCGRTG  114 (231)
Q Consensus        97 ~d~P~~~~~y~qr~GR~g  114 (231)
                      ++ |.+.++|+||+||+|
T Consensus       341 ~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       341 FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             EC-CCCHHHHhhhcccCC
Confidence            55 899999999999987

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.

>KOG0353|consensus

Probab=99.59  E-value=2e-15  Score=130.21  Aligned_cols=120  Identities=17%  Similarity=0.267  Sum_probs=108.7

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDV   88 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldi   88 (231)
                      .+..+|+....++.-||||-++  ..++.++..|...|+.+..+|+.|.|++|..+-+.|-.|++.|+|+|-++++|+|-
T Consensus       306 di~k~i~~~f~gqsgiiyc~sq--~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgidk  383 (695)
T KOG0353|consen  306 DIAKLIKGDFAGQSGIIYCFSQ--KDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGIDK  383 (695)
T ss_pred             HHHHHhccccCCCcceEEEecc--ccHHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCCC
Confidence            3445556556677777799887  56999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcEEEEecCCCCHhHHHH-------------------------------------------HhcccCCCCCceeEEEE
Q psy17587         89 KHLNLVVNYDCPNHYEDYVH-------------------------------------------RCGRTGRAGNKGFAYTF  125 (231)
Q Consensus        89 p~v~~VI~~d~P~~~~~y~q-------------------------------------------r~GR~gR~g~~g~~i~~  125 (231)
                      |+|++||+..+|.+.+.|.|                                           ..||+||.+.+..||++
T Consensus       384 pdvrfvihhsl~ksienyyqasarillrmtkqknksdtggstqinilevctnfkiffavfsekesgragrd~~~a~cily  463 (695)
T KOG0353|consen  384 PDVRFVIHHSLPKSIENYYQASARILLRMTKQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILY  463 (695)
T ss_pred             CCeeEEEecccchhHHHHHHHHHHHHHHHhhhcccccCCCcceeehhhhhccceeeeeeecchhccccccCCCcccEEEE
Confidence            99999999999999999999                                           77999999999999999


Q ss_pred             ecccc
Q psy17587        126 ITLEQ  130 (231)
Q Consensus       126 ~~~~~  130 (231)
                      +.-.+
T Consensus       464 y~~~d  468 (695)
T KOG0353|consen  464 YGFAD  468 (695)
T ss_pred             echHH
Confidence            87554

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.59  E-value=9.8e-15  Score=142.05  Aligned_cols=122  Identities=24%  Similarity=0.331  Sum_probs=103.3

Q ss_pred             chhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC---CccEEEecCc
Q psy17587          6 PCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG---KVRLLIATSV   81 (231)
Q Consensus         6 k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g---~~~vLvaT~~   81 (231)
                      |+..|..+|.... .+.++||||...  ...+.|.++|...|+....+||+++..+|..+++.|...   ...+|++|.+
T Consensus       472 Kl~lLdkLL~~Lk~~g~KVLIFSQft--~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLSTrA  549 (1033)
T PLN03142        472 KMVLLDKLLPKLKERDSRVLIFSQMT--RLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRA  549 (1033)
T ss_pred             HHHHHHHHHHHHHhcCCeEEeehhHH--HHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEeccc
Confidence            4555555554433 478999999965  789999999999999999999999999999999999753   3457899999


Q ss_pred             cccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCcee--EEEEeccc
Q psy17587         82 AARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGF--AYTFITLE  129 (231)
Q Consensus        82 ~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~--~i~~~~~~  129 (231)
                      ++.|||++.+++||+||+||+|....|++||+.|.|+...  ++.|++.+
T Consensus       550 GGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~g  599 (1033)
T PLN03142        550 GGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEY  599 (1033)
T ss_pred             cccCCchhhCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCC
Confidence            9999999999999999999999999999999999998644  45566554

>PRK14701 reverse gyrase; Provisional

Probab=99.55  E-value=4.3e-15  Score=150.28  Aligned_cols=121  Identities=15%  Similarity=0.107  Sum_probs=97.8

Q ss_pred             hhhhccccccCCCCeEEEEcCChhH-HHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec----Ccc
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVR-LLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT----SVA   82 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~-~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT----~~~   82 (231)
                      ..|.++++..  +...||||+++.. +.++.+++.|...|+++..+||+     |..++++|++|+++|||||    +++
T Consensus       320 ~~L~~ll~~~--g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~~F~~G~~~VLVaT~s~~gva  392 (1638)
T PRK14701        320 EHVRELLKKL--GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFDLFEEGEIDYLIGVATYYGTL  392 (1638)
T ss_pred             HHHHHHHHhC--CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHHHHHcCCCCEEEEecCCCCee
Confidence            3566666655  3567779998622 24699999999999999999995     8899999999999999999    589


Q ss_pred             ccccCCCC-CcEEEEecCCC---CHhHHHHHh-------------cccCCCCCceeEEEEecccchHHHH
Q psy17587         83 ARGLDVKH-LNLVVNYDCPN---HYEDYVHRC-------------GRTGRAGNKGFAYTFITLEQERHAG  135 (231)
Q Consensus        83 ~~Gldip~-v~~VI~~d~P~---~~~~y~qr~-------------GR~gR~g~~g~~i~~~~~~~~~~~~  135 (231)
                      +||||+|+ |++|||||+|.   +.+.|.|..             ||+||.|.++.+++.....+....+
T Consensus       393 aRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~~~a~~~g~~~~~~~~~~~~~~~~~~  462 (1638)
T PRK14701        393 VRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKIEEELKEGIPIEGVLDVFPEDVEFLR  462 (1638)
T ss_pred             EecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHhhhhcccCCcchhHHHhHHHHHHHHH
Confidence            99999999 99999999999   888777765             9999999887777544444444333

>PRK09694 helicase Cas3; Provisional

Probab=99.55  E-value=1.1e-13  Score=133.47  Aligned_cols=98  Identities=24%  Similarity=0.323  Sum_probs=84.5

Q ss_pred             ccCCCCeEEEEcCChhHHHHHHHHHHHHHCC---CCeeeccCCCCHHHH----HHHHHHH-hCCC---ccEEEecCcccc
Q psy17587         16 QYDRDSTIVDFKNGKVRLLVCAIVKELMKAG---YPCLSLHGGIDQYDR----DSTIVDF-KNGK---VRLLIATSVAAR   84 (231)
Q Consensus        16 ~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~---~~~~~lhg~~~~~~R----~~~~~~F-~~g~---~~vLvaT~~~~~   84 (231)
                      ....+++++||||+.  ..+..+++.|...+   .++..+||.+++.+|    .++++.| ++|+   ..|||||+++++
T Consensus       556 ~~~~g~~vLVf~NTV--~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~  633 (878)
T PRK09694        556 AANAGAQVCLICNLV--DDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQ  633 (878)
T ss_pred             HHhcCCEEEEEECCH--HHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhh
Confidence            345678899999988  67999999998754   679999999999999    4567788 6666   479999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCC
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGN  118 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~  118 (231)
                      |+|+ +++++|....|  .+.|+||+||++|.+.
T Consensus       634 GLDI-d~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        634 SLDL-DFDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             eeec-CCCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            9999 57999998888  7899999999999875

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.55  E-value=7.3e-14  Score=133.12  Aligned_cols=114  Identities=22%  Similarity=0.338  Sum_probs=93.1

Q ss_pred             ccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-------------------------------------CCCeeeccCCC
Q psy17587         14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-------------------------------------GYPCLSLHGGI   56 (231)
Q Consensus        14 L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-------------------------------------~~~~~~lhg~~   56 (231)
                      +.....+..++|||+++  ..+...++.|...                                     ...+.++|+||
T Consensus       247 ~~~~~~~~qvLvFv~sR--~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL  324 (766)
T COG1204         247 LESLAEGGQVLVFVHSR--KEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGL  324 (766)
T ss_pred             HHHHhcCCeEEEEEecC--chHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCC
Confidence            34555678899999987  5577777776520                                     13466899999


Q ss_pred             CHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEE----Eec-----CCCCHhHHHHHhcccCCCCC--ceeEEEE
Q psy17587         57 DQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV----NYD-----CPNHYEDYVHRCGRTGRAGN--KGFAYTF  125 (231)
Q Consensus        57 ~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI----~~d-----~P~~~~~y~qr~GR~gR~g~--~g~~i~~  125 (231)
                      +.++|..+.+.|+.|+++|||||+.+++|+|+|.-.+||    -||     .+-++.+|.|+.|||||+|-  .|.++++
T Consensus       325 ~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRPg~d~~G~~~i~  404 (766)
T COG1204         325 PREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIIL  404 (766)
T ss_pred             CHHHHHHHHHHHhcCCceEEEechHHhhhcCCcceEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCCCcCCCCcEEEE
Confidence            999999999999999999999999999999999877666    377     56679999999999999995  5777777


Q ss_pred             eccc
Q psy17587        126 ITLE  129 (231)
Q Consensus       126 ~~~~  129 (231)
                      .+..
T Consensus       405 ~~~~  408 (766)
T COG1204         405 ATSH  408 (766)
T ss_pred             ecCc
Confidence            7444

>PRK09401 reverse gyrase; Reviewed

Probab=99.54  E-value=8.9e-15  Score=144.89  Aligned_cols=103  Identities=16%  Similarity=0.176  Sum_probs=86.6

Q ss_pred             chhhhhccccccCCCCeEEEEcCChh-HHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEe----cC
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKV-RLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIA----TS   80 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~-~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLva----T~   80 (231)
                      |...|.++++...  ...||||+++. .+.++.+++.|...|+++..+||+|     .+.+++|++|+++||||    ||
T Consensus       316 k~~~L~~ll~~l~--~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F~~G~~~VLVatas~td  388 (1176)
T PRK09401        316 SVEKLVELVKRLG--DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASYYG  388 (1176)
T ss_pred             HHHHHHHHHHhcC--CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHHHCCCCCEEEEecCCCC
Confidence            4556666776553  46777999751 2349999999999999999999999     23469999999999999    69


Q ss_pred             ccccccCCCC-CcEEEEecCCC------CHhHHHHHhcccCC
Q psy17587         81 VAARGLDVKH-LNLVVNYDCPN------HYEDYVHRCGRTGR  115 (231)
Q Consensus        81 ~~~~Gldip~-v~~VI~~d~P~------~~~~y~qr~GR~gR  115 (231)
                      +++||||+|+ |++|||||+|.      ..+.|.||+||+..
T Consensus       389 v~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~  430 (1176)
T PRK09401        389 VLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLS  430 (1176)
T ss_pred             ceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHh
Confidence            9999999999 89999999998      67889999999863

>KOG0329|consensus

Probab=99.50  E-value=8.6e-15  Score=120.40  Aligned_cols=76  Identities=36%  Similarity=0.696  Sum_probs=65.8

Q ss_pred             EEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhCCCCCchh
Q psy17587         76 LIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEASGVPIPED  151 (231)
Q Consensus        76 LvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~~~~~~~~  151 (231)
                      ||||++++||+|+..|++|+|||+|.+.++|+||+|||||-|..|.+|+|++.. +...+..+.+........+|+.
T Consensus       302 ~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf~v~i~eLpde  378 (387)
T KOG0329|consen  302 LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRFEVNIKELPDE  378 (387)
T ss_pred             hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhhhccHhhcCcc
Confidence            899999999999999999999999999999999999999999999999999876 4555566666666555556654

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

Probab=99.45  E-value=5.7e-13  Score=120.73  Aligned_cols=107  Identities=17%  Similarity=0.327  Sum_probs=95.5

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      ...+..++.....+.+++|||...  .+++.++..+...++ +..+.|..++.+|..+++.|+.|++++||++.++.+|+
T Consensus       270 ~~~~~~~~~~~~~~~~~lif~~~~--~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~fr~g~~~~lv~~~vl~EGv  346 (442)
T COG1061         270 IAAVRGLLLKHARGDKTLIFASDV--EHAYEIAKLFLAPGI-VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGV  346 (442)
T ss_pred             HHHHHHHHHHhcCCCcEEEEeccH--HHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHHHcCCCCEEEEeeecccee
Confidence            344444454443577888899988  789999999988887 88999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCCCHhHHHHHhcccCCC
Q psy17587         87 DVKHLNLVVNYDCPNHYEDYVHRCGRTGRA  116 (231)
Q Consensus        87 dip~v~~VI~~d~P~~~~~y~qr~GR~gR~  116 (231)
                      |+|+++++|...+..+...|+||+||.-|.
T Consensus       347 DiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         347 DIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             cCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            999999999999999999999999999993

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

Probab=99.42  E-value=1.8e-12  Score=125.33  Aligned_cols=118  Identities=18%  Similarity=0.321  Sum_probs=100.8

Q ss_pred             hhccc-cccCCCCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587         10 LHGGI-DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus        10 L~~~L-~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      +.+.| ++...++.+-..+|..  +.++.+++.|+..  ..++.+.||.|+..+-+.+|.+|.+|+.+|||||.+.+-||
T Consensus       792 ireAI~REl~RgGQvfYv~NrV--~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGI  869 (1139)
T COG1197         792 IREAILRELLRGGQVFYVHNRV--ESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGI  869 (1139)
T ss_pred             HHHHHHHHHhcCCEEEEEecch--hhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCc
Confidence            33334 4445577777567876  7799999999764  57799999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         87 DVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        87 dip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      |+|+++++|..+.-. ..++..|..||+||.+..+.|++++.+.
T Consensus       870 DIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~  913 (1139)
T COG1197         870 DIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQ  913 (1139)
T ss_pred             CCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCc
Confidence            999999988776554 7999999999999999999999998764

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

Probab=99.42  E-value=8.8e-12  Score=111.78  Aligned_cols=121  Identities=20%  Similarity=0.277  Sum_probs=106.6

Q ss_pred             Cchhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..+.-|++-|+. ...+.+++|-+-++  ..++.|.++|...|+++.++|++...-+|.+++.+.|.|.++|||.-+.+-
T Consensus       430 ~QvdDL~~EI~~r~~~~eRvLVTtLTK--kmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLR  507 (663)
T COG0556         430 GQVDDLLSEIRKRVAKNERVLVTTLTK--KMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLR  507 (663)
T ss_pred             CcHHHHHHHHHHHHhcCCeEEEEeehH--HHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhh
Confidence            445566666654 44578999888888  889999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEec-----CCCCHhHHHHHhcccCCCCCceeEEEEecc
Q psy17587         84 RGLDVKHLNLVVNYD-----CPNHYEDYVHRCGRTGRAGNKGFAYTFITL  128 (231)
Q Consensus        84 ~Gldip~v~~VI~~d-----~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~  128 (231)
                      +|+|+|.|++|..+|     +..+-.+++|-+|||+|. ..|.+|++...
T Consensus       508 EGLDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN-~~GkvIlYAD~  556 (663)
T COG0556         508 EGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-VNGKVILYADK  556 (663)
T ss_pred             ccCCCcceeEEEEeecCccccccccchHHHHHHHHhhc-cCCeEEEEchh
Confidence            999999999999887     456889999999999995 46899888753

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.41  E-value=1.3e-12  Score=124.18  Aligned_cols=123  Identities=22%  Similarity=0.229  Sum_probs=108.2

Q ss_pred             Cchhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|..++.+.+.. +..++.+||||+++  ..++.+++.|...|+++..+||.  +.+|...+..|+.++..|+|||++++
T Consensus       414 ~K~~aI~~~I~~~~~~grpVLIft~Si--~~se~Ls~~L~~~gi~~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAG  489 (830)
T PRK12904        414 EKFDAVVEDIKERHKKGQPVLVGTVSI--EKSELLSKLLKKAGIPHNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAG  489 (830)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcH--HHHHHHHHHHHHCCCceEeccCc--hHHHHHHHHHhcCCCceEEEeccccc
Confidence            466677777755 34578999999998  77999999999999999999996  78999999999999999999999999


Q ss_pred             cccCCCCC--------------------------------------cEEEEecCCCCHhHHHHHhcccCCCCCceeEEEE
Q psy17587         84 RGLDVKHL--------------------------------------NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTF  125 (231)
Q Consensus        84 ~Gldip~v--------------------------------------~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~  125 (231)
                      ||+||+--                                      =+||--..|.+..---|-.||+||.|.+|.+-.|
T Consensus       490 RGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~GGLhVigTerhesrRid~QlrGRagRQGdpGss~f~  569 (830)
T PRK12904        490 RGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAGGLHVIGTERHESRRIDNQLRGRSGRQGDPGSSRFY  569 (830)
T ss_pred             CCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcCCCEEEecccCchHHHHHHhhcccccCCCCCceeEE
Confidence            99999842                                      1788888999999999999999999999999999


Q ss_pred             ecccch
Q psy17587        126 ITLEQE  131 (231)
Q Consensus       126 ~~~~~~  131 (231)
                      ++-+|.
T Consensus       570 lSleD~  575 (830)
T PRK12904        570 LSLEDD  575 (830)
T ss_pred             EEcCcH
Confidence            887654

>TIGR01054 rgy reverse gyrase

Probab=99.38  E-value=1.1e-12  Score=130.22  Aligned_cols=89  Identities=17%  Similarity=0.230  Sum_probs=75.3

Q ss_pred             hhhhccccccCCCCeEEEEcCCh-hHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEe----cCcc
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGK-VRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIA----TSVA   82 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~-~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLva----T~~~   82 (231)
                      ..|.++|+...  ...||||+++ ..+.++.+++.|...|+++..+||+|++    .++++|++|+++||||    ||++
T Consensus       316 ~~L~~ll~~l~--~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l~~Fr~G~~~vLVata~~tdv~  389 (1171)
T TIGR01054       316 ETLLEIVKKLG--TGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDYEKFAEGEIDVLIGVASYYGTL  389 (1171)
T ss_pred             HHHHHHHHHcC--CCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHHHHHHcCCCCEEEEeccccCcc
Confidence            45666666553  4677799875 2245999999999999999999999973    6899999999999999    5999


Q ss_pred             ccccCCCC-CcEEEEecCCCC
Q psy17587         83 ARGLDVKH-LNLVVNYDCPNH  102 (231)
Q Consensus        83 ~~Gldip~-v~~VI~~d~P~~  102 (231)
                      +||||+|+ |++|||||+|..
T Consensus       390 aRGIDip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       390 VRGLDLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             cccCCCCccccEEEEECCCCE
Confidence            99999999 899999999974

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.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.36  E-value=3.4e-12  Score=121.76  Aligned_cols=122  Identities=16%  Similarity=0.147  Sum_probs=104.8

Q ss_pred             chhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          6 PCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         6 k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      |..++.+.+.+ +..++.+||||+++  +.++.+++.|...|+++..+||.+.+.++..+.+.|+.|.  |+|||++++|
T Consensus       429 k~~av~~~i~~~~~~g~PVLVgt~Si--e~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~--VtIATNmAGR  504 (896)
T PRK13104        429 KFQAIIEDVRECGVRKQPVLVGTVSI--EASEFLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA--VTIATNMAGR  504 (896)
T ss_pred             HHHHHHHHHHHHHhCCCCEEEEeCcH--HHHHHHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc--EEEeccCccC
Confidence            44455555543 44689999999998  7899999999999999999999999999999999999994  9999999999


Q ss_pred             ccCCCCC--------------------------------------cEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEe
Q psy17587         85 GLDVKHL--------------------------------------NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI  126 (231)
Q Consensus        85 Gldip~v--------------------------------------~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~  126 (231)
                      |+||.=-                                      =+||--..+.+..-=-|-.||+||.|.+|.+-.|+
T Consensus       505 GtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQGDPGss~f~l  584 (896)
T PRK13104        505 GTDIVLGGSLAADLANLPADASEQEKEAVKKEWQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQGDPGSSRFYL  584 (896)
T ss_pred             CcceecCCchhhhhhccccchhhHHHHHHHHHhhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEEE
Confidence            9998721                                      16777778888888899999999999999999998


Q ss_pred             cccch
Q psy17587        127 TLEQE  131 (231)
Q Consensus       127 ~~~~~  131 (231)
                      +-+|.
T Consensus       585 SleD~  589 (896)
T PRK13104        585 SLEDN  589 (896)
T ss_pred             EcCcH
Confidence            86654

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.35  E-value=4.4e-12  Score=120.45  Aligned_cols=99  Identities=20%  Similarity=0.237  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHHC--CCCeeeccCCCC--HHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE--ecCCCC-----
Q psy17587         34 LVCAIVKELMKA--GYPCLSLHGGID--QYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN--YDCPNH-----  102 (231)
Q Consensus        34 ~~~~l~~~L~~~--~~~~~~lhg~~~--~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~--~d~P~~-----  102 (231)
                      -++.+.+.|.+.  +.++..+|++++  ..++++++++|++|+++|||+|+++++|+|+|+|++|+.  .|.+.+     
T Consensus       438 G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~pdfr  517 (679)
T PRK05580        438 GTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFR  517 (679)
T ss_pred             cHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCCccc
Confidence            367788888764  789999999987  467899999999999999999999999999999998854  454443     


Q ss_pred             -----HhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587        103 -----YEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus       103 -----~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                           ...|+|++||+||.+..|.+++.....+..
T Consensus       518 a~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~~~  552 (679)
T PRK05580        518 ASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHP  552 (679)
T ss_pred             hHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCCCH
Confidence                 367999999999999999999887666544

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.33  E-value=5.4e-12  Score=120.26  Aligned_cols=123  Identities=16%  Similarity=0.214  Sum_probs=106.3

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|..++.+.+... ..++.+||||++.  ..++.++..|...|+++..+|+.+++.++..+.+.|+.|.  |+|||++++
T Consensus       433 ~K~~Aii~ei~~~~~~GrpVLV~t~sv--~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAG  508 (908)
T PRK13107        433 EKYQAIIKDIKDCRERGQPVLVGTVSI--EQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAG  508 (908)
T ss_pred             HHHHHHHHHHHHHHHcCCCEEEEeCcH--HHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcC
Confidence            3445555555433 4589999999998  7799999999999999999999999999999999999999  999999999


Q ss_pred             cccCCCC--------------------------------C-----cEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEe
Q psy17587         84 RGLDVKH--------------------------------L-----NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI  126 (231)
Q Consensus        84 ~Gldip~--------------------------------v-----~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~  126 (231)
                      ||+||.=                                |     =+||--..|.+..-=-|-.||+||.|.+|.+-.|+
T Consensus       509 RGTDIkLggn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQGDPGss~f~l  588 (908)
T PRK13107        509 RGTDIVLGGNWNMEIEALENPTAEQKAKIKADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQGDAGSSRFYL  588 (908)
T ss_pred             CCcceecCCchHHhhhhhcchhhHHHHHHHHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccCCCCCceeEEE
Confidence            9999872                                1     17888888888888899999999999999999999


Q ss_pred             cccch
Q psy17587        127 TLEQE  131 (231)
Q Consensus       127 ~~~~~  131 (231)
                      +-+|.
T Consensus       589 SlED~  593 (908)
T PRK13107        589 SMEDS  593 (908)
T ss_pred             EeCcH
Confidence            87664

>KOG0950|consensus

Probab=99.32  E-value=7.9e-12  Score=118.15  Aligned_cols=116  Identities=22%  Similarity=0.321  Sum_probs=96.7

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH--------------------------------------CCCCeeeccCCCCHHHH
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK--------------------------------------AGYPCLSLHGGIDQYDR   61 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~--------------------------------------~~~~~~~lhg~~~~~~R   61 (231)
                      +..+|+||+++  ..|+.++..+..                                      -.+.+.++|+|++.++|
T Consensus       460 ~~~~lvfc~sk--~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti~~GvAyHhaGLT~eER  537 (1008)
T KOG0950|consen  460 GSSVLVFCPSK--KNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTIPYGVAYHHAGLTSEER  537 (1008)
T ss_pred             CCeEEEEcCcc--cchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheeccccceecccccccchH
Confidence            56688899998  778887755421                                      14667899999999999


Q ss_pred             HHHHHHHhCCCccEEEecCccccccCCCCCcEEEEec----CCCCHhHHHHHhcccCCCCC--ceeEEEEecccchHHHH
Q psy17587         62 DSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD----CPNHYEDYVHRCGRTGRAGN--KGFAYTFITLEQERHAG  135 (231)
Q Consensus        62 ~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d----~P~~~~~y~qr~GR~gR~g~--~g~~i~~~~~~~~~~~~  135 (231)
                      ..+...|++|.+.|++||+.++.|+|+|..+++|-..    .+.+.-+|.||+|||||+|-  .|.+|+.+...+.....
T Consensus       538 ~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~gidT~GdsiLI~k~~e~~~~~  617 (1008)
T KOG0950|consen  538 EIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRTGIDTLGDSILIIKSSEKKRVR  617 (1008)
T ss_pred             HHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhcccccCcceEEEeeccchhHHH
Confidence            9999999999999999999999999999999888643    23468899999999999984  69999999998876544


Q ss_pred             HH
Q psy17587        136 EI  137 (231)
Q Consensus       136 ~~  137 (231)
                      ++
T Consensus       618 ~l  619 (1008)
T KOG0950|consen  618 EL  619 (1008)
T ss_pred             HH
Confidence            33

>TIGR00595 priA primosomal protein N'

Probab=99.32  E-value=9.1e-12  Score=114.51  Aligned_cols=97  Identities=24%  Similarity=0.357  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHC--CCCeeeccCCCCHHHH--HHHHHHHhCCCccEEEecCccccccCCCCCcEEE--EecC----CC---
Q psy17587         35 VCAIVKELMKA--GYPCLSLHGGIDQYDR--DSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV--NYDC----PN---  101 (231)
Q Consensus        35 ~~~l~~~L~~~--~~~~~~lhg~~~~~~R--~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI--~~d~----P~---  101 (231)
                      .+.+.+.|.+.  +.++..+|++++...+  ..++++|++|+.+|||+|+++++|+|+|+|++|+  +.|.    |.   
T Consensus       271 te~~~e~l~~~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra  350 (505)
T TIGR00595       271 TEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRA  350 (505)
T ss_pred             HHHHHHHHHhhCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccch
Confidence            56777777655  7889999999987766  8999999999999999999999999999999875  5664    32   


Q ss_pred             ---CHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587        102 ---HYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus       102 ---~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                         ....|+|++||+||.+..|.+++.....+.
T Consensus       351 ~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~  383 (505)
T TIGR00595       351 AERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNH  383 (505)
T ss_pred             HHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCC
Confidence               256789999999999999999876654444

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).

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

Probab=99.29  E-value=2.1e-11  Score=104.26  Aligned_cols=114  Identities=21%  Similarity=0.280  Sum_probs=90.7

Q ss_pred             hhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHH-HCC-CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          9 SLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELM-KAG-YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         9 ~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~-~~~-~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      .|..+|+... .+..++||.++.  +..+++++.|. ..+ ..+.+.|+.  +..|.+.++.||+|++.+|++|.+++||
T Consensus       293 kl~~~lekq~~~~~P~liF~p~I--~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~~~lLiTTTILERG  368 (441)
T COG4098         293 KLKRWLEKQRKTGRPVLIFFPEI--ETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGKITLLITTTILERG  368 (441)
T ss_pred             HHHHHHHHHHhcCCcEEEEecch--HHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCceEEEEEeehhhcc
Confidence            6777775444 478899999988  78999999994 334 345788875  5689999999999999999999999999


Q ss_pred             cCCCCCcEEEE-e-cCCCCHhHHHHHhcccCCCCC--ceeEEEEe
Q psy17587         86 LDVKHLNLVVN-Y-DCPNHYEDYVHRCGRTGRAGN--KGFAYTFI  126 (231)
Q Consensus        86 ldip~v~~VI~-~-d~P~~~~~y~qr~GR~gR~g~--~g~~i~~~  126 (231)
                      +.+|+|++.|. - ..-.+-+.++|..||+||.-.  .|..+.|-
T Consensus       369 VTfp~vdV~Vlgaeh~vfTesaLVQIaGRvGRs~~~PtGdv~FFH  413 (441)
T COG4098         369 VTFPNVDVFVLGAEHRVFTESALVQIAGRVGRSLERPTGDVLFFH  413 (441)
T ss_pred             cccccceEEEecCCcccccHHHHHHHhhhccCCCcCCCCcEEEEe
Confidence            99999997654 2 233578899999999999864  46555443

>KOG0384|consensus

Probab=99.26  E-value=6.6e-11  Score=114.20  Aligned_cols=122  Identities=18%  Similarity=0.281  Sum_probs=105.0

Q ss_pred             chhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhC---CCccEEEecCc
Q psy17587          6 PCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKN---GKVRLLIATSV   81 (231)
Q Consensus         6 k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~---g~~~vLvaT~~   81 (231)
                      |+.-|=.+|.+... +.+|+||+.-  +...+.|+++|...+++..-+.|.+..+-|+.+++.|..   ..+..|+||-+
T Consensus       684 KlVLLDKLL~rLk~~GHrVLIFSQM--VRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddFvFLLSTRA  761 (1373)
T KOG0384|consen  684 KLVLLDKLLPRLKEGGHRVLIFSQM--VRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDFVFLLSTRA  761 (1373)
T ss_pred             cEEeHHHHHHHHhcCCceEEEhHHH--HHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCceEEEEeccc
Confidence            44444444544443 6899999994  488999999999999999999999999999999999985   45778999999


Q ss_pred             cccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         82 AARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        82 ~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      .+-|||+...++||.||.-|+|..=+|...||.|.|++  -.+|-|++.+
T Consensus       762 GGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~  811 (1373)
T KOG0384|consen  762 GGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKN  811 (1373)
T ss_pred             CcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCC
Confidence            99999999999999999999999999999999999985  4457778766

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

Probab=99.25  E-value=4.9e-11  Score=118.06  Aligned_cols=103  Identities=21%  Similarity=0.281  Sum_probs=83.9

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC------C---CCeeeccCCCCHHHHHHHHHHHhCCCc-cEEEec
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA------G---YPCLSLHGGIDQYDRDSTIVDFKNGKV-RLLIAT   79 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~------~---~~~~~lhg~~~~~~R~~~~~~F~~g~~-~vLvaT   79 (231)
                      |.+.+.... ..+.||||.++  .+++.+.+.|...      +   ..+..+||+++  ++..++++|+++.. .|+|++
T Consensus       689 l~~~l~~~~-~~KtiIF~~s~--~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsv  763 (1123)
T PRK11448        689 LAKYLDPTG-EGKTLIFAATD--AHADMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTV  763 (1123)
T ss_pred             HHHHHhccC-CCcEEEEEcCH--HHHHHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEe
Confidence            334443333 36777799987  7899888887642      2   24567999986  46789999999886 699999


Q ss_pred             CccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCC
Q psy17587         80 SVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAG  117 (231)
Q Consensus        80 ~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g  117 (231)
                      +++..|+|+|.|.+||++.+|.+...|+||+||+.|..
T Consensus       764 dmL~TG~DvP~v~~vVf~rpvkS~~lf~QmIGRgtR~~  801 (1123)
T PRK11448        764 DLLTTGIDVPSICNLVFLRRVRSRILYEQMLGRATRLC  801 (1123)
T ss_pred             cccccCCCcccccEEEEecCCCCHHHHHHHHhhhccCC
Confidence            99999999999999999999999999999999999964

>KOG0953|consensus

Probab=99.19  E-value=1.3e-10  Score=104.60  Aligned_cols=113  Identities=20%  Similarity=0.386  Sum_probs=93.0

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCCHHHHHHHHHHHhC--CCccEEEecCccccc
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGIDQYDRDSTIVDFKN--GKVRLLIATSVAARG   85 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~~~~R~~~~~~F~~--g~~~vLvaT~~~~~G   85 (231)
                      .+++-|....++++||-|+...    +-.+...+.+.|.. +.+++|++||+.|..--..|.+  ++.+||||||+.++|
T Consensus       347 ~~~~sl~nlk~GDCvV~FSkk~----I~~~k~kIE~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMG  422 (700)
T KOG0953|consen  347 TALGSLSNLKPGDCVVAFSKKD----IFTVKKKIEKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMG  422 (700)
T ss_pred             hhhhhhccCCCCCeEEEeehhh----HHHHHHHHHHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeecccccc
Confidence            4566677788899999887744    78888888888765 9999999999999999999986  899999999999999


Q ss_pred             cCCCCCcEEEEecC---------CCCHhHHHHHhcccCCCCC---ceeEEEEe
Q psy17587         86 LDVKHLNLVVNYDC---------PNHYEDYVHRCGRTGRAGN---KGFAYTFI  126 (231)
Q Consensus        86 ldip~v~~VI~~d~---------P~~~~~y~qr~GR~gR~g~---~g~~i~~~  126 (231)
                      +|+ +++-||.|++         |-+.++-.|-.|||||-|.   .|.+.+|-
T Consensus       423 LNL-~IrRiiF~sl~Kysg~e~~~it~sqikQIAGRAGRf~s~~~~G~vTtl~  474 (700)
T KOG0953|consen  423 LNL-NIRRIIFYSLIKYSGRETEDITVSQIKQIAGRAGRFGSKYPQGEVTTLH  474 (700)
T ss_pred             ccc-ceeEEEEeecccCCcccceeccHHHHHHHhhcccccccCCcCceEEEee
Confidence            998 4677777764         3468888999999999875   36555553

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

Probab=99.13  E-value=1.3e-10  Score=112.42  Aligned_cols=107  Identities=22%  Similarity=0.435  Sum_probs=93.9

Q ss_pred             CCCeEEEEcCChhHHHHHHHH----HHHHHCC----CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIV----KELMKAG----YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKH   90 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~----~~L~~~~----~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~   90 (231)
                      .+-+.++|+.++  ..++.+.    ..+...+    ..+..++|+|+.++|.++...|++|+..++++|+++.-|+|+.+
T Consensus       305 ~~~~tL~F~~sr--~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~~~~~~st~AlelgidiG~  382 (851)
T COG1205         305 NGIQTLVFFRSR--KQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGS  382 (851)
T ss_pred             cCceEEEEEehh--hhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCCccEEecchhhhhceeehh
Confidence            467778899987  6688886    4444444    67889999999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEec
Q psy17587         91 LNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus        91 v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                      ++.||.+..|. +..++.||.||+||.++.+..+..+.
T Consensus       383 ldavi~~g~P~~s~~~~~Q~~GRaGR~~~~~l~~~v~~  420 (851)
T COG1205         383 LDAVIAYGYPGVSVLSFRQRAGRAGRRGQESLVLVVLR  420 (851)
T ss_pred             hhhHhhcCCCCchHHHHHHhhhhccCCCCCceEEEEeC
Confidence            99999999999 89999999999999997776666665

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.07  E-value=6e-10  Score=106.83  Aligned_cols=110  Identities=20%  Similarity=0.350  Sum_probs=91.3

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHh----CCCccEEEecCccccccCCCC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFK----NGKVRLLIATSVAARGLDVKH   90 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~----~g~~~vLvaT~~~~~Gldip~   90 (231)
                      .....+++++|.||+.  ..+..++..|+..+.++..+||.++..+|.+.++.+.    .+...|+|||++.+.|+|+. 
T Consensus       435 ~~~~~~~kvlvI~NTV--~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQVIEagvDid-  511 (733)
T COG1203         435 EEVKEGKKVLVIVNTV--DRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDID-  511 (733)
T ss_pred             hhhccCCcEEEEEecH--HHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEeeEEEEEeccc-
Confidence            4455678999999998  6699999999888778999999999999999888744    56889999999999999994 


Q ss_pred             CcEEEEecCCCCHhHHHHHhcccCCCC--CceeEEEEeccc
Q psy17587         91 LNLVVNYDCPNHYEDYVHRCGRTGRAG--NKGFAYTFITLE  129 (231)
Q Consensus        91 v~~VI~~d~P~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~  129 (231)
                      .+++|  .=|..+++.+||+||++|.|  ..|..+.+....
T Consensus       512 fd~mI--Te~aPidSLIQR~GRv~R~g~~~~~~~~v~~~~~  550 (733)
T COG1203         512 FDVLI--TELAPIDSLIQRAGRVNRHGKKENGKIYVYNDEE  550 (733)
T ss_pred             cCeee--ecCCCHHHHHHHHHHHhhcccccCCceeEeeccc
Confidence            45554  44555999999999999999  567777776544

>KOG4150|consensus

Probab=99.05  E-value=3.4e-10  Score=102.47  Aligned_cols=127  Identities=19%  Similarity=0.220  Sum_probs=101.4

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----C----CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----G----YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKH   90 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~----~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~   90 (231)
                      .+-+.|-||.++  ..|+.+....+.-    +    -.+..+.||...++|.++..++--|+..-+|+|++++-|||+..
T Consensus       524 ~~~R~IAFC~~R--~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~L~giIaTNALELGIDIG~  601 (1034)
T KOG4150|consen  524 HGLRCIAFCPSR--KLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGKLCGIIATNALELGIDIGH  601 (1034)
T ss_pred             cCCcEEEeccHH--HHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCeeeEEEecchhhhcccccc
Confidence            356778899976  6687766654321    1    23567899999999999999999999999999999999999999


Q ss_pred             CcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEec--ccchHHHHHHHHHHHhCCCC
Q psy17587         91 LNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT--LEQERHAGEIIRALEASGVP  147 (231)
Q Consensus        91 v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~--~~~~~~~~~~~~~l~~~~~~  147 (231)
                      .+.|+...+|.+...+.|..||+||.++...++.++.  |-|+..+.--...+..++.+
T Consensus       602 LDAVl~~GFP~S~aNl~QQ~GRAGRRNk~SLavyva~~~PVDQ~Y~~HP~~l~~~pN~E  660 (1034)
T KOG4150|consen  602 LDAVLHLGFPGSIANLWQQAGRAGRRNKPSLAVYVAFLGPVDQYYMSHPDKLFGSPNEE  660 (1034)
T ss_pred             ceeEEEccCchhHHHHHHHhccccccCCCceEEEEEeccchhhHhhcCcHHHhCCCcce
Confidence            9999999999999999999999999998877766554  44666555555555544444

>KOG0947|consensus

Probab=99.04  E-value=6.2e-09  Score=98.87  Aligned_cols=118  Identities=22%  Similarity=0.251  Sum_probs=88.3

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC---------------------------------------CCC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA---------------------------------------GYP   48 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~---------------------------------------~~~   48 (231)
                      ..|+..|+... --.+|+||-++.+  |+.-+++|...                                       .-.
T Consensus       556 l~lin~L~k~~-lLP~VvFvFSkkr--Cde~a~~L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RG  632 (1248)
T KOG0947|consen  556 LDLINHLRKKN-LLPVVVFVFSKKR--CDEYADYLTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRG  632 (1248)
T ss_pred             HHHHHHHhhcc-cCceEEEEEcccc--HHHHHHHHhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhc
Confidence            34444444332 3466779988744  88888876421                                       112


Q ss_pred             eeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCCC---------CHhHHHHHhcccCCCCC-
Q psy17587         49 CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPN---------HYEDYVHRCGRTGRAGN-  118 (231)
Q Consensus        49 ~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~---------~~~~y~qr~GR~gR~g~-  118 (231)
                      +.++|||+=|--+.-+..-|..|-++||+||..+++|+|.|.-.+|+. .+-.         .+.+|.|++|||||.|- 
T Consensus       633 iaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFAMGVNMPARtvVF~-Sl~KhDG~efR~L~PGEytQMAGRAGRRGlD  711 (1248)
T KOG0947|consen  633 IAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFAMGVNMPARTVVFS-SLRKHDGNEFRELLPGEYTQMAGRAGRRGLD  711 (1248)
T ss_pred             chhhcccchHHHHHHHHHHHhcCceEEEeehhhhhhhcCCCceeEEee-ehhhccCcceeecCChhHHhhhccccccccC
Confidence            568999999999999999999999999999999999999998555543 3222         48899999999999984 


Q ss_pred             -ceeEEEEeccc
Q psy17587        119 -KGFAYTFITLE  129 (231)
Q Consensus       119 -~g~~i~~~~~~  129 (231)
                       .|.++++....
T Consensus       712 ~tGTVii~~~~~  723 (1248)
T KOG0947|consen  712 ETGTVIIMCKDS  723 (1248)
T ss_pred             cCceEEEEecCC
Confidence             68888777644

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

Probab=99.03  E-value=6.1e-10  Score=106.69  Aligned_cols=108  Identities=25%  Similarity=0.407  Sum_probs=93.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV   95 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI   95 (231)
                      .+.|+||.++.  ..++.+.+.|..    ..+.+.++||.|+.+++.++++--..|+-+|++||++++-+|.||+|.+||
T Consensus       259 ~GdILvFLpG~--~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VI  336 (845)
T COG1643         259 SGSILVFLPGQ--REIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVI  336 (845)
T ss_pred             CCCEEEECCcH--HHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEe
Confidence            67788899998  679999999987    457899999999999999988887778777999999999999999999999


Q ss_pred             E--------ecC----------CCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         96 N--------YDC----------PNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        96 ~--------~d~----------P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      .        ||+          |-+-.+..||.|||||.+ +|.||-+++.++
T Consensus       337 DsG~ak~~~y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~-pGicyRLyse~~  388 (845)
T COG1643         337 DSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTG-PGICYRLYSEED  388 (845)
T ss_pred             cCCcccccccccccCceeeeEEEechhhhhhhccccccCC-CceEEEecCHHH
Confidence            7        332          346778899999999975 799999998754

>KOG0385|consensus

Probab=99.03  E-value=1.9e-09  Score=100.37  Aligned_cols=123  Identities=20%  Similarity=0.279  Sum_probs=103.4

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCC---ccEEEecC
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK---VRLLIATS   80 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~---~~vLvaT~   80 (231)
                      .|+..|=.+|... ..+.+|+||+.-  ....+.|-.+..-.++...-+.|.++.++|...++.|....   .-.|++|-
T Consensus       471 GKm~vLDkLL~~Lk~~GhRVLIFSQm--t~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTR  548 (971)
T KOG0385|consen  471 GKMLVLDKLLPKLKEQGHRVLIFSQM--TRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTR  548 (971)
T ss_pred             cceehHHHHHHHHHhCCCeEEEeHHH--HHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEecc
Confidence            3555555555443 348999999984  47899999999999999999999999999999999998654   34689999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCcee--EEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGF--AYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~--~i~~~~~~  129 (231)
                      +++-|||+...++||.||.-|+|..-+|.+.||.|.|+...  ++-+++..
T Consensus       549 AGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLiten  599 (971)
T KOG0385|consen  549 AGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITEN  599 (971)
T ss_pred             ccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccc
Confidence            99999999999999999999999999999999999998544  45555544

>KOG0922|consensus

Probab=98.96  E-value=1.5e-09  Score=99.72  Aligned_cols=114  Identities=23%  Similarity=0.333  Sum_probs=95.2

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHC----C----CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----G----YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~----~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      +..++..-|+||.++.  +.++.+++.|...    +    .-+.++||.|+.+++.++++.--.|.-+|+++|++++-.+
T Consensus       253 h~~E~~GDILvFLtGq--eEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSl  330 (674)
T KOG0922|consen  253 HLTEPPGDILVFLTGQ--EEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSL  330 (674)
T ss_pred             HccCCCCCEEEEeCCH--HHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeE
Confidence            3446677899999998  7789888888654    1    1246899999999999999998889999999999999999


Q ss_pred             CCCCCcEEEE--------ecC----------CCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         87 DVKHLNLVVN--------YDC----------PNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        87 dip~v~~VI~--------~d~----------P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      .||.+.+||.        |++          |-+-.+-.||.|||||.| +|.|+-+++..+.
T Consensus       331 TI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~-pGkcyRLYte~~~  392 (674)
T KOG0922|consen  331 TIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG-PGKCYRLYTESAY  392 (674)
T ss_pred             EecceEEEEcCCceEEEeeccccCccceeEEechHHHHhhhcccCCCCC-CceEEEeeeHHHH
Confidence            9999999996        443          456778899999999976 7999999986653

>KOG0951|consensus

Probab=98.93  E-value=4.1e-09  Score=102.31  Aligned_cols=117  Identities=17%  Similarity=0.272  Sum_probs=88.1

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHH-------------------------------------CCCCeeecc
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK-------------------------------------AGYPCLSLH   53 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~-------------------------------------~~~~~~~lh   53 (231)
                      ++-+.+......++||+.++  ......++.++.                                     ..+....+|
T Consensus       537 yeKVm~~agk~qVLVFVHsR--kET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHh  614 (1674)
T KOG0951|consen  537 YEKVLEHAGKNQVLVFVHSR--KETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHH  614 (1674)
T ss_pred             HHHHHHhCCCCcEEEEEEec--hHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeec
Confidence            34444444558888999876  445555554431                                     146678999


Q ss_pred             CCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ecC------CCCHhHHHHHhcccCCCCC--cee
Q psy17587         54 GGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YDC------PNHYEDYVHRCGRTGRAGN--KGF  121 (231)
Q Consensus        54 g~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d~------P~~~~~y~qr~GR~gR~g~--~g~  121 (231)
                      +||+..+|..+.+-|+.|.++|||+|-.+++|+|+|.-.++|-    ||+      +.++.+-+||.||+||++.  .|.
T Consensus       615 AGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpahtViikgtqvy~pekg~w~elsp~dv~qmlgragrp~~D~~ge  694 (1674)
T KOG0951|consen  615 AGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPAHTVIIKGTQVYDPEKGRWTELSPLDVMQMLGRAGRPQYDTCGE  694 (1674)
T ss_pred             cCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCcceEEecCccccCcccCccccCCHHHHHHHHhhcCCCccCcCCc
Confidence            9999999999999999999999999999999999998665552    664      3468999999999999985  455


Q ss_pred             EEEEeccc
Q psy17587        122 AYTFITLE  129 (231)
Q Consensus       122 ~i~~~~~~  129 (231)
                      .++.....
T Consensus       695 giiit~~s  702 (1674)
T KOG0951|consen  695 GIIITDHS  702 (1674)
T ss_pred             eeeccCch
Confidence            55554433

>KOG0390|consensus

Probab=98.92  E-value=6.5e-09  Score=98.26  Aligned_cols=108  Identities=17%  Similarity=0.182  Sum_probs=90.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCc--c-EEEecCccccccCCCCCcEEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV--R-LLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~--~-vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      ...+++..|-+  .+.+.+.+..+-.|+.+..+||.|+..+|+++++.|.+...  . .|.+|-+.+.||++-+.+-||.
T Consensus       595 ~~~~v~Isny~--~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil  672 (776)
T KOG0390|consen  595 LVKSVLISNYT--QTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLIL  672 (776)
T ss_pred             ceEEEEeccHH--HHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEE
Confidence            34555455655  66777777777779999999999999999999999986432  3 5788999999999999999999


Q ss_pred             ecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         97 YDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        97 ~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      ||++|||+.-.|.++|+-|.|++  ..+|-|++.+
T Consensus       673 ~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatG  707 (776)
T KOG0390|consen  673 FDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATG  707 (776)
T ss_pred             eCCCCCchhHHHHHHHhccCCCcceEEEEEeecCC
Confidence            99999999999999999999985  5556677655

>KOG0387|consensus

Probab=98.87  E-value=6.8e-09  Score=96.98  Aligned_cols=123  Identities=19%  Similarity=0.264  Sum_probs=104.9

Q ss_pred             CchhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHH-HCCCCeeeccCCCCHHHHHHHHHHHhCCC-cc-EEEecC
Q psy17587          5 YPCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELM-KAGYPCLSLHGGIDQYDRDSTIVDFKNGK-VR-LLIATS   80 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~-~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~-vLvaT~   80 (231)
                      .|+..|..+|..... +.+++.|+.++  ...+.|-..|. ..|++..-+.|..+-..|...+++|.++. +. .|++|.
T Consensus       530 GKm~vl~~ll~~W~kqg~rvllFsqs~--~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lVd~Fne~~s~~VFLLTTr  607 (923)
T KOG0387|consen  530 GKMKVLAKLLKDWKKQGDRVLLFSQSR--QMLDILESFLRRAKGYSYLRMDGTTPAALRQKLVDRFNEDESIFVFLLTTR  607 (923)
T ss_pred             chHHHHHHHHHHHhhCCCEEEEehhHH--HHHHHHHHHHHhcCCceEEEecCCCccchhhHHHHhhcCCCceEEEEEEec
Confidence            467777777755544 67999999987  78999999998 58999999999999999999999999765 34 478999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc-e-eEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK-G-FAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~-g-~~i~~~~~~  129 (231)
                      |.+-|+|+...+-||.||+-|+|+.=.|..-|+-|.|++ . .+|-+++.+
T Consensus       608 vGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~g  658 (923)
T KOG0387|consen  608 VGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAG  658 (923)
T ss_pred             ccccccccccCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCC
Confidence            999999999999999999999999999999999999985 3 345566655

>KOG0948|consensus

Probab=98.87  E-value=3.3e-09  Score=98.52  Aligned_cols=81  Identities=25%  Similarity=0.397  Sum_probs=67.7

Q ss_pred             eeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ecCC---C-CHhHHHHHhcccCCCCC--
Q psy17587         49 CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YDCP---N-HYEDYVHRCGRTGRAGN--  118 (231)
Q Consensus        49 ~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d~P---~-~~~~y~qr~GR~gR~g~--  118 (231)
                      +..+|||+-|--++.+.--|.+|-+++|+||..++.|+|.|.-.+|.-    ||--   | +.-+|+|+.|||||.|.  
T Consensus       449 IGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMPAkTVvFT~~rKfDG~~fRwissGEYIQMSGRAGRRG~Dd  528 (1041)
T KOG0948|consen  449 IGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMPAKTVVFTAVRKFDGKKFRWISSGEYIQMSGRAGRRGIDD  528 (1041)
T ss_pred             cccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCcceeEEEeeccccCCcceeeecccceEEecccccccCCCC
Confidence            457999999999999999999999999999999999999998554442    3321   1 57789999999999985  


Q ss_pred             ceeEEEEeccc
Q psy17587        119 KGFAYTFITLE  129 (231)
Q Consensus       119 ~g~~i~~~~~~  129 (231)
                      .|.||+++...
T Consensus       529 rGivIlmiDek  539 (1041)
T KOG0948|consen  529 RGIVILMIDEK  539 (1041)
T ss_pred             CceEEEEecCc
Confidence            69999998755

>KOG0952|consensus

Probab=98.86  E-value=1.6e-08  Score=96.90  Aligned_cols=114  Identities=20%  Similarity=0.317  Sum_probs=86.0

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHC-----------------------CCCeeeccCCCCHHHHHHHHHHHhCCCc
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKA-----------------------GYPCLSLHGGIDQYDRDSTIVDFKNGKV   73 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----------------------~~~~~~lhg~~~~~~R~~~~~~F~~g~~   73 (231)
                      ...+..++|||.++  ...-..++.|...                       ......+|+||...+|......|..|.+
T Consensus       346 ~~~g~qVlvFvhsR--~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E~~F~~G~i  423 (1230)
T KOG0952|consen  346 LQEGHQVLVFVHSR--NETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVEKEFKEGHI  423 (1230)
T ss_pred             HHcCCeEEEEEecC--hHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHHHHHhcCCc
Confidence            34578889999876  3344445544321                       1235689999999999999999999999


Q ss_pred             cEEEecCccccccCCCCCcEEEE----ecCCC------CHhHHHHHhcccCCCC--CceeEEEEecccchH
Q psy17587         74 RLLIATSVAARGLDVKHLNLVVN----YDCPN------HYEDYVHRCGRTGRAG--NKGFAYTFITLEQER  132 (231)
Q Consensus        74 ~vLvaT~~~~~Gldip~v~~VI~----~d~P~------~~~~y~qr~GR~gR~g--~~g~~i~~~~~~~~~  132 (231)
                      +||+||..++.|+|+|+--+||-    ||.-.      +..+-+|..|||||++  ..|.++++.+.+...
T Consensus       424 ~vL~cTaTLAwGVNLPA~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGRPqFd~~G~giIiTt~dkl~  494 (1230)
T KOG0952|consen  424 KVLCCTATLAWGVNLPAYAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGRPQFDSSGEGIIITTRDKLD  494 (1230)
T ss_pred             eEEEecceeeeccCCcceEEEecCCcccccccCceeeehHHHHHHHHhccCCCCCCCCceEEEEecccHHH
Confidence            99999999999999998444442    55443      4677899999999986  578888887665433

>KOG0920|consensus

Probab=98.86  E-value=6.1e-09  Score=100.03  Aligned_cols=119  Identities=22%  Similarity=0.352  Sum_probs=99.7

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-------CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-------GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      ..|+..|......+.|+||.++.  ..+..+.+.|...       .+-+..+|+.|+..+++.++..--.|.-+|+++|+
T Consensus       401 ~~li~~I~~~~~~GaILVFLPG~--~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RKIIlaTN  478 (924)
T KOG0920|consen  401 EDLIEYIDEREFEGAILVFLPGW--EEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRKIILATN  478 (924)
T ss_pred             HHHHHhcccCCCCceEEEEcCCH--HHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcchhhhhhh
Confidence            45666677677789999999998  6688888888632       36788999999999999999999999999999999


Q ss_pred             ccccccCCCCCcEEEE--------ecCCCC----------HhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVN--------YDCPNH----------YEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~--------~d~P~~----------~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      +++-.|.||+|-+||.        ||+-.+          -..-.||.|||||. ..|.|+.+++..
T Consensus       479 IAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv-~~G~cy~L~~~~  544 (924)
T KOG0920|consen  479 IAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRV-RPGICYHLYTRS  544 (924)
T ss_pred             hHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCc-cCCeeEEeechh
Confidence            9999999999999997        565443          44458999999997 479999998754

>KOG0923|consensus

Probab=98.83  E-value=8e-09  Score=94.99  Aligned_cols=123  Identities=18%  Similarity=0.262  Sum_probs=94.2

Q ss_pred             CCCCchhhhhccc--cccCCCCeEEEEcCChhHHHHHHHHHHHHH----C-----CCCeeeccCCCCHHHHHHHHHHHhC
Q psy17587          2 KAGYPCLSLHGGI--DQYDRDSTIVDFKNGKVRLLVCAIVKELMK----A-----GYPCLSLHGGIDQYDRDSTIVDFKN   70 (231)
Q Consensus         2 ~~~~k~~~L~~~L--~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~-----~~~~~~lhg~~~~~~R~~~~~~F~~   70 (231)
                      +|.|-=.++...+  +...+.+-|+||..+.  +.++...+.|..    .     .+-+.++|+.+|...+.++++---.
T Consensus       453 EAdYldAai~tVlqIH~tqp~GDILVFltGQ--eEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~  530 (902)
T KOG0923|consen  453 EADYLDAAIVTVLQIHLTQPLGDILVFLTGQ--EEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPP  530 (902)
T ss_pred             chhHHHHHHhhheeeEeccCCccEEEEeccH--HHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCC
Confidence            3444433333333  4455678888898875  445555554432    2     4667899999999999999999999


Q ss_pred             CCccEEEecCccccccCCCCCcEEEEe--------cC----------CCCHhHHHHHhcccCCCCCceeEEEEec
Q psy17587         71 GKVRLLIATSVAARGLDVKHLNLVVNY--------DC----------PNHYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus        71 g~~~vLvaT~~~~~Gldip~v~~VI~~--------d~----------P~~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                      |.-+|++||++++-.|.|++|.+||.-        ++          |-+-.+-.||.|||||.| +|.|+-+++
T Consensus       531 gaRKVVLATNIAETSlTIdgI~yViDpGf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRtg-PGKCfRLYt  604 (902)
T KOG0923|consen  531 GARKVVLATNIAETSLTIDGIKYVIDPGFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRTG-PGKCFRLYT  604 (902)
T ss_pred             CceeEEEeecchhhceeecCeEEEecCccccccCcCCCcCceeEEEeeechhhhhhhccccCCCC-CCceEEeec
Confidence            999999999999999999999999963        32          445677799999999987 799999987

>KOG0392|consensus

Probab=98.78  E-value=3.1e-08  Score=96.10  Aligned_cols=108  Identities=24%  Similarity=0.338  Sum_probs=94.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCC---eeeccCCCCHHHHHHHHHHHhCC-CccEE-EecCccccccCCCCCcEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYP---CLSLHGGIDQYDRDSTIVDFKNG-KVRLL-IATSVAARGLDVKHLNLV   94 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~---~~~lhg~~~~~~R~~~~~~F~~g-~~~vL-vaT~~~~~Gldip~v~~V   94 (231)
                      +.+++|||.=+  ...+.+.+.|.+....   ...+.|..++.+|.++.++|.++ .++|| .+|-|.+-|+|+.+.+.|
T Consensus      1340 qHRiLIFcQlK--~mlDlVekDL~k~~mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTV 1417 (1549)
T KOG0392|consen 1340 QHRILIFCQLK--SMLDLVEKDLFKKYMPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTV 1417 (1549)
T ss_pred             cceeEEeeeHH--HHHHHHHHHHhhhhcCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceE
Confidence            46899999987  7899999999776443   44799999999999999999988 78875 778899999999999999


Q ss_pred             EEecCCCCHhHHHHHhcccCCCCCcee--EEEEeccc
Q psy17587         95 VNYDCPNHYEDYVHRCGRTGRAGNKGF--AYTFITLE  129 (231)
Q Consensus        95 I~~d~P~~~~~y~qr~GR~gR~g~~g~--~i~~~~~~  129 (231)
                      |.++=-|||..-+|.+-||.|-|++-.  ++-+++.+
T Consensus      1418 VFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrG 1454 (1549)
T KOG0392|consen 1418 VFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRG 1454 (1549)
T ss_pred             EEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhcc
Confidence            999999999999999999999998644  46666665

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.70  E-value=8.2e-08  Score=91.61  Aligned_cols=122  Identities=24%  Similarity=0.287  Sum_probs=97.0

Q ss_pred             Cchhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccEEEecCcc
Q psy17587          5 YPCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRLLIATSVA   82 (231)
Q Consensus         5 ~k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLvaT~~~   82 (231)
                      .|..++.+.+.. +..++.|+|.|.+.  +..+.|++.|.+.|++..++++...  +++..+-. ..| .-.|.|||+.+
T Consensus       410 ~K~~Aii~ei~~~~~~gqPVLVgT~SI--e~SE~ls~~L~~~gi~h~vLNAk~~--e~EA~IIa-~AG~~GaVTIATNMA  484 (925)
T PRK12903        410 AKWKAVVKEVKRVHKKGQPILIGTAQV--EDSETLHELLLEANIPHTVLNAKQN--AREAEIIA-KAGQKGAITIATNMA  484 (925)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcH--HHHHHHHHHHHHCCCCceeecccch--hhHHHHHH-hCCCCCeEEEecccc
Confidence            344556666654 45689999999988  7799999999999999999998744  33333322 455 45689999999


Q ss_pred             ccccCCCCCc--------EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         83 ARGLDVKHLN--------LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        83 ~~Gldip~v~--------~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +||.||.--.        +||....|.+..---|-.||+||.|.+|.+-.|++-+|.
T Consensus       485 GRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQGDpGss~f~lSLeD~  541 (925)
T PRK12903        485 GRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQGDVGESRFFISLDDQ  541 (925)
T ss_pred             cCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccCCCCCcceEEEecchH
Confidence            9999997322        899999999988888999999999999999888886653

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

Probab=98.70  E-value=1.3e-07  Score=91.98  Aligned_cols=123  Identities=18%  Similarity=0.189  Sum_probs=103.0

Q ss_pred             Cchhhhhccc-c-ccCCCC--eEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC--CccEEEe
Q psy17587          5 YPCLSLHGGI-D-QYDRDS--TIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG--KVRLLIA   78 (231)
Q Consensus         5 ~k~~~L~~~L-~-~~~~~~--~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g--~~~vLva   78 (231)
                      .|+..+.++| . ....+.  ++++|++-.  ...+.+...|...++....++|+++.++|...++.|.++  ..-++++
T Consensus       692 ~k~~~l~~ll~~~~~~~~~~~kvlifsq~t--~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls  769 (866)
T COG0553         692 GKLQALDELLLDKLLEEGHYHKVLIFSQFT--PVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLS  769 (866)
T ss_pred             hHHHHHHHHHHHHHHhhcccccEEEEeCcH--HHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEE
Confidence            4667777777 2 333355  899999966  789999999999888999999999999999999999986  4556788


Q ss_pred             cCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCcee--EEEEeccc
Q psy17587         79 TSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGF--AYTFITLE  129 (231)
Q Consensus        79 T~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~--~i~~~~~~  129 (231)
                      |.+++.|+|+...++||.||+.|++....|...|+.|.|+...  ++-+++.+
T Consensus       770 ~kagg~glnLt~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~  822 (866)
T COG0553         770 LKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRG  822 (866)
T ss_pred             ecccccceeecccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCC
Confidence            8999999999999999999999999999999999999887544  45555544

>KOG0924|consensus

Probab=98.67  E-value=2.8e-08  Score=91.80  Aligned_cols=112  Identities=20%  Similarity=0.301  Sum_probs=89.2

Q ss_pred             cCCCCeEEEEcCChh--HHHHHHHHHHHHHC------CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCC
Q psy17587         17 YDRDSTIVDFKNGKV--RLLVCAIVKELMKA------GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDV   88 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~--~~~~~~l~~~L~~~------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldi   88 (231)
                      ..+..-|+||.++..  .-+++.+.+.|.+.      ++.+..+++.||..-+.++++.-..|.-+++|||++++-.+.+
T Consensus       560 ~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi  639 (1042)
T KOG0924|consen  560 SGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTI  639 (1042)
T ss_pred             cCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceee
Confidence            334577888988741  12344555555432      6889999999999999999999989999999999999999999


Q ss_pred             CCCcEEEEec------------------CCCCHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         89 KHLNLVVNYD------------------CPNHYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        89 p~v~~VI~~d------------------~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      |++.+||...                  .|-+-..--||.|||||.| +|.|+-+++..
T Consensus       640 ~gI~yVID~Gy~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~-pG~cYRlYTe~  697 (1042)
T KOG0924|consen  640 PGIRYVIDTGYCKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG-PGTCYRLYTED  697 (1042)
T ss_pred             cceEEEEecCceeeeecccccccceeEEEechhccchhhccccCCCC-Ccceeeehhhh
Confidence            9999999743                  3455666789999999976 79999998753

>KOG0388|consensus

Probab=98.63  E-value=1.6e-07  Score=87.24  Aligned_cols=123  Identities=19%  Similarity=0.266  Sum_probs=104.9

Q ss_pred             CchhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCcc-EEEecCcc
Q psy17587          5 YPCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR-LLIATSVA   82 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~-vLvaT~~~   82 (231)
                      .|+..|=++|.+... +.++++|..-  +..++.+.++|.-.++...-+.|...-.+|...+.+|...++- .|++|.+.
T Consensus      1028 gKL~~LDeLL~kLkaegHRvL~yfQM--TkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAG 1105 (1185)
T KOG0388|consen 1028 GKLVVLDELLPKLKAEGHRVLMYFQM--TKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAG 1105 (1185)
T ss_pred             cceeeHHHHHHHhhcCCceEEehhHH--HHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccC
Confidence            466677777766554 6788888884  4789999999999999999999999999999999999987655 47999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCcee--EEEEeccc
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGF--AYTFITLE  129 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~--~i~~~~~~  129 (231)
                      +-|||+...+.||.||..|+|.--.|.+.||.|.|+...  ++-+++.+
T Consensus      1106 GLGINLTAADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rg 1154 (1185)
T KOG0388|consen 1106 GLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRG 1154 (1185)
T ss_pred             cccccccccceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccc
Confidence            999999999999999999999999999999999998544  45555544

>KOG0389|consensus

Probab=98.60  E-value=3.5e-07  Score=85.73  Aligned_cols=122  Identities=22%  Similarity=0.309  Sum_probs=102.6

Q ss_pred             chhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCC-cc-EEEecCcc
Q psy17587          6 PCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK-VR-LLIATSVA   82 (231)
Q Consensus         6 k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~-vLvaT~~~   82 (231)
                      |...|-.+|..... +.+|+||+.  ++...+.|-..|...+++..-+.|...-.+|+..+.+|...+ +. .|++|-+.
T Consensus       762 K~r~L~~LLp~~k~~G~RVLiFSQ--FTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAG  839 (941)
T KOG0389|consen  762 KCRKLKELLPKIKKKGDRVLIFSQ--FTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAG  839 (941)
T ss_pred             hHhHHHHHHHHHhhcCCEEEEeeH--HHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccC
Confidence            45555566644443 599999998  558899999999999999999999999999999999998543 44 47999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      +-|||+...++||.+|+-.+|-.=.|.--||.|.|+.  -.++-+++.+
T Consensus       840 G~GINLt~An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~  888 (941)
T KOG0389|consen  840 GFGINLTCANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKS  888 (941)
T ss_pred             cceecccccceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecC
Confidence            9999999999999999999999999999999999974  4556677665

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.59  E-value=2.6e-07  Score=86.95  Aligned_cols=121  Identities=21%  Similarity=0.278  Sum_probs=95.3

Q ss_pred             chhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCC-ccEEEecCccc
Q psy17587          6 PCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK-VRLLIATSVAA   83 (231)
Q Consensus         6 k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLvaT~~~~   83 (231)
                      |..++.+.+.+ +..++.|+|.|.+.  +..+.++..|.+.|+++..+++.-...| ..++.  ..|. -.|.|||+.++
T Consensus       412 k~~Aii~ei~~~~~~GrPVLVgt~sI--~~SE~ls~~L~~~gI~h~vLNAk~~~~E-A~IIa--~AG~~gaVTIATNMAG  486 (764)
T PRK12326        412 KNDAIVEHIAEVHETGQPVLVGTHDV--AESEELAERLRAAGVPAVVLNAKNDAEE-ARIIA--EAGKYGAVTVSTQMAG  486 (764)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEeCCH--HHHHHHHHHHHhCCCcceeeccCchHhH-HHHHH--hcCCCCcEEEEecCCC
Confidence            44555555533 45689999999988  7799999999999999999998754333 22222  2343 46899999999


Q ss_pred             cccCCCC----------Cc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         84 RGLDVKH----------LN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        84 ~Gldip~----------v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||.||.-          |.     +||--..|.+..--.|-.||+||.|.+|.+-.|++-+|.
T Consensus       487 RGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRaGRQGDpGss~f~lSleDd  549 (764)
T PRK12326        487 RGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRAGRQGDPGSSVFFVSLEDD  549 (764)
T ss_pred             CccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhcccccCCCCCceeEEEEcchh
Confidence            9999872          21     789899999999999999999999999999988886654

>KOG0391|consensus

Probab=98.52  E-value=5.5e-07  Score=87.44  Aligned_cols=122  Identities=17%  Similarity=0.227  Sum_probs=95.3

Q ss_pred             chhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCC--ccEEEecCcc
Q psy17587          6 PCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK--VRLLIATSVA   82 (231)
Q Consensus         6 k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~--~~vLvaT~~~   82 (231)
                      |+.+|--+|++.. .+.+++||+.-.  ...+-|-.+|.-+|+...-+.|...-++|+..+++|....  .+.+++|-..
T Consensus      1261 KLQtLAiLLqQLk~eghRvLIfTQMt--kmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSg 1338 (1958)
T KOG0391|consen 1261 KLQTLAILLQQLKSEGHRVLIFTQMT--KMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSG 1338 (1958)
T ss_pred             hHHHHHHHHHHHHhcCceEEehhHHH--HHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCC
Confidence            4444444444433 378999999954  8899999999999999999999999999999999998643  5678899999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      +.|||+...+.||.||--||+.---|.--|+.|.|+.  -..|-|++..
T Consensus      1339 gvGiNLtgADTVvFYDsDwNPtMDaQAQDrChRIGqtRDVHIYRLISe~ 1387 (1958)
T KOG0391|consen 1339 GVGINLTGADTVVFYDSDWNPTMDAQAQDRCHRIGQTRDVHIYRLISER 1387 (1958)
T ss_pred             ccccccccCceEEEecCCCCchhhhHHHHHHHhhcCccceEEEEeeccc
Confidence            9999999999999999999977666655555555542  3345555543

>KOG1002|consensus

Probab=98.51  E-value=4.8e-07  Score=81.19  Aligned_cols=122  Identities=23%  Similarity=0.253  Sum_probs=98.8

Q ss_pred             chhhhhccc---cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccE-EEecC
Q psy17587          6 PCLSLHGGI---DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRL-LIATS   80 (231)
Q Consensus         6 k~~~L~~~L---~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~v-LvaT~   80 (231)
                      |+.+|.+.|   .+.+..-+.|||+.  +....+.+.-.|.+.|++++.+-|+|++..|..+++.|++. +++| |++-.
T Consensus       621 KIEAL~EEl~~l~~rd~t~KsIVFSQ--FTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLk  698 (791)
T KOG1002|consen  621 KIEALVEELYFLRERDRTAKSIVFSQ--FTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLK  698 (791)
T ss_pred             HHHHHHHHHHHHHHcccchhhhhHHH--HHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEec
Confidence            455565555   33344445566988  45789999999999999999999999999999999999865 5666 67888


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCC--ceeEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGN--KGFAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~--~g~~i~~~~~~  129 (231)
                      +.+..+|+...+.|+..|+-|++..-.|...|..|.|+  +-.++.|+..+
T Consensus       699 AGGVALNLteASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEn  749 (791)
T KOG1002|consen  699 AGGVALNLTEASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIEN  749 (791)
T ss_pred             cCceEeeechhceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhc
Confidence            99999999999999999999999999998888888886  44556666544

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.47  E-value=1.1e-06  Score=84.90  Aligned_cols=121  Identities=19%  Similarity=0.178  Sum_probs=93.7

Q ss_pred             chhhhhccc-cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCC-ccEEEecCccc
Q psy17587          6 PCLSLHGGI-DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK-VRLLIATSVAA   83 (231)
Q Consensus         6 k~~~L~~~L-~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLvaT~~~~   83 (231)
                      |..++.+.+ ..+..++.|+|-|.+.  +..+.++..|.+.|++...+++.-...|- .++  -..|. -.|.|||+.++
T Consensus       553 k~~ai~~ei~~~~~~grPvLigt~si--~~se~ls~~L~~~gi~h~vLNak~~~~Ea-~ii--a~AG~~g~VTIATNmAG  627 (970)
T PRK12899        553 KYHAIVAEIASIHRKGNPILIGTESV--EVSEKLSRILRQNRIEHTVLNAKNHAQEA-EII--AGAGKLGAVTVATNMAG  627 (970)
T ss_pred             HHHHHHHHHHHHHhCCCCEEEEeCcH--HHHHHHHHHHHHcCCcceecccchhhhHH-HHH--HhcCCCCcEEEeecccc
Confidence            334444444 3445678899999988  78999999999999999999987432222 222  23444 56899999999


Q ss_pred             cccCCCC---Cc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         84 RGLDVKH---LN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        84 ~Gldip~---v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||.||.-   |.     +||.-..|.+..--.|-.||+||.|.+|.+-.|++-+|.
T Consensus       628 RGTDIkl~~~v~~~GGLhVIgTer~es~Rid~Ql~GRagRQGdpGss~f~lSlEDd  683 (970)
T PRK12899        628 RGTDIKLDEEAVAVGGLYVIGTSRHQSRRIDRQLRGRCARLGDPGAAKFFLSFEDR  683 (970)
T ss_pred             CCcccccCchHHhcCCcEEEeeccCchHHHHHHHhcccccCCCCCceeEEEEcchH
Confidence            9999872   22     788899999999999999999999999999999987664

>KOG0926|consensus

Probab=98.44  E-value=3e-07  Score=86.40  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=58.5

Q ss_pred             eeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE--------ecCCCCH----------hHHHHHh
Q psy17587         49 CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN--------YDCPNHY----------EDYVHRC  110 (231)
Q Consensus        49 ~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~--------~d~P~~~----------~~y~qr~  110 (231)
                      |..+++=++.+++.++++.--.|.-=++|+|+|++-.+.||+|.+||.        ||--..+          .+--||+
T Consensus       607 vLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAETSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRA  686 (1172)
T KOG0926|consen  607 VLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAETSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRA  686 (1172)
T ss_pred             EeehhhhcCHHHhhhhccCCCCCceEEEEeccchhcccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhc
Confidence            344455555555555555555566668999999999999999999997        4544433          3447999


Q ss_pred             cccCCCCCceeEEEEecc
Q psy17587        111 GRTGRAGNKGFAYTFITL  128 (231)
Q Consensus       111 GR~gR~g~~g~~i~~~~~  128 (231)
                      |||||.| +|.|+-+++.
T Consensus       687 GRAGRtg-pGHcYRLYSS  703 (1172)
T KOG0926|consen  687 GRAGRTG-PGHCYRLYSS  703 (1172)
T ss_pred             cccCCCC-CCceeehhhh
Confidence            9999987 6999988864

>KOG0949|consensus

Probab=98.39  E-value=1.1e-06  Score=84.17  Aligned_cols=81  Identities=23%  Similarity=0.285  Sum_probs=66.5

Q ss_pred             eeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEec-CCCCHhHHHHHhcccCCCCC--ceeEEEE
Q psy17587         49 CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD-CPNHYEDYVHRCGRTGRAGN--KGFAYTF  125 (231)
Q Consensus        49 ~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d-~P~~~~~y~qr~GR~gR~g~--~g~~i~~  125 (231)
                      +.++|+||+...|..+.--||.|...||+||..++-|||.|.-.+|.--| +-.++..|.|+.|||||.|=  -|.++.+
T Consensus       965 iG~HHaglNr~yR~~VEvLFR~g~L~VlfaT~TLsLGiNMPCrTVvF~gDsLQL~plny~QmaGRAGRRGFD~lGnV~Fm 1044 (1330)
T KOG0949|consen  965 IGVHHAGLNRKYRSLVEVLFRQGHLQVLFATETLSLGINMPCRTVVFAGDSLQLDPLNYKQMAGRAGRRGFDTLGNVVFM 1044 (1330)
T ss_pred             ccccccccchHHHHHHHHHhhcCceEEEEEeeehhcccCCCceeEEEeccccccCchhHHhhhccccccccccccceEEE
Confidence            45899999999999999999999999999999999999999644444433 45589999999999999884  4666555


Q ss_pred             eccc
Q psy17587        126 ITLE  129 (231)
Q Consensus       126 ~~~~  129 (231)
                      -.|.
T Consensus      1045 giP~ 1048 (1330)
T KOG0949|consen 1045 GIPR 1048 (1330)
T ss_pred             eCcH
Confidence            4443

>KOG1000|consensus

Probab=98.37  E-value=2.3e-06  Score=76.88  Aligned_cols=115  Identities=17%  Similarity=0.182  Sum_probs=97.8

Q ss_pred             Cchhhhhccccc-----cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccE-EE
Q psy17587          5 YPCLSLHGGIDQ-----YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRL-LI   77 (231)
Q Consensus         5 ~k~~~L~~~L~~-----~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~v-Lv   77 (231)
                      -|+..+-++|..     ..+..+++|||.-.  ...+.+...+..+++..+-+.|..++.+|....+.|+.. ++.| ++
T Consensus       472 aK~~av~eyi~~~~~l~d~~~~KflVFaHH~--~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvl  549 (689)
T KOG1000|consen  472 AKAAAVCEYILENYFLPDAPPRKFLVFAHHQ--IVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVL  549 (689)
T ss_pred             cccHHHHHHHHhCcccccCCCceEEEEehhH--HHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEE
Confidence            455555555544     33578999999976  779999999999999999999999999999999999854 5555 56


Q ss_pred             ecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCcee
Q psy17587         78 ATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGF  121 (231)
Q Consensus        78 aT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~  121 (231)
                      +-.+++.|+++...+.||...+||++.-++|.-.|+.|.|++..
T Consensus       550 sItA~gvGLt~tAa~~VVFaEL~wnPgvLlQAEDRaHRiGQkss  593 (689)
T KOG1000|consen  550 SITAAGVGLTLTAASVVVFAELHWNPGVLLQAEDRAHRIGQKSS  593 (689)
T ss_pred             EEeecccceeeeccceEEEEEecCCCceEEechhhhhhccccce
Confidence            77899999999999999999999999999999999999997543

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.34  E-value=1.9e-06  Score=83.63  Aligned_cols=122  Identities=18%  Similarity=0.251  Sum_probs=95.7

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccEEEecCcc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRLLIATSVA   82 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLvaT~~~   82 (231)
                      .|..++.+.+... ..++.|+|-|.+.  +..+.|+..|...|++..++++....+|-. ++.  ..| .-.|-|||+.+
T Consensus       612 eK~~Aii~ei~~~~~~GrPVLVGT~SV--e~SE~lS~~L~~~gI~H~VLNAK~h~~EAe-IVA--~AG~~GaVTIATNMA  686 (1112)
T PRK12901        612 EKYNAVIEEITELSEAGRPVLVGTTSV--EISELLSRMLKMRKIPHNVLNAKLHQKEAE-IVA--EAGQPGTVTIATNMA  686 (1112)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEeCcH--HHHHHHHHHHHHcCCcHHHhhccchhhHHH-HHH--hcCCCCcEEEeccCc
Confidence            3455566655444 4589999999987  789999999999999999998875544332 222  233 34688999999


Q ss_pred             ccccCCC---CC-----cEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         83 ARGLDVK---HL-----NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        83 ~~Gldip---~v-----~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      +||.||.   .|     =+||--..|.+..---|-.||+||.|.+|.+-.|++-+|.
T Consensus       687 GRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQGDPGsS~f~lSLEDd  743 (1112)
T PRK12901        687 GRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQGDPGSSQFYVSLEDN  743 (1112)
T ss_pred             CCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccCCCCCcceEEEEcccH
Confidence            9999997   22     3788899999999999999999999999999988886653

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

Probab=98.31  E-value=6.5e-06  Score=78.36  Aligned_cols=99  Identities=24%  Similarity=0.380  Sum_probs=75.7

Q ss_pred             HHHHHHHHH--CCCCeeeccCCCCHHH--HHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecC------CC----
Q psy17587         36 CAIVKELMK--AGYPCLSLHGGIDQYD--RDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDC------PN----  101 (231)
Q Consensus        36 ~~l~~~L~~--~~~~~~~lhg~~~~~~--R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~------P~----  101 (231)
                      +.+.+.|..  .+.++..+.++.+...  =...+..|.+|+.+|||.|..++.|.|+|++..|...|.      |.    
T Consensus       494 erieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA~  573 (730)
T COG1198         494 ERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRAS  573 (730)
T ss_pred             HHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcchH
Confidence            444444433  3678999999877544  357799999999999999999999999999998665443      22    


Q ss_pred             --CHhHHHHHhcccCCCCCceeEEEEecccchHHH
Q psy17587        102 --HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHA  134 (231)
Q Consensus       102 --~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~  134 (231)
                        ...-+.|-.||+||.+.+|.+++-....+...+
T Consensus       574 Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~hp~i  608 (730)
T COG1198         574 ERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDHPAI  608 (730)
T ss_pred             HHHHHHHHHHHhhhccCCCCCeEEEEeCCCCcHHH
Confidence              255578888999999999999888776665533

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.28  E-value=1.9e-06  Score=83.00  Aligned_cols=122  Identities=20%  Similarity=0.206  Sum_probs=94.9

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccEEEecCcc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRLLIATSVA   82 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLvaT~~~   82 (231)
                      .|..++.+.+... ..++.|+|-|.+.  +..+.|++.|...|++..++++....+|- .++.  ..| .-.|.|||+.+
T Consensus       433 eK~~Ai~~ei~~~~~~GrPVLVGT~SV--e~SE~ls~~L~~~gi~h~VLNAk~~~~EA-~IIa--~AG~~GaVTIATNMA  507 (913)
T PRK13103        433 EKYAAIITDIKECMALGRPVLVGTATI--ETSEHMSNLLKKEGIEHKVLNAKYHEKEA-EIIA--QAGRPGALTIATNMA  507 (913)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEEeCCH--HHHHHHHHHHHHcCCcHHHhccccchhHH-HHHH--cCCCCCcEEEeccCC
Confidence            3455555555443 4589999999988  78999999999999999888887543332 2222  345 45689999999


Q ss_pred             ccccCCC--------------------------------CCc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEE
Q psy17587         83 ARGLDVK--------------------------------HLN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTF  125 (231)
Q Consensus        83 ~~Gldip--------------------------------~v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~  125 (231)
                      +||.||.                                .|.     +||--..|.+..-=.|-.||+||.|.+|.+-.|
T Consensus       508 GRGTDIkLg~n~~~~~~~~~~~~~~~~~~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQGDPGsS~f~  587 (913)
T PRK13103        508 GRGTDILLGGNWEVEVAALENPTPEQIAQIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQGDPGSSRFY  587 (913)
T ss_pred             CCCCCEecCCchHHHHHhhhhhhHHHHHHHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccCCCCCceEEE
Confidence            9999994                                122     788888999988889999999999999999999


Q ss_pred             ecccch
Q psy17587        126 ITLEQE  131 (231)
Q Consensus       126 ~~~~~~  131 (231)
                      ++-+|.
T Consensus       588 lSlED~  593 (913)
T PRK13103        588 LSLEDS  593 (913)
T ss_pred             EEcCcH
Confidence            887653

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

Probab=98.26  E-value=7.2e-06  Score=80.30  Aligned_cols=101  Identities=23%  Similarity=0.251  Sum_probs=73.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCc--E
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLN--L   93 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~--~   93 (231)
                      ..+++||+++.  ..++.+++.|..    .++.+  +..+.. ..|.+++++|++++..||++|+.+.+|+|+|+..  +
T Consensus       674 ~g~~LVlftS~--~~l~~v~~~L~~~~~~~~~~~--l~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~  748 (850)
T TIGR01407       674 SPKILVLFTSY--EMLHMVYDMLNELPEFEGYEV--LAQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVC  748 (850)
T ss_pred             CCCEEEEeCCH--HHHHHHHHHHhhhccccCceE--EecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEE
Confidence            35677799987  679999999864    23333  333333 5788999999999999999999999999999766  5


Q ss_pred             EEEecCCCC------------------------------HhHHHHHhcccCCCCC-ceeEEEE
Q psy17587         94 VVNYDCPNH------------------------------YEDYVHRCGRTGRAGN-KGFAYTF  125 (231)
Q Consensus        94 VI~~d~P~~------------------------------~~~y~qr~GR~gR~g~-~g~~i~~  125 (231)
                      ||...+|..                              ...+.|.+||.=|..+ .|..+++
T Consensus       749 viI~~LPf~~p~dp~~~a~~~~~~~~g~~~f~~~~lP~A~~~l~Qa~GRlIRs~~D~G~v~il  811 (850)
T TIGR01407       749 LVIPRLPFANPKHPLTKKYWQKLEQEGKNPFYDYVLPMAIIRLRQALGRLIRRENDRGSIVIL  811 (850)
T ss_pred             EEEeCCCCCCCCCHHHHHHHHHHHHhcCCchHHhhHHHHHHHHHHhhccccccCCceEEEEEE
Confidence            666555531                              2335788899999775 4544443

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.

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

Probab=98.21  E-value=3.5e-06  Score=82.31  Aligned_cols=81  Identities=22%  Similarity=0.277  Sum_probs=68.2

Q ss_pred             eeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ec----CCCCHhHHHHHhcccCCCCC--c
Q psy17587         50 LSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YD----CPNHYEDYVHRCGRTGRAGN--K  119 (231)
Q Consensus        50 ~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d----~P~~~~~y~qr~GR~gR~g~--~  119 (231)
                      ..+|+||=|..+..+..-|..|-+.|+++|.+++.|+|.|.-.+|+-    +|    -+-++.+|.|+.|||||.|-  .
T Consensus       448 avHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmPartvv~~~l~K~dG~~~r~L~~gEy~QmsGRAGRRGlD~~  527 (1041)
T COG4581         448 AVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMPARTVVFTSLSKFDGNGHRWLSPGEYTQMSGRAGRRGLDVL  527 (1041)
T ss_pred             hhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCcccceeeeeeEEecCCceeecChhHHHHhhhhhcccccccc
Confidence            38999999999999999999999999999999999999998655552    22    34469999999999999996  5


Q ss_pred             eeEEEEecccc
Q psy17587        120 GFAYTFITLEQ  130 (231)
Q Consensus       120 g~~i~~~~~~~  130 (231)
                      |.+++...+..
T Consensus       528 G~vI~~~~~~~  538 (1041)
T COG4581         528 GTVIVIEPPFE  538 (1041)
T ss_pred             ceEEEecCCCC
Confidence            88887755443

>KOG1015|consensus

Probab=98.14  E-value=7.8e-06  Score=78.36  Aligned_cols=121  Identities=18%  Similarity=0.186  Sum_probs=100.7

Q ss_pred             CchhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHHH----------------------CCCCeeeccCCCCHHHH
Q psy17587          5 YPCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELMK----------------------AGYPCLSLHGGIDQYDR   61 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~~----------------------~~~~~~~lhg~~~~~~R   61 (231)
                      .|+..|++.|+..+. +.+++||+.+-  ...+.|-.+|..                      .|.....+.|..+...|
T Consensus      1126 gKmiLLleIL~mceeIGDKlLVFSQSL--~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R 1203 (1567)
T KOG1015|consen 1126 GKMILLLEILRMCEEIGDKLLVFSQSL--ISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSR 1203 (1567)
T ss_pred             cceehHHHHHHHHHHhcceeEEeeccc--chhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHH
Confidence            578889999987766 78999999986  557777777642                      26677889999999999


Q ss_pred             HHHHHHHhCCC----ccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeE--EEEec
Q psy17587         62 DSTIVDFKNGK----VRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFA--YTFIT  127 (231)
Q Consensus        62 ~~~~~~F~~g~----~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~--i~~~~  127 (231)
                      .+...+|.+-.    --.||+|-+.+-|+|+-..+-||.||..|+|+--.|.+=|+-|.|+.-.|  |-|+.
T Consensus      1204 ~k~~~~FNdp~NlRaRl~LISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyRfGQtKPvyiYRfiA 1275 (1567)
T KOG1015|consen 1204 KKWAEEFNDPTNLRARLFLISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYRFGQTKPVYIYRFIA 1275 (1567)
T ss_pred             HHHHHHhcCcccceeEEEEEeeccCccccceeecceEEEEecccCCccchHHHHHHHhhcCcCceeehhhhh
Confidence            99999998642    23689999999999999999999999999999999999999999985444  44444

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

Probab=98.07  E-value=1.8e-05  Score=62.59  Aligned_cols=76  Identities=20%  Similarity=0.297  Sum_probs=55.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCC----CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC--ccccccCCCC--C
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAG----YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS--VAARGLDVKH--L   91 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~----~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~--~~~~Gldip~--v   91 (231)
                      +..++||+++.  ...+.+.+.+....    +.+. ..   +..++...++.|+.+.-.||+++.  .+.+|+|+|+  +
T Consensus         9 ~g~~lv~f~Sy--~~l~~~~~~~~~~~~~~~~~v~-~q---~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~   82 (167)
T PF13307_consen    9 PGGVLVFFPSY--RRLEKVYERLKERLEEKGIPVF-VQ---GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLL   82 (167)
T ss_dssp             SSEEEEEESSH--HHHHHHHTT-TSS-E-ETSCEE-ES---TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESE
T ss_pred             CCCEEEEeCCH--HHHHHHHHHHHhhcccccceee-ec---CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchh
Confidence            37777899988  67999999886543    3332 22   355788999999999999999999  9999999995  7


Q ss_pred             cEEEEecCCC
Q psy17587         92 NLVVNYDCPN  101 (231)
Q Consensus        92 ~~VI~~d~P~  101 (231)
                      +.||...+|.
T Consensus        83 r~vii~glPf   92 (167)
T PF13307_consen   83 RAVIIVGLPF   92 (167)
T ss_dssp             EEEEEES---
T ss_pred             heeeecCCCC
Confidence            7899888774

>KOG1123|consensus

Probab=97.99  E-value=3.5e-05  Score=69.60  Aligned_cols=107  Identities=21%  Similarity=0.366  Sum_probs=81.1

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHh-CCCccEEEecCccccccCCCCCcEEEEe
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFK-NGKVRLLIATSVAARGLDVKHLNLVVNY   97 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~-~g~~~vLvaT~~~~~Gldip~v~~VI~~   97 (231)
                      .+.+||||..+.     -.|-++-.+.|.  -+++|..++.||.++++.|+ +..++.++-+.++.-.+|+|..+++|+.
T Consensus       542 RgDKiIVFsDnv-----fALk~YAikl~K--pfIYG~Tsq~ERm~ILqnFq~n~~vNTIFlSKVgDtSiDLPEAnvLIQI  614 (776)
T KOG1123|consen  542 RGDKIIVFSDNV-----FALKEYAIKLGK--PFIYGPTSQNERMKILQNFQTNPKVNTIFLSKVGDTSIDLPEANVLIQI  614 (776)
T ss_pred             cCCeEEEEeccH-----HHHHHHHHHcCC--ceEECCCchhHHHHHHHhcccCCccceEEEeeccCccccCCcccEEEEE
Confidence            578999999864     344444333332  37899999999999999998 6789999999999999999999999997


Q ss_pred             cCCC-CHhHHHHHhcccCCCCC------ceeEEEEecccchH
Q psy17587         98 DCPN-HYEDYVHRCGRTGRAGN------KGFAYTFITLEQER  132 (231)
Q Consensus        98 d~P~-~~~~y~qr~GR~gR~g~------~g~~i~~~~~~~~~  132 (231)
                      ..-. +-.+-.||.||.-|+.+      ...-+++++.+..+
T Consensus       615 SSH~GSRRQEAQRLGRILRAKk~~de~fnafFYSLVS~DTqE  656 (776)
T KOG1123|consen  615 SSHGGSRRQEAQRLGRILRAKKRNDEEFNAFFYSLVSKDTQE  656 (776)
T ss_pred             cccccchHHHHHHHHHHHHHhhcCccccceeeeeeeecchHH
Confidence            6654 45667899999988743      23445666655443

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

Probab=97.95  E-value=1.9e-05  Score=76.32  Aligned_cols=88  Identities=20%  Similarity=0.295  Sum_probs=71.4

Q ss_pred             hhhhhccccccCCCCeEEEEcCC-hhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec----Cc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNG-KVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT----SV   81 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~-~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT----~~   81 (231)
                      +..+.++++...  ...|||++. .-++.++.|+++|+..|+++..+|++     ..+.++.|..|++++||..    .+
T Consensus       324 ~e~~~elvk~lG--~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~~~le~F~~GeidvLVGvAsyYG~  396 (1187)
T COG1110         324 LEKVVELVKKLG--DGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KEEALEDFEEGEVDVLVGVASYYGV  396 (1187)
T ss_pred             HHHHHHHHHHhC--CCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----chhhhhhhccCceeEEEEecccccc
Confidence            445566667664  355668886 22378999999999999999999983     3778999999999999885    58


Q ss_pred             cccccCCC-CCcEEEEecCCC
Q psy17587         82 AARGLDVK-HLNLVVNYDCPN  101 (231)
Q Consensus        82 ~~~Gldip-~v~~VI~~d~P~  101 (231)
                      +.||+|+| -+.++|.|++|.
T Consensus       397 lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         397 LVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             eeecCCchhheeEEEEecCCc
Confidence            99999999 567999999994

>KOG0386|consensus

Probab=97.95  E-value=2.6e-05  Score=75.16  Aligned_cols=106  Identities=18%  Similarity=0.221  Sum_probs=94.3

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCcc---EEEecCccccccCCCCCcEEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR---LLIATSVAARGLDVKHLNLVVN   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~---vLvaT~~~~~Gldip~v~~VI~   96 (231)
                      +.+|+.||.-.  ...+.+..+|.-.++....+.|....++|-..+..|...+..   .|.+|.+.+.|+|+.-.+.||.
T Consensus       726 gHRVLlF~qMT--rlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtvii  803 (1157)
T KOG0386|consen  726 GHRVLLFSQMT--RLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVII  803 (1157)
T ss_pred             CcchhhHHHHH--HHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEE
Confidence            78999999965  779999999999999999999999999999999999976543   5789999999999999999999


Q ss_pred             ecCCCCHhHHHHHhcccCCCCCceeEEEEec
Q psy17587         97 YDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus        97 ~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                      ||.-|++....|+--|+.|.|+...+-++..
T Consensus       804 fdsdwnp~~d~qaqdrahrigq~~evRv~rl  834 (1157)
T KOG0386|consen  804 FDSDWNPHQDLQAQDRAHRIGQKKEVRVLRL  834 (1157)
T ss_pred             ecCCCCchhHHHHHHHHHHhhchhheeeeee
Confidence            9999999999999999999998655544443

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.94  E-value=7.3e-05  Score=72.03  Aligned_cols=80  Identities=18%  Similarity=0.144  Sum_probs=58.4

Q ss_pred             chhhhhccc-cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHH-HHHHHHHhCC-CccEEEecCcc
Q psy17587          6 PCLSLHGGI-DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDR-DSTIVDFKNG-KVRLLIATSVA   82 (231)
Q Consensus         6 k~~~L~~~L-~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R-~~~~~~F~~g-~~~vLvaT~~~   82 (231)
                      |..++.+.+ ..+..++.|+|-|.+.  +..+.+++.|...|++..++++.-...++ ..++.+  .| .-.|.|||+.+
T Consensus       409 K~~AI~~ei~~~~~~grPVLIgT~SI--e~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIA~--AG~~G~VTIATNMA  484 (870)
T CHL00122        409 KWRAIADECLQMHQTGRPILIGTTTI--EKSELLSQLLKEYRLPHQLLNAKPENVRRESEIVAQ--AGRKGSITIATNMA  484 (870)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEeeCCH--HHHHHHHHHHHHcCCccceeeCCCccchhHHHHHHh--cCCCCcEEEecccc
Confidence            334444443 4455689999999988  77999999999999999999986322222 233333  34 45689999999


Q ss_pred             ccccCCC
Q psy17587         83 ARGLDVK   89 (231)
Q Consensus        83 ~~Gldip   89 (231)
                      +||.||.
T Consensus       485 GRGTDI~  491 (870)
T CHL00122        485 GRGTDII  491 (870)
T ss_pred             CCCcCee
Confidence            9999975

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

Probab=97.93  E-value=0.00013  Score=69.75  Aligned_cols=105  Identities=17%  Similarity=0.186  Sum_probs=76.0

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHH---------------------HHHHHHHHHhC-CCc
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQY---------------------DRDSTIVDFKN-GKV   73 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~---------------------~R~~~~~~F~~-g~~   73 (231)
                      .+..|||.++  ..|..+.+.|...     +.....+++..+..                     .....+++|++ +.+
T Consensus       515 ~kamvv~~sr--~~a~~~~~~l~~~~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~  592 (667)
T TIGR00348       515 FKAMVVAISR--YACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENP  592 (667)
T ss_pred             CceeEEEecH--HHHHHHHHHHHhhcccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCc
Confidence            5566699987  7798888887553     24556677664433                     12468888976 689


Q ss_pred             cEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCC-C--C-ceeEEEEecc
Q psy17587         74 RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRA-G--N-KGFAYTFITL  128 (231)
Q Consensus        74 ~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~-g--~-~g~~i~~~~~  128 (231)
                      +|||+++.+..|.|.|.+++++..-+-. ...++|.+||+.|. .  + .|..+-|+..
T Consensus       593 ~ilIVvdmllTGFDaP~l~tLyldKplk-~h~LlQai~R~nR~~~~~K~~g~IvDy~g~  650 (667)
T TIGR00348       593 KLLIVVDMLLTGFDAPILNTLYLDKPLK-YHGLLQAIARTNRIDGKDKTFGLIVDYRGL  650 (667)
T ss_pred             eEEEEEcccccccCCCccceEEEecccc-ccHHHHHHHHhccccCCCCCCEEEEECcCh
Confidence            9999999999999999998776655444 45689999999994 3  2 3556555543

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

>KOG4439|consensus

Probab=97.83  E-value=0.00016  Score=67.72  Aligned_cols=104  Identities=20%  Similarity=0.248  Sum_probs=88.3

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHh--CCCccE-EEecCccccccCCCCCcE
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFK--NGKVRL-LIATSVAARGLDVKHLNL   93 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~--~g~~~v-LvaT~~~~~Gldip~v~~   93 (231)
                      ...+.++||...=.  ...+.+...|.+.|+....+||.....+|+.+++.|.  +|..+| |++-.+.+.|+|+-..++
T Consensus       743 ~~skeK~viVSQwt--svLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNH  820 (901)
T KOG4439|consen  743 TSSKEKVVIVSQWT--SVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANH  820 (901)
T ss_pred             hcccceeeehhHHH--HHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccce
Confidence            44567777665533  4578888899999999999999999999999999996  455666 577788999999999999


Q ss_pred             EEEecCCCCHhHHHHHhcccCCCCCceeE
Q psy17587         94 VVNYDCPNHYEDYVHRCGRTGRAGNKGFA  122 (231)
Q Consensus        94 VI~~d~P~~~~~y~qr~GR~gR~g~~g~~  122 (231)
                      +|..|+-|++.---|.+.|..|.|++-.+
T Consensus       821 lilvDlHWNPaLEqQAcDRIYR~GQkK~V  849 (901)
T KOG4439|consen  821 LILVDLHWNPALEQQACDRIYRMGQKKDV  849 (901)
T ss_pred             EEEEecccCHHHHHHHHHHHHHhcccCce
Confidence            99999999999999999999999986444

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=97.72  E-value=0.00084  Score=60.70  Aligned_cols=127  Identities=12%  Similarity=0.115  Sum_probs=98.8

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc--cccccC
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV--AARGLD   87 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~--~~~Gld   87 (231)
                      ++..|.+....+.++||+++...  --.|-++|.+.+++...+|--.++.+-.++-..|..|+.+||+.|.=  +=+=..
T Consensus       290 iLP~l~~~~~~~~~LIfIPSYfD--fVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~iLL~TER~HFfrRy~  367 (442)
T PF06862_consen  290 ILPQLKRDSKMSGTLIFIPSYFD--FVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPILLYTERFHFFRRYR  367 (442)
T ss_pred             HHHHhhhccCCCcEEEEecchhh--hHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceEEEEEhHHhhhhhce
Confidence            34444433446788889999733  66788889999999999999999999999999999999999999972  334455


Q ss_pred             CCCCcEEEEecCCCCHhHHHHHhcccCCCCC------ceeEEEEecccchHHHHHHH
Q psy17587         88 VKHLNLVVNYDCPNHYEDYVHRCGRTGRAGN------KGFAYTFITLEQERHAGEII  138 (231)
Q Consensus        88 ip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~------~g~~i~~~~~~~~~~~~~~~  138 (231)
                      +.++..||.|.+|.++.-|...+.-.+....      .+.|.++++.-|.-.++.++
T Consensus       368 irGi~~viFY~~P~~p~fY~El~n~~~~~~~~~~~~~~~~~~~lysk~D~~~LErIV  424 (442)
T PF06862_consen  368 IRGIRHVIFYGPPENPQFYSELLNMLDESSGGEVDAADATVTVLYSKYDALRLERIV  424 (442)
T ss_pred             ecCCcEEEEECCCCChhHHHHHHhhhcccccccccccCceEEEEecHhHHHHHHHHh
Confidence            7788999999999999999887755554432      57888888887776555443

; GO: 0005634 nucleus

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

Probab=97.69  E-value=0.00025  Score=67.55  Aligned_cols=102  Identities=17%  Similarity=0.165  Sum_probs=74.3

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHHCCC-CeeeccCCCCHHHHHHHHHHHhCCCc-cEEEecCccccccCCCC--CcEEEE
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMKAGY-PCLSLHGGIDQYDRDSTIVDFKNGKV-RLLIATSVAARGLDVKH--LNLVVN   96 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~~~~-~~~~lhg~~~~~~R~~~~~~F~~g~~-~vLvaT~~~~~Gldip~--v~~VI~   96 (231)
                      ++++||+++.  +.++.+.+.+..... .....+|..+   +...++.|+.+.- -++|+|..+.+|+|+|+  ++.||.
T Consensus       480 ~~~lvlF~Sy--~~l~~~~~~~~~~~~~~~v~~q~~~~---~~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI  554 (654)
T COG1199         480 GGVLVLFPSY--EYLKRVAERLKDERSTLPVLTQGEDE---REELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVI  554 (654)
T ss_pred             CCEEEEeccH--HHHHHHHHHHhhcCccceeeecCCCc---HHHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEE
Confidence            3677788887  679999999976554 2455665544   4478888886555 89999999999999994  467887


Q ss_pred             ecCCCC------------------------------HhHHHHHhcccCCCCC-ceeEEEEec
Q psy17587         97 YDCPNH------------------------------YEDYVHRCGRTGRAGN-KGFAYTFIT  127 (231)
Q Consensus        97 ~d~P~~------------------------------~~~y~qr~GR~gR~g~-~g~~i~~~~  127 (231)
                      ..+|..                              .....|.+||+=|... .|..+++-.
T Consensus       555 ~~lPfp~p~dp~~~~r~~~~~~~g~~~f~~~~l~~A~~~l~QavGRlIR~~~D~G~ivllD~  616 (654)
T COG1199         555 VGLPFPNPDDPLLKARLEFLKRLGGDPFEEFYLPPAVIKLRQAVGRLIRSEDDRGVIVLLDK  616 (654)
T ss_pred             EecCCCCCCCHHHHHHHHHHHHhcCCCceEeehHHHHHHHHHhhccccccCCCceEEEEecc
Confidence            666642                              4456899999999654 466655533

>COG4889 Predicted helicase [General function prediction only]

Probab=97.63  E-value=4.3e-05  Score=73.06  Aligned_cols=105  Identities=19%  Similarity=0.295  Sum_probs=78.8

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHH-----------H--CCC--CeeeccCCCCHHHHHHHHH---HHhCCCccEEEecCcc
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELM-----------K--AGY--PCLSLHGGIDQYDRDSTIV---DFKNGKVRLLIATSVA   82 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~-----------~--~~~--~~~~lhg~~~~~~R~~~~~---~F~~g~~~vLvaT~~~   82 (231)
                      ++.|-||.+.  .+..++++.+.           +  .++  ++-...|.|.-.+|.....   .|...+++||--..++
T Consensus       461 ~RAIaF~k~I--~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~neckIlSNaRcL  538 (1518)
T COG4889         461 QRAIAFAKDI--KTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPNECKILSNARCL  538 (1518)
T ss_pred             HHHHHHHHhh--HHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcchheeeccchhh
Confidence            5666788875  45555555432           2  234  4445667899888854443   2556788999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCC---CceeEEEEec
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAG---NKGFAYTFIT  127 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g---~~g~~i~~~~  127 (231)
                      ++|+|+|..+.||.+|+..+.-+.+|.+||+.|-.   ..|..|+-+.
T Consensus       539 SEGVDVPaLDsViFf~pr~smVDIVQaVGRVMRKa~gK~yGYIILPIa  586 (1518)
T COG4889         539 SEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMRKAKGKKYGYIILPIA  586 (1518)
T ss_pred             hcCCCccccceEEEecCchhHHHHHHHHHHHHHhCcCCccceEEEEec
Confidence            99999999999999999999999999999999954   2577776654

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

Probab=97.61  E-value=0.00042  Score=68.60  Aligned_cols=103  Identities=17%  Similarity=0.198  Sum_probs=70.0

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHHCCC--CeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCC--CcEEEE
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMKAGY--PCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKH--LNLVVN   96 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~~~~--~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~--v~~VI~   96 (231)
                      +.++||.++.  ...+.+++.|.....  ....+.-+++...|.+.++.|++++-.||++|..+.+|+|+|+  +++||.
T Consensus       753 g~~LVLFtSy--~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI  830 (928)
T PRK08074        753 GRMLVLFTSY--EMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVI  830 (928)
T ss_pred             CCEEEEECCH--HHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEE
Confidence            4555566666  668888888865422  1222222444456888999999988899999999999999995  467877


Q ss_pred             ecCCC----C--------------------------HhHHHHHhcccCCCCC-ceeEEEE
Q psy17587         97 YDCPN----H--------------------------YEDYVHRCGRTGRAGN-KGFAYTF  125 (231)
Q Consensus        97 ~d~P~----~--------------------------~~~y~qr~GR~gR~g~-~g~~i~~  125 (231)
                      ..+|.    +                          ...+.|-+||.=|... .|..+++
T Consensus       831 ~kLPF~~p~dp~~~a~~~~~~~~g~~~F~~~~lP~A~~~lkQg~GRlIRs~~D~G~v~il  890 (928)
T PRK08074        831 VRLPFAPPDQPVMEAKSEWAKEQGENPFQELSLPQAVLRFKQGFGRLIRTETDRGTVFVL  890 (928)
T ss_pred             ecCCCCCCCCHHHHHHHHHHHHhCCCchhhhhhHHHHHHHHhhhhhhcccCCceEEEEEe
Confidence            66553    2                          2234777889888765 4544333

>PF13959 DUF4217: Domain of unknown function (DUF4217)

Probab=97.57  E-value=5.5e-05  Score=50.27  Aligned_cols=40  Identities=18%  Similarity=0.057  Sum_probs=34.7

Q ss_pred             HHHHHHhcCCCCcHHHHHHHHhhHHHHHhHHHH-HHHHHHh
Q psy17587        190 IIRALEASGVPIPEDLDKILAEGLVWLRDYKQR-VDQRIAR  229 (231)
Q Consensus       190 ~~~~l~~~~~~~~~~l~~~~~~~~s~~r~y~~~-~~~~i~~  229 (231)
                      ++..++.....+++..+.+.++++||+|+|..| +.+.||+
T Consensus         2 iq~~l~~~~~~d~~l~~lA~~Af~SyvraY~~~~~~k~iF~   42 (65)
T PF13959_consen    2 IQQKLEKLVAKDRELKELAQKAFVSYVRAYASHKELKDIFN   42 (65)
T ss_pred             HHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhhhhhCC
Confidence            456777777778888999999999999999999 8899986

>PF13871 Helicase_C_4: Helicase_C-like

Probab=97.57  E-value=0.00044  Score=58.85  Aligned_cols=80  Identities=20%  Similarity=0.388  Sum_probs=61.6

Q ss_pred             HHHHHHhCCCccEEEecCccccccCCCC--------CcEEEEecCCCCHhHHHHHhcccCCCCCc-eeEEEEecc---cc
Q psy17587         63 STIVDFKNGKVRLLIATSVAARGLDVKH--------LNLVVNYDCPNHYEDYVHRCGRTGRAGNK-GFAYTFITL---EQ  130 (231)
Q Consensus        63 ~~~~~F~~g~~~vLvaT~~~~~Gldip~--------v~~VI~~d~P~~~~~y~qr~GR~gR~g~~-g~~i~~~~~---~~  130 (231)
                      ...+.|.+|+..|+|.|++++.|+-+.+        -++-|...+||+.+..+|..||+.|.|+. ...+.++..   .|
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE  131 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGE  131 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHH
Confidence            4566899999999999999999998873        23667789999999999999999999973 445555543   35


Q ss_pred             hHHHHHHHHHHH
Q psy17587        131 ERHAGEIIRALE  142 (231)
Q Consensus       131 ~~~~~~~~~~l~  142 (231)
                      ...+..+.+.|.
T Consensus       132 ~Rfas~va~rL~  143 (278)
T PF13871_consen  132 RRFASTVARRLE  143 (278)
T ss_pred             HHHHHHHHHHHh
Confidence            555555555554

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

Probab=97.52  E-value=0.00043  Score=66.03  Aligned_cols=104  Identities=16%  Similarity=0.203  Sum_probs=79.2

Q ss_pred             hhhccccc--cCC-CCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhC--CCccEEEe
Q psy17587          9 SLHGGIDQ--YDR-DSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKN--GKVRLLIA   78 (231)
Q Consensus         9 ~L~~~L~~--~~~-~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~--g~~~vLva   78 (231)
                      .|.+.|+.  ... -.+.||||.+.  .+++.+...|...     |--+..+.|+-.  +-+..+..|..  .-.+|.|+
T Consensus       412 ~~~~~l~~~~~g~~~~KTIvFa~n~--dHAe~i~~~~~~~ype~~~~~a~~IT~d~~--~~q~~Id~f~~ke~~P~Iait  487 (875)
T COG4096         412 ELTEYLKRGATGDEIGKTIVFAKNH--DHAERIREALVNEYPEYNGRYAMKITGDAE--QAQALIDNFIDKEKYPRIAIT  487 (875)
T ss_pred             HHHHHhccccCCCccCceEEEeeCc--HHHHHHHHHHHHhCccccCceEEEEeccch--hhHHHHHHHHhcCCCCceEEe
Confidence            44555555  332 35667799988  8899999999754     233667777644  33445666653  45779999


Q ss_pred             cCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCC
Q psy17587         79 TSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRA  116 (231)
Q Consensus        79 T~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~  116 (231)
                      .+.+.-|+|+|.|..+|.+-.-.+..-|-|++||.=|.
T Consensus       488 vdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl  525 (875)
T COG4096         488 VDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRL  525 (875)
T ss_pred             hhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCcccc
Confidence            99999999999999999999999999999999998775

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.49  E-value=0.0013  Score=63.26  Aligned_cols=74  Identities=19%  Similarity=0.210  Sum_probs=53.4

Q ss_pred             eEEEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHHHHHHHHHHHh----CCCccEEEecCccccccCCCC--CcEE
Q psy17587         22 TIVDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFK----NGKVRLLIATSVAARGLDVKH--LNLV   94 (231)
Q Consensus        22 ~iiiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~----~g~~~vLvaT~~~~~Gldip~--v~~V   94 (231)
                      .++||.++.  ...+.+++.|... +.. +..+|..   .+...++.|+    .++-.||++|..+.+|||+|+  +++|
T Consensus       536 g~LVlFtSy--~~l~~v~~~l~~~~~~~-ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~v  609 (697)
T PRK11747        536 GSLVLFASR--RQMQKVADLLPRDLRLM-LLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQV  609 (697)
T ss_pred             CEEEEeCcH--HHHHHHHHHHHHhcCCc-EEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEE
Confidence            356677766  6688998888643 333 4556643   4667787776    467789999999999999995  6788


Q ss_pred             EEecCCC
Q psy17587         95 VNYDCPN  101 (231)
Q Consensus        95 I~~d~P~  101 (231)
                      |...+|.
T Consensus       610 II~kLPF  616 (697)
T PRK11747        610 IITKIPF  616 (697)
T ss_pred             EEEcCCC
Confidence            8766553

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

Probab=97.44  E-value=0.0018  Score=63.34  Aligned_cols=101  Identities=17%  Similarity=0.120  Sum_probs=69.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCC--CCcEEEEe
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK--HLNLVVNY   97 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip--~v~~VI~~   97 (231)
                      +++++|+.+|.  +..+.+++.|....+.+ ...|.-.  .+.+.+++|++++-.||++|..+.+|+|+|  +...||..
T Consensus       647 ~g~~LVLFtS~--~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vLlG~~sFwEGVD~p~~~~~~viI~  721 (820)
T PRK07246        647 QQPILVLFNSK--KHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQILLGLGSFWEGVDFVQADRMIEVIT  721 (820)
T ss_pred             CCCEEEEECcH--HHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEEEecchhhCCCCCCCCCeEEEEEe
Confidence            45555566666  66888888887655554 4445322  245689999999889999999999999998  34555554


Q ss_pred             cCC----CC--------------------------HhHHHHHhcccCCCCC-ceeEEEE
Q psy17587         98 DCP----NH--------------------------YEDYVHRCGRTGRAGN-KGFAYTF  125 (231)
Q Consensus        98 d~P----~~--------------------------~~~y~qr~GR~gR~g~-~g~~i~~  125 (231)
                      -+|    .+                          ...+.|-+||.=|... .|..+++
T Consensus       722 kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~il  780 (820)
T PRK07246        722 RLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVLIL  780 (820)
T ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEEEE
Confidence            444    22                          2335788899888765 5755444

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.42  E-value=0.00029  Score=68.37  Aligned_cols=49  Identities=12%  Similarity=0.133  Sum_probs=36.5

Q ss_pred             EecCccccccCCCC----------------------C----------cEEEEecCCCCHhHHHH--HhcccCCCCCceeE
Q psy17587         77 IATSVAARGLDVKH----------------------L----------NLVVNYDCPNHYEDYVH--RCGRTGRAGNKGFA  122 (231)
Q Consensus        77 vaT~~~~~Gldip~----------------------v----------~~VI~~d~P~~~~~y~q--r~GR~gR~g~~g~~  122 (231)
                      |+|.+...|+|+|.                      +          ++||.|++-.+...-+|  |.||.||.   +.+
T Consensus       431 ~~~~~~~e~~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~---~rV  507 (814)
T TIGR00596       431 FEIIDEENDIDIYSGAEFDNLPQHITHFLWGERDEYVLRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRP---LRV  507 (814)
T ss_pred             ccccccccccccchhhccccccceeeeecccccchhhHHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCC---cEE
Confidence            77888999999997                      5          89999997766666666  66665554   566


Q ss_pred             EEEecc
Q psy17587        123 YTFITL  128 (231)
Q Consensus       123 i~~~~~  128 (231)
                      +.++..
T Consensus       508 yfL~y~  513 (814)
T TIGR00596       508 YFLYYG  513 (814)
T ss_pred             EEEEEC
Confidence            666643

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

>KOG0925|consensus

Probab=97.42  E-value=0.00034  Score=63.21  Aligned_cols=108  Identities=18%  Similarity=0.312  Sum_probs=78.0

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHC---------CCCeeeccCCCCHHHHHHHHHHHh---CC--CccEEEecC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA---------GYPCLSLHGGIDQYDRDSTIVDFK---NG--KVRLLIATS   80 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~---------~~~~~~lhg~~~~~~R~~~~~~F~---~g--~~~vLvaT~   80 (231)
                      ...+..+-|++|..+.  +.++..++.+...         ..+|..+|    +.++..+++-..   +|  .-+|+|+|+
T Consensus       248 h~~ee~GDilvFLtge--eeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~~~RkvVvstn  321 (699)
T KOG0925|consen  248 HMCEEPGDILVFLTGE--EEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGAYGRKVVVSTN  321 (699)
T ss_pred             HhccCCCCEEEEecCH--HHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCCccceEEEEec
Confidence            4444567788899886  5577777766421         47888999    444454444332   22  357999999


Q ss_pred             ccccccCCCCCcEEEEec------------------CCCCHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYD------------------CPNHYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d------------------~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      +++-.+.++.|.+||.-.                  .|-+..+-.||.||+||. ++|.|+-+++..
T Consensus       322 iaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt-~pGkcfrLYte~  387 (699)
T KOG0925|consen  322 IAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEE  387 (699)
T ss_pred             chheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC-CCCceEEeecHH
Confidence            999999999999999733                  255677788999999985 579999998744

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=97.32  E-value=0.0042  Score=47.74  Aligned_cols=67  Identities=21%  Similarity=0.234  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHCCC------CeeeccCCCCHHHHHHHHHHHhCCC-ccEEEecCccccccCCCC--CcEEEEecCCC
Q psy17587         35 VCAIVKELMKAGY------PCLSLHGGIDQYDRDSTIVDFKNGK-VRLLIATSVAARGLDVKH--LNLVVNYDCPN  101 (231)
Q Consensus        35 ~~~l~~~L~~~~~------~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLvaT~~~~~Gldip~--v~~VI~~d~P~  101 (231)
                      .+.+...+...+.      .-..+.-+.+..+...+++.|+... ..||++|.-+.+|+|+|+  ++.||...+|.
T Consensus         4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492        4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            4555555554443      1233444455656789999998654 379999988999999995  45788777664

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.29  E-value=0.0015  Score=63.41  Aligned_cols=80  Identities=15%  Similarity=0.140  Sum_probs=58.8

Q ss_pred             chhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCC-CCHHHHHHHHHHHhCCC-ccEEEecCcc
Q psy17587          6 PCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGG-IDQYDRDSTIVDFKNGK-VRLLIATSVA   82 (231)
Q Consensus         6 k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~-~~~~~R~~~~~~F~~g~-~~vLvaT~~~   82 (231)
                      |..++.+.+.. +..++.|+|-|.+.  +..+.+++.|...|+++.++++. ...+.=..++.+  .|. -.|-|||+.+
T Consensus       424 K~~Ai~~ei~~~~~~GrPVLIgT~SV--e~SE~ls~~L~~~gi~h~vLNAk~~~~~~EA~IIa~--AG~~GaVTIATNMA  499 (939)
T PRK12902        424 KWRAVANETAEMHKQGRPVLVGTTSV--EKSELLSALLQEQGIPHNLLNAKPENVEREAEIVAQ--AGRKGAVTIATNMA  499 (939)
T ss_pred             HHHHHHHHHHHHHhCCCCEEEeeCCH--HHHHHHHHHHHHcCCchheeeCCCcchHhHHHHHHh--cCCCCcEEEeccCC
Confidence            44455555543 45689999999988  78999999999999999999986 222222233333  443 4688999999


Q ss_pred             ccccCCC
Q psy17587         83 ARGLDVK   89 (231)
Q Consensus        83 ~~Gldip   89 (231)
                      +||.||.
T Consensus       500 GRGTDIk  506 (939)
T PRK12902        500 GRGTDII  506 (939)
T ss_pred             CCCcCEe
Confidence            9999876

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=97.19  E-value=0.0014  Score=64.45  Aligned_cols=82  Identities=16%  Similarity=0.154  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHH----CC--CCeeeccCCCCHHHHHHHHHHH----------------------hC----CCccEEEecCc
Q psy17587         34 LVCAIVKELMK----AG--YPCLSLHGGIDQYDRDSTIVDF----------------------KN----GKVRLLIATSV   81 (231)
Q Consensus        34 ~~~~l~~~L~~----~~--~~~~~lhg~~~~~~R~~~~~~F----------------------~~----g~~~vLvaT~~   81 (231)
                      .+-.+++.|..    .+  +.+.++|+..+...|..+.+..                      .+    +...|+|+|++
T Consensus       768 p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv  847 (1110)
T TIGR02562       768 PLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPV  847 (1110)
T ss_pred             HHHHHHHHHHhhccccCCceeEEEecccChHHHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeee
Confidence            35555665543    23  4577899999888887766553                      11    35689999999


Q ss_pred             cccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCC
Q psy17587         82 AARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGN  118 (231)
Q Consensus        82 ~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~  118 (231)
                      .+.|+|+. .+++  +.-|.+..+.+|++||+.|.+.
T Consensus       848 ~E~g~D~d-fd~~--~~~~~~~~sliQ~aGR~~R~~~  881 (1110)
T TIGR02562       848 EEVGRDHD-YDWA--IADPSSMRSIIQLAGRVNRHRL  881 (1110)
T ss_pred             EEEEeccc-CCee--eeccCcHHHHHHHhhccccccc
Confidence            99999983 3444  4456779999999999999875

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.

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=97.14  E-value=0.0052  Score=47.22  Aligned_cols=66  Identities=17%  Similarity=0.237  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHCCC----CeeeccCCCCHHHHHHHHHHHhCCCc---cEEEecCc--cccccCCCC--CcEEEEecCCC
Q psy17587         35 VCAIVKELMKAGY----PCLSLHGGIDQYDRDSTIVDFKNGKV---RLLIATSV--AARGLDVKH--LNLVVNYDCPN  101 (231)
Q Consensus        35 ~~~l~~~L~~~~~----~~~~lhg~~~~~~R~~~~~~F~~g~~---~vLvaT~~--~~~Gldip~--v~~VI~~d~P~  101 (231)
                      .+.+.+.+...+.    .....-+ ....+....++.|++..-   .||+++.-  +++|+|+|+  ++.||...+|.
T Consensus         4 m~~v~~~~~~~~~~~~~~~i~~e~-~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491        4 LEQVVEYWKENGILEINKPVFIEG-KDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             HHHHHHHHHhcCccccCceEEEEC-CCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCC
Confidence            5566666655432    2223323 333355788999987544   68888877  999999996  56888877774

>KOG1016|consensus

Probab=97.00  E-value=0.0034  Score=59.76  Aligned_cols=134  Identities=17%  Similarity=0.186  Sum_probs=99.9

Q ss_pred             CCCCchhhhhccccccCC-CCeEEEEcCChhHHHHHHHHHHHHHC------------------CCCeeeccCCCCHHHHH
Q psy17587          2 KAGYPCLSLHGGIDQYDR-DSTIVDFKNGKVRLLVCAIVKELMKA------------------GYPCLSLHGGIDQYDRD   62 (231)
Q Consensus         2 ~~~~k~~~L~~~L~~~~~-~~~iiiF~~~~~~~~~~~l~~~L~~~------------------~~~~~~lhg~~~~~~R~   62 (231)
                      +.|+|+..+++.+...-. +.++|+|+.+.  ...+.|-+.|.+.                  +.+..-+.|..+..+|.
T Consensus       700 en~pk~V~~~~~~des~~~g~kil~fSq~l--~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~re  777 (1387)
T KOG1016|consen  700 ENGPKIVISLEILDESTQIGEKILIFSQNL--TALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADRE  777 (1387)
T ss_pred             cCCCceEEEEeeeccccccCceEEEeecch--hHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHH
Confidence            457888888888865544 78999999886  3466666666543                  23344678888899999


Q ss_pred             HHHHHHhCC--Cc-cEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHH
Q psy17587         63 STIVDFKNG--KV-RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEI  137 (231)
Q Consensus        63 ~~~~~F~~g--~~-~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~  137 (231)
                      +.+++|.+-  -. -+|++|....-|+|+=..+-+|.||.-|++---.|.+-|+-|.|+...|+++-.-.+....+++
T Consensus       778 kLinqfN~e~~lsWlfllstrag~lGinLIsanr~~ifda~wnpchdaqavcRvyrYGQ~KpcfvYRlVmD~~lEkkI  855 (1387)
T KOG1016|consen  778 KLINQFNSEPGLSWLFLLSTRAGSLGINLISANRCIIFDACWNPCHDAQAVCRVYRYGQQKPCFVYRLVMDNSLEKKI  855 (1387)
T ss_pred             HHHHhccCCCCceeeeeehhccccccceeeccceEEEEEeecCccccchhhhhhhhhcCcCceeEEeehhhhhhHHHH
Confidence            999999853  22 4678999999999999889999999999998888988999999986566554433333333333

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=96.96  E-value=0.0028  Score=60.87  Aligned_cols=86  Identities=15%  Similarity=0.240  Sum_probs=68.1

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-cc
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-AA   83 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-~~   83 (231)
                      .++-.+.....+.+++|.++++  ..+.+.++.+..    .|+++..+||+++..+|...+....+|+.+|+|+|.. +.
T Consensus       299 a~~~il~~~~~g~q~lilaPT~--~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~  376 (681)
T PRK10917        299 AALAALAAIEAGYQAALMAPTE--ILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQ  376 (681)
T ss_pred             HHHHHHHHHHcCCeEEEEeccH--HHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhc
Confidence            3334444445567888889987  778888777654    3789999999999999999999999999999999975 44


Q ss_pred             cccCCCCCcEEEE
Q psy17587         84 RGLDVKHLNLVVN   96 (231)
Q Consensus        84 ~Gldip~v~~VI~   96 (231)
                      ..+.++++.+||.
T Consensus       377 ~~v~~~~l~lvVI  389 (681)
T PRK10917        377 DDVEFHNLGLVII  389 (681)
T ss_pred             ccchhcccceEEE
Confidence            4577888888775

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

Probab=96.70  E-value=0.0023  Score=61.66  Aligned_cols=123  Identities=22%  Similarity=0.229  Sum_probs=84.3

Q ss_pred             CCchhhhhcccc-ccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          4 GYPCLSLHGGID-QYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         4 ~~k~~~L~~~L~-~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ..|..++++.+. .+..++.++|-+.+.  +..+.+++.|.+.|++...+...-.  ++..-+-.+.-..-.|-|||+.+
T Consensus       412 ~~K~~Aiv~~I~~~~~~gqPvLvgT~si--e~SE~ls~~L~~~~i~h~VLNAk~h--~~EA~Iia~AG~~gaVTiATNMA  487 (822)
T COG0653         412 EEKFKAIVEDIKERHEKGQPVLVGTVSI--EKSELLSKLLRKAGIPHNVLNAKNH--AREAEIIAQAGQPGAVTIATNMA  487 (822)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEcCcce--ecchhHHHHHHhcCCCceeeccccH--HHHHHHHhhcCCCCccccccccc
Confidence            345556666664 444689999899987  7799999999999999988888766  33333333332234578999999


Q ss_pred             ccccCCCCCc-----------EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         83 ARGLDVKHLN-----------LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        83 ~~Gldip~v~-----------~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      +||-||.--.           +||--.--.+-.-=.|-.||+||.|-+|.+-.|++-.+
T Consensus       488 GRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQGDpG~S~F~lSleD  546 (822)
T COG0653         488 GRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLED  546 (822)
T ss_pred             cCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCCCcchhhhhhhhHH
Confidence            9999986222           23332222222222477799999999999877776544

>PRK05580 primosome assembly protein PriA; Validated

Probab=96.56  E-value=0.011  Score=56.88  Aligned_cols=77  Identities=19%  Similarity=0.273  Sum_probs=63.8

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH-CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEe
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK-AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY   97 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~-~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~   97 (231)
                      .+++++|.++++  ..+.++.+.|.. .|..+..+||+++..+|...+.+..+|+.+|+|+|..+.. +.++++.+||.-
T Consensus       189 ~g~~vLvLvPt~--~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-~p~~~l~liVvD  265 (679)
T PRK05580        189 QGKQALVLVPEI--ALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-LPFKNLGLIIVD  265 (679)
T ss_pred             cCCeEEEEeCcH--HHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-ccccCCCEEEEE
Confidence            467888899987  779999999976 3788999999999999999999999999999999975432 556678877754


Q ss_pred             c
Q psy17587         98 D   98 (231)
Q Consensus        98 d   98 (231)
                      +
T Consensus       266 E  266 (679)
T PRK05580        266 E  266 (679)
T ss_pred             C
Confidence            3

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=96.55  E-value=0.023  Score=54.81  Aligned_cols=79  Identities=18%  Similarity=0.243  Sum_probs=55.7

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCC-------CeeeccCCCCHHHHHHHHHHHhC----CCccEEEec--Ccccccc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGY-------PCLSLHGGIDQYDRDSTIVDFKN----GKVRLLIAT--SVAARGL   86 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~-------~~~~lhg~~~~~~R~~~~~~F~~----g~~~vLvaT--~~~~~Gl   86 (231)
                      .+.++||.++.  ...+.+.+.+...+.       ..++.-+. ...++..++++|+.    |.-.||+|+  ..+++||
T Consensus       522 pgg~lvfFpSy--~~l~~v~~~~~~~~~~~~i~~~k~i~~E~~-~~~~~~~~l~~f~~~~~~~~gavL~av~gGk~sEGI  598 (705)
T TIGR00604       522 PDGIVVFFPSY--SYLENIVSTWKEMGILENIEKKKLIFVETK-DAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGI  598 (705)
T ss_pred             CCcEEEEccCH--HHHHHHHHHHHhcCHHHHHhcCCCEEEeCC-CcchHHHHHHHHHHHHhcCCceEEEEecCCcccCcc
Confidence            35666688887  668888887765321       22222221 22578889999964    455699998  8899999


Q ss_pred             CCCC--CcEEEEecCCC
Q psy17587         87 DVKH--LNLVVNYDCPN  101 (231)
Q Consensus        87 dip~--v~~VI~~d~P~  101 (231)
                      |+++  ++.||...+|.
T Consensus       599 Df~~~~~r~ViivGlPf  615 (705)
T TIGR00604       599 DFCDDLGRAVIMVGIPY  615 (705)
T ss_pred             ccCCCCCcEEEEEccCC
Confidence            9995  67888888875

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).

>TIGR00595 priA primosomal protein N'

Probab=96.46  E-value=0.014  Score=54.13  Aligned_cols=76  Identities=20%  Similarity=0.282  Sum_probs=62.8

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEe
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY   97 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~   97 (231)
                      .+++++|.+++.  ..+.++.+.|+.. +..+..+||+++..+|...+.+..+|+.+|+|+|..+.- ..++++.+||.-
T Consensus        24 ~g~~vLvlvP~i--~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIVD  100 (505)
T TIGR00595        24 LGKSVLVLVPEI--ALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIVD  100 (505)
T ss_pred             cCCeEEEEeCcH--HHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEEE
Confidence            467788889987  7789999998754 778999999999999999999999999999999976432 456677877753

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).

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=96.37  E-value=0.0094  Score=56.77  Aligned_cols=86  Identities=15%  Similarity=0.233  Sum_probs=67.4

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc-
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA-   83 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~-   83 (231)
                      .++-.+.....+.++++.++++  ..+.++++.+.+    .|+++..+||+++..+|...++...+|+.+|+|+|...- 
T Consensus       273 a~l~il~~~~~g~qvlilaPT~--~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~  350 (630)
T TIGR00643       273 AALAMLAAIEAGYQVALMAPTE--ILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQ  350 (630)
T ss_pred             HHHHHHHHHHcCCcEEEECCHH--HHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHh
Confidence            3344444445567788889977  778888877654    379999999999999999999999999999999998644 


Q ss_pred             cccCCCCCcEEEE
Q psy17587         84 RGLDVKHLNLVVN   96 (231)
Q Consensus        84 ~Gldip~v~~VI~   96 (231)
                      ..+++.++.+||.
T Consensus       351 ~~~~~~~l~lvVI  363 (630)
T TIGR00643       351 EKVEFKRLALVII  363 (630)
T ss_pred             ccccccccceEEE
Confidence            3567778887775

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

Probab=96.17  E-value=0.12  Score=49.30  Aligned_cols=78  Identities=21%  Similarity=0.109  Sum_probs=55.4

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhC----CCccEEEecCccccccCC------
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKN----GKVRLLIATSVAARGLDV------   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~----g~~~vLvaT~~~~~Gldi------   88 (231)
                      .++..|.|++-   ..++.+++.|...---...+.|..+  .+...+++|++    |.-.||++|+.+-+|+|+      
T Consensus       470 ~G~~lvLfTS~---~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~  544 (636)
T TIGR03117       470 QGGTLVLTTAF---SHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVS  544 (636)
T ss_pred             CCCEEEEechH---HHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCC
Confidence            35666656653   4688888888543112346666543  34668888887    478999999999999999      


Q ss_pred             --C--CCcEEEEecCCC
Q psy17587         89 --K--HLNLVVNYDCPN  101 (231)
Q Consensus        89 --p--~v~~VI~~d~P~  101 (231)
                        |  .++.||..-+|.
T Consensus       545 p~~G~~Ls~ViI~kLPF  561 (636)
T TIGR03117       545 PDKDNLLTDLIITCAPF  561 (636)
T ss_pred             CCCCCcccEEEEEeCCC
Confidence              2  577898877773

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.

>KOG0701|consensus

Probab=96.00  E-value=0.0046  Score=63.39  Aligned_cols=92  Identities=29%  Similarity=0.438  Sum_probs=70.8

Q ss_pred             EEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHH-----------HHHHHHHHHhCCCccEEEecCccccccCCCCC
Q psy17587         24 VDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQY-----------DRDSTIVDFKNGKVRLLIATSVAARGLDVKHL   91 (231)
Q Consensus        24 iiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~-----------~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v   91 (231)
                      +|||+..  ..+..+.+.++.. -..+..+.|.+.+.           .+..++..|+...+++|++|.++.+|+|+|.+
T Consensus       296 i~~~~~~--~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~  373 (1606)
T KOG0701|consen  296 IIFVDQR--YTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKC  373 (1606)
T ss_pred             eeecccc--hHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhh
Confidence            4488765  4466666666543 12333455543221           25678888999999999999999999999999


Q ss_pred             cEEEEecCCCCHhHHHHHhcccCCCC
Q psy17587         92 NLVVNYDCPNHYEDYVHRCGRTGRAG  117 (231)
Q Consensus        92 ~~VI~~d~P~~~~~y~qr~GR~gR~g  117 (231)
                      +.|+.++.|....+|+|..||+-...
T Consensus       374 ~~~~~~~~~~~~~~~vq~~~r~~~~~  399 (1606)
T KOG0701|consen  374 NLVVLFDAPTYYRSYVQKKGRARAAD  399 (1606)
T ss_pred             hhheeccCcchHHHHHHhhcccccch
Confidence            99999999999999999999987654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.91  E-value=0.021  Score=56.56  Aligned_cols=77  Identities=14%  Similarity=0.167  Sum_probs=63.6

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-cccccCCCCCc
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-AARGLDVKHLN   92 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-~~~Gldip~v~   92 (231)
                      ..+.+++|.+++.  ..+.+.++.+..    .++++..++|..+..++.+.++.+++|+++|+|+|.. +...+.+.++.
T Consensus       498 ~~g~qvlvLvPT~--~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~  575 (926)
T TIGR00580       498 LDGKQVAVLVPTT--LLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLG  575 (926)
T ss_pred             HhCCeEEEEeCcH--HHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCC
Confidence            3457888899987  789988887764    3678889999999999999999999999999999984 44557788888


Q ss_pred             EEEE
Q psy17587         93 LVVN   96 (231)
Q Consensus        93 ~VI~   96 (231)
                      +||.
T Consensus       576 llVI  579 (926)
T TIGR00580       576 LLII  579 (926)
T ss_pred             EEEe
Confidence            8775

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.

>KOG1001|consensus

Probab=95.80  E-value=0.0035  Score=59.80  Aligned_cols=116  Identities=16%  Similarity=0.120  Sum_probs=93.9

Q ss_pred             CchhhhhccccccCC-C-CeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccE-EEecC
Q psy17587          5 YPCLSLHGGIDQYDR-D-STIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRL-LIATS   80 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~-~-~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~v-LvaT~   80 (231)
                      +|+..+...|..... . .++|||+.-.  ...+.+.-.|...++....+-|.|+...|.+.+..|..+ ...| +++.-
T Consensus       522 ~ki~~~~~~l~~~~~s~~~kiiifsq~~--~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slk  599 (674)
T KOG1001|consen  522 SKIYAFLKILQAKEMSEQPKIVIFSQLI--WGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLK  599 (674)
T ss_pred             hhhHHHHHHHhhccCCCCCceeeehhHH--HHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHH
Confidence            344444444432222 2 3899999954  778888888888899999999999999999999999854 3444 57889


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeE
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFA  122 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~  122 (231)
                      +.+.|+|+...++|+..|+-|++..--|.+-|+.|-|+.-.+
T Consensus       600 ag~~glnlt~a~~v~~~d~~wnp~~eeQaidR~hrigq~k~v  641 (674)
T KOG1001|consen  600 AGKVGLNLTAASHVLLMDPWWNPAVEEQAIDRAHRIGQTKPV  641 (674)
T ss_pred             HhhhhhchhhhhHHHhhchhcChHHHHHHHHHHHHhccccee
Confidence            999999999999999999999999999999999999976444

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

Probab=95.68  E-value=0.029  Score=55.14  Aligned_cols=61  Identities=20%  Similarity=0.297  Sum_probs=46.3

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----C-CCeee-ccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----G-YPCLS-LHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~-~~~~~-lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ++++.+..++.  ..+.+.++.|.+.    + ..+.. +||.|+.+++..++++|.+|+.+|||+|+.+
T Consensus       125 gkr~yii~PT~--~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~F  191 (1187)
T COG1110         125 GKRVYIIVPTT--TLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQF  191 (1187)
T ss_pred             CCeEEEEecCH--HHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHH
Confidence            45566566655  5577777776543    3 43333 9999999999999999999999999999764

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases

Probab=95.46  E-value=0.094  Score=43.89  Aligned_cols=100  Identities=15%  Similarity=0.270  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCC----ccEEEecCccccccCCCCCcEEEEecCCCCHhHHHH
Q psy17587         33 LLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGK----VRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVH  108 (231)
Q Consensus        33 ~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~----~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~q  108 (231)
                      +..+.|.+.+.. ++.+..++++.+...     -+|.++.    ..|+|.=+.++||+.+++..+....--|.+.+++.|
T Consensus        98 ei~~~l~~~~~~-~~~v~~vNS~~~~~~-----ldy~~~~~~~~~~I~VGGn~LsRGlTleGL~vsYf~R~s~~~DTL~Q  171 (239)
T PF10593_consen   98 EIKPELPKAISD-GIEVVVVNSGSSDDS-----LDYDDGENLGLNVIAVGGNKLSRGLTLEGLTVSYFLRNSKQYDTLMQ  171 (239)
T ss_pred             HHHHHHHHHHhc-CceEEEEeCCCcccc-----ccccccccCCceEEEECCccccCceeECCcEEEEecCCCchHHHHHH
Confidence            334555555554 799999998766543     4555554    789999999999999999988888888889999999


Q ss_pred             HhcccC-CCCCceeEEEEecccchHHHHHHH
Q psy17587        109 RCGRTG-RAGNKGFAYTFITLEQERHAGEII  138 (231)
Q Consensus       109 r~GR~g-R~g~~g~~i~~~~~~~~~~~~~~~  138 (231)
                      |.-..| |.|....|=++.++.-...+..+.
T Consensus       172 mgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~  202 (239)
T PF10593_consen  172 MGRWFGYRPGYEDLCRIYMPEELYDWFRHIA  202 (239)
T ss_pred             HhhcccCCcccccceEEecCHHHHHHHHHHH
Confidence            887777 777788888887766555444443

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

>PRK14873 primosome assembly protein PriA; Provisional

Probab=95.23  E-value=0.051  Score=52.03  Aligned_cols=90  Identities=19%  Similarity=0.146  Sum_probs=67.2

Q ss_pred             chhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHC-C-CCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          6 PCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKA-G-YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         6 k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~-~-~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      |....+.++.+. ..++.+||.++..  ..+.++.+.|... | ..+..+|+++++.+|.+++.+..+|+.+|+|.|-.+
T Consensus       173 KTevyl~~i~~~l~~Gk~vLvLvPEi--~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSA  250 (665)
T PRK14873        173 WARRLAAAAAATLRAGRGALVVVPDQ--RDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSA  250 (665)
T ss_pred             HHHHHHHHHHHHHHcCCeEEEEecch--hhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEccee
Confidence            344444455333 2477888899987  6789999999754 4 679999999999999999999999999999999763


Q ss_pred             ccccCCCCCcEEEEec
Q psy17587         83 ARGLDVKHLNLVVNYD   98 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d   98 (231)
                      . =..+++...||..+
T Consensus       251 v-FaP~~~LgLIIvdE  265 (665)
T PRK14873        251 V-FAPVEDLGLVAIWD  265 (665)
T ss_pred             E-EeccCCCCEEEEEc
Confidence            2 23344666666533

>KOG0921|consensus

Probab=95.16  E-value=0.029  Score=54.45  Aligned_cols=117  Identities=18%  Similarity=0.355  Sum_probs=88.6

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-------CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-------GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      .+|+..+....-.+.|++|.+.=  ..+-.|..+|...       .+.+...|+.++..+..++.+....|..+++++|.
T Consensus       631 Eal~~~i~s~~i~gailvflpgw--a~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv~kii~stn  708 (1282)
T KOG0921|consen  631 EALLNDIASRNIDGAVLVFLPGW--AEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGVTKIILSTN  708 (1282)
T ss_pred             HHHHhhhcccCCccceeeecCch--HHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccccccccccc
Confidence            34445555555578888898775  4466666666432       47788999999999999999999999999999999


Q ss_pred             ccccccCCCCCcEEEEecC------------------CCCHhHHHHHhcccCCCCCceeEEEEec
Q psy17587         81 VAARGLDVKHLNLVVNYDC------------------PNHYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~------------------P~~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                      ++.-.+.+.++.+||..+.                  -.+..+..||-||+||. ++|.|..+.+
T Consensus       709 iaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grv-R~G~~f~lcs  772 (1282)
T KOG0921|consen  709 IAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRV-RPGFCFHLCS  772 (1282)
T ss_pred             eeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCcee-cccccccccH
Confidence            9999999998777775332                  22456679999999985 4678877664

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

Probab=94.98  E-value=0.041  Score=52.97  Aligned_cols=88  Identities=18%  Similarity=0.202  Sum_probs=67.3

Q ss_pred             chhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          6 PCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         6 k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      |....++.+.+.- .++.+||-++.+  ....++.+.+... |.++..+|+++++.+|..+..+.++|+.+|+|.|-.+ 
T Consensus       230 KTEvYl~~i~~~L~~GkqvLvLVPEI--~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSA-  306 (730)
T COG1198         230 KTEVYLEAIAKVLAQGKQVLVLVPEI--ALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSA-  306 (730)
T ss_pred             HHHHHHHHHHHHHHcCCEEEEEeccc--cchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCceEEEEechh-
Confidence            4555566664433 467888889987  6688888888644 8899999999999999999999999999999998753 


Q ss_pred             cccCCCCCcEEEE
Q psy17587         84 RGLDVKHLNLVVN   96 (231)
Q Consensus        84 ~Gldip~v~~VI~   96 (231)
                      -=..+++...||.
T Consensus       307 lF~Pf~~LGLIIv  319 (730)
T COG1198         307 LFLPFKNLGLIIV  319 (730)
T ss_pred             hcCchhhccEEEE
Confidence            1233446666664

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

Probab=94.95  E-value=0.081  Score=50.04  Aligned_cols=92  Identities=13%  Similarity=0.184  Sum_probs=72.7

Q ss_pred             CchhhhhccccccCCCCeEEEEcCCh--hHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGK--VRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-   81 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~--~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-   81 (231)
                      -.+.+++..+.....+..+.+-+++.  -+++.+.+.+.|...|+.+..+.|.+....|.+++++..+|+++++|.|-+ 
T Consensus       296 KTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHAL  375 (677)
T COG1200         296 KTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHAL  375 (677)
T ss_pred             HHHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchh
Confidence            34566777777777777777688874  113445555666677999999999999999999999999999999999986 


Q ss_pred             cccccCCCCCcEEEE
Q psy17587         82 AARGLDVKHLNLVVN   96 (231)
Q Consensus        82 ~~~Gldip~v~~VI~   96 (231)
                      +-..+++.+.-+||.
T Consensus       376 iQd~V~F~~LgLVIi  390 (677)
T COG1200         376 IQDKVEFHNLGLVII  390 (677)
T ss_pred             hhcceeecceeEEEE
Confidence            566788888887765

>cd00268 DEADc DEAD-box helicases

Probab=94.77  E-value=0.17  Score=40.46  Aligned_cols=81  Identities=14%  Similarity=0.142  Sum_probs=53.7

Q ss_pred             hhcccccc--CCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc--
Q psy17587         10 LHGGIDQY--DRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV--   81 (231)
Q Consensus        10 L~~~L~~~--~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~--   81 (231)
                      ++..+...  ..+.++||.|++.  ..+.+..+.+...    ++.+..++|+.+..+......    +...|+|+|.-  
T Consensus        57 ~l~~~~~~~~~~~~~viii~p~~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~iiv~T~~~l  130 (203)
T cd00268          57 ILEKLDPSPKKDGPQALILAPTR--ELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLK----RGPHIVVATPGRL  130 (203)
T ss_pred             HHHHHHhhcccCCceEEEEcCCH--HHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhc----CCCCEEEEChHHH
Confidence            33444443  3456788889987  6688777766543    678889999998766554333    67889999952  


Q ss_pred             ---c-ccccCCCCCcEEEE
Q psy17587         82 ---A-ARGLDVKHLNLVVN   96 (231)
Q Consensus        82 ---~-~~Gldip~v~~VI~   96 (231)
                         + ..-.++++++++|.
T Consensus       131 ~~~l~~~~~~~~~l~~lIv  149 (203)
T cd00268         131 LDLLERGKLDLSKVKYLVL  149 (203)
T ss_pred             HHHHHcCCCChhhCCEEEE
Confidence               2 22256667777664

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.

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=94.70  E-value=0.12  Score=49.98  Aligned_cols=98  Identities=14%  Similarity=0.093  Sum_probs=71.3

Q ss_pred             cccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCc
Q psy17587         13 GIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLN   92 (231)
Q Consensus        13 ~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~   92 (231)
                      ++.....++.|-|||++.  ..++.+++.....+.++..++|.-+..+.    +.  =++.+|++=|+++..|+++.+..
T Consensus       275 L~~~L~~gknIcvfsSt~--~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~--W~~~~VviYT~~itvG~Sf~~~H  346 (824)
T PF02399_consen  275 LLARLNAGKNICVFSSTV--SFAEIVARFCARFTKKVLVLNSTDKLEDV----ES--WKKYDVVIYTPVITVGLSFEEKH  346 (824)
T ss_pred             HHHHHhCCCcEEEEeChH--HHHHHHHHHHHhcCCeEEEEcCCCCcccc----cc--ccceeEEEEeceEEEEeccchhh
Confidence            345666788999999987  66888888888888899999887665522    22  35689999999999999997543


Q ss_pred             --EEEEe--cCC--CCHhHHHHHhcccCCCCC
Q psy17587         93 --LVVNY--DCP--NHYEDYVHRCGRTGRAGN  118 (231)
Q Consensus        93 --~VI~~--d~P--~~~~~y~qr~GR~gR~g~  118 (231)
                        -|.-|  ...  .+..+..|++||+-....
T Consensus       347 F~~~f~yvk~~~~gpd~~s~~Q~lgRvR~l~~  378 (824)
T PF02399_consen  347 FDSMFAYVKPMSYGPDMVSVYQMLGRVRSLLD  378 (824)
T ss_pred             ceEEEEEecCCCCCCcHHHHHHHHHHHHhhcc
Confidence              34333  222  245568999999865443

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

>KOG1513|consensus

Probab=94.69  E-value=0.057  Score=51.94  Aligned_cols=77  Identities=22%  Similarity=0.371  Sum_probs=58.8

Q ss_pred             HHHhCCCccEEEecCccccccCCCCCcEEE--------EecCCCCHhHHHHHhcccCCCCC-ceeEEEEecc---cchHH
Q psy17587         66 VDFKNGKVRLLIATSVAARGLDVKHLNLVV--------NYDCPNHYEDYVHRCGRTGRAGN-KGFAYTFITL---EQERH  133 (231)
Q Consensus        66 ~~F~~g~~~vLvaT~~~~~Gldip~v~~VI--------~~d~P~~~~~y~qr~GR~gR~g~-~g~~i~~~~~---~~~~~  133 (231)
                      ++|..|+..|-|-+.+++-||-++.=+-|+        -..+||+.+.-+|..||+.|.++ .+.-++|+..   ++..+
T Consensus       851 qrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPWSADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErRF  930 (1300)
T KOG1513|consen  851 QRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPWSADRAIQQFGRTHRSNQVSAPEYVFLISELAGERRF  930 (1300)
T ss_pred             hhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCcchhHHHHHhcccccccccCCCeEEEEehhhccchHH
Confidence            569999999999999999999998544444        47899999999999999999987 4555666643   35555


Q ss_pred             HHHHHHHHH
Q psy17587        134 AGEIIRALE  142 (231)
Q Consensus       134 ~~~~~~~l~  142 (231)
                      ...+.+.|+
T Consensus       931 AS~VAKRLE  939 (1300)
T KOG1513|consen  931 ASIVAKRLE  939 (1300)
T ss_pred             HHHHHHHHH
Confidence            554555544

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.66  E-value=0.1  Score=52.99  Aligned_cols=76  Identities=14%  Similarity=0.133  Sum_probs=61.7

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-cccccCCCCCcE
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-AARGLDVKHLNL   93 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-~~~Gldip~v~~   93 (231)
                      .+.+++|.|+++  ..+.++++.+..    .++.+..++|+.+..++..+++..++|.++|+|+|.- +...+.+.++.+
T Consensus       648 ~g~qvlvLvPT~--eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~l  725 (1147)
T PRK10689        648 NHKQVAVLVPTT--LLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGL  725 (1147)
T ss_pred             cCCeEEEEeCcH--HHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCE
Confidence            467788899987  788888888764    2567888999999999999999999999999999974 444566778887


Q ss_pred             EEE
Q psy17587         94 VVN   96 (231)
Q Consensus        94 VI~   96 (231)
                      +|.
T Consensus       726 LVI  728 (1147)
T PRK10689        726 LIV  728 (1147)
T ss_pred             EEE
Confidence            764

>PRK14873 primosome assembly protein PriA; Provisional

Probab=94.25  E-value=0.37  Score=46.31  Aligned_cols=80  Identities=15%  Similarity=0.196  Sum_probs=52.4

Q ss_pred             HHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC----ccccccCCCCCcEEEEecC------CC--
Q psy17587         36 CAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS----VAARGLDVKHLNLVVNYDC------PN--  101 (231)
Q Consensus        36 ~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~----~~~~Gldip~v~~VI~~d~------P~--  101 (231)
                      +.+.+.|.+.  +.++..+.+       +.+++.|. ++.+|||+|.    +++     +++..|+..|.      |.  
T Consensus       441 er~eeeL~~~FP~~~V~r~d~-------d~~l~~~~-~~~~IlVGTqgaepm~~-----g~~~lV~ildaD~~L~~pDfR  507 (665)
T PRK14873        441 RRTAEELGRAFPGVPVVTSGG-------DQVVDTVD-AGPALVVATPGAEPRVE-----GGYGAALLLDAWALLGRQDLR  507 (665)
T ss_pred             HHHHHHHHHHCCCCCEEEECh-------HHHHHhhc-cCCCEEEECCCCccccc-----CCceEEEEEcchhhhcCCCcC
Confidence            4444444332  455554432       35788996 5999999998    555     35676665543      32  


Q ss_pred             ----CHhHHHHHhcccCCCCCceeEEEEecc
Q psy17587        102 ----HYEDYVHRCGRTGRAGNKGFAYTFITL  128 (231)
Q Consensus       102 ----~~~~y~qr~GR~gR~g~~g~~i~~~~~  128 (231)
                          ...-+.|-.||+||....|.+++...+
T Consensus       508 A~Er~~qll~qvagragr~~~~G~V~iq~~p  538 (665)
T PRK14873        508 AAEDTLRRWMAAAALVRPRADGGQVVVVAES  538 (665)
T ss_pred             hHHHHHHHHHHHHHhhcCCCCCCEEEEEeCC
Confidence                245567888999999889999887533

>PRK14701 reverse gyrase; Provisional

Probab=94.06  E-value=0.17  Score=53.07  Aligned_cols=61  Identities=15%  Similarity=0.246  Sum_probs=52.1

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH------CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK------AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~------~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      .+.+++|.++++  ..+.++.+.|..      .+..+..+||+++..++...++.+++|+.+|||+|+-
T Consensus       121 ~g~~aLVl~PTr--eLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        121 KGKKCYIILPTT--LLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             cCCeEEEEECHH--HHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            356788899977  788988888875      2467789999999999999999999999999999985

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

Probab=93.78  E-value=0.25  Score=46.04  Aligned_cols=68  Identities=26%  Similarity=0.403  Sum_probs=54.0

Q ss_pred             EEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----ccccc-cCCCCC
Q psy17587         23 IVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAARG-LDVKHL   91 (231)
Q Consensus        23 iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~~G-ldip~v   91 (231)
                      .+|.++++  +.+.++++.+...     ++.+.+++||++...+...   ++.| .+|+|+|+     .+.++ +++..+
T Consensus       102 aLil~PTR--ELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~---l~~~-~~ivVaTPGRllD~i~~~~l~l~~v  175 (513)
T COG0513         102 ALILAPTR--ELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEA---LKRG-VDIVVATPGRLLDLIKRGKLDLSGV  175 (513)
T ss_pred             eEEECCCH--HHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHH---HhcC-CCEEEECccHHHHHHHcCCcchhhc
Confidence            78899987  8899999887532     5778999999998776644   4446 99999997     56666 888888


Q ss_pred             cEEEE
Q psy17587         92 NLVVN   96 (231)
Q Consensus        92 ~~VI~   96 (231)
                      .++|.
T Consensus       176 ~~lVl  180 (513)
T COG0513         176 ETLVL  180 (513)
T ss_pred             CEEEe
Confidence            88775

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=93.53  E-value=0.29  Score=46.70  Aligned_cols=72  Identities=18%  Similarity=0.278  Sum_probs=51.3

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH-----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----ccccc-cC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK-----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAARG-LD   87 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~-----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~~G-ld   87 (231)
                      ...++||.|+++  +.+.++++.+..     .++.+..+||+.+...+...+    .....|+|+|+     .+.++ ++
T Consensus        73 ~~~~~LIL~PTr--eLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l----~~~~~IVVgTPgrl~d~l~r~~l~  146 (629)
T PRK11634         73 KAPQILVLAPTR--ELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL----RQGPQIVVGTPGRLLDHLKRGTLD  146 (629)
T ss_pred             CCCeEEEEeCcH--HHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh----cCCCCEEEECHHHHHHHHHcCCcc
Confidence            345788899987  788888877653     278899999998876554433    24578999995     33333 67


Q ss_pred             CCCCcEEEE
Q psy17587         88 VKHLNLVVN   96 (231)
Q Consensus        88 ip~v~~VI~   96 (231)
                      +.++.+||.
T Consensus       147 l~~l~~lVl  155 (629)
T PRK11634        147 LSKLSGLVL  155 (629)
T ss_pred             hhhceEEEe
Confidence            778887764

>KOG0951|consensus

Probab=93.46  E-value=0.49  Score=47.96  Aligned_cols=112  Identities=13%  Similarity=0.162  Sum_probs=78.3

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----------------------CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----------------------AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLI   77 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----------------------~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLv   77 (231)
                      .+..++|++++  ..+..++..|..                      ...+...=|-+|+..+..-+-.-|..|.+.|+|
T Consensus      1359 ~k~~~vf~p~r--k~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v 1436 (1674)
T KOG0951|consen 1359 RKPAIVFLPTR--KHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCV 1436 (1674)
T ss_pred             CCCeEEEeccc--hhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEE
Confidence            46667799876  567666554321                      123333338899999999888899999999998


Q ss_pred             ecCccccccCCCCCcEEEE----ec------CCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHH
Q psy17587         78 ATSVAARGLDVKHLNLVVN----YD------CPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEI  137 (231)
Q Consensus        78 aT~~~~~Gldip~v~~VI~----~d------~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~  137 (231)
                      ...- ..|+-...--+|+.    ||      .+.+.....|++|+|.|   .|.|+++........++++
T Consensus      1437 ~s~~-~~~~~~~~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~---~~k~vi~~~~~~k~yykkf 1502 (1674)
T KOG0951|consen 1437 MSRD-CYGTKLKAHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG---AGKCVIMCHTPKKEYYKKF 1502 (1674)
T ss_pred             EEcc-cccccccceEEEEecceeecccccccccCchhHHHHHhhhhcC---CccEEEEecCchHHHHHHh
Confidence            8766 77776654333332    44      34458899999999988   5678888887776654443

>KOG0339|consensus

Probab=93.31  E-value=1.2  Score=41.24  Aligned_cols=71  Identities=14%  Similarity=0.259  Sum_probs=51.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHH---HH-HHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC------ccccccCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVK---EL-MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS------VAARGLDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~---~L-~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~------~~~~Gldip   89 (231)
                      +.-.||.|+++  +.+-++..   .| ...|+.++++|||++.-++.+.++    -...++|||+      +--.++|+.
T Consensus       296 gPi~vilvPTr--ela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~  369 (731)
T KOG0339|consen  296 GPIGVILVPTR--ELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLS  369 (731)
T ss_pred             CCeEEEEeccH--HHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccce
Confidence            34556668876  55665554   45 445899999999999988877766    3568999997      344678888


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      .|++.|.
T Consensus       370 rvS~LV~  376 (731)
T KOG0339|consen  370 RVSYLVL  376 (731)
T ss_pred             eeeEEEE
Confidence            8887664

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=93.30  E-value=0.32  Score=44.43  Aligned_cols=71  Identities=18%  Similarity=0.229  Sum_probs=52.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----ccc-cccCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAA-RGLDV   88 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~-~Gldi   88 (231)
                      ..+++|.|+++  +.+.++++.+...     ++.+..++|+.+...+...+.    ...+|+|+|+     .+. ..+++
T Consensus        72 ~~~~lil~Ptr--eLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~----~~~~IvV~Tp~rl~~~l~~~~~~l  145 (460)
T PRK11776         72 RVQALVLCPTR--ELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE----HGAHIIVGTPGRILDHLRKGTLDL  145 (460)
T ss_pred             CceEEEEeCCH--HHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc----CCCCEEEEChHHHHHHHHcCCccH
Confidence            34678899987  8899988877642     678899999998766544333    5689999995     333 34778


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      .++++||.
T Consensus       146 ~~l~~lVi  153 (460)
T PRK11776        146 DALNTLVL  153 (460)
T ss_pred             HHCCEEEE
Confidence            88888875

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=92.68  E-value=0.68  Score=41.87  Aligned_cols=71  Identities=10%  Similarity=0.224  Sum_probs=51.7

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------cccccCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------AARGLDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~~~Gldip   89 (231)
                      ..+++|.++++  +.+.++.+.+..    .++++..++|+.+...+...+    .+..+|+|+|+-      ....+++.
T Consensus        73 ~~~~lil~Pt~--eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l----~~~~~IlV~Tp~rl~~~~~~~~~~~~  146 (434)
T PRK11192         73 PPRILILTPTR--ELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF----SENQDIVVATPGRLLQYIKEENFDCR  146 (434)
T ss_pred             CceEEEECCcH--HHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHh----cCCCCEEEEChHHHHHHHHcCCcCcc
Confidence            46788899987  778887776543    478899999999877654433    356789999972      22456778


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      ++++||.
T Consensus       147 ~v~~lVi  153 (434)
T PRK11192        147 AVETLIL  153 (434)
T ss_pred             cCCEEEE
Confidence            8888775

>TIGR01054 rgy reverse gyrase

Probab=92.60  E-value=0.37  Score=49.26  Aligned_cols=60  Identities=17%  Similarity=0.261  Sum_probs=49.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCe---eeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPC---LSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~---~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      +.+++|.++++  +.+.++++.+...    ++.+   ..+||+++..++...++.+.+|..+|+|+|+-
T Consensus       121 g~~vLIL~PTr--eLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~  187 (1171)
T TIGR01054       121 GKRCYIILPTT--LLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTM  187 (1171)
T ss_pred             CCeEEEEeCHH--HHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            57788899987  8889888887643    4443   36899999999999999999999999999974

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=91.86  E-value=0.66  Score=42.60  Aligned_cols=60  Identities=23%  Similarity=0.319  Sum_probs=52.9

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      ....||.++.+  +.+......|...|+++..++|+.+..++..++.....|..+++++|+-
T Consensus        51 ~~~~lVi~P~~--~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe  110 (470)
T TIGR00614        51 DGITLVISPLI--SLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPE  110 (470)
T ss_pred             CCcEEEEecHH--HHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHH
Confidence            45667789976  7788888889999999999999999999999999999999999999974

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

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=91.21  E-value=0.95  Score=42.83  Aligned_cols=60  Identities=18%  Similarity=0.188  Sum_probs=51.5

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      .+.+||.++.+  ..+......|...|+.+..+||+++..++..++.....|..++++.|+-
T Consensus        53 ~g~~lVisPl~--sL~~dq~~~l~~~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe  112 (591)
T TIGR01389        53 KGLTVVISPLI--SLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPE  112 (591)
T ss_pred             CCcEEEEcCCH--HHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChh
Confidence            34566678876  6788888888889999999999999999999999999999999998854

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.

>KOG0331|consensus

Probab=90.40  E-value=1.9  Score=39.98  Aligned_cols=91  Identities=14%  Similarity=0.196  Sum_probs=67.1

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----ccccc-cCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAARG-LDV   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~~G-ldi   88 (231)
                      ...+++|-++++  +.+.++.+.....    ++++.|++||.+...+...+++    .++|+|+|+     .+..| +|+
T Consensus       164 ~~P~vLVL~PTR--ELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~----gvdiviaTPGRl~d~le~g~~~l  237 (519)
T KOG0331|consen  164 DGPIVLVLAPTR--ELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLER----GVDVVIATPGRLIDLLEEGSLNL  237 (519)
T ss_pred             CCCeEEEEcCcH--HHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhc----CCcEEEeCChHHHHHHHcCCccc
Confidence            367899999987  8899988887654    4668899999987766554432    478999995     56666 788


Q ss_pred             CCCcEEEE--------ecCCCCHhHHHHHhcccCC
Q psy17587         89 KHLNLVVN--------YDCPNHYEDYVHRCGRTGR  115 (231)
Q Consensus        89 p~v~~VI~--------~d~P~~~~~y~qr~GR~gR  115 (231)
                      ..|.++|.        .++-..+...++++++..|
T Consensus       238 ~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  238 SRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             cceeEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            88888875        3344456777777777666

>KOG2340|consensus

Probab=90.27  E-value=1.4  Score=40.86  Aligned_cols=113  Identities=17%  Similarity=0.132  Sum_probs=81.3

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc--cccccCCCCCcEEEEe
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV--AARGLDVKHLNLVVNY   97 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~--~~~Gldip~v~~VI~~   97 (231)
                      .+.++|+.++.+.  --.+-+++.+.+++...+|---+...-.++-.-|-.|...||+-|.=  .=+--++.+|..||.|
T Consensus       552 ~s~~LiyIPSYfD--FVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLyTER~hffrR~~ikGVk~vVfY  629 (698)
T KOG2340|consen  552 ESGILIYIPSYFD--FVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLYTERAHFFRRYHIKGVKNVVFY  629 (698)
T ss_pred             cCceEEEecchhh--HHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEEehhhhhhhhheecceeeEEEe
Confidence            4677889998733  55667788777777777776555666666777799999999999874  4567788999999999


Q ss_pred             cCCCCHhHH---HHHhcccCCCCC----ceeEEEEecccchHHH
Q psy17587         98 DCPNHYEDY---VHRCGRTGRAGN----KGFAYTFITLEQERHA  134 (231)
Q Consensus        98 d~P~~~~~y---~qr~GR~gR~g~----~g~~i~~~~~~~~~~~  134 (231)
                      .+|.+|.-|   +.+.+|+.-.|+    .-.|.++++.-|.-.+
T Consensus       630 qpP~~P~FYsEiinm~~k~~~~gn~d~d~~t~~ilytKyD~i~L  673 (698)
T KOG2340|consen  630 QPPNNPHFYSEIINMSDKTTSQGNTDLDIFTVRILYTKYDRIRL  673 (698)
T ss_pred             cCCCCcHHHHHHHhhhhhhhccCCccccceEEEEEeechhhHHH
Confidence            999997766   445566654332    3456667776665433

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=90.17  E-value=1.5  Score=40.02  Aligned_cols=70  Identities=16%  Similarity=0.248  Sum_probs=51.0

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC------ccccccCCCC
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS------VAARGLDVKH   90 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~------~~~~Gldip~   90 (231)
                      .++||.|+++  +.+.++.+.+...    ++.+..++|+.+.......   + .+..+|+|||+      .....+++..
T Consensus        76 ~~aLil~Ptr--eLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~---l-~~~~~IiV~TP~rL~~~~~~~~~~l~~  149 (456)
T PRK10590         76 VRALILTPTR--ELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK---L-RGGVDVLVATPGRLLDLEHQNAVKLDQ  149 (456)
T ss_pred             ceEEEEeCcH--HHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHH---H-cCCCcEEEEChHHHHHHHHcCCccccc
Confidence            3688899987  7888888877643    6778889999886654322   2 36789999996      2344567888


Q ss_pred             CcEEEE
Q psy17587         91 LNLVVN   96 (231)
Q Consensus        91 v~~VI~   96 (231)
                      ++++|.
T Consensus       150 v~~lVi  155 (456)
T PRK10590        150 VEILVL  155 (456)
T ss_pred             ceEEEe
Confidence            888775

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=89.90  E-value=0.59  Score=32.34  Aligned_cols=41  Identities=20%  Similarity=0.333  Sum_probs=32.5

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      .....++.+|+||++-  ..+...+..|+..|+++..+.||++
T Consensus        46 ~~~~~~~~vvl~c~~g--~~a~~~a~~L~~~G~~v~~l~GG~~   86 (90)
T cd01524          46 NELPKDKEIIVYCAVG--LRGYIAARILTQNGFKVKNLDGGYK   86 (90)
T ss_pred             HhcCCCCcEEEEcCCC--hhHHHHHHHHHHCCCCEEEecCCHH
Confidence            3345678899999875  3477788899999999999999975

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=88.76  E-value=1.4  Score=41.71  Aligned_cols=71  Identities=20%  Similarity=0.258  Sum_probs=51.5

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----cccc--ccCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAAR--GLDV   88 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~~--Gldi   88 (231)
                      ..++||.++++  +.+.++.+.+..    .++.+..+||+.+...+...+    .+..+|+|+|+     .+..  .+++
T Consensus        84 ~~raLIl~PTr--eLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l----~~~~dIiV~TP~rL~~~l~~~~~~~l  157 (572)
T PRK04537         84 DPRALILAPTR--ELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELL----QQGVDVIIATPGRLIDYVKQHKVVSL  157 (572)
T ss_pred             CceEEEEeCcH--HHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHH----hCCCCEEEECHHHHHHHHHhccccch
Confidence            35788899987  889888887754    367889999999877655444    34678999996     2322  3667


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      ..+.+||.
T Consensus       158 ~~v~~lVi  165 (572)
T PRK04537        158 HACEICVL  165 (572)
T ss_pred             hheeeeEe
Confidence            77777664

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=88.53  E-value=0.69  Score=32.62  Aligned_cols=41  Identities=22%  Similarity=0.269  Sum_probs=32.8

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      ....+++.+|++|.+-.+  ....+..|...|+.+..+.||+.
T Consensus        56 ~~~~~~~~ivv~C~~G~r--s~~aa~~L~~~G~~~~~l~GG~~   96 (100)
T cd01523          56 DQLPDDQEVTVICAKEGS--SQFVAELLAERGYDVDYLAGGMK   96 (100)
T ss_pred             hhCCCCCeEEEEcCCCCc--HHHHHHHHHHcCceeEEeCCcHH
Confidence            444567899999987533  77888899999999889999975

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>KOG0347|consensus

Probab=88.23  E-value=1  Score=41.99  Aligned_cols=53  Identities=13%  Similarity=0.217  Sum_probs=45.1

Q ss_pred             eEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587         22 TIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus        22 ~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      -.+||++++  +.+.++.+.|..    .++.+..+.|||+...+++.+..    ...|+|||+
T Consensus       265 ~~LV~tPTR--ELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATP  321 (731)
T KOG0347|consen  265 IALVVTPTR--ELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATP  321 (731)
T ss_pred             eeEEecChH--HHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecc
Confidence            367799977  889999998864    48999999999999988888877    578999997

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=87.61  E-value=2.3  Score=40.42  Aligned_cols=59  Identities=15%  Similarity=0.210  Sum_probs=51.2

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      ...+||.++.+  ..+......|...|+.+.+++++++..++..++.....|+++++++|+
T Consensus        65 ~g~tlVisPl~--sL~~dqv~~l~~~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tP  123 (607)
T PRK11057         65 DGLTLVVSPLI--SLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAP  123 (607)
T ss_pred             CCCEEEEecHH--HHHHHHHHHHHHcCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEECh
Confidence            34567688876  778888888999999999999999999999999999999999998885

>KOG0298|consensus

Probab=87.23  E-value=0.85  Score=46.19  Aligned_cols=102  Identities=19%  Similarity=0.136  Sum_probs=78.3

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCcc-EEEecCccccccCCC
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR-LLIATSVAARGLDVK   89 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~-vLvaT~~~~~Gldip   89 (231)
                      ...|+..+...++|+|+.-.  ...+-+...+...++....--+   .++-...+..|++  +. .|+-+...+-|+|+-
T Consensus      1212 il~iK~k~~qekvIvfsqws--~~ldV~e~~~~~N~I~~~~~~~---t~d~~dc~~~fk~--I~clll~~~~~~~GLNL~ 1284 (1394)
T KOG0298|consen 1212 ILYIKFKNEQEKVIVFSQWS--VVLDVKELRYLMNLIKKQLDGE---TEDFDDCIICFKS--IDCLLLFVSKGSKGLNLI 1284 (1394)
T ss_pred             HHHHhccCcCceEEEEEehH--HHHHHHHHHHHhhhhHhhhccC---Ccchhhhhhhccc--ceEEEEEeccCcccccHH
Confidence            34455555678999999865  4577777777776666544333   3345567777776  44 467788999999999


Q ss_pred             CCcEEEEecCCCCHhHHHHHhcccCCCCCc
Q psy17587         90 HLNLVVNYDCPNHYEDYVHRCGRTGRAGNK  119 (231)
Q Consensus        90 ~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~  119 (231)
                      +..+|+..++-.++..-.|.+||+.|-|+.
T Consensus      1285 eA~Hvfl~ePiLN~~~E~QAigRvhRiGQ~ 1314 (1394)
T KOG0298|consen 1285 EATHVFLVEPILNPGDEAQAIGRVHRIGQK 1314 (1394)
T ss_pred             hhhhhheeccccCchHHHhhhhhhhhcccc
Confidence            999999999999999999999999999974

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=86.59  E-value=3.8  Score=36.93  Aligned_cols=71  Identities=17%  Similarity=0.158  Sum_probs=50.3

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----c-ccccCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----A-ARGLDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~-~~Gldip   89 (231)
                      ..++||.++++  +.+.++.+.+..    .++++..++|+.+.......+    ....+|+|+|+-     + ...+++.
T Consensus        83 ~~~~lil~Ptr--eLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l----~~~~~IlV~TP~~l~~~l~~~~~~l~  156 (423)
T PRK04837         83 QPRALIMAPTR--ELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVL----ESGVDILIGTTGRLIDYAKQNHINLG  156 (423)
T ss_pred             CceEEEECCcH--HHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----cCCCCEEEECHHHHHHHHHcCCcccc
Confidence            35788899987  788888776543    378899999998765543332    345799999972     2 2356788


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      .+.++|.
T Consensus       157 ~v~~lVi  163 (423)
T PRK04837        157 AIQVVVL  163 (423)
T ss_pred             cccEEEE
Confidence            8888775

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

Probab=85.83  E-value=4.2  Score=31.00  Aligned_cols=72  Identities=19%  Similarity=0.332  Sum_probs=48.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHH-HHHHHHHHHhCCCccEEEecCc------cccccC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLIATSV------AARGLD   87 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~-~R~~~~~~F~~g~~~vLvaT~~------~~~Gld   87 (231)
                      +..++++.++++  ..++++.+.+...    +.++..+||+.+.. +....+    .+..+|+|+|..      ....++
T Consensus        43 ~~~~~lii~P~~--~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ilv~T~~~l~~~~~~~~~~  116 (169)
T PF00270_consen   43 KDARVLIIVPTR--ALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVL----SNQADILVTTPEQLLDLISNGKIN  116 (169)
T ss_dssp             SSSEEEEEESSH--HHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHH----HTTSSEEEEEHHHHHHHHHTTSST
T ss_pred             CCceEEEEeecc--cccccccccccccccccccccccccccccccccccccc----cccccccccCcchhhccccccccc
Confidence            345888899987  7788888887654    46788999998854 322223    667899999863      112235


Q ss_pred             CCCCcEEEE
Q psy17587         88 VKHLNLVVN   96 (231)
Q Consensus        88 ip~v~~VI~   96 (231)
                      +..+++||.
T Consensus       117 ~~~~~~iVi  125 (169)
T PF00270_consen  117 ISRLSLIVI  125 (169)
T ss_dssp             GTTESEEEE
T ss_pred             cccceeecc
Confidence            555666554

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 ....

>KOG0389|consensus

Probab=85.25  E-value=2.1  Score=41.51  Aligned_cols=74  Identities=14%  Similarity=0.100  Sum_probs=55.2

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCC--CccEEEecCcc
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNG--KVRLLIATSVA   82 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g--~~~vLvaT~~~   82 (231)
                      +.+.+.+|++.+....-+|.|++-   +.+.+...+.+.  .+.+.++||.  +.+|...-..+.++  .++|||+|--+
T Consensus       435 vIaFlayLkq~g~~gpHLVVvPsS---TleNWlrEf~kwCPsl~Ve~YyGS--q~ER~~lR~~i~~~~~~ydVllTTY~l  509 (941)
T KOG0389|consen  435 VIAFLAYLKQIGNPGPHLVVVPSS---TLENWLREFAKWCPSLKVEPYYGS--QDERRELRERIKKNKDDYDVLLTTYNL  509 (941)
T ss_pred             HHHHHHHHHHcCCCCCcEEEecch---hHHHHHHHHHHhCCceEEEeccCc--HHHHHHHHHHHhccCCCccEEEEEeec
Confidence            345667777777766666678763   467777777664  6889999997  58888888888765  79999999665


Q ss_pred             ccc
Q psy17587         83 ARG   85 (231)
Q Consensus        83 ~~G   85 (231)
                      +.|
T Consensus       510 a~~  512 (941)
T KOG0389|consen  510 AAS  512 (941)
T ss_pred             ccC
Confidence            554

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

Probab=84.92  E-value=3.5  Score=41.94  Aligned_cols=60  Identities=18%  Similarity=0.255  Sum_probs=49.6

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhC--CCccEEEecCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKN--GKVRLLIATSV   81 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~--g~~~vLvaT~~   81 (231)
                      ...+||.++.+  ..+..-...|...|+.+..+.|+++..++..++..+..  |+++||++|+-
T Consensus       500 ~GiTLVISPLi--SLmqDQV~~L~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPE  561 (1195)
T PLN03137        500 PGITLVISPLV--SLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPE  561 (1195)
T ss_pred             CCcEEEEeCHH--HHHHHHHHHHHhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChH
Confidence            35677788976  66765556667789999999999999999999999877  89999999984

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

Probab=84.27  E-value=4.6  Score=40.94  Aligned_cols=77  Identities=14%  Similarity=0.154  Sum_probs=62.3

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHH----HHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-ccccccCCCCCc
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKE----LMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-VAARGLDVKHLN   92 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~----L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-~~~~Gldip~v~   92 (231)
                      ..++.+.|.|++.  -.+++=++.    +...++++..+..=.+.++...+++..++|+++|+|.|- +++.++-+.+..
T Consensus       641 ~~GKQVAvLVPTT--lLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLG  718 (1139)
T COG1197         641 MDGKQVAVLVPTT--LLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLG  718 (1139)
T ss_pred             cCCCeEEEEcccH--HhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCC
Confidence            3568888899974  445554444    455578888999999999999999999999999999996 677888888888


Q ss_pred             EEEE
Q psy17587         93 LVVN   96 (231)
Q Consensus        93 ~VI~   96 (231)
                      .+|.
T Consensus       719 LlII  722 (1139)
T COG1197         719 LLII  722 (1139)
T ss_pred             eEEE
Confidence            8775

>PRK09401 reverse gyrase; Reviewed

Probab=83.80  E-value=2.9  Score=42.91  Aligned_cols=60  Identities=22%  Similarity=0.333  Sum_probs=46.9

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CCCee--eccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCL--SLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~--~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      .+.+++|.++++  +.+.++++.+...    ++.+.  ..|++++..++....+.+.+|..+|+|+|+
T Consensus       122 ~g~~alIL~PTr--eLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp  187 (1176)
T PRK09401        122 KGKKSYIIFPTR--LLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTS  187 (1176)
T ss_pred             cCCeEEEEeccH--HHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECH
Confidence            367788899987  8899999988754    34443  445667778888888899999999999995

>PTZ00110 helicase; Provisional

Probab=83.72  E-value=5.2  Score=37.60  Aligned_cols=71  Identities=14%  Similarity=0.177  Sum_probs=50.0

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----ccccc-cCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAARG-LDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~~G-ldip   89 (231)
                      +..+||.++++  +.+.++.+.+...    ++.+.+++|+.+.......+   +. ..+|+|+|+     .+..+ +++.
T Consensus       203 gp~~LIL~PTr--eLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l---~~-~~~IlVaTPgrL~d~l~~~~~~l~  276 (545)
T PTZ00110        203 GPIVLVLAPTR--ELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYAL---RR-GVEILIACPGRLIDFLESNVTNLR  276 (545)
T ss_pred             CcEEEEECChH--HHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHH---Hc-CCCEEEECHHHHHHHHHcCCCChh
Confidence            45688889987  8888888887653    57788899998866544333   33 478999996     33333 5677


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      .+.+||.
T Consensus       277 ~v~~lVi  283 (545)
T PTZ00110        277 RVTYLVL  283 (545)
T ss_pred             hCcEEEe
Confidence            7777664

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=83.30  E-value=6.4  Score=36.11  Aligned_cols=72  Identities=17%  Similarity=0.281  Sum_probs=51.2

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------cccccCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------AARGLDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~~~Gldip   89 (231)
                      ..++||.++++  +.+.++.+.+..    .++.+..++|+.+....   .+.+..+..+|+|+|+-      -...+.+.
T Consensus       162 ~~~aLil~Ptr--eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~---~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~  236 (475)
T PRK01297        162 EPRALIIAPTR--ELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQ---LKQLEARFCDILVATPGRLLDFNQRGEVHLD  236 (475)
T ss_pred             CceEEEEeCcH--HHHHHHHHHHHHhhccCCCEEEEEEccCChHHH---HHHHhCCCCCEEEECHHHHHHHHHcCCcccc
Confidence            35788889987  778888877654    36788899999875443   34555678899999973      22345667


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      ++++||.
T Consensus       237 ~l~~lVi  243 (475)
T PRK01297        237 MVEVMVL  243 (475)
T ss_pred             cCceEEe
Confidence            7777765

>smart00450 RHOD Rhodanese Homology Domain

Probab=83.28  E-value=2.1  Score=29.21  Aligned_cols=39  Identities=21%  Similarity=0.287  Sum_probs=31.6

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      ..++..+|+||.+.  ..+..++..|...|++ +..+.||+.
T Consensus        53 ~~~~~~iv~~c~~g--~~a~~~~~~l~~~G~~~v~~l~GG~~   92 (100)
T smart00450       53 LDKDKPVVVYCRSG--NRSAKAAWLLRELGFKNVYLLDGGYK   92 (100)
T ss_pred             CCCCCeEEEEeCCC--cHHHHHHHHHHHcCCCceEEecCCHH
Confidence            44578999999876  3478888999999987 889999974

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

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

Probab=82.02  E-value=5.1  Score=37.92  Aligned_cols=58  Identities=19%  Similarity=0.257  Sum_probs=46.7

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      +..||.++=.  .....=.+.|+..|+.+.++++.++.++|..++..+..|.+++|.-++
T Consensus        58 G~TLVVSPLi--SLM~DQV~~l~~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisP  115 (590)
T COG0514          58 GLTLVVSPLI--SLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISP  115 (590)
T ss_pred             CCEEEECchH--HHHHHHHHHHHHcCceeehhhcccCHHHHHHHHHHHhcCceeEEEECc
Confidence            3455566644  455555667778899999999999999999999999999999986654

>PRK13766 Hef nuclease; Provisional

Probab=81.95  E-value=5.4  Score=38.96  Aligned_cols=74  Identities=15%  Similarity=0.206  Sum_probs=52.4

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHC-CC---CeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------cccccC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKA-GY---PCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------AARGLD   87 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~---~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~~~Gld   87 (231)
                      ..++++||.|+++  ..+++..+.+... +.   .+..++|+.+..+|.....     ..+|+|+|+-      ...-++
T Consensus        56 ~~~~~vLvl~Pt~--~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~-----~~~iiv~T~~~l~~~l~~~~~~  128 (773)
T PRK13766         56 KKGGKVLILAPTK--PLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE-----KAKVIVATPQVIENDLIAGRIS  128 (773)
T ss_pred             hCCCeEEEEeCcH--HHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHh-----CCCEEEECHHHHHHHHHcCCCC
Confidence            3567899899987  6788888777653 33   7888999999888765543     3579999963      233456


Q ss_pred             CCCCcEEEEec
Q psy17587         88 VKHLNLVVNYD   98 (231)
Q Consensus        88 ip~v~~VI~~d   98 (231)
                      +.++++||.-.
T Consensus       129 ~~~~~liVvDE  139 (773)
T PRK13766        129 LEDVSLLIFDE  139 (773)
T ss_pred             hhhCcEEEEEC
Confidence            66778777543

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=81.12  E-value=2.8  Score=28.95  Aligned_cols=45  Identities=24%  Similarity=0.392  Sum_probs=33.7

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      .+.+....+++.+||+|++-  ..+...+..|...|+. +..+.|++.
T Consensus        47 ~~~~~~~~~~~~ivv~c~~g--~~s~~a~~~l~~~G~~~v~~l~gG~~   92 (96)
T cd01444          47 DDWLGDLDRDRPVVVYCYHG--NSSAQLAQALREAGFTDVRSLAGGFE   92 (96)
T ss_pred             HHHHhhcCCCCCEEEEeCCC--ChHHHHHHHHHHcCCceEEEcCCCHH
Confidence            33444556788999999876  3478888899988885 778888864

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=81.09  E-value=3.8  Score=28.49  Aligned_cols=38  Identities=29%  Similarity=0.385  Sum_probs=29.6

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHCCC-CeeeccCCCC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKAGY-PCLSLHGGID   57 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~-~~~~lhg~~~   57 (231)
                      .+++.||++|++-.  .+...+..|...|+ ++..+.|||.
T Consensus        54 ~~~~~ivv~c~~g~--~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          54 GRATRYVLTCDGSL--LARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCCCEEEEeCChH--HHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            45788999998763  36777788888888 5888999874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=80.50  E-value=2.6  Score=29.68  Aligned_cols=38  Identities=21%  Similarity=0.361  Sum_probs=28.9

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      .+++.+||+|.+-.+  ....+..|...|++ +..+.||+.
T Consensus        59 ~~~~~ivvyC~~G~r--s~~a~~~L~~~G~~~v~~l~GG~~   97 (101)
T cd01518          59 LKGKKVLMYCTGGIR--CEKASAYLKERGFKNVYQLKGGIL   97 (101)
T ss_pred             cCCCEEEEECCCchh--HHHHHHHHHHhCCcceeeechhHH
Confidence            567889999987433  55667788888985 778898874

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=80.24  E-value=4.6  Score=39.30  Aligned_cols=54  Identities=9%  Similarity=0.023  Sum_probs=40.9

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHH----HCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELM----KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~----~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      +..+.|.+++.  ..+.+.++.+.    ..|+++.++.|+++.++|.....      .+|+++|+.
T Consensus        97 G~~V~VvTpt~--~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~------~dIvyGT~~  154 (745)
T TIGR00963        97 GKGVHVVTVND--YLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYA------CDITYGTNN  154 (745)
T ss_pred             CCCEEEEcCCH--HHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcC------CCEEEECCC
Confidence            45677788875  56666666553    45899999999999888776653      689999987

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	231
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		5e-25
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		2e-24
2jgn_A	185	Ddx3 Helicase Domain Length = 185		8e-21
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		9e-21
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-19
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-19
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-19
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-19
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-19
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-19
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		1e-18
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-18
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-17
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		4e-17
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		7e-17
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		7e-17
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		7e-17
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-16
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		7e-16
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		8e-16
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		8e-16
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		2e-15
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		6e-15
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		6e-15
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-14
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-14
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		4e-14
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		4e-14
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		6e-14
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		6e-14
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		8e-14
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		2e-13
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		4e-13
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		6e-13
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		8e-13
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		8e-13
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		8e-13
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-12
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-12
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-12
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-12
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		5e-12
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		8e-12
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-11
1wp9_A	494	Crystal Structure Of Pyrococcus Furiosus Hef Helica		6e-07
4gl2_A	699	Structural Basis For Dsrna Duplex Backbone Recognit		4e-05
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		6e-05
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		8e-05
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		9e-05
4i1s_A	243	Melanoma Differentiation Associated Protein-5 Helic		9e-05

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

Iteration: 1
 Score =  110 bits (276), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 53/112 (47%), Positives = 77/112 (68%), Gaps = 1/112 (0%)
Query: 42  LMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPN 101
           L +  +P  S+HG   Q  R+  + DFKNG +++LIATSVA+RGLD+K++  V+NYD P+
Sbjct: 320 LSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPS 379
Query: 102 HYEDYVHRCGRTGRAGNKGFAYTFITLEQERH-AGEIIRALEASGVPIPEDL 152
             +DYVHR GRTGR GN G A +F   E++R  A ++++ LE SG  +P+ L
Sbjct: 380 KIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431

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

Iteration: 1
 Score =  109 bits (272), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 52/103 (50%), Positives = 71/103 (68%)
Query: 35  VCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLV 94
           V  +  EL   GYPC  +HGG+ Q DR   + +FK G+ R L+AT VAARG+D+++++LV
Sbjct: 48  VNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLV 107
Query: 95  VNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEI 137
           +NYD P   E YVHR GRTGRAGNKG A +F+T  ++R   +I
Sbjct: 108 INYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADI 150

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 97.1 bits (240), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 54/156 (34%), Positives = 85/156 (54%), Gaps = 11/156 (7%)
Query: 14  IDQYDRDSTIVDFKN--GKVRLLVCAIVKE---------LMKAGYPCLSLHGGIDQYDRD 62
           +++ D+ S ++D  N  GK  L +  +  +         L   GY C S+HG   Q DR+
Sbjct: 27  VEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDRE 86
Query: 63  STIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFA 122
             +  F++GK  +L+AT+VAARGLD+ ++  V+N+D P+  E+YVHR GRTGR GN G A
Sbjct: 87  EALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLA 146
Query: 123 YTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAE 158
            +F          +++  L  +   +P  L+ M  E
Sbjct: 147 TSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 182

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 96.7 bits (239), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 52/156 (33%), Positives = 83/156 (53%), Gaps = 11/156 (7%)
Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-----------GYPCLSLHGGIDQYDRD 62
           +++ D+ S ++D  N   +  +  +  E  K            GY C S+HG   Q DR+
Sbjct: 257 VEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDRE 316
Query: 63  STIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFA 122
             +  F++GK  +L+AT+VAARGLD+ ++  V+N+D P+  E+YVHR GRTGR GN G A
Sbjct: 317 EALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLA 376
Query: 123 YTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAE 158
            +F          +++  L  +   +P  L+ M  E
Sbjct: 377 TSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYE 412

>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 = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 63/89 (70%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + +++ +A +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NY
Sbjct: 293 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 352
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           D PN+ E Y+HR GR+GR G KG A  F+
Sbjct: 353 DLPNNRELYIHRIGRSGRYGRKGVAINFV 381

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 63/89 (70%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + +++ +A +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NY
Sbjct: 292 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 351
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           D PN+ E Y+HR GR+GR G KG A  F+
Sbjct: 352 DLPNNRELYIHRIGRSGRYGRKGVAINFV 380

>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 = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 63/89 (70%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + +++ +A +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NY
Sbjct: 293 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 352
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           D PN+ E Y+HR GR+GR G KG A  F+
Sbjct: 353 DLPNNRELYIHRIGRSGRYGRKGVAINFV 381

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 92.8 bits (229), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 63/89 (70%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + +++ +A +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NY
Sbjct: 271 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 330
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           D PN+ E Y+HR GR+GR G KG A  F+
Sbjct: 331 DLPNNRELYIHRIGRSGRYGRKGVAINFV 359

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 92.4 bits (228), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 63/89 (70%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + +++ +A +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NY
Sbjct: 256 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 315
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           D PN+ E Y+HR GR+GR G KG A  F+
Sbjct: 316 DLPNNRELYIHRIGRSGRYGRKGVAVNFV 344

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 92.4 bits (228), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/89 (43%), Positives = 63/89 (70%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + +++ +A +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NY
Sbjct: 256 LTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY 315
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           D PN+ E Y+HR GR+GR G KG A  F+
Sbjct: 316 DLPNNRELYIHRIGRSGRYGRKGVAVNFV 344

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/129 (35%), Positives = 71/129 (55%), Gaps = 2/129 (1%)
Query: 26  FKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG 85
           F N   R+ + A  K++ + GY C  +H  + Q  R+    DF+NG  R L+ T +  RG
Sbjct: 50  FCNSSQRVELLA--KKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRG 107
Query: 86  LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG 145
           +D++ +N+V+N+D P   E Y+HR GR+GR G+ G A   IT +   +   I   L    
Sbjct: 108 IDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEI 167
Query: 146 VPIPEDLDK 154
            PIP ++DK
Sbjct: 168 KPIPSNIDK 176

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/93 (47%), Positives = 59/93 (63%)
Query: 35  VCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLV 94
           V AI + L+  G   +++HGG DQ +R   I  F+ GK  +L+AT VA++GLD   +  V
Sbjct: 67  VDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHV 126
Query: 95  VNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT 127
           +NYD P   E+YVHR GRTG +GN G A TFI 
Sbjct: 127 INYDMPEEIENYVHRIGRTGCSGNTGIATTFIN 159

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 85.9 bits (211), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 43/95 (45%), Positives = 57/95 (60%)
Query: 46  GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
           G+   ++HG + Q  R+  I  FK  K+R+LIAT V +RG+DV  LN V+NY  P + E 
Sbjct: 262 GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPES 321
Query: 106 YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRA 140
           Y HR GRTGRAG KG A + I   + +    I RA
Sbjct: 322 YXHRIGRTGRAGKKGKAISIINRREYKKLRYIERA 356

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 84.7 bits (208), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 38/119 (31%), Positives = 72/119 (60%), Gaps = 1/119 (0%)
Query: 36  CAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV 95
            A+ + L++  +P +++H G+ Q +R S    FK+ + R+L+AT++  RG+D++ +N+  
Sbjct: 45  IALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF 104
Query: 96  NYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE-RHAGEIIRALEASGVPIPEDLD 153
           NYD P   + Y+HR  R GR G KG A TF++ E + +   ++    E +   +P+++D
Sbjct: 105 NYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEID 163

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 84.0 bits (206), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 38/118 (32%), Positives = 72/118 (61%), Gaps = 1/118 (0%)
Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN 96
           A+ + L++  +P +++H G+ Q +R S    FK+ + R+L+AT++  RG+D++ +N+  N
Sbjct: 264 ALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFN 323
Query: 97  YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE-RHAGEIIRALEASGVPIPEDLD 153
           YD P   + Y+HR  R GR G KG A TF++ E + +   ++    E +   +P+++D
Sbjct: 324 YDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEID 381

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 84.0 bits (206), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 38/118 (32%), Positives = 72/118 (61%), Gaps = 1/118 (0%)
Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN 96
           A+ + L++  +P +++H G+ Q +R S    FK+ + R+L+AT++  RG+D++ +N+  N
Sbjct: 265 ALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFN 324
Query: 97  YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE-RHAGEIIRALEASGVPIPEDLD 153
           YD P   + Y+HR  R GR G KG A TF++ E + +   ++    E +   +P+++D
Sbjct: 325 YDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEID 382

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 84.0 bits (206), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 38/118 (32%), Positives = 72/118 (61%), Gaps = 1/118 (0%)
Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN 96
           A+ + L++  +P +++H G+ Q +R S    FK+ + R+L+AT++  RG+D++ +N+  N
Sbjct: 265 ALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFN 324
Query: 97  YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE-RHAGEIIRALEASGVPIPEDLD 153
           YD P   + Y+HR  R GR G KG A TF++ E + +   ++    E +   +P+++D
Sbjct: 325 YDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEID 382

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 83.2 bits (204), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 64/117 (54%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + K++   GY C   H  + Q +R+    +F+ GKVR L+ + +  RG+D++ +N+V+N+
Sbjct: 274 LAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINF 333
Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDK 154
           D P   E Y+HR GR+GR G+ G A   I      +  +I + L      IP  +DK
Sbjct: 334 DFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDK 390

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 80.5 bits (197), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 9/108 (8%)
Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
           +L   G+    LHG +   +RD  I DF+ G+ ++LI T+V ARG+D+  +++VVNYD P
Sbjct: 262 KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321
Query: 101 ---NHYED---YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
              N   D   Y+HR GRTGR G KG A +F+    ++++  I+ A++
Sbjct: 322 TLANGQADPATYIHRIGRTGRFGRKGVAISFV---HDKNSFNILSAIQ 366

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 80.5 bits (197), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 9/108 (8%)
Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
           +L   G+    LHG +   +RD  I DF+ G+ ++LI T+V ARG+D+  +++VVNYD P
Sbjct: 262 KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321
Query: 101 ---NHYED---YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
              N   D   Y+HR GRTGR G KG A +F+    ++++  I+ A++
Sbjct: 322 TLANGQADPATYIHRIGRTGRFGRKGVAISFV---HDKNSFNILSAIQ 366

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 80.1 bits (196), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 47/128 (36%), Positives = 71/128 (55%), Gaps = 19/128 (14%)
Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
           E+++ G+    L G +    R S I  F++GK ++LI T+V ARG+DVK + +VVN+D P
Sbjct: 53  EMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLP 112
Query: 101 ------NHYEDYVHRCGRTGRAGNKGFAYTFITLEQ-------ERHAGEIIRALEASGVP 147
                   YE Y+HR GRTGR G KG A+  I +++       + H    I+ L A    
Sbjct: 113 VKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNA---- 168
Query: 148 IPEDLDKM 155
             ED+D++
Sbjct: 169 --EDMDEI 174

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 66/108 (61%), Gaps = 9/108 (8%)
Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
           +L   G+    LHG +   +RD  I DF+ G+ ++LI T+V ARG+D+  +++VVNYD P
Sbjct: 54  KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 113
Query: 101 ---NHYED---YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
              N   D   Y+HR GRTGR G KG A +F+    ++++  I+ A++
Sbjct: 114 TLANGQADPATYIHRIGRTGRFGRKGVAISFV---HDKNSFNILSAIQ 158

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 77.4 bits (189), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 65/108 (60%), Gaps = 9/108 (8%)
Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
           +L   G+    LHG +   +RD  I DF+ G+ ++LI T+V ARG+D+  ++ VVNYD P
Sbjct: 56  KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLP 115
Query: 101 ---NHYED---YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
              N   D   Y+HR GRTGR G KG A +F+    ++++  I+ A++
Sbjct: 116 TLANGQADPATYIHRIGRTGRFGRKGVAISFV---HDKNSFNILSAIQ 160

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 77.4 bits (189), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 42/108 (38%), Positives = 65/108 (60%), Gaps = 9/108 (8%)
Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
           +L   G+    LHG +   +RD  I DF+ G+ ++LI T+V ARG+D+  ++ VVNYD P
Sbjct: 55  KLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLP 114
Query: 101 ---NHYED---YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
              N   D   Y+HR GRTGR G KG A +F+    ++++  I+ A++
Sbjct: 115 TLANGQADPATYIHRIGRTGRFGRKGVAISFV---HDKNSFNILSAIQ 159

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 75.5 bits (184), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/91 (41%), Positives = 53/91 (58%)
Query: 39  VKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD 98
           V +L++     + L G + Q  R+  I  F+ G+  +LI T VA+RGLD+  +  V+N+D
Sbjct: 233 VAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFD 292
Query: 99  CPNHYEDYVHRCGRTGRAGNKGFAYTFITLE 129
            P     Y+HR GRTGR G KG A TFI  E
Sbjct: 293 APQDLRTYIHRIGRTGRMGRKGEAITFILNE 323

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 74.7 bits (182), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 59/112 (52%), Gaps = 3/112 (2%)
Query: 18  DRDST---IVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR 74
           +RDS    I+     K    +C+I+K   K   P L  HG I Q  R S +  FK  +  
Sbjct: 29  ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESG 88
Query: 75  LLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           +L+ T V ARG+D  +++ V+    P+   +Y+HR GRT R+G +G +  FI
Sbjct: 89  ILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 74.7 bits (182), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 59/112 (52%), Gaps = 3/112 (2%)
Query: 18  DRDST---IVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR 74
           +RDS    I+     K    +C+I+K   K   P L  HG I Q  R S +  FK  +  
Sbjct: 29  ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESG 88
Query: 75  LLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           +L+ T V ARG+D  +++ V+    P+   +Y+HR GRT R+G +G +  FI
Sbjct: 89  ILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 74.7 bits (182), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 59/112 (52%), Gaps = 3/112 (2%)
Query: 18  DRDST---IVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR 74
           +RDS    I+     K    +C+I+K   K   P L  HG I Q  R S +  FK  +  
Sbjct: 29  ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESG 88
Query: 75  LLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           +L+ T V ARG+D  +++ V+    P+   +Y+HR GRT R+G +G +  FI
Sbjct: 89  ILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140

>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 = 74.3 bits (181), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 53/97 (54%)
Query: 30  KVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK 89
           K    +C+I+K   K   P L  HG I Q  R S +  FK  +  +L+ T V ARG+D  
Sbjct: 299 KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFP 358
Query: 90  HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           +++ V+    P+   +Y+HR GRT R+G +G +  FI
Sbjct: 359 NVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 395

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 74.3 bits (181), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 53/97 (54%)
Query: 30  KVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK 89
           K    +C+I+K   K   P L  HG I Q  R S +  FK  +  +L+ T V ARG+D  
Sbjct: 350 KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFP 409
Query: 90  HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           +++ V+    P+   +Y+HR GRT R+G +G +  FI
Sbjct: 410 NVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 446

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 73.6 bits (179), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 53/97 (54%)
Query: 30  KVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK 89
           K    +C+I+K   K   P L  HG I Q  R S +  FK  +  +L+ T V ARG+D  
Sbjct: 299 KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFP 358
Query: 90  HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI 126
           +++ V+    P+   +Y+HR GRT R+G +G +  FI
Sbjct: 359 NVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 395

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 31/71 (43%), Positives = 49/71 (69%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           I + L++ G+P  +LHG + Q +R+  +  F+ G+VR+L+AT VAARGLD+  ++LVV+Y
Sbjct: 44  IAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHY 103
Query: 98  DCPNHYEDYVH 108
             P+  E Y H
Sbjct: 104 RMPDRAEAYQH 114

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 71.6 bits (174), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/71 (43%), Positives = 49/71 (69%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           I + L++ G+P  +LHG + Q +R+  +  F+ G+VR+L+AT VAARGLD+  ++LVV+Y
Sbjct: 47  IAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHY 106
Query: 98  DCPNHYEDYVH 108
             P+  E Y H
Sbjct: 107 RLPDRAEAYQH 117

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 70.5 bits (171), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 39/91 (42%), Positives = 61/91 (67%)
Query: 47  YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDY 106
           +   ++HG +DQ +RD  + +F++G  R+LI T + ARG+DV+ ++LV+NYD P + E+Y
Sbjct: 279 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
Query: 107 VHRCGRTGRAGNKGFAYTFITLEQERHAGEI 137
           +HR GR GR G KG A   +T E +R   +I
Sbjct: 339 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDI 369

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 70.5 bits (171), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 56/101 (55%)
Query: 42  LMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPN 101
           L +AG     L G + Q  R+  I     G+V +L+AT VAARG+D+  ++ V N+D P 
Sbjct: 50  LREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPR 109
Query: 102 HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
             + Y+HR GRT RAG KG A + +        G++ R +E
Sbjct: 110 SGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIE 150

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 70.5 bits (171), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 39/91 (42%), Positives = 61/91 (67%)
Query: 47  YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDY 106
           +   ++HG +DQ +RD  + +F++G  R+LI T + ARG+DV+ ++LV+NYD P + E+Y
Sbjct: 305 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
Query: 107 VHRCGRTGRAGNKGFAYTFITLEQERHAGEI 137
           +HR GR GR G KG A   +T E +R   +I
Sbjct: 365 IHRIGRGGRFGRKGVAINMVTEEDKRTLRDI 395

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 9/111 (8%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  EL K G+    L G +    R + I  F+ GK ++L+ T+V ARG+DV+ +++V+N+
Sbjct: 349 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 408
Query: 98  DCP------NHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
           D P         E Y+HR GRTGR G +G A   +     +H+  I+  ++
Sbjct: 409 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMV---DSKHSMNILNRIQ 456

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 9/111 (8%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  EL K G+    L G +    R + I  F+ GK ++L+ T+V ARG+DV+ +++V+N+
Sbjct: 298 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 357
Query: 98  DCP------NHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
           D P         E Y+HR GRTGR G +G A   +     +H+  I+  ++
Sbjct: 358 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMV---DSKHSMNILNRIQ 405

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 9/111 (8%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  EL K G+    L G +    R + I  F+ GK ++L+ T+V ARG+DV+ +++V+N+
Sbjct: 319 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 378
Query: 98  DCP------NHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
           D P         E Y+HR GRTGR G +G A   +     +H+  I+  ++
Sbjct: 379 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMV---DSKHSMNILNRIQ 426

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 37/111 (33%), Positives = 61/111 (54%), Gaps = 9/111 (8%)
Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  EL K G+    L G +    R + I  F+ GK ++L+ T+V ARG+DV+ +++V+N+
Sbjct: 282 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 341
Query: 98  DCP------NHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
           D P         E Y+HR GRTGR G +G A   +     +H+  I+  ++
Sbjct: 342 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMV---DSKHSMNILNRIQ 389

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 67.8 bits (164), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 71/125 (56%), Gaps = 5/125 (4%)
Query: 5   YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDST 64
           Y CL+     D YD  S          R  V  +  +L    +   +++  + Q +RD+ 
Sbjct: 248 YECLT-----DLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTI 302
Query: 65  IVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYT 124
           + +F++G  R+LI+T + ARG+DV+ ++LV+NYD P + E+Y+HR GR GR G KG A  
Sbjct: 303 MKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAIN 362
Query: 125 FITLE 129
           F+T E
Sbjct: 363 FVTNE 367

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 67.0 bits (162), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 48/148 (32%), Positives = 78/148 (52%), Gaps = 5/148 (3%)
Query: 5   YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDST 64
           Y CL+     D YD  S          R  V  +  +L    +   +++  + Q +RD+ 
Sbjct: 18  YECLT-----DLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTI 72
Query: 65  IVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYT 124
           + +F++G  R+LI+T + ARG+DV+ ++LV+NYD P + E+Y+HR GR GR G KG A  
Sbjct: 73  MKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAIN 132
Query: 125 FITLEQERHAGEIIRALEASGVPIPEDL 152
           F+T E      E+ +        +P D+
Sbjct: 133 FVTNEDVGAMRELEKFYSTQIEELPSDI 160

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 66.6 bits (161), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 70/125 (56%), Gaps = 5/125 (4%)
Query: 5   YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDST 64
           Y CL+     D YD  S          R  V  +  +L    +   +++  + Q +RD+ 
Sbjct: 247 YECLT-----DLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTI 301
Query: 65  IVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYT 124
             +F++G  R+LI+T + ARG+DV+ ++LV+NYD P + E+Y+HR GR GR G KG A  
Sbjct: 302 XKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAIN 361
Query: 125 FITLE 129
           F+T E
Sbjct: 362 FVTNE 366

>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase Domain Length = 494

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 52/108 (48%), Gaps = 10/108 (9%)
Query: 16  QYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHG--------GIDQYDRDSTIVD 67
           Q  ++S I+ F N   R     IV EL+K G       G        G+ Q ++   + +
Sbjct: 357 QRKQNSKIIVFTN--YRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDE 414
Query: 68  FKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGR 115
           F  G+  +L+ATSV   GLDV  ++LVV Y+        + R GRTGR
Sbjct: 415 FARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR 462

>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By Mda5 Length = 699

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 28/42 (66%)
Query: 56  IDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           + Q ++   I  F+ GK+ LLIAT+VA  GLD+K  N+V+ Y
Sbjct: 448 MTQNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRY 489

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 46/89 (51%), Gaps = 4/89 (4%)
Query: 42  LMKAGYPCLSL---HGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD 98
           L K  +P   L   HG + Q ++D  +++F  G+  +L++T+V   G+DV   N++V  +
Sbjct: 606 LSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIEN 665
Query: 99  CPNHYEDYVHRC-GRTGRAGNKGFAYTFI 126
                   +H+  GR GR G + + +  +
Sbjct: 666 PERFGLAQLHQLRGRVGRGGQEAYCFLVV 694

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%)
Query: 42  LMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPN 101
           L   G    + H G++   R      F+   +++++AT     G++  ++  VV++D P 
Sbjct: 256 LQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR 315
Query: 102 HYEDYVHRCGRTGRAGNKGFAYTF 125
           + E Y    GR GR G    A  F
Sbjct: 316 NIESYYQETGRAGRDGLPAEAMLF 339

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%)
Query: 42  LMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPN 101
           L   G    + H G++   R      F+   +++++AT     G++  ++  VV++D P 
Sbjct: 256 LQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPR 315
Query: 102 HYEDYVHRCGRTGRAGNKGFAYTF 125
           + E Y    GR GR G    A  F
Sbjct: 316 NIESYYQETGRAGRDGLPAEAXLF 339

>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase Domain Complex With Inhibitor Non-structural Protein V Length = 243

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 58  QYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           Q ++   I  F+ GK+ LLIAT+VA  GLD+K  N+V+ Y
Sbjct: 200 QNEQREVISKFRTGKINLLIATTVAEEGLDIKECNIVIRY 239

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	231
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	6e-61
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-58
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	5e-52
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	2e-49
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	1e-44
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-43
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-43
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-42
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-42
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	1e-42
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	9e-42
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	1e-41
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-41
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	8e-41
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-40
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-39
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	5e-39
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	7e-39
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	3e-38
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	6e-38
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	8e-38
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	9e-38
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	6e-37
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-36
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-22
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	3e-20
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	4e-11
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	1e-10
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-10
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	5e-10
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	1e-07

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  195 bits (499), Expect = 6e-61
 Identities = 47/121 (38%), Positives = 70/121 (57%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +   L   GY C S+HG   Q DR+  +  F++GK  +L+AT+VAARGLD+ ++  V+N+
Sbjct: 292 LEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINF 351

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA 157
           D P+  E+YVHR GRTGR GN G A +F          +++  L  +   +P  L+ M  
Sbjct: 352 DLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY 411

Query: 158 E 158
           E
Sbjct: 412 E 412

>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 =  190 bits (485), Expect = 1e-58
 Identities = 53/116 (45%), Positives = 78/116 (67%), Gaps = 1/116 (0%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +   L +  +P  S+HG   Q  R+  + DFKNG +++LIATSVA+RGLD+K++  V+NY
Sbjct: 316 LASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINY 375

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH-AGEIIRALEASGVPIPEDL 152
           D P+  +DYVHR GRTGR GN G A +F   E++R  A ++++ LE SG  +P+ L
Sbjct: 376 DMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score =  165 bits (420), Expect = 5e-52
 Identities = 46/118 (38%), Positives = 69/118 (58%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +   L   GY C S+HG   Q DR+  +  F++GK  +L+AT+VAARGLD+ ++  V+N+
Sbjct: 62  LEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINF 121

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKM 155
           D P+  E+YVHR GRTGR GN G A +F          +++  L  +   +P  L+ M
Sbjct: 122 DLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENM 179

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

 Score =  159 bits (404), Expect = 2e-49
 Identities = 47/120 (39%), Positives = 67/120 (55%), Gaps = 1/120 (0%)

Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN 96
           AI + L+  G   +++HGG DQ +R   I  F+ GK  +L+AT VA++GLD   +  V+N
Sbjct: 69  AIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVIN 128

Query: 97  YDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ-ERHAGEIIRALEASGVPIPEDLDKM 155
           YD P   E+YVHR GRTG +GN G A TFI     E    ++   L  +   +P  L  +
Sbjct: 129 YDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVL 188

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  146 bits (370), Expect = 1e-44
 Identities = 59/137 (43%), Positives = 82/137 (59%), Gaps = 6/137 (4%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +   + DS I+ F   K    V  +  EL   GYPC  +HGG+ Q DR   + +FK G+ 
Sbjct: 30  LMTENPDSCII-FCRTKEH--VNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEY 86

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R L+AT VAARG+D+++++LV+NYD P   E YVHR GRTGRAGNKG A +F+T  ++R 
Sbjct: 87  RYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRF 146

Query: 134 AGEIIRALEASGVPIPE 150
             +I       G  I +
Sbjct: 147 LADIEE---YIGFEIQK 160

>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 =  150 bits (380), Expect = 1e-43
 Identities = 44/141 (31%), Positives = 72/141 (51%), Gaps = 3/141 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
             +   +  I+ F N   R  V  + K++   GY C   H  + Q +R+    +F+ GKV
Sbjct: 253 FSKLQINQAII-FCNSTNR--VELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKV 309

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R L+ + +  RG+D++ +N+V+N+D P   E Y+HR GR+GR G+ G A   I      +
Sbjct: 310 RTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFN 369

Query: 134 AGEIIRALEASGVPIPEDLDK 154
             +I + L      IP  +DK
Sbjct: 370 LYKIEQELGTEIAAIPATIDK 390

>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 =  147 bits (373), Expect = 1e-42
 Identities = 41/142 (28%), Positives = 79/142 (55%), Gaps = 4/142 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +D  + +  ++ F     R    A+ + L++  +P +++H G+ Q +R S    FK+ + 
Sbjct: 245 LDVLEFNQVVI-FVKSVQR--CIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR 301

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+L+AT++  RG+D++ +N+  NYD P   + Y+HR  R GR G KG A TF++ E +  
Sbjct: 302 RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 361

Query: 134 A-GEIIRALEASGVPIPEDLDK 154
              ++    E +   +P+++D 
Sbjct: 362 ILNDVQDRFEVNISELPDEIDI 383

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A Length = 212

 Score =  142 bits (360), Expect = 1e-42
 Identities = 56/185 (30%), Positives = 86/185 (46%), Gaps = 7/185 (3%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +     D  +V F   K       I + L++ G+P  +LHG + Q +R+  +  F+ G+V
Sbjct: 26  LYVASPDRAMV-FTRTKAE--TEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEV 82

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+L+AT VAARGLD+  ++LVV+Y  P+  E Y HR GRTGRAG  G         + R 
Sbjct: 83  RVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRD 142

Query: 134 AGEIIRA----LEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGE 189
              + RA     +    P PE++ +     L+ R       +      F          E
Sbjct: 143 VEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVE 202

Query: 190 IIRAL 194
           ++ AL
Sbjct: 203 VVAAL 207

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19 Length = 172

 Score =  141 bits (357), Expect = 1e-42
 Identities = 41/142 (28%), Positives = 79/142 (55%), Gaps = 4/142 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +D  + +  ++ F     R    A+ + L++  +P +++H G+ Q +R S    FK+ + 
Sbjct: 26  LDVLEFNQVVI-FVKSVQR--CIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR 82

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+L+AT++  RG+D++ +N+  NYD P   + Y+HR  R GR G KG A TF++ E +  
Sbjct: 83  RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 142

Query: 134 A-GEIIRALEASGVPIPEDLDK 154
              ++    E +   +P+++D 
Sbjct: 143 ILNDVQDRFEVNISELPDEIDI 164

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score =  142 bits (361), Expect = 9e-42
 Identities = 56/185 (30%), Positives = 86/185 (46%), Gaps = 7/185 (3%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +     D  +V F   K       I + L++ G+P  +LHG + Q +R+  +  F+ G+V
Sbjct: 23  LYVASPDRAMV-FTRTKAE--TEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEV 79

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+L+AT VAARGLD+  ++LVV+Y  P+  E Y HR GRTGRAG  G         + R 
Sbjct: 80  RVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRD 139

Query: 134 AGEIIRA----LEASGVPIPEDLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGE 189
              + RA     +    P PE++ +     L+ R       +      F          E
Sbjct: 140 VEALERAVGRRFKRVNPPTPEEVLEAKWRHLLARLARVPEKDYRLYQDFAGRLFAEGRVE 199

Query: 190 IIRAL 194
           ++ AL
Sbjct: 200 VVAAL 204

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score =  138 bits (350), Expect = 1e-41
 Identities = 43/132 (32%), Positives = 65/132 (49%), Gaps = 9/132 (6%)

Query: 14  IDQYDRDSTIVDF---KNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKN 70
           + Q +   +IV F   +     L        L +AG     L G + Q  R+  I     
Sbjct: 25  LKQPEATRSIV-FVRKRERVHEL-----ANWLREAGINNCYLEGEMVQGKRNEAIKRLTE 78

Query: 71  GKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ 130
           G+V +L+AT VAARG+D+  ++ V N+D P   + Y+HR GRT RAG KG A + +    
Sbjct: 79  GRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHD 138

Query: 131 ERHAGEIIRALE 142
               G++ R +E
Sbjct: 139 HLLLGKVGRYIE 150

>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 =  144 bits (366), Expect = 1e-41
 Identities = 43/142 (30%), Positives = 77/142 (54%), Gaps = 3/142 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
            D       ++ F N + +  V  +  +L    +   +++  + Q +RD+ + +F++G  
Sbjct: 254 YDSISVTQAVI-FCNTRRK--VEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS 310

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+LI+T + ARG+DV+ ++LV+NYD P + E+Y+HR GR GR G KG A  F+T E    
Sbjct: 311 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGA 370

Query: 134 AGEIIRALEASGVPIPEDLDKM 155
             E+ +        +P D+  +
Sbjct: 371 MRELEKFYSTQIEELPSDIATL 392

>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 =  143 bits (362), Expect = 8e-41
 Identities = 47/138 (34%), Positives = 79/138 (57%), Gaps = 3/138 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
            D       ++ F N K +  V  + +++ +A +   S+HG + Q +R+S + +F++G  
Sbjct: 271 YDTLTITQAVI-FCNTKRK--VDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGAS 327

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+LI+T V ARGLDV  ++L++NYD PN+ E Y+HR GR+GR G KG A  F+  +  R 
Sbjct: 328 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRI 387

Query: 134 AGEIIRALEASGVPIPED 151
             +I +        +P +
Sbjct: 388 LRDIEQYYSTQIDEMPMN 405

>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 =  141 bits (359), Expect = 2e-40
 Identities = 44/138 (31%), Positives = 77/138 (55%), Gaps = 3/138 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
            +       ++ F N + +  V  + +++    +   ++HG +DQ +RD  + +F++G  
Sbjct: 275 YETLTITQAVI-FINTRRK--VDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS 331

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+LI T + ARG+DV+ ++LV+NYD P + E+Y+HR GR GR G KG A   +T E +R 
Sbjct: 332 RVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRT 391

Query: 134 AGEIIRALEASGVPIPED 151
             +I      S   +P +
Sbjct: 392 LRDIETFYNTSIEEMPLN 409

>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 =  138 bits (349), Expect = 3e-39
 Identities = 46/127 (36%), Positives = 65/127 (51%), Gaps = 4/127 (3%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +   +    +  F   K       +   L   G+   ++HG + Q  R+  I  FK  K+
Sbjct: 234 LKNKEFYGLV--FCKTKRD--TKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKI 289

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+LIAT V +RG+DV  LN V+NY  P + E Y+HR GRTGRAG KG A + I   + + 
Sbjct: 290 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKK 349

Query: 134 AGEIIRA 140
              I RA
Sbjct: 350 LRYIERA 356

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  131 bits (333), Expect = 5e-39
 Identities = 40/121 (33%), Positives = 70/121 (57%)

Query: 35  VCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLV 94
           V  +  +L    +   +++  + Q +RD+ + +F++G  R+LI+T + ARG+DV+ ++LV
Sbjct: 43  VEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLV 102

Query: 95  VNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDK 154
           +NYD P + E+Y+HR GR GR G KG A  F+T E      E+ +        +P D+  
Sbjct: 103 INYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIAT 162

Query: 155 M 155
           +
Sbjct: 163 L 163

>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 =  136 bits (344), Expect = 7e-39
 Identities = 42/116 (36%), Positives = 60/116 (51%), Gaps = 7/116 (6%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           + +      IV F   + R      V +L++     + L G + Q  R+  I  F+ G+ 
Sbjct: 215 LRENKDKGVIV-FVRTRNR------VAKLVRLFDNAIELRGDLPQSVRNRNIDAFREGEY 267

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE 129
            +LI T VA+RGLD+  +  V+N+D P     Y+HR GRTGR G KG A TFI  E
Sbjct: 268 DMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFILNE 323

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score =  130 bits (328), Expect = 3e-38
 Identities = 42/120 (35%), Positives = 66/120 (55%), Gaps = 6/120 (5%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  E+++ G+    L G +    R S I  F++GK ++LI T+V ARG+DVK + +VVN+
Sbjct: 50  LTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNF 109

Query: 98  DCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPED 151
           D P        YE Y+HR GRTGR G KG A+  I +++     +I     +S   +  +
Sbjct: 110 DLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSIKQLNAE 169

>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 =  135 bits (342), Expect = 6e-38
 Identities = 39/132 (29%), Positives = 67/132 (50%), Gaps = 17/132 (12%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  EL K G+    L G +    R + I  F+ GK ++L+ T+V ARG+DV+ +++V+N+
Sbjct: 282 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 341

Query: 98  DCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQ--------ERHAGEIIRALEA 143
           D P         E Y+HR GRTGR G +G A   +  +         + H  + I  L+ 
Sbjct: 342 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDT 401

Query: 144 SGVPIPEDLDKM 155
                 ++++K+
Sbjct: 402 ---DDLDEIEKI 410

>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 =  134 bits (341), Expect = 8e-38
 Identities = 44/135 (32%), Positives = 71/135 (52%), Gaps = 12/135 (8%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
                  S+I+ F   K       +  +L   G+    LHG +   +RD  I DF+ G+ 
Sbjct: 238 YGLMTIGSSII-FVATKKT--ANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRS 294

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNH------YEDYVHRCGRTGRAGNKGFAYTFIT 127
           ++LI T+V ARG+D+  +++VVNYD P           Y+HR GRTGR G KG A +F+ 
Sbjct: 295 KVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVH 354

Query: 128 LEQERHAGEIIRALE 142
              ++++  I+ A++
Sbjct: 355 ---DKNSFNILSAIQ 366

>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 =  136 bits (344), Expect = 9e-38
 Identities = 39/132 (29%), Positives = 67/132 (50%), Gaps = 17/132 (12%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  EL K G+    L G +    R + I  F+ GK ++L+ T+V ARG+DV+ +++V+N+
Sbjct: 349 LAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINF 408

Query: 98  DCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQ--------ERHAGEIIRALEA 143
           D P         E Y+HR GRTGR G +G A   +  +         + H  + I  L+ 
Sbjct: 409 DLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLDT 468

Query: 144 SGVPIPEDLDKM 155
                 ++++K+
Sbjct: 469 ---DDLDEIEKI 477

>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 =  134 bits (340), Expect = 6e-37
 Identities = 39/137 (28%), Positives = 65/137 (47%), Gaps = 4/137 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
            ++      I+     K    +C+I+K   K   P L  HG I Q  R S +  FK  + 
Sbjct: 334 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDES 393

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
            +L+ T V ARG+D  +++ V+    P+   +Y+HR GRT R+G +G +  FI  ++   
Sbjct: 394 GILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF 453

Query: 134 AGEIIRALEASGVPIPE 150
               +R LE +   +  
Sbjct: 454 ----VRELEDAKNIVIA 466

>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 =  134 bits (338), Expect = 2e-36
 Identities = 39/137 (28%), Positives = 65/137 (47%), Gaps = 4/137 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
            ++      I+     K    +C+I+K   K   P L  HG I Q  R S +  FK  + 
Sbjct: 283 KERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDES 342

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
            +L+ T V ARG+D  +++ V+    P+   +Y+HR GRT R+G +G +  FI  ++   
Sbjct: 343 GILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPF 402

Query: 134 AGEIIRALEASGVPIPE 150
               +R LE +   +  
Sbjct: 403 ----VRELEDAKNIVIA 415

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 93.3 bits (232), Expect = 2e-22
 Identities = 26/152 (17%), Positives = 52/152 (34%), Gaps = 17/152 (11%)

Query: 19  RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIA 78
           RD  ++ F   +       + + L +  +            + +    DFK GK+ +LI 
Sbjct: 252 RDGILI-FAQTEEE--GKELYEYLKRFKFNVGETWS-----EFEKNFEDFKVGKINILIG 303

Query: 79  TSV----AARGLDVKH-LNLVVNYDCPNH--YEDYVHRCGRTGRAGNKGF--AYTFITLE 129
                    RG+D+   +  V+ +  P+      Y+   GR+ R  N       + I  E
Sbjct: 304 VQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEE 363

Query: 130 QERHAGEIIRALEASGVPIPEDLDKMWAEDLI 161
            E     +   L         +  +   ++L+
Sbjct: 364 DEEIFESLKTRLLLIAEEEIIEEAEANWKELV 395

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 87.5 bits (216), Expect = 3e-20
 Identities = 32/104 (30%), Positives = 46/104 (44%), Gaps = 9/104 (8%)

Query: 32  RLLVCAIVKELMKAGYPCLSLHG--------GIDQYDRDSTIVDFKNGKVRLLIATSVAA 83
           R     IV EL+K G       G        G+ Q ++   + +F  G+  +L+ATSV  
Sbjct: 371 RETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGE 430

Query: 84  RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT 127
            GLDV  ++LVV Y+        + R GRTGR    G     + 
Sbjct: 431 EGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMA 473

>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* Length = 556

 Score = 61.1 bits (147), Expect = 4e-11
 Identities = 25/70 (35%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 53  HGGIDQYDRDSTIVDFKNGKV-RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCG 111
             G+    +   +  FK  K  RLLIATSVA  G+D+   NLVV Y+   +    +   G
Sbjct: 433 TTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRG 492

Query: 112 RTGRAGNKGF 121
           R GRA     
Sbjct: 493 R-GRAAGSKC 501

>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} Length = 936

 Score = 60.4 bits (145), Expect = 8e-11
 Identities = 30/94 (31%), Positives = 40/94 (42%), Gaps = 4/94 (4%)

Query: 46  GYPCLSLHGGIDQYDRDSTIVDFKNGKV-RLLIATSVAARGLDVKHLNLVVNYDCPNHYE 104
           G        G+    +   +  FK  K  RLLIATSVA  G+D+   NLVV Y+   +  
Sbjct: 667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVT 726

Query: 105 DYVHRCGRTGRAGNKGFAYTFITLEQERHAGEII 138
             +   GR GRA   G     +T + E    E  
Sbjct: 727 KMIQVRGR-GRA--AGSKCILVTSKTEVVENEKC 757

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 59.5 bits (143), Expect = 1e-10
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 55  GIDQYDRDSTIVDFK-NGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRT 113
           G+    +   +  F+ +G   +LIATSVA  G+D+   NLV+ Y+   +    +   GR 
Sbjct: 434 GMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR- 492

Query: 114 GRAGN 118
           GRA +
Sbjct: 493 GRARD 497

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 59.6 bits (143), Expect = 1e-10
 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 3/98 (3%)

Query: 46  GYPCLSLHGGIDQYDRDSTIVDFK-NGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYE 104
           G    + + G+    +   +  FK +G   +LIATSVA  G+D+   NLV+ Y+   +  
Sbjct: 434 GRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVI 493

Query: 105 DYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
             +   GR GRA      +   +        +I    E
Sbjct: 494 KMIQTRGR-GRARGSKC-FLLTSNAGVIEKEQINMYKE 529

>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} Length = 797

 Score = 57.7 bits (138), Expect = 5e-10
 Identities = 30/94 (31%), Positives = 40/94 (42%), Gaps = 4/94 (4%)

Query: 46  GYPCLSLHGGIDQYDRDSTIVDFKNGKV-RLLIATSVAARGLDVKHLNLVVNYDCPNHYE 104
           G        G+    +   +  FK  K  RLLIATSVA  G+D+   NLVV Y+   +  
Sbjct: 667 GRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVT 726

Query: 105 DYVHRCGRTGRAGNKGFAYTFITLEQERHAGEII 138
             +   GR GRA   G     +T + E    E  
Sbjct: 727 KMIQVRGR-GRA--AGSKCILVTSKTEVVENEKC 757

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 51.2 bits (122), Expect = 1e-07
 Identities = 19/131 (14%), Positives = 41/131 (31%), Gaps = 12/131 (9%)

Query: 42  LMKAGYPCLSLHGGIDQYDRDSTIVDFKN--GKVRLLIATSVAARGLDVKHLNLVVNYDC 99
             + G      H G+   +RD     F       ++L+ + + + G + +  + +V +D 
Sbjct: 524 REREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDL 583

Query: 100 PNHYEDYVHRCGRTGRAGNKG--FAYTFIT--------LEQERHAGEIIRALEASGVPIP 149
           P + +    R GR  R G       +            +       +       +G  I 
Sbjct: 584 PFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHEGLDAFEHTCPTGRTIY 643

Query: 150 EDLDKMWAEDL 160
           + +       L
Sbjct: 644 DSVYNDLINYL 654

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	231
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	100.0
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.97
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.97
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.97
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.97
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.97
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.97
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.96
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.96
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.96
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.91
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.95
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.94
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.94
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.94
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.93
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.93
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.93
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.93
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.93
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.92
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.92
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.9
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.89
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.89
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.89
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.89
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.88
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.88
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.88
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.87
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.87
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.87
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.87
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.87
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.86
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.86
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.86
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.86
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.84
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.84
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.83
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.83
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.82
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.81
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.81
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.81
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.81
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.8
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.8
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.8
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.8
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.8
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.8
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.8
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.8
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.8
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.79
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.79
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.78
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.78
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.78
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.76
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.75
3h1t_A	590	Type I site-specific restriction-modification syst	99.74
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.71
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.68
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.37
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.29
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.98
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	97.97
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	97.29
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	96.53
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	96.27
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	95.98
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	95.52
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	95.09
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	94.89
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	94.37
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	94.3
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	94.13
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	93.84
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	93.59
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	93.49
3bor_A	237	Human initiation factor 4A-II; translation initiat	93.36
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	92.99
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	92.58
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	92.35
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	92.1
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	91.52
2l82_A	162	Designed protein OR32; structural genomics, northe	91.28
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	91.24
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	91.06
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	90.99
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	90.0
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	89.98
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	89.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	88.93
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	88.65
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	88.03
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	87.88
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	87.77
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	87.72
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	87.2
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	86.89
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	86.63
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	85.97
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	85.86
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	85.8
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	85.01
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	84.94
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	84.93
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	84.62
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	83.71
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	83.08
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	81.89
1tq1_A	129	AT5G66040, senescence-associated family protein; C	80.86
2jtq_A	85	Phage shock protein E; solution structure rhodanes	80.75
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	80.5

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=100.00  E-value=2.7e-32  Score=218.41  Aligned_cols=152  Identities=34%  Similarity=0.530  Sum_probs=128.9

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|+..|.++|+...++.++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+++|||||++++
T Consensus        30 ~~K~~~L~~ll~~~~~~~k~lVF~~~~--~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  107 (185)
T 2jgn_A           30 SDKRSFLLDLLNATGKDSLTLVFVETK--KGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAA  107 (185)
T ss_dssp             GGHHHHHHHHHHHC-CCSCEEEEESCH--HHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC---
T ss_pred             HHHHHHHHHHHHhcCCCCeEEEEECCH--HHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcChhh
Confidence            467888999998877788899999998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHh
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA  157 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~  157 (231)
                      +|+|+|++++||+||+|+++.+|+||+||+||.|+.|.|++|+++.+...++.+.+.+....+++|+++.++..
T Consensus       108 ~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~a~  181 (185)
T 2jgn_A          108 RGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY  181 (185)
T ss_dssp             ---CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHHHC
T ss_pred             cCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchhhHHHHHHHHHHHHhccCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999887754

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

Probab=99.97  E-value=2.2e-31  Score=214.24  Aligned_cols=148  Identities=34%  Similarity=0.518  Sum_probs=133.6

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|+..|.++|...  +.++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||++++
T Consensus        40 ~~K~~~L~~~l~~~--~~~~lVF~~~~--~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~  115 (191)
T 2p6n_A           40 EAKMVYLLECLQKT--PPPVLIFAEKK--ADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVAS  115 (191)
T ss_dssp             GGHHHHHHHHHTTS--CSCEEEECSCH--HHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHH
T ss_pred             HHHHHHHHHHHHhC--CCCEEEEECCH--HHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchh
Confidence            46788888888765  35788899998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhCCCCCchhHHHH
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEASGVPIPEDLDKM  155 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~~~~~~~~l~~~  155 (231)
                      +|+|+|++++||+||+|+++.+|+||+||+||.|+.|.+++|+++. +...+..+.+.+...++++|+.+.++
T Consensus       116 ~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~~~~l~~~l~~~~~~~p~~l~~~  188 (191)
T 2p6n_A          116 KGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVL  188 (191)
T ss_dssp             TTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHHHHHHHHHHHHTTCCCCHHHHST
T ss_pred             cCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHHHHHHHHHHHHccCcCCHHHHhh
Confidence            9999999999999999999999999999999999999999999986 67788889999999999999987654

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

Probab=99.97  E-value=1.6e-30  Score=203.80  Aligned_cols=139  Identities=40%  Similarity=0.600  Sum_probs=127.3

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ...|+..|.++|.... +.++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+++
T Consensus        19 ~~~K~~~L~~ll~~~~-~~~~lVF~~~~--~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~   95 (163)
T 2hjv_A           19 EENKFSLLKDVLMTEN-PDSCIIFCRTK--EHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVA   95 (163)
T ss_dssp             GGGHHHHHHHHHHHHC-CSSEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGG
T ss_pred             hHHHHHHHHHHHHhcC-CCcEEEEECCH--HHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChh
Confidence            3567888888887654 56778899998  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhC
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEAS  144 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~  144 (231)
                      ++|+|+|++++||+||+|+++.+|+||+||+||.|+.|.+++|+.+.+...++.+.+.+..+
T Consensus        96 ~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~  157 (163)
T 2hjv_A           96 ARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAFEKRFLADIEEYIGFE  157 (163)
T ss_dssp             TTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGGGHHHHHHHHHHHTSC
T ss_pred             hcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHHHHHHHHHHHHHHCCC
Confidence            99999999999999999999999999999999999999999999999988888887776443

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

Probab=99.97  E-value=6.8e-31  Score=207.82  Aligned_cols=146  Identities=28%  Similarity=0.504  Sum_probs=129.2

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ...|+..|.++|+.. ...++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+++
T Consensus        15 ~~~K~~~L~~ll~~~-~~~~~lVF~~~~--~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~~   91 (172)
T 1t5i_A           15 DNEKNRKLFDLLDVL-EFNQVVIFVKSV--QRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLF   91 (172)
T ss_dssp             GGGHHHHHHHHHHHS-CCSSEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCC
T ss_pred             hHHHHHHHHHHHHhC-CCCcEEEEECCH--HHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCch
Confidence            356888888888766 456788899998  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhCCCCCchh
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEASGVPIPED  151 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~~~~~~~~  151 (231)
                      ++|+|+|++++||+||+|+++.+|+||+||+||.|+.|.+++|+++. +...++.+.+.+.....++|..
T Consensus        92 ~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  161 (172)
T 1t5i_A           92 GRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDE  161 (172)
T ss_dssp             STTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC--
T ss_pred             hcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChh
Confidence            99999999999999999999999999999999999999999999876 4566777777776655556554

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

Probab=99.97  E-value=2.9e-31  Score=208.25  Aligned_cols=144  Identities=32%  Similarity=0.522  Sum_probs=126.2

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      +|+..|.+++... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++
T Consensus        16 ~K~~~l~~ll~~~-~~~~~lVF~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~   92 (165)
T 1fuk_A           16 YKYECLTDLYDSI-SVTQAVIFCNTR--RKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR   92 (165)
T ss_dssp             GHHHHHHHHHHHT-TCSCEEEEESSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTT
T ss_pred             hHHHHHHHHHHhC-CCCCEEEEECCH--HHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcChhhc
Confidence            4888888888876 456788899988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchh
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPED  151 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~  151 (231)
                      |+|+|++++||+||+|+++.+|+||+||+||.|+.|.|++|+++.+...+..+.+.+.....++|..
T Consensus        93 G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (165)
T 1fuk_A           93 GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSD  159 (165)
T ss_dssp             TCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSC
T ss_pred             CCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcchHHHHHHHHHHHHccCccccCcc
Confidence            9999999999999999999999999999999999999999999999888888888776665555543

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.97  E-value=2.9e-30  Score=204.40  Aligned_cols=138  Identities=32%  Similarity=0.483  Sum_probs=122.3

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|+..|.++++.. ..+++||||+++  ..++.++..|...|+.+..+||+|++.+|..+++.|++|+.+|||||+++++
T Consensus        20 ~K~~~L~~ll~~~-~~~~~lVF~~~~--~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~   96 (175)
T 2rb4_A           20 DKYQALCNIYGSI-TIGQAIIFCQTR--RNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCAR   96 (175)
T ss_dssp             HHHHHHHHHHTTS-CCSEEEEECSCH--HHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCT
T ss_pred             hHHHHHHHHHHhC-CCCCEEEEECCH--HHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhc
Confidence            3778888888765 466888899988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCC------CCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         85 GLDVKHLNLVVNYDCP------NHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        85 Gldip~v~~VI~~d~P------~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      |+|+|++++||+||+|      .++.+|+||+||+||.|+.|.+++|+.+.+...+..+.+.+....
T Consensus        97 Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~  163 (175)
T 2rb4_A           97 GIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVDELPSLMKIQDHFNSSI  163 (175)
T ss_dssp             TTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGGGHHHHHHHHHHHTCCC
T ss_pred             CCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccchHHHHHHHHHHhcCcc
Confidence            9999999999999999      899999999999999999999999999999887777777765443

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=99.97  E-value=9e-30  Score=207.87  Aligned_cols=140  Identities=33%  Similarity=0.483  Sum_probs=126.9

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ...|+..|.+++.... ++++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+++
T Consensus        15 ~~~k~~~l~~ll~~~~-~~~~lVF~~~~--~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~   91 (212)
T 3eaq_A           15 VRGRLEVLSDLLYVAS-PDRAMVFTRTK--AETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVA   91 (212)
T ss_dssp             TTSHHHHHHHHHHHHC-CSCEEEECSSH--HHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTT
T ss_pred             HHHHHHHHHHHHHhCC-CCeEEEEeCCH--HHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChh
Confidence            4678888888887654 56788899998  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      ++|+|+|++++||+||+|+++.+|+||+||+||.|+.|.|++|+++.+...++.+.+.+....
T Consensus        92 ~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~  154 (212)
T 3eaq_A           92 ARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRF  154 (212)
T ss_dssp             TCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGGGHHHHHHHHHHHSSCC
T ss_pred             hcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchhHHHHHHHHHHHhcCcC
Confidence            999999999999999999999999999999999999999999999999888888887776543

>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=99.96  E-value=4.3e-29  Score=223.84  Aligned_cols=146  Identities=38%  Similarity=0.580  Sum_probs=133.1

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|...|.+.|.....  ++||||+++  ..++.+++.|...|+.+..+||+|++.+|..++++|++|+.+|||||+++++
T Consensus       287 ~k~~~l~~~l~~~~~--~~lVF~~t~--~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~r  362 (434)
T 2db3_A          287 AKRSKLIEILSEQAD--GTIVFVETK--RGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASR  362 (434)
T ss_dssp             GHHHHHHHHHHHCCT--TEEEECSSH--HHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTS
T ss_pred             HHHHHHHHHHHhCCC--CEEEEEeCc--HHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhC
Confidence            456677777776543  388899998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhCCCCCchhHHH
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEASGVPIPEDLDK  154 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~~~~~~~~l~~  154 (231)
                      |+|+|+|++||+||+|.++++|+||+||+||.|+.|.|++|+++. +......+.+.+...++++|+++.+
T Consensus       363 GlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          363 GLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             SCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTTCGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             CCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccccHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            999999999999999999999999999999999999999999954 6778888999999999999998654

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

Probab=99.96  E-value=5.8e-29  Score=213.13  Aligned_cols=140  Identities=33%  Similarity=0.483  Sum_probs=124.9

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ...|+..|.++++... +.++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+++
T Consensus        12 ~~~K~~~L~~ll~~~~-~~~~LVF~~t~--~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va   88 (300)
T 3i32_A           12 VRGRLEVLSDLLYVAS-PDRAMVFTRTK--AETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVA   88 (300)
T ss_dssp             SSSHHHHHHHHHHHHC-CSSEEEECSSH--HHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTT
T ss_pred             HHHHHHHHHHHHHhcC-CCCEEEEECCH--HHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechh
Confidence            4678888998888776 67788899998  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      ++|+|+|++++||+||+|+++.+|+||+||+||.|+.|.|++|+++.+...++.+.+.+....
T Consensus        89 ~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~e~~~~~~ie~~~~~~~  151 (300)
T 3i32_A           89 ARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPRERRDVEALERAVGRRF  151 (300)
T ss_dssp             TCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSSTHHHHHHHHHHHTCCC
T ss_pred             hcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChHHHHHHHHHHHHhCCcc
Confidence            999999999999999999999999999999999999999999999999888888888776543

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

Probab=99.96  E-value=3.4e-28  Score=215.05  Aligned_cols=152  Identities=34%  Similarity=0.530  Sum_probs=140.4

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|...|.++++....+.++||||+++  ..++.+++.|...++.+..+||+|++++|..+++.|++|+.+|||||++++
T Consensus       260 ~~~~~~l~~~l~~~~~~~~~lVf~~~~--~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~  337 (417)
T 2i4i_A          260 SDKRSFLLDLLNATGKDSLTLVFVETK--KGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAA  337 (417)
T ss_dssp             GGHHHHHHHHHHTCCTTCEEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHH
T ss_pred             HhHHHHHHHHHHhcCCCCeEEEEECCH--HHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhh
Confidence            345667778888777788999999998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHHHh
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWA  157 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~  157 (231)
                      +|+|+|++++||+||+|+++.+|+||+||+||.|+.|.|++|+++.+...+..+.+.+.....++|.++.++..
T Consensus       338 ~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~  411 (417)
T 2i4i_A          338 RGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAY  411 (417)
T ss_dssp             TTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC--CCEEEEEEECGGGGGGHHHHHHHHHHTTCCCCHHHHHHHT
T ss_pred             cCCCcccCCEEEEEcCCCCHHHHHHhcCccccCCCCceEEEEEccccHHHHHHHHHHHHHhcCcCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999887765

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.91  E-value=5.2e-30  Score=202.14  Aligned_cols=137  Identities=31%  Similarity=0.432  Sum_probs=124.5

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|+..|.++++.. .+.++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||++++
T Consensus        15 ~~k~~~l~~ll~~~-~~~~~iVF~~~~--~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~   91 (170)
T 2yjt_D           15 EHKTALLVHLLKQP-EATRSIVFVRKR--ERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAA   91 (170)
Confidence            56788888888764 456788899988  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHh
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                      +|+|+|++++||+||+|+++.+|+||+||+||.|+.|.+++++.+.+...+..+.+.+..
T Consensus        92 ~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~  151 (170)
T 2yjt_D           92 RGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEE  151 (170)
Confidence            999999999999999999999999999999999999999999999888777777665543

>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=99.95  E-value=1.3e-26  Score=213.41  Aligned_cols=129  Identities=28%  Similarity=0.458  Sum_probs=116.9

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC---CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccC
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA---GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLD   87 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gld   87 (231)
                      ...+.....+.++||||+++  ..++.+++.|...   ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|
T Consensus       330 ~~~~~~~~~~~~~iVF~~s~--~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~GiD  407 (563)
T 3i5x_A          330 KKQIKERDSNYKAIIFAPTV--KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMD  407 (563)
T ss_dssp             HHHHHHTTTCCEEEEECSCH--HHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCC
T ss_pred             HHHHhhcCCCCcEEEEcCcH--HHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcchhhcCCC
Confidence            33444446678999999998  7799999999876   899999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHH
Q psy17587         88 VKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRAL  141 (231)
Q Consensus        88 ip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l  141 (231)
                      +|+|++||+||+|.++.+|+||+||+||.|+.|.|++|+.+.+...++.+.+..
T Consensus       408 ip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~  461 (563)
T 3i5x_A          408 FPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAK  461 (563)
T ss_dssp             CTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHH
T ss_pred             cccCCEEEEECCCCchhhhhhhcCccccCCCCceEEEEEchhHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999887666665544

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

Probab=99.94  E-value=4.2e-26  Score=211.14  Aligned_cols=129  Identities=28%  Similarity=0.458  Sum_probs=117.1

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC---CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccC
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA---GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLD   87 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gld   87 (231)
                      ...+.....+.++||||+++  ..++.+++.|...   ++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|
T Consensus       279 ~~~~~~~~~~~~~iVF~~t~--~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~GiD  356 (579)
T 3sqw_A          279 KKQIKERDSNYKAIIFAPTV--KFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMD  356 (579)
T ss_dssp             HHHHHHTTTCCEEEEECSSH--HHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSCC
T ss_pred             HHHHhhcCCCCcEEEECCcH--HHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCCC
Confidence            34444446678899999988  7799999999876   899999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHH
Q psy17587         88 VKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRAL  141 (231)
Q Consensus        88 ip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l  141 (231)
                      +|+|++||+||+|.++.+|+||+||+||.|+.|.|++|+.+.+...++.+.+..
T Consensus       357 ip~v~~VI~~~~p~s~~~y~Qr~GRagR~g~~g~~i~~~~~~e~~~~~~l~~~~  410 (579)
T 3sqw_A          357 FPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAK  410 (579)
T ss_dssp             CTTCCEEEEESCCSSTTHHHHHHTTSSCTTCCEEEEEEEEGGGHHHHHHHHHHH
T ss_pred             cccCCEEEEcCCCCCHHHhhhhccccccCCCCceEEEEEcccHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999888766666554

>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=99.94  E-value=1.3e-26  Score=204.92  Aligned_cols=144  Identities=34%  Similarity=0.516  Sum_probs=129.5

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ++|...|.+++.... ..++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||++++
T Consensus       261 ~~k~~~l~~~~~~~~-~~~~lVf~~~~--~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~  337 (410)
T 2j0s_A          261 EWKFDTLCDLYDTLT-ITQAVIFCNTK--RKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWA  337 (410)
T ss_dssp             THHHHHHHHHHHHHT-SSEEEEECSSH--HHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGS
T ss_pred             HhHHHHHHHHHHhcC-CCcEEEEEcCH--HHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhh
Confidence            346666777666553 45788899998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCch
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPE  150 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~  150 (231)
                      +|+|+|++++||+||+|+++..|+||+||+||.|+.|.|++|+.+.+...++.+.+++.....++|.
T Consensus       338 ~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~  404 (410)
T 2j0s_A          338 RGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPM  404 (410)
T ss_dssp             SSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCS
T ss_pred             CcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHHHHHHHHHHHHHhCCCceeccc
Confidence            9999999999999999999999999999999999999999999999999888888888766555554

>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=99.94  E-value=2.9e-26  Score=201.76  Aligned_cols=144  Identities=28%  Similarity=0.508  Sum_probs=129.5

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|...+..++... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++
T Consensus       244 ~k~~~l~~~~~~~-~~~~~lVf~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~  320 (400)
T 1s2m_A          244 QKLHCLNTLFSKL-QINQAIIFCNST--NRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTR  320 (400)
T ss_dssp             GHHHHHHHHHHHS-CCSEEEEECSSH--HHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSS
T ss_pred             hHHHHHHHHHhhc-CCCcEEEEEecH--HHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCcccc
Confidence            4555566666544 456888899988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchh
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPED  151 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~  151 (231)
                      |+|+|++++||+||+|+++.+|+||+||+||.|+.|.|++++++.+...++.+.+.+.....++|..
T Consensus       321 Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~  387 (400)
T 1s2m_A          321 GIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPAT  387 (400)
T ss_dssp             SCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSS
T ss_pred             CCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccchHHHHHHHHHHhCCCccccccc
Confidence            9999999999999999999999999999999999999999999999988888888887666666654

>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=99.93  E-value=1.6e-26  Score=204.01  Aligned_cols=148  Identities=31%  Similarity=0.518  Sum_probs=116.3

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .+|+..|.+++.... ..++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||++++
T Consensus       265 ~~~~~~l~~~~~~~~-~~~~lvf~~~~--~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~  341 (414)
T 3eiq_A          265 EWKLDTLCDLYETLT-ITQAVIFINTR--RKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLA  341 (414)
T ss_dssp             TTHHHHHHHHHHSSC-CSSCEEECSCH--HHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC
T ss_pred             HhHHHHHHHHHHhCC-CCcEEEEeCCH--HHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccc
Confidence            346667777766553 45677799988  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHH
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDK  154 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~  154 (231)
                      +|+|+|++++||+||+|++..+|+||+||+||.|+.|.|++|+++.+...++.+.+.+.....++|..+.+
T Consensus       342 ~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  412 (414)
T 3eiq_A          342 RGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVAD  412 (414)
T ss_dssp             --CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECSTHHHHHHHHHHHTTCCCEECCC----
T ss_pred             cCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHHHHHHHHHHHHHHcCCccccChhhhh
Confidence            99999999999999999999999999999999999999999999999998888988888777777766544

>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=99.93  E-value=1.7e-25  Score=195.98  Aligned_cols=144  Identities=28%  Similarity=0.510  Sum_probs=125.3

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|...|.+++... ...++||||+++  ..++.+++.|...|+.+..+||+|++.+|..+++.|++|+.+|||||+++++
T Consensus       236 ~~~~~l~~~l~~~-~~~~~lvf~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~  312 (391)
T 1xti_A          236 EKNRKLFDLLDVL-EFNQVVIFVKSV--QRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGR  312 (391)
T ss_dssp             GHHHHHHHHHHHS-CCSEEEEECSCH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSS
T ss_pred             hHHHHHHHHHHhc-CCCcEEEEeCcH--HHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhc
Confidence            4455666666655 567888899998  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccc-hHHHHHHHHHHHhCCCCCchh
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ-ERHAGEIIRALEASGVPIPED  151 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~-~~~~~~~~~~l~~~~~~~~~~  151 (231)
                      |+|+|++++||++++|+++.+|+||+||+||.|+.|.|++++.+.+ ...++.+.+.+.....++|..
T Consensus       313 Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  380 (391)
T 1xti_A          313 GMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDE  380 (391)
T ss_dssp             CBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCCEECCSC
T ss_pred             CCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCChhhCCcc
Confidence            9999999999999999999999999999999999999999998774 455566666665555555543

>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=99.93  E-value=1.5e-25  Score=208.13  Aligned_cols=130  Identities=13%  Similarity=0.191  Sum_probs=118.5

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      ++..|.++|.....+.++||||+++  ..++.+++.|...|+.+..+||+|++.+|..++++|++|+++|||||+++++|
T Consensus       253 ~~~~l~~~l~~~~~~~~~IVf~~sr--~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~G  330 (591)
T 2v1x_A          253 FIEDIVKLINGRYKGQSGIIYCFSQ--KDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMG  330 (591)
T ss_dssp             HHHHHHHHHTTTTTTCEEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTT
T ss_pred             HHHHHHHHHHHhccCCCeEEEeCcH--HHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcC
Confidence            3456777776665778899999988  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHH
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEI  137 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~  137 (231)
                      +|+|+|++||+|++|.++++|+||+||+||.|.+|.|++++.+.+......+
T Consensus       331 ID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~G~~g~~i~l~~~~D~~~~~~~  382 (591)
T 2v1x_A          331 IDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSM  382 (591)
T ss_dssp             CCCSCEEEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHH
T ss_pred             CCcccccEEEEeCCCCCHHHHHHHhccCCcCCCCceEEEEEChHHHHHHHHH
Confidence            9999999999999999999999999999999999999999998876544433

>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=99.93  E-value=2.4e-25  Score=204.02  Aligned_cols=132  Identities=20%  Similarity=0.335  Sum_probs=119.0

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .+...|.++|... .+.++||||+++  ..++.+++.|...|+.+..+||+|++++|..+++.|++|+.+|||||+++++
T Consensus       222 ~~~~~l~~~l~~~-~~~~~IVf~~sr--~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~  298 (523)
T 1oyw_A          222 KPLDQLMRYVQEQ-RGKSGIIYCNSR--AKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGM  298 (523)
T ss_dssp             SHHHHHHHHHHHT-TTCCEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCT
T ss_pred             CHHHHHHHHHHhc-CCCcEEEEeCCH--HHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhC
Confidence            4566677777655 566788899988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHH
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIR  139 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~  139 (231)
                      |+|+|+|++||+||+|.++++|+||+||+||.|..|.|++++.+.+....+.++.
T Consensus       299 GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g~~~~~~l~~~~~d~~~~~~~~~  353 (523)
T 1oyw_A          299 GINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLE  353 (523)
T ss_dssp             TTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHHH
T ss_pred             CCCccCccEEEEECCCCCHHHHHHHhccccCCCCCceEEEEeCHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999887765544443

>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=99.93  E-value=3.6e-25  Score=191.72  Aligned_cols=138  Identities=34%  Similarity=0.472  Sum_probs=124.5

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      .|+..|.+.++  ..+.++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++
T Consensus       225 ~~~~~l~~~l~--~~~~~~lvf~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~  300 (367)
T 1hv8_A          225 ERFEALCRLLK--NKEFYGLVFCKTK--RDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSR  300 (367)
T ss_dssp             GHHHHHHHHHC--STTCCEEEECSSH--HHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHH
T ss_pred             HHHHHHHHHHh--cCCCcEEEEECCH--HHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhc
Confidence            45566666666  3467788899988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCC
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGV  146 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~  146 (231)
                      |+|+|++++||++++|+++.+|+||+||+||.|+.|.+++++.+.+...+..+.+.++.+..
T Consensus       301 Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~~~~~~~~i~~~~~~~~~  362 (367)
T 1hv8_A          301 GIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLKIK  362 (367)
T ss_dssp             HCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCCCC
T ss_pred             CCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHHHHHHHHHHHHHhCCCCc
Confidence            99999999999999999999999999999999999999999999998888888777755433

>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=99.92  E-value=8.9e-25  Score=192.45  Aligned_cols=141  Identities=27%  Similarity=0.412  Sum_probs=121.2

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |...|.+++... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++|
T Consensus       253 ~~~~l~~~~~~~-~~~~~lvf~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~G  329 (412)
T 3fht_A          253 KFQALCNLYGAI-TIAQAMIFCHTR--KTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARG  329 (412)
T ss_dssp             HHHHHHHHHHHH-SSSEEEEECSSH--HHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSS
T ss_pred             HHHHHHHHHhhc-CCCCEEEEeCCH--HHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccC
Confidence            445555555544 356788899998  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCC------CHhHHHHHhcccCCCCCceeEEEEecccc-hHHHHHHHHHHHhCCCCCc
Q psy17587         86 LDVKHLNLVVNYDCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQ-ERHAGEIIRALEASGVPIP  149 (231)
Q Consensus        86 ldip~v~~VI~~d~P~------~~~~y~qr~GR~gR~g~~g~~i~~~~~~~-~~~~~~~~~~l~~~~~~~~  149 (231)
                      +|+|++++||+||+|+      +..+|+||+||+||.|+.|.|++++.+.+ ...++.+.+.+.....+++
T Consensus       330 idip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  400 (412)
T 3fht_A          330 IDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIERLD  400 (412)
T ss_dssp             CCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHHTCCCEEC-
T ss_pred             CCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHHHHHHHHHHCCccccCC
Confidence            9999999999999995      67899999999999999999999998775 6666677777755544444

>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=99.92  E-value=3.5e-24  Score=187.28  Aligned_cols=131  Identities=32%  Similarity=0.488  Sum_probs=113.8

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLD   87 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gld   87 (231)
                      ..+..++... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++|+|
T Consensus       232 ~~l~~~~~~~-~~~~~lvf~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gid  308 (395)
T 3pey_A          232 DVLTELYGLM-TIGSSIIFVATK--KTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGID  308 (395)
T ss_dssp             HHHHHHHTTT-TSSEEEEECSCH--HHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCC
T ss_pred             HHHHHHHHhc-cCCCEEEEeCCH--HHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCC
Confidence            3344444333 467888899998  7799999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcEEEEecCCC------CHhHHHHHhcccCCCCCceeEEEEecccchH-HHHHHHHHH
Q psy17587         88 VKHLNLVVNYDCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQER-HAGEIIRAL  141 (231)
Q Consensus        88 ip~v~~VI~~d~P~------~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~-~~~~~~~~l  141 (231)
                      +|++++||+||+|+      ++.+|+||+||+||.|+.|.|++++.+.+.. ....+.+.+
T Consensus       309 ip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~  369 (395)
T 3pey_A          309 IPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYF  369 (395)
T ss_dssp             CTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHT
T ss_pred             cccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHh
Confidence            99999999999999      9999999999999999999999999876543 334444443

>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=7.7e-26  Score=198.16  Aligned_cols=146  Identities=32%  Similarity=0.521  Sum_probs=0.0

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      +|...+.+.+... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||+++++
T Consensus       245 ~~~~~l~~~~~~~-~~~~~lVf~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~  321 (394)
T 1fuu_A          245 YKYECLTDLYDSI-SVTQAVIFCNTR--RKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLAR  321 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hHHHHHHHHHhcC-CCCcEEEEECCH--HHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChhhc
Confidence            3555566665544 456788899988  7799999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHH
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLD  153 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~  153 (231)
                      |+|+|++++||++|+|+++.+|+||+||+||.|+.|.|++++++.+...++.+.+.+.....++|..+.
T Consensus       322 Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  390 (394)
T 1fuu_A          322 GIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIA  390 (394)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             CCCcccCCEEEEeCCCCCHHHHHHHcCcccCCCCCceEEEEEchhHHHHHHHHHHHhCCcccccCcchh
Confidence            999999999999999999999999999999999999999999999888888888877766666665443

>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=99.90  E-value=4.8e-24  Score=194.77  Aligned_cols=125  Identities=26%  Similarity=0.296  Sum_probs=68.5

Q ss_pred             CCchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHC------------CCCeeeccCCCCHHHHHHHHHHH
Q psy17587          4 GYPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKA------------GYPCLSLHGGIDQYDRDSTIVDF   68 (231)
Q Consensus         4 ~~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~------------~~~~~~lhg~~~~~~R~~~~~~F   68 (231)
                      ..|+..|.+.|...   ..+.++||||+++  ..++.+++.|...            |.....+||+|++.+|..++++|
T Consensus       371 ~~K~~~L~~~l~~~~~~~~~~k~lVF~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F  448 (556)
T 4a2p_A          371 NPKLEELVCILDDAYRYNPQTRTLLFAKTR--ALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAF  448 (556)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEEESSH--HHHHHHHHHHTTCSGGGSCCEEC-------------------------
T ss_pred             ChHHHHHHHHHHHHhcCCCCceEEEEEccH--HHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHh
Confidence            34677788888654   5678999999988  7899999999765            55566778889999999999999


Q ss_pred             hC-CCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587         69 KN-GKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus        69 ~~-g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                      ++ |+++|||||+++++|+|+|+|++||+||+|+++..|+||+|| ||. +.|.++.|+++.+..
T Consensus       449 ~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~  511 (556)
T 4a2p_A          449 KTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  511 (556)
T ss_dssp             -----CCEEEEEC-----------CEEEEETCCSCHHHHHHC----------CCEEEEESCHHHH
T ss_pred             cccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCcchH
Confidence            99 999999999999999999999999999999999999999999 998 789999999887543

>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=99.89  E-value=2.7e-25  Score=200.92  Aligned_cols=141  Identities=27%  Similarity=0.401  Sum_probs=0.0

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      +++...|..++... ...++||||+++  ..++.+++.|...++.+..+||+|++.+|..+++.|++|+.+|||||++++
T Consensus       318 ~~~~~~l~~~~~~~-~~~~~lvF~~s~--~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~  394 (479)
T 3fmp_B          318 DEKFQALCNLYGAI-TIAQAMIFCHTR--KTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCA  394 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHhhc-cCCceEEEeCcH--HHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccc
Confidence            45566666666544 356788899988  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCC------CHhHHHHHhcccCCCCCceeEEEEecccc-hHHHHHHHHHHHhCCCC
Q psy17587         84 RGLDVKHLNLVVNYDCPN------HYEDYVHRCGRTGRAGNKGFAYTFITLEQ-ERHAGEIIRALEASGVP  147 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~------~~~~y~qr~GR~gR~g~~g~~i~~~~~~~-~~~~~~~~~~l~~~~~~  147 (231)
                      +|+|+|++++||+||+|.      +..+|+||+||+||.|+.|.|++|+.+.+ ...++.+.+.+......
T Consensus       395 ~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~g~~G~~i~~~~~~~~~~~~~~i~~~~~~~~~~  465 (479)
T 3fmp_B          395 RGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHFNKKIER  465 (479)
T ss_dssp             -----------------------------------------------------------------------
T ss_pred             cCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccCCCCceEEEEEcCcchHHHHHHHHHHhCCCceE
Confidence            999999999999999995      56899999999999999999999998765 55555565655444333

>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=99.89  E-value=1.5e-23  Score=179.65  Aligned_cols=117  Identities=34%  Similarity=0.587  Sum_probs=104.8

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEe
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY   97 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~   97 (231)
                      ..++++||||+++  ..++.+++.|.    .+..+||+|++.+|..++++|++|+.+|||||+++++|+|+|++++||+|
T Consensus       218 ~~~~~~lvf~~~~--~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~  291 (337)
T 2z0m_A          218 NKDKGVIVFVRTR--NRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINF  291 (337)
T ss_dssp             CCCSSEEEECSCH--HHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEEES
T ss_pred             CCCCcEEEEEcCH--HHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEEEe
Confidence            3567788899988  77999988885    68899999999999999999999999999999999999999999999999


Q ss_pred             cCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHH
Q psy17587         98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRAL  141 (231)
Q Consensus        98 d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l  141 (231)
                      ++|+++.+|+||+||+||.|+.|.|++++. .+...++.+.+.+
T Consensus       292 ~~~~s~~~~~Q~~GR~gR~g~~g~~~~~~~-~~~~~~~~i~~~~  334 (337)
T 2z0m_A          292 DAPQDLRTYIHRIGRTGRMGRKGEAITFIL-NEYWLEKEVKKVS  334 (337)
T ss_dssp             SCCSSHHHHHHHHTTBCGGGCCEEEEEEES-SCHHHHHHHC---
T ss_pred             cCCCCHHHhhHhcCccccCCCCceEEEEEe-CcHHHHHHHHHHh
Confidence            999999999999999999999999999999 7776666665554

>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=99.89  E-value=2.6e-23  Score=185.25  Aligned_cols=125  Identities=30%  Similarity=0.392  Sum_probs=112.5

Q ss_pred             CCchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccC--------CCCHHHHHHHHHHHhCCC
Q psy17587          4 GYPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHG--------GIDQYDRDSTIVDFKNGK   72 (231)
Q Consensus         4 ~~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg--------~~~~~~R~~~~~~F~~g~   72 (231)
                      ..|+..|.++|...   ..+.++||||+++  ..++.+++.|...|+.+..+||        +|++.+|..+++.|++|+
T Consensus       342 ~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~--~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~  419 (494)
T 1wp9_A          342 HPKMDKLKEIIREQLQRKQNSKIIVFTNYR--ETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE  419 (494)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCH--HHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTS
T ss_pred             ChHHHHHHHHHHHHhccCCCCeEEEEEccH--HHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCC
Confidence            34677788888765   4678899999988  7899999999999999999999        999999999999999999


Q ss_pred             ccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         73 VRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        73 ~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      .+|||||+++++|+|+|++++||+||+|+++..|+||+||+||.|+ |.++.|++++..
T Consensus       420 ~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g~-g~~~~l~~~~t~  477 (494)
T 1wp9_A          420 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMP-GRVIILMAKGTR  477 (494)
T ss_dssp             CSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCCC-SEEEEEEETTSH
T ss_pred             ceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCCC-ceEEEEEecCCH
Confidence            9999999999999999999999999999999999999999999998 999999988753

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

Probab=99.89  E-value=9.4e-24  Score=192.43  Aligned_cols=126  Identities=21%  Similarity=0.267  Sum_probs=88.6

Q ss_pred             Cchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHCC------------CCeeeccCCCCHHHHHHHHHHHh
Q psy17587          5 YPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKAG------------YPCLSLHGGIDQYDRDSTIVDFK   69 (231)
Q Consensus         5 ~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~~------------~~~~~lhg~~~~~~R~~~~~~F~   69 (231)
                      .|+..|.++|...   .++.++||||+++  ..++.+++.|...+            .....+||+|++.+|..++++|+
T Consensus       371 ~k~~~l~~~l~~~~~~~~~~k~lVF~~~~--~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          371 PKLRDLYLVLQEEYHLKPETKTILFVKTR--ALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSSH--HHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeCcH--HHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            4667777777654   4568899999988  78999999998763            34445566999999999999999


Q ss_pred             C-CCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHH
Q psy17587         70 N-GKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHA  134 (231)
Q Consensus        70 ~-g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~  134 (231)
                      + |+++|||||+++++|+|+|+|++||+||+|+++..|+||+|| ||. +.|.++.|+++.+....
T Consensus       449 ~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR~-~~g~~~~l~~~~~~~~~  512 (555)
T 3tbk_A          449 ASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIEK  512 (555)
T ss_dssp             ---CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CTT-TSCEEEEEESCHHHHHH
T ss_pred             cCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-CcC-CCceEEEEEcCCCHHHH
Confidence            9 999999999999999999999999999999999999999999 998 88999999988765443

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.88  E-value=9.5e-23  Score=172.23  Aligned_cols=125  Identities=18%  Similarity=0.180  Sum_probs=96.6

Q ss_pred             CCCchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHHHHHHHHHHHhCC-Ccc-EEEe
Q psy17587          3 AGYPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFKNG-KVR-LLIA   78 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~-vLva   78 (231)
                      ...|+..|.++|... ..+.++||||+..  ..++.+...|... |+.+..+||++++.+|..++++|+++ +++ +|++
T Consensus        94 ~s~K~~~L~~ll~~~~~~~~kvlIFs~~~--~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~s  171 (271)
T 1z5z_A           94 RSGKMIRTMEIIEEALDEGDKIAIFTQFV--DMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLS  171 (271)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCH--HHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             cCHHHHHHHHHHHHHHhCCCeEEEEeccH--HHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEe
Confidence            345778888888765 3467899999987  7799999999875 99999999999999999999999998 677 7899


Q ss_pred             cCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeE--EEEeccc
Q psy17587         79 TSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFA--YTFITLE  129 (231)
Q Consensus        79 T~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~--i~~~~~~  129 (231)
                      |+++++|+|++.+++||+||+||++..|.||+||++|.|+.+.+  +.+++.+
T Consensus       172 t~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~Gq~~~v~v~~li~~~  224 (271)
T 1z5z_A          172 VKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  224 (271)
T ss_dssp             CCTTCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             hhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccccCCCCceEEEEEeeCC
Confidence            99999999999999999999999999999999999999986554  5566655

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

Probab=99.88  E-value=2.6e-22  Score=177.97  Aligned_cols=125  Identities=21%  Similarity=0.288  Sum_probs=107.7

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCee-eccCCCCHHHHHHHHHHHhCCCccEEEe----cC
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCL-SLHGGIDQYDRDSTIVDFKNGKVRLLIA----TS   80 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~-~lhg~~~~~~R~~~~~~F~~g~~~vLva----T~   80 (231)
                      +...|.++|+..  +.++||||+++  ..++.+++.|...|+++. .+||.    +|.  ++.|++|+++||||    |+
T Consensus       240 ~~~~l~~~l~~~--~~~~lVF~~~~--~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~~~vLvat~s~T~  309 (414)
T 3oiy_A          240 SKEKLVELLEIF--RDGILIFAQTE--EEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGKINILIGVQAYYG  309 (414)
T ss_dssp             CHHHHHHHHHHH--CSSEEEEESSH--HHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTSCSEEEEECCTTC
T ss_pred             HHHHHHHHHHHc--CCCEEEEECCH--HHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCCCeEEEEecCcCc
Confidence            455666777663  47788899998  779999999999999998 99995    344  99999999999999    99


Q ss_pred             ccccccCCCC-CcEEEEecCC--CCHhHHHHHhcccCCCC----CceeEEEEecccchHHHHHHHHHHH
Q psy17587         81 VAARGLDVKH-LNLVVNYDCP--NHYEDYVHRCGRTGRAG----NKGFAYTFITLEQERHAGEIIRALE  142 (231)
Q Consensus        81 ~~~~Gldip~-v~~VI~~d~P--~~~~~y~qr~GR~gR~g----~~g~~i~~~~~~~~~~~~~~~~~l~  142 (231)
                      ++++|+|+|+ |++||+||+|  .++.+|+||+||+||.|    +.|.+++|+  .+...+..+.+.+.
T Consensus       310 ~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g~~~~~~g~~i~~~--~~~~~~~~l~~~~~  376 (414)
T 3oiy_A          310 KLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  376 (414)
T ss_dssp             CCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             hhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCCCCCCcceEEEEEE--ccHHHHHHHHHHhc
Confidence            9999999999 9999999999  99999999999999988    589999999  55555666666664

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

Probab=99.88  E-value=3.9e-23  Score=194.39  Aligned_cols=127  Identities=22%  Similarity=0.252  Sum_probs=80.1

Q ss_pred             CCchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHCC----CCeeec--------cCCCCHHHHHHHHHHH
Q psy17587          4 GYPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKAG----YPCLSL--------HGGIDQYDRDSTIVDF   68 (231)
Q Consensus         4 ~~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~~----~~~~~l--------hg~~~~~~R~~~~~~F   68 (231)
                      ..|+..|.++|...   .++.++||||+++  ..++.+++.|...+    +++..+        ||+|++++|..++++|
T Consensus       379 ~~k~~~L~~ll~~~~~~~~~~~~IIF~~~~--~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F  456 (696)
T 2ykg_A          379 NPKLEDLCFILQEEYHLNPETITILFVKTR--ALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAF  456 (696)
T ss_dssp             CHHHHHHHHHHHHHHTTCTTCCEEEECSCH--HHHHHHHHHHHHCTTCCSCCEEC-------------------------
T ss_pred             CHHHHHHHHHHHHHhccCCCCcEEEEeCcH--HHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHH
Confidence            34677777777655   3567889999988  77999999999887    899999        5599999999999999


Q ss_pred             hC-CCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHH
Q psy17587         69 KN-GKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHA  134 (231)
Q Consensus        69 ~~-g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~  134 (231)
                      ++ |+.+|||||+++++|||+|+|++||+||+|+++.+|+||+|| ||. +.|.++++++..+....
T Consensus       457 ~~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~-~~g~~~~l~~~~~~~~~  521 (696)
T 2ykg_A          457 KASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA-RGSKCFLLTSNAGVIEK  521 (696)
T ss_dssp             ----CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC-----------CCCEEEEEESCHHHHHH
T ss_pred             HhcCCccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC-CCceEEEEecCCCHHHH
Confidence            98 999999999999999999999999999999999999999999 998 67999999987765433

>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=99.87  E-value=1.1e-22  Score=191.32  Aligned_cols=119  Identities=25%  Similarity=0.365  Sum_probs=96.4

Q ss_pred             CchhhhhccccccC---C-CCeEEEEcCChhHHHHHHHHHHHHHC------CCCeeeccCC--------CCHHHHHHHHH
Q psy17587          5 YPCLSLHGGIDQYD---R-DSTIVDFKNGKVRLLVCAIVKELMKA------GYPCLSLHGG--------IDQYDRDSTIV   66 (231)
Q Consensus         5 ~k~~~L~~~L~~~~---~-~~~iiiF~~~~~~~~~~~l~~~L~~~------~~~~~~lhg~--------~~~~~R~~~~~   66 (231)
                      .|+..|.+.|....   + +.++||||+++  ..++.|++.|...      |+++..+||+        |++.+|..+++
T Consensus       381 ~k~~~L~~~L~~~~~~~~~~~~~IVF~~s~--~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~  458 (699)
T 4gl2_A          381 EKLTKLRNTIMEQYTRTEESARGIIFTKTR--QSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVIS  458 (699)
T ss_dssp             -CSSCSHHHHHHHHHHSSSCCCEEEECSCH--HHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCcEEEEECcH--HHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHH
Confidence            45666666665421   2 68888899988  7899999999877      8999999999        99999999999


Q ss_pred             HHhCCCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecc
Q psy17587         67 DFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITL  128 (231)
Q Consensus        67 ~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~  128 (231)
                      +|++|+++|||||+++++|||+|+|++||+||+|+++.+|+||+||+||.|   .+++++.+
T Consensus       459 ~F~~g~~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr~g---~~~~l~~~  517 (699)
T 4gl2_A          459 KFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE---STYVLVAH  517 (699)
T ss_dssp             HHCC---CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCSSS---CEEEEEEE
T ss_pred             HHhcCCCcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCCCC---ceEEEEEe
Confidence            999999999999999999999999999999999999999999999977655   44444443

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=99.87  E-value=7.1e-22  Score=185.50  Aligned_cols=126  Identities=21%  Similarity=0.275  Sum_probs=112.4

Q ss_pred             hhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          7 CLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         7 ~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      ...|+..|... ..+.++||||+++  ..++.+++.|...|+++.++||+|++.+|..++++|++|+++|||||+++++|
T Consensus       431 ~~~Ll~~l~~~~~~~~~vlVf~~t~--~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~G  508 (661)
T 2d7d_A          431 IDDLIGEIQARIERNERVLVTTLTK--KMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREG  508 (661)
T ss_dssp             HHHHHHHHHHHHTTTCEEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTT
T ss_pred             HHHHHHHHHHHHhcCCeEEEEECCH--HHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCC
Confidence            44555555544 3567999999998  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecC-----CCCHhHHHHHhcccCCCCCceeEEEEecccchHHHH
Q psy17587         86 LDVKHLNLVVNYDC-----PNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAG  135 (231)
Q Consensus        86 ldip~v~~VI~~d~-----P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~  135 (231)
                      +|+|+|++||++|.     |.+..+|+||+||+||. ..|.|++|+++.+....+
T Consensus       509 lDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~-~~G~~i~~~~~~~~~~~~  562 (661)
T 2d7d_A          509 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN-AEGRVIMYADKITKSMEI  562 (661)
T ss_dssp             CCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS-TTCEEEEECSSCCHHHHH
T ss_pred             cccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC-CCCEEEEEEeCCCHHHHH
Confidence            99999999999997     99999999999999998 689999999887654443

>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=99.87  E-value=1.8e-22  Score=193.17  Aligned_cols=124  Identities=26%  Similarity=0.297  Sum_probs=73.3

Q ss_pred             Cchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHC------------CCCeeeccCCCCHHHHHHHHHHHh
Q psy17587          5 YPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKA------------GYPCLSLHGGIDQYDRDSTIVDFK   69 (231)
Q Consensus         5 ~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~------------~~~~~~lhg~~~~~~R~~~~~~F~   69 (231)
                      .|+..|.+.|...   ..+.++||||+++  ..++.|++.|...            |..+..+||+|++.+|..++++|+
T Consensus       613 ~K~~~L~~lL~~~~~~~~~~kvLIF~~~~--~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~  690 (797)
T 4a2q_A          613 PKLEELVCILDDAYRYNPQTRTLLFAKTR--ALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK  690 (797)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCEEEEESSH--HHHHHHHHHHHTCSTTCSCCCEEC-------------------------
T ss_pred             hHHHHHHHHHHHHhccCCCCeEEEEECcH--HHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhh
Confidence            3677788888652   5578999999988  7899999999763            566677899999999999999999


Q ss_pred             C-CCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587         70 N-GKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus        70 ~-g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                      + |+++|||||+++++|||+|+|++||+||+|+++..|+||+|| ||. +.|.++.|+++.+..
T Consensus       691 ~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~-~~g~~i~l~~~~~~e  752 (797)
T 4a2q_A          691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVV  752 (797)
T ss_dssp             ---CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC---------CCCEEEEECCHHHH
T ss_pred             ccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCceEEEEEeCCcHH
Confidence            9 999999999999999999999999999999999999999999 998 789999999877543

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=99.87  E-value=1.2e-21  Score=184.07  Aligned_cols=128  Identities=21%  Similarity=0.314  Sum_probs=112.6

Q ss_pred             hhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          7 CLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         7 ~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      ...|+..|... ..+.++||||+++  ..++.|++.|...|+++.++||+|++.+|..++++|++|+++|||||+++++|
T Consensus       425 ~~~Ll~~l~~~~~~~~~vlVf~~t~--~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~G  502 (664)
T 1c4o_A          425 ILDLMEGIRERAARGERTLVTVLTV--RMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREG  502 (664)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTT
T ss_pred             HHHHHHHHHHHHhcCCEEEEEECCH--HHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcC
Confidence            44455555443 3578999999998  77999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecC-----CCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHH
Q psy17587         86 LDVKHLNLVVNYDC-----PNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEI  137 (231)
Q Consensus        86 ldip~v~~VI~~d~-----P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~  137 (231)
                      +|+|+|++||++|.     |.+..+|+||+||+||.+ .|.+++++.+.+....+.+
T Consensus       503 lDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~~-~G~~i~~~~~~~~~~~~~i  558 (664)
T 1c4o_A          503 LDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA-RGEVWLYADRVSEAMQRAI  558 (664)
T ss_dssp             CCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTST-TCEEEEECSSCCHHHHHHH
T ss_pred             ccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcCC-CCEEEEEEcCCCHHHHHHH
Confidence            99999999999998     999999999999999985 7999999988765444333

>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=99.87  E-value=1.9e-22  Score=190.61  Aligned_cols=123  Identities=21%  Similarity=0.193  Sum_probs=108.9

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...|.+.|... ..++.+||||+++  ..++.|++.|...|+++..+||++++++|..+.+.|+.|  .|+||||+++
T Consensus       416 ~K~~al~~~i~~~~~~~~pvLVft~s~--~~se~Ls~~L~~~gi~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAg  491 (844)
T 1tf5_A          416 GKFKAVAEDVAQRYMTGQPVLVGTVAV--ETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAG  491 (844)
T ss_dssp             HHHHHHHHHHHHHHHHTCCEEEEESCH--HHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSS
T ss_pred             HHHHHHHHHHHHHHhcCCcEEEEECCH--HHHHHHHHHHHHCCCCEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccc
Confidence            4566777777653 4567899999998  779999999999999999999999999988776667665  6999999999


Q ss_pred             cccCCC--------CCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         84 RGLDVK--------HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        84 ~Gldip--------~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||+|++        ++.+|||||+|.+...|+||+||+||.|.+|.+++|++..|.
T Consensus       492 RG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~G~s~~~vs~eD~  547 (844)
T 1tf5_A          492 RGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDE  547 (844)
T ss_dssp             TTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTSS
T ss_pred             cCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCCCeEEEEecHHHH
Confidence            999999        788999999999999999999999999999999999997763

>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=99.86  E-value=4.4e-22  Score=178.76  Aligned_cols=124  Identities=17%  Similarity=0.195  Sum_probs=100.9

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE---
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN---   96 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~---   96 (231)
                      +.+++|||+++  ..++.+++.|...++++..+||    .+|..+++.|++|+++|||||+++++|+|+| +++||+   
T Consensus       177 ~~~~lVF~~s~--~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~  249 (440)
T 1yks_A          177 KRPTAWFLPSI--RAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRT  249 (440)
T ss_dssp             CSCEEEECSCH--HHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCE
T ss_pred             CCCEEEEeCCH--HHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCc
Confidence            56788899998  7799999999999999999999    4688999999999999999999999999999 999986   


Q ss_pred             ----------------ecCCCCHhHHHHHhcccCCC-CCceeEEEEe---cccchHHHHHHHHHHHhCCCCCch
Q psy17587         97 ----------------YDCPNHYEDYVHRCGRTGRA-GNKGFAYTFI---TLEQERHAGEIIRALEASGVPIPE  150 (231)
Q Consensus        97 ----------------~d~P~~~~~y~qr~GR~gR~-g~~g~~i~~~---~~~~~~~~~~~~~~l~~~~~~~~~  150 (231)
                                      ++.|.+.++|+||+||+||. |..|.|++|+   ++.+...+..+...+.....+++.
T Consensus       250 ~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~g~~~~l~~~~~~~~~~~l~~l~~~~~~~~~~l~~  323 (440)
T 1yks_A          250 AFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASMLLDNMEVRG  323 (440)
T ss_dssp             EEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHHHHTTSCCGG
T ss_pred             cceeeecccccceeeccccccCHHHHHHhccccCCCCCCCceEEEEeccCChhhhhhhhhhhHHhccccccccc
Confidence                            99999999999999999997 6799999996   566766666776666555555554

>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=99.86  E-value=4.8e-22  Score=193.13  Aligned_cols=123  Identities=26%  Similarity=0.305  Sum_probs=73.8

Q ss_pred             Cchhhhhcccccc---CCCCeEEEEcCChhHHHHHHHHHHHHHC------------CCCeeeccCCCCHHHHHHHHHHHh
Q psy17587          5 YPCLSLHGGIDQY---DRDSTIVDFKNGKVRLLVCAIVKELMKA------------GYPCLSLHGGIDQYDRDSTIVDFK   69 (231)
Q Consensus         5 ~k~~~L~~~L~~~---~~~~~iiiF~~~~~~~~~~~l~~~L~~~------------~~~~~~lhg~~~~~~R~~~~~~F~   69 (231)
                      .|+..|.++|...   ..+.++||||+++  ..++.|++.|...            |..+..+||+|++.+|..++++|+
T Consensus       613 ~K~~~L~~lL~~~~~~~~~~rvLIF~~t~--~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr  690 (936)
T 4a2w_A          613 PKLEELVCILDDAYRYNPQTRTLLFAKTR--ALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFK  690 (936)
T ss_dssp             HHHHHHHHHHHHTTTSCTTCCEEEEESSH--HHHHHHHHHHHHCSTTSSCCCEEC-------------------------
T ss_pred             HHHHHHHHHHHHHhccCCCCeEEEEeCCH--HHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhh
Confidence            3677777777654   4578999999988  7899999999876            555667789999999999999999


Q ss_pred             C-CCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         70 N-GKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        70 ~-g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      + |+++|||||+++++|||+|+|++||+||+|+++.+|+||+|| ||. ..|.++.+++..+.
T Consensus       691 ~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~-~~g~vi~Li~~~t~  751 (936)
T 4a2w_A          691 TSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEV  751 (936)
T ss_dssp             ---CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC---------CCCEEEEESCHHH
T ss_pred             ccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC-CCCEEEEEEeCCCH
Confidence            9 999999999999999999999999999999999999999999 998 67999999887643

>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=99.86  E-value=1.5e-21  Score=182.02  Aligned_cols=133  Identities=20%  Similarity=0.189  Sum_probs=113.0

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDV   88 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldi   88 (231)
                      .++..|.+.  ..++||||+++  ..++.+++.|...++++..+||+    +|.+++++|++|+.+||||||++++|+|+
T Consensus       346 ~ll~~l~~~--~~~~LVF~~s~--~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi  417 (618)
T 2whx_A          346 TGFDWITDY--QGKTVWFVPSI--KAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANF  417 (618)
T ss_dssp             SSCHHHHHC--CSCEEEECSSH--HHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCC
T ss_pred             HHHHHHHhC--CCCEEEEECCh--hHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCccc
Confidence            344444432  56788899998  77999999999999999999985    68889999999999999999999999999


Q ss_pred             CCCcEE--------------------EEecCCCCHhHHHHHhcccCCCCC-ceeEEEEec---ccchHHHHHHHHHHHhC
Q psy17587         89 KHLNLV--------------------VNYDCPNHYEDYVHRCGRTGRAGN-KGFAYTFIT---LEQERHAGEIIRALEAS  144 (231)
Q Consensus        89 p~v~~V--------------------I~~d~P~~~~~y~qr~GR~gR~g~-~g~~i~~~~---~~~~~~~~~~~~~l~~~  144 (231)
                      | +++|                    |+||+|.+.++|+||+||+||.|. .|.|++|++   +.+...+..++..+...
T Consensus       418 ~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~g~~~G~ai~l~~~~~~~d~~~l~~le~~i~l~  496 (618)
T 2whx_A          418 R-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLD  496 (618)
T ss_dssp             C-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTCHHHHHHHHHHT
T ss_pred             C-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCCCCCCCeEEEEccCCchhhHHHHHHHHhHhccc
Confidence            8 8887                    888999999999999999999975 899999998   67777777777766665


Q ss_pred             CCCCch
Q psy17587        145 GVPIPE  150 (231)
Q Consensus       145 ~~~~~~  150 (231)
                      ...+++
T Consensus       497 ~~~~~~  502 (618)
T 2whx_A          497 NIYTPE  502 (618)
T ss_dssp             TCCCTT
T ss_pred             cccCCc
Confidence            555554

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=99.86  E-value=1.4e-21  Score=190.35  Aligned_cols=135  Identities=16%  Similarity=0.229  Sum_probs=115.6

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHH-CCCCeeeccCCCCHHHHHHHHHHHhCCC--ccEEEecCc
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK-AGYPCLSLHGGIDQYDRDSTIVDFKNGK--VRLLIATSV   81 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~-~~~~~~~lhg~~~~~~R~~~~~~F~~g~--~~vLvaT~~   81 (231)
                      .|+..|.+++.. ..+.++||||+++  ..++.+++.|.. .|+++..+||+|++.+|..+++.|++|+  ++|||||++
T Consensus       489 ~K~~~L~~ll~~-~~~~k~iVF~~~~--~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v  565 (968)
T 3dmq_A          489 PRVEWLMGYLTS-HRSQKVLVICAKA--ATALQLEQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEI  565 (968)
T ss_dssp             HHHHHHHHHHHH-TSSSCCCEECSST--HHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCC
T ss_pred             HHHHHHHHHHHh-CCCCCEEEEeCcH--HHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecch
Confidence            467778888776 4567788899998  779999999984 5999999999999999999999999998  999999999


Q ss_pred             cccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHH
Q psy17587         82 AARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE  142 (231)
Q Consensus        82 ~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~  142 (231)
                      +++|+|+|++++||+||+|+++..|.||+||+||.|+.+.++++....+....+.+.+.+.
T Consensus       566 ~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~Gq~~~v~v~~~~~~~t~ee~i~~~~~  626 (968)
T 3dmq_A          566 GSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYH  626 (968)
T ss_dssp             TTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSSSCSCCEEEEEEETTSHHHHHHHHHH
T ss_pred             hhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCCCCceEEEEEecCCChHHHHHHHHHH
Confidence            9999999999999999999999999999999999999887766654444444444555553

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.84  E-value=3.3e-21  Score=179.38  Aligned_cols=123  Identities=20%  Similarity=0.221  Sum_probs=107.8

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...|.+.+... ..++.+||||+++  ..++.|++.|...|+++..+||++.++++..+.+.|+.|  .|+||||+++
T Consensus       458 eK~~al~~~I~~~~~~gqpVLVFt~S~--e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVATdmAg  533 (822)
T 3jux_A          458 EKYEKIVEEIEKRYKKGQPVLVGTTSI--EKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIATNMAG  533 (822)
T ss_dssp             HHHHHHHHHHHHHHHHTCCEEEEESSH--HHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEETTTT
T ss_pred             HHHHHHHHHHHHHhhCCCCEEEEECCH--HHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEcchhh
Confidence            4566777777654 3578899999998  779999999999999999999997777777666677766  6999999999


Q ss_pred             cccCCC--------CCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         84 RGLDVK--------HLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        84 ~Gldip--------~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||+||+        +..+|||+++|.+...|+||+||+||.|.+|.+++|++.+|.
T Consensus       534 RGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG~~G~a~~fvsleD~  589 (822)
T 3jux_A          534 RGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDD  589 (822)
T ss_dssp             TTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSSCCCEEEEEEETTSH
T ss_pred             CCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCCCCeeEEEEechhHH
Confidence            999998        566999999999999999999999999999999999998873

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

Probab=99.84  E-value=6.1e-21  Score=179.26  Aligned_cols=116  Identities=20%  Similarity=0.229  Sum_probs=102.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE--
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN--   96 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~--   96 (231)
                      .+.++||||+++  ..++.+++.|...++++..+||+    +|.++++.|++|+++|||||+++++|+|+| +++||+  
T Consensus       409 ~~~~~lVF~~s~--~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI~~g  481 (673)
T 2wv9_A          409 YAGKTVWFVASV--KMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVIDCR  481 (673)
T ss_dssp             CCSCEEEECSSH--HHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEEECC
T ss_pred             CCCCEEEEECCH--HHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcceeeC-CcEEEECC
Confidence            367888899998  77999999999999999999994    799999999999999999999999999999 999998  


Q ss_pred             ------------------ecCCCCHhHHHHHhcccCCC-CCceeEEEEe---cccchHHHHHHHHHH
Q psy17587         97 ------------------YDCPNHYEDYVHRCGRTGRA-GNKGFAYTFI---TLEQERHAGEIIRAL  141 (231)
Q Consensus        97 ------------------~d~P~~~~~y~qr~GR~gR~-g~~g~~i~~~---~~~~~~~~~~~~~~l  141 (231)
                                        ||+|.+.++|+||+||+||. |+.|.|++|+   .+.+...+..+...+
T Consensus       482 ~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~~g~~G~ai~l~~~~~~~d~~~l~~ie~~~  548 (673)
T 2wv9_A          482 KSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRNPSQIGDEYHYGGGTSEDDTMLAHWTEAKI  548 (673)
T ss_dssp             EECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCCSSCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             CcccceeeecccccceecccCCCCHHHHHHHhhccCCCCCCCCEEEEEEecCChhHHHHHHHHHHHH
Confidence                              67999999999999999999 7899999996   455655555554444

>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=99.83  E-value=9.4e-21  Score=178.85  Aligned_cols=123  Identities=17%  Similarity=0.150  Sum_probs=111.1

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...|.+.+... ..++.+||||+++  ..++.|++.|...|+++.++||++.++++..+.++|+.|  .|+||||+++
T Consensus       425 ~K~~al~~~i~~~~~~gqpvLVft~si--e~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAg  500 (853)
T 2fsf_A          425 EKIQAIIEDIKERTAKGQPVLVGTISI--EKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAG  500 (853)
T ss_dssp             HHHHHHHHHHHHHHTTTCCEEEEESSH--HHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCS
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEECcH--HHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEeccccc
Confidence            4667777777654 4578899999998  779999999999999999999999999998888999988  6999999999


Q ss_pred             cccCCCCC-------------------------------------cEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEe
Q psy17587         84 RGLDVKHL-------------------------------------NLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFI  126 (231)
Q Consensus        84 ~Gldip~v-------------------------------------~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~  126 (231)
                      ||+||+..                                     .+||+++.|.+...|.||+||+||.|.+|.+++|+
T Consensus       501 RGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fl  580 (853)
T 2fsf_A          501 RGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYL  580 (853)
T ss_dssp             SCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEE
T ss_pred             CCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEe
Confidence            99999974                                     59999999999999999999999999999999999


Q ss_pred             cccch
Q psy17587        127 TLEQE  131 (231)
Q Consensus       127 ~~~~~  131 (231)
                      +..|.
T Consensus       581 s~eD~  585 (853)
T 2fsf_A          581 SMEDA  585 (853)
T ss_dssp             ETTSG
T ss_pred             cccHH
Confidence            87763

>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=99.83  E-value=3e-21  Score=174.22  Aligned_cols=110  Identities=24%  Similarity=0.289  Sum_probs=96.6

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCC
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKH   90 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~   90 (231)
                      ++.|.+.  .+++||||+++  ..++.+++.|...++.+..+||.    +|..+++.|++|+.+|||||+++++|+|+|+
T Consensus       183 ~~~l~~~--~~~~LVF~~s~--~~~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~  254 (459)
T 2z83_A          183 YEWITEY--AGKTVWFVASV--KMGNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA  254 (459)
T ss_dssp             CHHHHHC--CSCEEEECSCH--HHHHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC
T ss_pred             HHHHHhc--CCCEEEEeCCh--HHHHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC
Confidence            3444443  56788899998  77999999999999999999995    7888999999999999999999999999999


Q ss_pred             CcEEEE--------------------ecCCCCHhHHHHHhcccCCCCC-ceeEEEEeccc
Q psy17587         91 LNLVVN--------------------YDCPNHYEDYVHRCGRTGRAGN-KGFAYTFITLE  129 (231)
Q Consensus        91 v~~VI~--------------------~d~P~~~~~y~qr~GR~gR~g~-~g~~i~~~~~~  129 (231)
                       ++||+                    ||+|.+..+|+||+||+||.|. .|.|++|+.+.
T Consensus       255 -~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g~~~G~~~~~~~~~  313 (459)
T 2z83_A          255 -SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNPNQVGDEYHYGGAT  313 (459)
T ss_dssp             -SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             -CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCCCCCCeEEEEEccc
Confidence             99999                    7899999999999999999997 89999999875

>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=99.82  E-value=2.3e-20  Score=168.07  Aligned_cols=103  Identities=19%  Similarity=0.184  Sum_probs=94.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEec-
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD-   98 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d-   98 (231)
                      ..++||||+++  ..++.+++.|...|+.+..+||++.    .++++.|++|+.+|||||+++++|+|+|+ ++||||| 
T Consensus       188 ~~~~lVF~~s~--~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~  260 (451)
T 2jlq_A          188 QGKTVWFVPSI--KAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRR  260 (451)
T ss_dssp             CSCEEEECSSH--HHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCE
T ss_pred             CCCEEEEcCCH--HHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCC
Confidence            45788899998  7799999999999999999999864    57899999999999999999999999999 9999999 


Q ss_pred             -------------------CCCCHhHHHHHhcccCCCCC-ceeEEEEeccc
Q psy17587         99 -------------------CPNHYEDYVHRCGRTGRAGN-KGFAYTFITLE  129 (231)
Q Consensus        99 -------------------~P~~~~~y~qr~GR~gR~g~-~g~~i~~~~~~  129 (231)
                                         .|.+..+|+||+||+||.|. .|.|++|....
T Consensus       261 ~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g~~~g~~~~~~~~~  311 (451)
T 2jlq_A          261 CLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDP  311 (451)
T ss_dssp             EEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCC
T ss_pred             cccccccccccceeeecccccCCHHHHHHhccccCCCCCCCccEEEEeCCc
Confidence                               99999999999999999998 88998887543

>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=99.81  E-value=8.9e-20  Score=172.70  Aligned_cols=123  Identities=16%  Similarity=0.193  Sum_probs=109.8

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|...|.+.+... ..++.+||||+++  +.++.|++.|...|+++.++||++.++++..+.+.|+.|  .|+||||+++
T Consensus       444 ~K~~al~~~i~~~~~~gqpvLVft~Si--e~sE~Ls~~L~~~Gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAg  519 (922)
T 1nkt_A          444 AKYIAVVDDVAERYAKGQPVLIGTTSV--ERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAG  519 (922)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEESCH--HHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCS
T ss_pred             HHHHHHHHHHHHHHhcCCcEEEEECCH--HHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecchhh
Confidence            3566777777553 4567899999998  779999999999999999999999888888888888888  6999999999


Q ss_pred             cccCCCCC----------------------------------------------------cEEEEecCCCCHhHHHHHhc
Q psy17587         84 RGLDVKHL----------------------------------------------------NLVVNYDCPNHYEDYVHRCG  111 (231)
Q Consensus        84 ~Gldip~v----------------------------------------------------~~VI~~d~P~~~~~y~qr~G  111 (231)
                      ||+||+.+                                                    .+||+++.|.+...|.||+|
T Consensus       520 RGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~G  599 (922)
T 1nkt_A          520 RGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRG  599 (922)
T ss_dssp             TTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHH
T ss_pred             cCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhc
Confidence            99999975                                                    49999999999999999999


Q ss_pred             ccCCCCCceeEEEEecccch
Q psy17587        112 RTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus       112 R~gR~g~~g~~i~~~~~~~~  131 (231)
                      |+||.|.+|.+++|++..|.
T Consensus       600 RTGRqGdpG~s~fflSleD~  619 (922)
T 1nkt_A          600 RSGRQGDPGESRFYLSLGDE  619 (922)
T ss_dssp             TSSGGGCCEEEEEEEETTSH
T ss_pred             ccccCCCCeeEEEEechhHH
Confidence            99999999999999988765

>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=99.81  E-value=7.9e-20  Score=179.36  Aligned_cols=129  Identities=17%  Similarity=0.237  Sum_probs=106.6

Q ss_pred             CchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEe----cC
Q psy17587          5 YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIA----TS   80 (231)
Q Consensus         5 ~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLva----T~   80 (231)
                      .|...|.++++..  +.++||||+++  ..++.+++.|... +++..+||+|.     .++++|++|+.+||||    |+
T Consensus       262 ~k~~~L~~ll~~~--~~~~LVF~~t~--~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Td  331 (1054)
T 1gku_B          262 ESISTLSSILEKL--GTGGIIYARTG--EEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYG  331 (1054)
T ss_dssp             CCTTTTHHHHTTS--CSCEEEEESSH--HHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC---
T ss_pred             hHHHHHHHHHhhc--CCCEEEEEcCH--HHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCC
Confidence            4555666666655  46788899998  7799999999887 99999999983     7889999999999999    99


Q ss_pred             ccccccCCCCC-cEEEEecCC-----------------------------------------------------------
Q psy17587         81 VAARGLDVKHL-NLVVNYDCP-----------------------------------------------------------  100 (231)
Q Consensus        81 ~~~~Gldip~v-~~VI~~d~P-----------------------------------------------------------  100 (231)
                      ++++|+|+|+| ++||++|+|                                                           
T Consensus       332 v~~rGIDip~VI~~VI~~~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  411 (1054)
T 1gku_B          332 TLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQA  411 (1054)
T ss_dssp             ---CCSCCTTTCCEEEEESCCEEEEECSCGGGSCHHHHHHHHTTTSCHHHHHTTCTTTSSCHHHHHHHHHHHHTTSCCSC
T ss_pred             eeEeccccCCcccEEEEeCCCcccccccccccChHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence            99999999996 999999999                                                           


Q ss_pred             ------------CCHhHHHHHhcccCCCCCce--eEEEEecccchHHHHHHHHHHHh
Q psy17587        101 ------------NHYEDYVHRCGRTGRAGNKG--FAYTFITLEQERHAGEIIRALEA  143 (231)
Q Consensus       101 ------------~~~~~y~qr~GR~gR~g~~g--~~i~~~~~~~~~~~~~~~~~l~~  143 (231)
                                  .+..+|+||+||+||.|..|  .+++++...+...+..+.+.+..
T Consensus       412 ~~~~~~~~~~~~~~~~~yiQr~GRagR~g~~g~~~g~~~~~~~d~~~~~~l~~~l~~  468 (1054)
T 1gku_B          412 KDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKL  468 (1054)
T ss_dssp             SSSEEETTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEECSCHHHHHHHHHHHHT
T ss_pred             cceeEeecceecCcHHHHhhhhchhhhccCCCCceEEEEEEecCHHHHHHHHHHHhh
Confidence                        78999999999999987765  47888888888888888887774

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

Probab=99.81  E-value=1.4e-19  Score=171.04  Aligned_cols=112  Identities=17%  Similarity=0.346  Sum_probs=96.6

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHCC------------------------------------CCeeeccCCCCHHHH
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKAG------------------------------------YPCLSLHGGIDQYDR   61 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~~------------------------------------~~~~~lhg~~~~~~R   61 (231)
                      ..++.+||||+++  ..++.+++.|....                                    ..+.++||+|++.+|
T Consensus       250 ~~~~~~LVF~~s~--~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r  327 (715)
T 2va8_A          250 SKNGQVLVFRNSR--KMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALR  327 (715)
T ss_dssp             TTTCCEEEECSSH--HHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHH
T ss_pred             hcCCCEEEEECCH--HHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHH
Confidence            3568889999998  77999999987542                                    248999999999999


Q ss_pred             HHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ec-------CCCCHhHHHHHhcccCCCC--CceeEEEEecc
Q psy17587         62 DSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YD-------CPNHYEDYVHRCGRTGRAG--NKGFAYTFITL  128 (231)
Q Consensus        62 ~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d-------~P~~~~~y~qr~GR~gR~g--~~g~~i~~~~~  128 (231)
                      ..+++.|++|.++|||||+++++|+|+|++++||+    ||       .|.+..+|.||+|||||.|  ..|.|+.++++
T Consensus       328 ~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~  407 (715)
T 2va8_A          328 DLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRD  407 (715)
T ss_dssp             HHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCTTTCSCEEEEEECSC
T ss_pred             HHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEeCC
Confidence            99999999999999999999999999999999999    99       8999999999999999998  47999999987


Q ss_pred             cch
Q psy17587        129 EQE  131 (231)
Q Consensus       129 ~~~  131 (231)
                      .+.
T Consensus       408 ~~~  410 (715)
T 2va8_A          408 KED  410 (715)
T ss_dssp             GGG
T ss_pred             chH
Confidence            653

>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=99.81  E-value=1.4e-20  Score=179.44  Aligned_cols=110  Identities=19%  Similarity=0.265  Sum_probs=101.3

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH-----------CCCCeeeccCCCCHHHHHHHHHHHh-----CCCccEEEecCcc
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK-----------AGYPCLSLHGGIDQYDRDSTIVDFK-----NGKVRLLIATSVA   82 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~-----------~~~~~~~lhg~~~~~~R~~~~~~F~-----~g~~~vLvaT~~~   82 (231)
                      ....+||||+++  ..++.+++.|..           .++.+..+||+|++++|..+++.|+     +|..+|||||+++
T Consensus       302 ~~g~iLVF~~~~--~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~ia  379 (773)
T 2xau_A          302 EAGDILLFLTGE--DEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIA  379 (773)
T ss_dssp             CSCEEEEECSCH--HHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHH
T ss_pred             CCCCEEEECCCH--HHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHH
Confidence            467899999998  779999999874           5788999999999999999999999     9999999999999


Q ss_pred             ccccCCCCCcEEEEecC------------------CCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         83 ARGLDVKHLNLVVNYDC------------------PNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~------------------P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ++|||+|+|++||++++                  |.+..+|+||+|||||. ..|.|+.|+++.+.
T Consensus       380 e~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~-~~G~~~~l~~~~~~  445 (773)
T 2xau_A          380 ETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRLYTEEAF  445 (773)
T ss_dssp             HHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS-SSEEEEESSCHHHH
T ss_pred             HhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC-CCCEEEEEecHHHh
Confidence            99999999999999877                  89999999999999999 78999999976543

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

Probab=99.80  E-value=1.3e-19  Score=176.92  Aligned_cols=119  Identities=19%  Similarity=0.266  Sum_probs=103.0

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC---------------------------------------
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP---------------------------------------   48 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~---------------------------------------   48 (231)
                      ..+...+... ...++||||+++  ..++.++..|...++.                                       
T Consensus       332 ~~l~~~l~~~-~~~~~IVF~~sr--~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~g  408 (1010)
T 2xgj_A          332 YKIVKMIWKK-KYNPVIVFSFSK--RDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRG  408 (1010)
T ss_dssp             HHHHHHHHHH-TCCSEEEEESSH--HHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhc-CCCCEEEEECCH--HHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCC
Confidence            3344444433 244677799998  7799999988765443                                       


Q ss_pred             eeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ecC----CCCHhHHHHHhcccCCCCC--
Q psy17587         49 CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YDC----PNHYEDYVHRCGRTGRAGN--  118 (231)
Q Consensus        49 ~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d~----P~~~~~y~qr~GR~gR~g~--  118 (231)
                      +..+||+|++.+|..+++.|++|.++|||||+++++|+|+|++++||+    ||.    |.++.+|+||+||+||.|.  
T Consensus       409 I~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G~d~  488 (1010)
T 2xgj_A          409 IGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDD  488 (1010)
T ss_dssp             EEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTTTCS
T ss_pred             eeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCCCCC
Confidence            778999999999999999999999999999999999999999999999    999    9999999999999999996  


Q ss_pred             ceeEEEEeccc
Q psy17587        119 KGFAYTFITLE  129 (231)
Q Consensus       119 ~g~~i~~~~~~  129 (231)
                      .|.|++++.+.
T Consensus       489 ~G~vi~l~~~~  499 (1010)
T 2xgj_A          489 RGIVIMMIDEK  499 (1010)
T ss_dssp             SEEEEEEECSC
T ss_pred             ceEEEEEECCC
Confidence            59999999866

>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=99.80  E-value=1.6e-19  Score=171.01  Aligned_cols=110  Identities=18%  Similarity=0.252  Sum_probs=99.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC---------------------------------CCCeeeccCCCCHHHHHHHH
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA---------------------------------GYPCLSLHGGIDQYDRDSTI   65 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~---------------------------------~~~~~~lhg~~~~~~R~~~~   65 (231)
                      .+..+||||+++  ..++.++..|...                                 ...+.++||+|++.+|..++
T Consensus       236 ~~~~~LVF~~sr--~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~  313 (720)
T 2zj8_A          236 KKKGALIFVNMR--RKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVE  313 (720)
T ss_dssp             TTCCEEEECSCH--HHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHH
T ss_pred             CCCCEEEEecCH--HHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHH
Confidence            467888899988  7799999888642                                 12489999999999999999


Q ss_pred             HHHhCCCccEEEecCccccccCCCCCcEEEE----ec----CCCCHhHHHHHhcccCCCC--CceeEEEEecccc
Q psy17587         66 VDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YD----CPNHYEDYVHRCGRTGRAG--NKGFAYTFITLEQ  130 (231)
Q Consensus        66 ~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d----~P~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~~  130 (231)
                      +.|++|.++|||||+++++|+|+|++++||+    ||    .|.+..+|.||+|||||.|  ..|.|++++++.+
T Consensus       314 ~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  388 (720)
T 2zj8_A          314 ENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDD  388 (720)
T ss_dssp             HHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTCSEEEEEEECSSSC
T ss_pred             HHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999999999999999999999    77    6899999999999999998  4799999998776

>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=99.80  E-value=3.4e-20  Score=167.06  Aligned_cols=116  Identities=22%  Similarity=0.360  Sum_probs=100.7

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccc
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARG   85 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~G   85 (231)
                      |+..|.++|.. ..+.++||||++.  ..++.+++.|     .+..+||++++.+|..++++|++|+++|||||+++++|
T Consensus       336 k~~~l~~~l~~-~~~~k~lvF~~~~--~~~~~l~~~l-----~~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~G  407 (472)
T 2fwr_A          336 KIRKLREILER-HRKDKIIIFTRHN--ELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEG  407 (472)
T ss_dssp             HHHHHHHHHHH-TSSSCBCCBCSCH--HHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSS
T ss_pred             HHHHHHHHHHh-CCCCcEEEEECCH--HHHHHHHHHh-----CcceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcC
Confidence            55667777776 4567888899988  7799999887     36789999999999999999999999999999999999


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc---eeEEEEeccc
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK---GFAYTFITLE  129 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~---g~~i~~~~~~  129 (231)
                      +|+|++++||++|+|+++..|+||+||+||.|+.   ..++.++..+
T Consensus       408 ldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~k~~~~i~~lv~~~  454 (472)
T 2fwr_A          408 IDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISRG  454 (472)
T ss_dssp             SCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEECS
T ss_pred             cccccCcEEEEECCCCCHHHHHHHHhhccCCCCCCceEEEEEEEeCC
Confidence            9999999999999999999999999999999854   3445566544

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

Probab=99.80  E-value=1.8e-19  Score=161.41  Aligned_cols=111  Identities=23%  Similarity=0.192  Sum_probs=94.3

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLD   87 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gld   87 (231)
                      ..+++.+.+.  +.+++|||+++  ..++.+++.|...++.+..+||+    +|..++++|++|+++|||||+++++|+|
T Consensus       161 ~~~~~~l~~~--~~~~lVF~~~~--~~~~~l~~~L~~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiD  232 (431)
T 2v6i_A          161 NSGYEWITEF--DGRTVWFVHSI--KQGAEIGTCLQKAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGAN  232 (431)
T ss_dssp             SSCCHHHHSC--SSCEEEECSSH--HHHHHHHHHHHHTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCC
T ss_pred             HHHHHHHHcC--CCCEEEEeCCH--HHHHHHHHHHHHcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcc
Confidence            3444555443  45788899998  77999999999999999999997    5788999999999999999999999999


Q ss_pred             CCCCcE-----------------EEEecCCCCHhHHHHHhcccCCCCC-ceeEEEEec
Q psy17587         88 VKHLNL-----------------VVNYDCPNHYEDYVHRCGRTGRAGN-KGFAYTFIT  127 (231)
Q Consensus        88 ip~v~~-----------------VI~~d~P~~~~~y~qr~GR~gR~g~-~g~~i~~~~  127 (231)
                      +| +.+                 ||+++.|.+..+|+||+||+||.|. .|.++++..
T Consensus       233 ip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g~~~~~~~~~~~  289 (431)
T 2v6i_A          233 FK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNPEKLGDIYAYSG  289 (431)
T ss_dssp             CC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCCEEEECS
T ss_pred             cC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCCCCCCeEEEEcC
Confidence            99 544                 6889999999999999999999985 556666653

>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=99.80  E-value=1.9e-19  Score=169.96  Aligned_cols=110  Identities=19%  Similarity=0.326  Sum_probs=99.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC------------------------------CCCeeeccCCCCHHHHHHHHHHH
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA------------------------------GYPCLSLHGGIDQYDRDSTIVDF   68 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~------------------------------~~~~~~lhg~~~~~~R~~~~~~F   68 (231)
                      .++++||||+++  ..++.++..|...                              +..+.++||+|++++|..+++.|
T Consensus       241 ~~~~~LVF~~s~--~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f  318 (702)
T 2p6r_A          241 ENGGVLVFESTR--RGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAF  318 (702)
T ss_dssp             TTCCEEEECSSH--HHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHH
T ss_pred             cCCCEEEEcCCH--HHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHH
Confidence            567888899998  7799999888642                              24588999999999999999999


Q ss_pred             hCCCccEEEecCccccccCCCCCcEEEE----ec---CCCCHhHHHHHhcccCCCC--CceeEEEEecccc
Q psy17587         69 KNGKVRLLIATSVAARGLDVKHLNLVVN----YD---CPNHYEDYVHRCGRTGRAG--NKGFAYTFITLEQ  130 (231)
Q Consensus        69 ~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d---~P~~~~~y~qr~GR~gR~g--~~g~~i~~~~~~~  130 (231)
                      ++|.++|||||+++++|+|+|++++||+    ||   .|.+..+|.||+|||||.|  ..|.|++++++.+
T Consensus       319 ~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g~~~~G~~~~l~~~~~  389 (702)
T 2p6r_A          319 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRD  389 (702)
T ss_dssp             HTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGG
T ss_pred             HCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCCCCCCceEEEEecCcc
Confidence            9999999999999999999999999999    77   7999999999999999998  4799999998776

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.80  E-value=1.4e-19  Score=164.19  Aligned_cols=123  Identities=18%  Similarity=0.184  Sum_probs=102.5

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHHHHHHHHHHHhCC-Ccc-EEEecC
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFKNG-KVR-LLIATS   80 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~-vLvaT~   80 (231)
                      .|+..+.+.|.+. ..+.++||||+..  ..++.+.+.|... |+.+..+||++++.+|..++++|++| ..+ +|+||+
T Consensus       325 ~K~~~l~~~l~~~~~~~~k~lvF~~~~--~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~  402 (500)
T 1z63_A          325 GKMIRTMEIIEEALDEGDKIAIFTQFV--DMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK  402 (500)
T ss_dssp             HHHHHHHHHHHHHHTTTCCEEEECSCH--HHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECC
T ss_pred             hhHHHHHHHHHHHHccCCcEEEEEehH--HHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecc
Confidence            4666777777654 4578899999987  7799999999875 99999999999999999999999988 555 799999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeE--EEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFA--YTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~--i~~~~~~  129 (231)
                      ++++|+|+|.+++||+||+||++..|.|++||++|.|+...+  +.++..+
T Consensus       403 ~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~Gq~~~v~v~~lv~~~  453 (500)
T 1z63_A          403 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  453 (500)
T ss_dssp             CC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTTTTTSCEEEEEEEETT
T ss_pred             cccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHcCCCCeeEEEEEEeCC
Confidence            999999999999999999999999999999999999986544  5555554

>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=99.80  E-value=1.8e-19  Score=178.10  Aligned_cols=114  Identities=15%  Similarity=0.243  Sum_probs=104.5

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCc
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLN   92 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~   92 (231)
                      .....+.+++||||+.  ..++.+++.|...  +..+..+||+|++.+|..++++|++|+++|||||+++++|+|+|+++
T Consensus       807 ~~l~~g~qvlvf~~~v--~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~  884 (1151)
T 2eyq_A          807 REILRGGQVYYLYNDV--ENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTAN  884 (1151)
T ss_dssp             HHHTTTCEEEEECCCS--SCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEE
T ss_pred             HHHhcCCeEEEEECCH--HHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCc
Confidence            4445678899999998  6799999999876  88999999999999999999999999999999999999999999999


Q ss_pred             EEEEecC-CCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         93 LVVNYDC-PNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        93 ~VI~~d~-P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      +||+++. ++++.+|+||+||+||.|+.|.|++++.+.+
T Consensus       885 ~VIi~~~~~~~l~~l~Qr~GRvgR~g~~g~~~ll~~~~~  923 (1151)
T 2eyq_A          885 TIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPK  923 (1151)
T ss_dssp             EEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGG
T ss_pred             EEEEeCCCCCCHHHHHHHHhccCcCCCceEEEEEECCcc
Confidence            9999998 5799999999999999999999999987653

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

Probab=99.80  E-value=4.6e-19  Score=166.39  Aligned_cols=101  Identities=17%  Similarity=0.275  Sum_probs=92.3

Q ss_pred             EEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhC--CCccEEEecCccccccCCCCCcEEEEecC--
Q psy17587         24 VDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKN--GKVRLLIATSVAARGLDVKHLNLVVNYDC--   99 (231)
Q Consensus        24 iiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~--g~~~vLvaT~~~~~Gldip~v~~VI~~d~--   99 (231)
                      +|||+++  ..++.+++.|...++.+..+||+|++++|..+++.|++  |..+|||||+++++|+|+ ++++||++++  
T Consensus       324 iIf~~s~--~~ie~la~~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k  400 (677)
T 3rc3_A          324 CIVCFSK--NDIYSVSRQIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIK  400 (677)
T ss_dssp             EEECSSH--HHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC
T ss_pred             EEEEcCH--HHHHHHHHHHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccc
Confidence            4589987  67999999999999999999999999999999999999  889999999999999999 8999999999  


Q ss_pred             ------------CCCHhHHHHHhcccCCCCCc---eeEEEEec
Q psy17587        100 ------------PNHYEDYVHRCGRTGRAGNK---GFAYTFIT  127 (231)
Q Consensus       100 ------------P~~~~~y~qr~GR~gR~g~~---g~~i~~~~  127 (231)
                                  |.+..+|+||+|||||.|..   |.|+.+..
T Consensus       401 ~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g~~g~~G~v~~l~~  443 (677)
T 3rc3_A          401 PSINEKGERELEPITTSQALQIAGRAGRFSSRFKEGEVTTMNH  443 (677)
T ss_dssp             -----------CBCCHHHHHHHHTTBTCTTSSCSSEEEEESST
T ss_pred             cccccCCccccccCCHHHHHHHhcCCCCCCCCCCCEEEEEEec
Confidence                        88999999999999999964   66665543

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

Probab=99.80  E-value=1.9e-19  Score=177.04  Aligned_cols=125  Identities=22%  Similarity=0.295  Sum_probs=105.7

Q ss_pred             chhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCee-eccCCCCHHHHHHHHHHHhCCCccEEEe----cC
Q psy17587          6 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCL-SLHGGIDQYDRDSTIVDFKNGKVRLLIA----TS   80 (231)
Q Consensus         6 k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~-~lhg~~~~~~R~~~~~~F~~g~~~vLva----T~   80 (231)
                      |...|.++|...  +.++||||+++  ..++.++..|...|+.+. .+||     +|.+ +++|++|+++||||    |+
T Consensus       297 k~~~L~~ll~~~--~~~~LVF~~s~--~~a~~l~~~L~~~g~~~~~~lhg-----~rr~-l~~F~~G~~~VLVatas~Td  366 (1104)
T 4ddu_A          297 SKEKLVELLEIF--RDGILIFAQTE--EEGKELYEYLKRFKFNVGETWSE-----FEKN-FEDFKVGKINILIGVQAYYG  366 (1104)
T ss_dssp             CHHHHHHHHHHH--CSSEEEEESSS--HHHHHHHHHHHHTTCCEEESSSS-----HHHH-HHHHHHTSCSEEEEETTTHH
T ss_pred             HHHHHHHHHHhc--CCCEEEEECcH--HHHHHHHHHHHhCCCCeeeEecC-----cHHH-HHHHHCCCCCEEEEecCCCC
Confidence            556677777764  37788899998  779999999999999998 9999     2555 99999999999999    99


Q ss_pred             ccccccCCCC-CcEEEEecCCC----------------------------------------------------------
Q psy17587         81 VAARGLDVKH-LNLVVNYDCPN----------------------------------------------------------  101 (231)
Q Consensus        81 ~~~~Gldip~-v~~VI~~d~P~----------------------------------------------------------  101 (231)
                      ++++|+|+|+ |++|||||+|.                                                          
T Consensus       367 vlarGIDip~~V~~VI~~d~P~~~~Sle~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~e~~~~~l~~~~~~~~i~~~~~  446 (1104)
T 4ddu_A          367 KLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRFVLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFR  446 (1104)
T ss_dssp             HHCCSCCCTTTCCEEEEESCCEEEEECSSSSCCHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCC
T ss_pred             eeEecCcCCCCCCEEEEECCCCCCCCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHhhccc
Confidence            9999999999 99999999998                                                          


Q ss_pred             --------------CHhHHHHHhcccCCCCC----ceeEEEEecccchHHHHHHHHHHH
Q psy17587        102 --------------HYEDYVHRCGRTGRAGN----KGFAYTFITLEQERHAGEIIRALE  142 (231)
Q Consensus       102 --------------~~~~y~qr~GR~gR~g~----~g~~i~~~~~~~~~~~~~~~~~l~  142 (231)
                                    ++.+|+||+|||||.|.    .|.+++++  ++...+..+.+.+.
T Consensus       447 ~l~~~~~~~~~~~pd~~tYihr~GRtgR~~~gg~~~Glsi~~~--~d~~~~~~l~~~~~  503 (1104)
T 4ddu_A          447 GVVVKDEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFE--EDEEIFESLKTRLL  503 (1104)
T ss_dssp             SSEEETTTTEEEEECHHHHHHHHHTTCCEETTEECCEEEEEEC--CCHHHHHHHHHHHH
T ss_pred             eEEecCCeeEEEecChhhhhcccCchhcccCCCcccceEEEEE--ecHHHHHHHHHHHh
Confidence                          78899999999999653    45666665  66677777777665

>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=99.79  E-value=3.2e-19  Score=166.43  Aligned_cols=102  Identities=23%  Similarity=0.350  Sum_probs=92.0

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEE---
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV---   95 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI---   95 (231)
                      ...++||||+++  ..++.+++.|...++++..+||+|++++       |+++..+||||||++++|||+| +++||   
T Consensus       395 ~~~~vLVFv~Tr--~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~G  464 (666)
T 3o8b_A          395 RGGRHLIFCHSK--KKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCN  464 (666)
T ss_dssp             SSSEEEEECSCH--HHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECC
T ss_pred             cCCcEEEEeCCH--HHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecC
Confidence            467889999998  7799999999999999999999999875       5566779999999999999997 99988   


Q ss_pred             -------Eec-----------CCCCHhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587         96 -------NYD-----------CPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus        96 -------~~d-----------~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                             |||           +|.+.++|+||+||+|| |+.|. +.|+++.+..
T Consensus       465 l~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR-g~~G~-i~lvt~~e~~  517 (666)
T 3o8b_A          465 TCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR-GRRGI-YRFVTPGERP  517 (666)
T ss_dssp             EEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEE-EEESCCCCBC
T ss_pred             cccccccccccccccccccccCcCCHHHHHHHhccCCC-CCCCE-EEEEecchhh
Confidence                   788           89999999999999999 88999 9999877644

>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=99.79  E-value=1.3e-19  Score=178.31  Aligned_cols=119  Identities=18%  Similarity=0.248  Sum_probs=97.1

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC---------------------------------------e
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP---------------------------------------C   49 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~---------------------------------------~   49 (231)
                      .++..+... ...++||||+++  ..|+.++..|...++.                                       +
T Consensus       431 ~li~~l~~~-~~~~vIVF~~sr--~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV  507 (1108)
T 3l9o_A          431 KIVKMIWKK-KYNPVIVFSFSK--RDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGI  507 (1108)
T ss_dssp             HHHHHHHHT-TCCCEEEEESCH--HHHHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTE
T ss_pred             HHHHHHHhc-CCCCEEEEeCcH--HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCe
Confidence            344444433 356788899998  7799999987542222                                       7


Q ss_pred             eeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCCC--------CHhHHHHHhcccCCCC--Cc
Q psy17587         50 LSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPN--------HYEDYVHRCGRTGRAG--NK  119 (231)
Q Consensus        50 ~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~--------~~~~y~qr~GR~gR~g--~~  119 (231)
                      ..+||+|++.+|..+++.|++|.++|||||+++++|||+|++++||+++.|+        ++.+|+||+|||||.|  ..
T Consensus       508 ~~~Hg~l~~~~R~~v~~~F~~G~ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G~d~~  587 (1108)
T 3l9o_A          508 GIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRGLDDR  587 (1108)
T ss_dssp             EEECSCSCHHHHHHHHHHHHHTCCCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSSSCSS
T ss_pred             eeecCCCCHHHHHHHHHHHhCCCCeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCCCCCc
Confidence            8999999999999999999999999999999999999999999999876643        6778999999999999  68


Q ss_pred             eeEEEEecccc
Q psy17587        120 GFAYTFITLEQ  130 (231)
Q Consensus       120 g~~i~~~~~~~  130 (231)
                      |.|++++.+..
T Consensus       588 G~~ill~~~~~  598 (1108)
T 3l9o_A          588 GIVIMMIDEKM  598 (1108)
T ss_dssp             EEEEEEECCCC
T ss_pred             eEEEEEecCCc
Confidence            99999988763

>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=99.78  E-value=7.6e-20  Score=174.06  Aligned_cols=122  Identities=18%  Similarity=0.271  Sum_probs=101.0

Q ss_pred             hhhcccc-ccCCCCeEEEEcCChhH------HHHHHHHHHHHH---CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEe
Q psy17587          9 SLHGGID-QYDRDSTIVDFKNGKVR------LLVCAIVKELMK---AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIA   78 (231)
Q Consensus         9 ~L~~~L~-~~~~~~~iiiF~~~~~~------~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLva   78 (231)
                      .+.+.+. ....+.+++|||+....      ..++.+++.|..   .++.+..+||+|++.+|..++++|++|+++||||
T Consensus       566 ~l~~~i~~~l~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~ILVa  645 (780)
T 1gm5_A          566 EVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVS  645 (780)
T ss_dssp             HHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCC
T ss_pred             HHHHHHHHHHhcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEEEE
Confidence            3444443 33456778889986411      246788888877   4789999999999999999999999999999999


Q ss_pred             cCccccccCCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         79 TSVAARGLDVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        79 T~~~~~Gldip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      |+++++|+|+|++++||++|+|. +...|.||+||+||.|..|.|++++.+.+
T Consensus       646 T~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~g~~g~~ill~~~~~  698 (780)
T 1gm5_A          646 TTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVG  698 (780)
T ss_dssp             SSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCC
T ss_pred             CCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcCCCCCEEEEEECCCC
Confidence            99999999999999999999996 78899999999999999999999988433

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.78  E-value=2.7e-19  Score=162.59  Aligned_cols=106  Identities=22%  Similarity=0.163  Sum_probs=95.7

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec-CccccccCCCCCcEEEEe
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT-SVAARGLDVKHLNLVVNY   97 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT-~~~~~Gldip~v~~VI~~   97 (231)
                      .++.+||||+ .  ..++.+++.|...+.++..+||+|++.+|..+++.|++|+.+||||| +++++|+|+|++++||++
T Consensus       347 ~~~~~ivf~~-~--~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~~GiDip~v~~vi~~  423 (510)
T 2oca_A          347 DENAFVMFKH-V--SHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFSTGISVKNLHHVVLA  423 (510)
T ss_dssp             TCEEEEEESS-H--HHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHHHSCCCCSEEEEEES
T ss_pred             CCCeEEEEec-H--HHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhhcccccccCcEEEEe
Confidence            3577787888 4  56888999999888899999999999999999999999999999999 999999999999999999


Q ss_pred             cCCCCHhHHHHHhcccCCCCCceeEEEEec
Q psy17587         98 DCPNHYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus        98 d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                      ++|+++..|+|++||+||.|+.+.+++++.
T Consensus       424 ~~~~s~~~~~Q~~GR~gR~g~~~~~v~i~~  453 (510)
T 2oca_A          424 HGVKSKIIVLQTIGRVLRKHGSKTIATVWD  453 (510)
T ss_dssp             SCCCSCCHHHHHHHHHHTTTCCCCCCEEEE
T ss_pred             CCCCCHHHHHHHHhcccccCCCCceEEEEE
Confidence            999999999999999999998764444443

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=99.78  E-value=1.5e-18  Score=162.54  Aligned_cols=122  Identities=17%  Similarity=0.196  Sum_probs=104.9

Q ss_pred             chhhhhcccccc--CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCcc---EEEecC
Q psy17587          6 PCLSLHGGIDQY--DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR---LLIATS   80 (231)
Q Consensus         6 k~~~L~~~L~~~--~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~---vLvaT~   80 (231)
                      |+..|..++...  ..+.++||||+..  ..++.+...|...|+.+..+||+++..+|..++++|++|+..   +|++|+
T Consensus       400 K~~~l~~ll~~~~~~~~~k~lIFs~~~--~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~  477 (644)
T 1z3i_X          400 KMLVLDYILAMTRTTTSDKVVLVSNYT--QTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  477 (644)
T ss_dssp             HHHHHHHHHHHHHHHCCCEEEEEESCH--HHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             HHHHHHHHHHHHhhcCCCEEEEEEccH--HHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecc
Confidence            344444444433  2478899999987  789999999999999999999999999999999999998764   899999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      ++++|+|++.+++||+||+||++..|.|++||++|.|+.  ..++.|++.+
T Consensus       478 a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~Gq~~~v~v~~lv~~~  528 (644)
T 1z3i_X          478 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  528 (644)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             cccCCcccccCCEEEEECCCCCccHHHHHHHhhhhcCCCCceEEEEEEECC
Confidence            999999999999999999999999999999999999975  4456666655

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

Probab=99.76  E-value=3.3e-18  Score=166.92  Aligned_cols=117  Identities=19%  Similarity=0.209  Sum_probs=98.1

Q ss_pred             hhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCC---------------------------------------
Q psy17587          7 CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGY---------------------------------------   47 (231)
Q Consensus         7 ~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~---------------------------------------   47 (231)
                      +..|+..|... ...++||||+++  ..|+.++..|...++                                       
T Consensus       324 ~~~li~~l~~~-~~~~~IVF~~sr--~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~  400 (997)
T 4a4z_A          324 WPEIVNYLRKR-ELLPMVVFVFSK--KRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLER  400 (997)
T ss_dssp             HHHHHHHHHHT-TCCSEEEECSCH--HHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhC-CCCCEEEEECCH--HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhc
Confidence            55666666655 345777799998  779999999976555                                       


Q ss_pred             CeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCC---------CCHhHHHHHhcccCCCC-
Q psy17587         48 PCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP---------NHYEDYVHRCGRTGRAG-  117 (231)
Q Consensus        48 ~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P---------~~~~~y~qr~GR~gR~g-  117 (231)
                      .+..+||+|++.+|..+++.|++|.++|||||+++++|+|+|++. ||++++|         .++.+|+||+|||||.| 
T Consensus       401 gi~~~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~~~-VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~G~  479 (997)
T 4a4z_A          401 GIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRT-VIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGL  479 (997)
T ss_dssp             TEEEECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCCSE-EEESCSEEEETTEEEECCHHHHHHHHGGGCCTTT
T ss_pred             CeeeecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCCce-EEEeccccccCccCCCCCHHHHhHHhcccccCCC
Confidence            478999999999999999999999999999999999999999954 5544444         49999999999999998 


Q ss_pred             -CceeEEEEec
Q psy17587        118 -NKGFAYTFIT  127 (231)
Q Consensus       118 -~~g~~i~~~~  127 (231)
                       ..|.|+++..
T Consensus       480 ~~~G~vi~l~~  490 (997)
T 4a4z_A          480 DSTGTVIVMAY  490 (997)
T ss_dssp             CSSEEEEEECC
T ss_pred             CcceEEEEecC
Confidence             5688888874

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.75  E-value=4.1e-18  Score=163.16  Aligned_cols=123  Identities=16%  Similarity=0.233  Sum_probs=108.1

Q ss_pred             CchhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCcc---EEEecC
Q psy17587          5 YPCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR---LLIATS   80 (231)
Q Consensus         5 ~k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~---vLvaT~   80 (231)
                      .|+..|.++|.... .+.++||||+..  ..++.|...|...|+++..+||+++..+|..++++|+++...   +|++|.
T Consensus       556 ~K~~~L~~lL~~~~~~g~kvLIFsq~~--~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlSt~  633 (800)
T 3mwy_W          556 GKMVLLDQLLTRLKKDGHRVLIFSQMV--RMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTR  633 (800)
T ss_dssp             HHHHHHHHHHHHHTTTTCCEEEEESCH--HHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEEHH
T ss_pred             hHHHHHHHHHHHHhhCCCeEEEEechH--HHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEecc
Confidence            46667777776654 467999999977  789999999999999999999999999999999999986654   899999


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      +++.|||+|.+++||+||+||++..+.|++||++|.|+.  ..++.|++.+
T Consensus       634 agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~RiGQ~k~V~Vyrlv~~~  684 (800)
T 3mwy_W          634 AGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKD  684 (800)
T ss_dssp             HHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSCSSCCSCEEEEEEEETT
T ss_pred             cccCCCCccccceEEEecCCCChhhHHHHHHHHHhcCCCceEEEEEEecCC
Confidence            999999999999999999999999999999999999975  4455666655

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.74  E-value=5.4e-18  Score=156.97  Aligned_cols=106  Identities=14%  Similarity=0.138  Sum_probs=91.2

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCC--------CeeeccCCCCHHHHHHHHHHHhCCCcc---EEEe
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGY--------PCLSLHGGIDQYDRDSTIVDFKNGKVR---LLIA   78 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~--------~~~~lhg~~~~~~R~~~~~~F~~g~~~---vLva   78 (231)
                      |.+.+.......++||||+++  ..++.+++.|...+.        .+..+||.++. +|..++++|++|+.+   ||||
T Consensus       429 l~~~l~~~~~~~k~lVF~~~~--~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvt  505 (590)
T 3h1t_A          429 LTDFMKRTDRFAKTIVFCVDQ--EHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHLSRFQELETSTPVILTT  505 (590)
T ss_dssp             HHHHHHHHCTTSEEEEEESSH--HHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEE
T ss_pred             HHHHHHhcCCCccEEEEECCH--HHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEE
Confidence            444455556678899999988  779999999976432        37789999864 799999999998866   8899


Q ss_pred             cCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCC
Q psy17587         79 TSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGN  118 (231)
Q Consensus        79 T~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~  118 (231)
                      |+++++|+|+|+|++||++++|+++..|+||+||+||.+.
T Consensus       506 t~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          506 SQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             SSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             CChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            9999999999999999999999999999999999999774

>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=99.71  E-value=2.3e-17  Score=167.87  Aligned_cols=125  Identities=13%  Similarity=0.193  Sum_probs=103.5

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC----------------------------------CCCeeeccC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----------------------------------GYPCLSLHG   54 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----------------------------------~~~~~~lhg   54 (231)
                      .+...+.....++.+||||+++  ..|+.++..|...                                  ...+.++||
T Consensus      1144 ~~~~~i~~~~~~~~~lVF~~sR--~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHa 1221 (1724)
T 4f92_B         1144 PVYHAITKHSPKKPVIVFVPSR--KQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHE 1221 (1724)
T ss_dssp             HHHHHHHHHCSSSCEEEEESSH--HHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECT
T ss_pred             hHHHHHHHhcCCCCeeeeCCCH--HHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECC
Confidence            3445556666778899999988  6688777665321                                  235789999


Q ss_pred             CCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ec------CCCCHhHHHHHhcccCCCCC--ceeE
Q psy17587         55 GIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YD------CPNHYEDYVHRCGRTGRAGN--KGFA  122 (231)
Q Consensus        55 ~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d------~P~~~~~y~qr~GR~gR~g~--~g~~  122 (231)
                      +|++.+|..+++.|++|.++|||||+++++|+|+|++.+||.    ||      .|.++.+|+||+|||||.|.  .|.|
T Consensus      1222 gL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~g~d~~G~a 1301 (1724)
T 4f92_B         1222 GLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRC 1301 (1724)
T ss_dssp             TSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCTTTCSCEEE
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCCCCCCceEE
Confidence            999999999999999999999999999999999999999983    33      46789999999999999996  7999


Q ss_pred             EEEecccchHHHH
Q psy17587        123 YTFITLEQERHAG  135 (231)
Q Consensus       123 i~~~~~~~~~~~~  135 (231)
                      ++++.+.+...++
T Consensus      1302 vll~~~~~~~~~~ 1314 (1724)
T 4f92_B         1302 VIMCQGSKKDFFK 1314 (1724)
T ss_dssp             EEEEEGGGHHHHH
T ss_pred             EEEecchHHHHHH
Confidence            9999887766443

>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=99.68  E-value=8.5e-17  Score=163.72  Aligned_cols=121  Identities=17%  Similarity=0.230  Sum_probs=99.3

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-------------------------------------CCCeeecc
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-------------------------------------GYPCLSLH   53 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-------------------------------------~~~~~~lh   53 (231)
                      .+.+.....+..++|||+++  ..++.+++.|...                                     ...+.++|
T Consensus       308 ~~~v~~~~~~~~~LVF~~sR--~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HH  385 (1724)
T 4f92_B          308 YEKIMEHAGKNQVLVFVHSR--KETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHH  385 (1724)
T ss_dssp             HHHHTTCCSSCCEEEECSST--TTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEEC
T ss_pred             HHHHHHHhcCCcEEEECCCH--HHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEc
Confidence            34445555567788899987  5577777766421                                     23478999


Q ss_pred             CCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEE----ecC------CCCHhHHHHHhcccCCCCC--cee
Q psy17587         54 GGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVN----YDC------PNHYEDYVHRCGRTGRAGN--KGF  121 (231)
Q Consensus        54 g~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~----~d~------P~~~~~y~qr~GR~gR~g~--~g~  121 (231)
                      |||++.+|..+.+.|++|.++|||||+++++|||+|.+++||.    ||+      |.++.+|.||+|||||.|.  .|.
T Consensus       386 agL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~g~d~~G~  465 (1724)
T 4f92_B          386 AGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGE  465 (1724)
T ss_dssp             SSSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCTTTCSCEE
T ss_pred             CCCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCCCCCCccE
Confidence            9999999999999999999999999999999999999999985    554      5689999999999999984  799


Q ss_pred             EEEEecccchHH
Q psy17587        122 AYTFITLEQERH  133 (231)
Q Consensus       122 ~i~~~~~~~~~~  133 (231)
                      ++++..+.+...
T Consensus       466 ~ii~~~~~~~~~  477 (1724)
T 4f92_B          466 GILITSHGELQY  477 (1724)
T ss_dssp             EEEEEESTTCCH
T ss_pred             EEEEecchhHHH
Confidence            999988776553

>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=99.37  E-value=2.8e-12  Score=125.30  Aligned_cols=106  Identities=19%  Similarity=0.115  Sum_probs=87.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCC------------CCe-eeccCC----------C----------CHH-------
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAG------------YPC-LSLHGG----------I----------DQY-------   59 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~------------~~~-~~lhg~----------~----------~~~-------   59 (231)
                      +.+.+|||+++  ..|..+++.|...+            +++ ..+||+          +          ++.       
T Consensus       537 g~kamVf~~S~--~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~  614 (1038)
T 2w00_A          537 GFNAMLAVSSV--DAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDA  614 (1038)
T ss_dssp             CCEEEEEESSH--HHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHH
T ss_pred             CCcEEEEECCH--HHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHH
Confidence            35678899988  77999999987643            555 456653          2          221       


Q ss_pred             ----------------------HHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCC
Q psy17587         60 ----------------------DRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAG  117 (231)
Q Consensus        60 ----------------------~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g  117 (231)
                                            +|..++++|++|+++|||+|+++.+|+|+|.+ .++++|.|.+...|+|++||++|.+
T Consensus       615 ~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~  693 (1038)
T 2w00_A          615 AIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIY  693 (1038)
T ss_dssp             HHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCC
Confidence                                  47889999999999999999999999999999 6789999999999999999999987


Q ss_pred             Cc----eeEEEEecc
Q psy17587        118 NK----GFAYTFITL  128 (231)
Q Consensus       118 ~~----g~~i~~~~~  128 (231)
                      ..    |.++.|+..
T Consensus       694 ~~~K~~G~IVdf~~~  708 (1038)
T 2w00_A          694 DATKTFGNIVTFRDL  708 (1038)
T ss_dssp             CTTCCSEEEEESSCC
T ss_pred             CCCCCcEEEEEcccc
Confidence            53    777777753

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.29  E-value=1.1e-06  Score=80.47  Aligned_cols=74  Identities=14%  Similarity=0.215  Sum_probs=47.6

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEE--ecCccccccCCCC----CcE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLI--ATSVAARGLDVKH----LNL   93 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLv--aT~~~~~Gldip~----v~~   93 (231)
                      ...++||+++.  ..++.+++.|..  .. ...+|..  .+|...++.|+++. .||+  +|+.+.+|||+|+    +++
T Consensus       384 ~g~~lvff~S~--~~~~~v~~~l~~--~~-~~~q~~~--~~~~~~l~~f~~~~-~il~~V~~~~~~EGiD~~~~~~~~~~  455 (540)
T 2vl7_A          384 SKSVLVFFPSY--EMLESVRIHLSG--IP-VIEENKK--TRHEEVLELMKTGK-YLVMLVMRAKESEGVEFREKENLFES  455 (540)
T ss_dssp             SSEEEEEESCH--HHHHHHHTTCTT--SC-EEESTTT--CCHHHHHHHHHTSC-CEEEEEC---------------CEEE
T ss_pred             CCCEEEEeCCH--HHHHHHHHHhcc--Cc-eEecCCC--CcHHHHHHHHhcCC-eEEEEEecCceecceecCCCcccccE
Confidence            46788899988  678999888754  33 4566654  46888999999865 6776  8999999999997    889


Q ss_pred             EEEecCCC
Q psy17587         94 VVNYDCPN  101 (231)
Q Consensus        94 VI~~d~P~  101 (231)
                      ||++++|.
T Consensus       456 Vii~~lPf  463 (540)
T 2vl7_A          456 LVLAGLPY  463 (540)
T ss_dssp             EEEESCCC
T ss_pred             EEEECCCC
Confidence            99999985

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=97.98  E-value=2.8e-05  Score=66.49  Aligned_cols=119  Identities=6%  Similarity=-0.049  Sum_probs=81.5

Q ss_pred             chhhhhccccccC-CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc
Q psy17587          6 PCLSLHGGIDQYD-RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR   84 (231)
Q Consensus         6 k~~~L~~~L~~~~-~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~   84 (231)
                      |...|-.+|.... .+.+|+||++..  ...+.+..++...+++..-+.|.....+ .+    -.++...+.+.|...+-
T Consensus       110 Kf~~L~~LL~~l~~~~~kVLIfsq~t--~~LDilE~~l~~~~~~y~RlDG~~~~~~-~k----~~~~~~~i~Lltsag~~  182 (328)
T 3hgt_A          110 KFSVLRDLINLVQEYETETAIVCRPG--RTMDLLEALLLGNKVHIKRYDGHSIKSA-AA----ANDFSCTVHLFSSEGIN  182 (328)
T ss_dssp             HHHHHHHHHHHHTTSCEEEEEEECST--HHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEEEEESSCCC
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEECCh--hHHHHHHHHHhcCCCceEeCCCCchhhh-hh----cccCCceEEEEECCCCC
Confidence            4344444443332 368999999977  7899999999999999999999855432 22    12456666666777777


Q ss_pred             ccC-----CCCCcEEEEecCCCCHhHH-HHHhcccCCCC----CceeEEEEecccch
Q psy17587         85 GLD-----VKHLNLVVNYDCPNHYEDY-VHRCGRTGRAG----NKGFAYTFITLEQE  131 (231)
Q Consensus        85 Gld-----ip~v~~VI~~d~P~~~~~y-~qr~GR~gR~g----~~g~~i~~~~~~~~  131 (231)
                      |+|     +...+.||.||.-|++..= +|.+-|+.|.|    +...++-+++.+-.
T Consensus       183 gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~~r~~R~~~gq~k~v~V~RLvt~~Ti  239 (328)
T 3hgt_A          183 FTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSI  239 (328)
T ss_dssp             TTTSCCCCCSCCSEEEECSTTCCTTSHHHHHHHCCC---------CCEEEEEETTSH
T ss_pred             CcCcccccCCCCCEEEEECCCCCCCChHHHHHHHHhhhccCCCCcceEEEEeCCCCH
Confidence            776     6788999999999999885 88887777763    35667888876643

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=97.97  E-value=2.1e-05  Score=75.20  Aligned_cols=120  Identities=18%  Similarity=0.246  Sum_probs=90.2

Q ss_pred             chhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHH-----------------------------------------
Q psy17587          6 PCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELM-----------------------------------------   43 (231)
Q Consensus         6 k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~-----------------------------------------   43 (231)
                      |..++.+.+... ..++.|+|+|.+.  +..+.|++.|.                                         
T Consensus       428 K~~AIv~eI~~~~~~GqPVLVgT~SI--e~SE~LS~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  505 (997)
T 2ipc_A          428 KFYAVVEEIAEKYERGQPVLVGTISI--EKSERLSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQL  505 (997)
T ss_dssp             HHHHHHHHHHHHHHHTCCEEEECSSH--HHHHHHHHHHHCGGGGHHHHHHHHHHHHHHHTTCCSHHHHHHHHHTSSSTTC
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEeCCH--HHHHHHHHHHhhccccchhhhhhhhhhhhhhhhccccchhhhhhhhhccccc
Confidence            445555555443 4589999999988  77999999998                                         


Q ss_pred             -----------------------------------HCCCCeeeccCCCCHHHHHHHHHHHhCC-CccEEEecCccccccC
Q psy17587         44 -----------------------------------KAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRLLIATSVAARGLD   87 (231)
Q Consensus        44 -----------------------------------~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLvaT~~~~~Gld   87 (231)
                                                         +.|++..++.+....+|- .++.+  .| .-.|-|||+.++||.|
T Consensus       506 ~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gI~H~VLNAK~he~EA-eIIAq--AG~~GaVTIATNMAGRGTD  582 (997)
T 2ipc_A          506 KDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGIPHQVLNAKHHAREA-EIVAQ--AGRSKTVTIATNMAGRGTD  582 (997)
T ss_dssp             SHHHHSGGGGGCCSSHHHHHHHHHHHHHHHHHHHHHHCCCCCEECSSSHHHHH-HHHHT--TTSTTCEEEECSSTTTTSC
T ss_pred             cccccccccccccccccccccccccchhhhhhHHHHcCCCeeeccccchHHHH-HHHHh--cCCCCeEEEEecccCCCcC
Confidence                                               567777777776543321 22222  33 3468899999999999


Q ss_pred             CCCC-------------------c-------------------------------------------------------E
Q psy17587         88 VKHL-------------------N-------------------------------------------------------L   93 (231)
Q Consensus        88 ip~v-------------------~-------------------------------------------------------~   93 (231)
                      |.--                   .                                                       +
T Consensus       583 IkLggn~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~V~e~GGLh  662 (997)
T 2ipc_A          583 IKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLF  662 (997)
T ss_dssp             CCSSCCHHHHHHHTTSSSCSSTTHHHHHHHHHHHHHTCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             eecCCCHHHHHHHHHHhhcccccccccccccccccccchhhccccchhhhhhhhHHHHHHHhhhhhhhhhhHHHhcCCeE
Confidence            8622                   1                                                       7


Q ss_pred             EEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         94 VVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        94 VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      ||--..+.+..-=.|-.||+||.|.+|.+-.|++-+|
T Consensus       663 VIGTeRhESrRIDnQLRGRaGRQGDPGsSrF~LSLeD  699 (997)
T 2ipc_A          663 IIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDD  699 (997)
T ss_dssp             EEESSCCSSHHHHHHHHHTSSCSSCCCEEEEEEESSS
T ss_pred             EEeccCCchHHHHHHHhcccccCCCCCCeEEEEECCh
Confidence            8888889999889999999999999999988887665

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=97.29  E-value=0.00079  Score=62.56  Aligned_cols=100  Identities=16%  Similarity=0.152  Sum_probs=65.0

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC--ccccccCCCC--CcEEE
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS--VAARGLDVKH--LNLVV   95 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~--~~~~Gldip~--v~~VI   95 (231)
                      ++.++||+++.  ...+.+++.|.  .+... ...+++..++...+++|+ +.-.||++|.  .+.+|||+|+  .+.||
T Consensus       448 ~g~~lvlF~Sy--~~l~~v~~~l~--~~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~v~~gsf~EGiD~~g~~l~~vi  521 (620)
T 4a15_A          448 KKNTIVYFPSY--SLMDRVENRVS--FEHMK-EYRGIDQKELYSMLKKFR-RDHGTIFAVSGGRLSEGINFPGNELEMII  521 (620)
T ss_dssp             CSCEEEEESCH--HHHHHHTSSCC--SCCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEEETTSCC--------CCCCEEE
T ss_pred             CCCEEEEeCCH--HHHHHHHHHHH--hcchh-ccCCCChhHHHHHHHHhc-cCCcEEEEEecCceeccccCCCCceEEEE
Confidence            34567788877  66888888775  23333 555666778999999999 8889999975  9999999994  66888


Q ss_pred             EecCCCCH-----------------------------hHHHHHhcccCCCCC-ceeEEEE
Q psy17587         96 NYDCPNHY-----------------------------EDYVHRCGRTGRAGN-KGFAYTF  125 (231)
Q Consensus        96 ~~d~P~~~-----------------------------~~y~qr~GR~gR~g~-~g~~i~~  125 (231)
                      ...+|...                             ....|-+||+=|... .|..+++
T Consensus       522 I~~lPfp~~~p~~~ar~~~~~~~~g~~~~~~y~~pa~~~l~Qa~GRlIR~~~D~G~v~ll  581 (620)
T 4a15_A          522 LAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVIL  581 (620)
T ss_dssp             ESSCCCCCCCHHHHHHHHHHHHHHSCHHHHHTHHHHHHHHHHHHHTTCCSTTCCEEEEEE
T ss_pred             EEcCCCCCCCHHHHHHHHHHHHhhCCCchHHhHHHHHHHHHHHhCccccCCCceEEEEEE
Confidence            88777531                             112588899888754 4555444

>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=96.53  E-value=0.0045  Score=59.01  Aligned_cols=80  Identities=16%  Similarity=0.283  Sum_probs=65.0

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc-ccccCCC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA-ARGLDVK   89 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~-~~Gldip   89 (231)
                      .....+.+++|.++++  ..+.++++.+...    ++++..+||+++..+|...++.+.+|..+|+|+|... ...+++.
T Consensus       412 ~~l~~g~qvlvlaPtr--~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~  489 (780)
T 1gm5_A          412 DNYEAGFQTAFMVPTS--ILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFK  489 (780)
T ss_dssp             HHHHHTSCEEEECSCH--HHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCS
T ss_pred             HHHHcCCeEEEEeCcH--HHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhcc
Confidence            3333467888899987  7788888777543    7999999999999999999999999999999999753 3457888


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      ++.+||.
T Consensus       490 ~l~lVVI  496 (780)
T 1gm5_A          490 NLGLVII  496 (780)
T ss_dssp             CCCEEEE
T ss_pred             CCceEEe
Confidence            8888775

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

Probab=96.27  E-value=0.0083  Score=52.19  Aligned_cols=81  Identities=11%  Similarity=0.097  Sum_probs=65.3

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHH---CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc----cccC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMK---AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA----RGLD   87 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~----~Gld   87 (231)
                      .....+.++||.++++  ..+.++++.+..   .++++..+||+.+..++......+..|+.+|+|+|+-.-    .-++
T Consensus        59 ~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~  136 (414)
T 3oiy_A           59 WLARKGKKSALVFPTV--TLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLS  136 (414)
T ss_dssp             HHHTTTCCEEEEESSH--HHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHT
T ss_pred             HHhcCCCEEEEEECCH--HHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhc
Confidence            3334577888899987  889999999987   588999999999999999999999999999999997432    1255


Q ss_pred             CCCCcEEEEe
Q psy17587         88 VKHLNLVVNY   97 (231)
Q Consensus        88 ip~v~~VI~~   97 (231)
                      ...+++||.-
T Consensus       137 ~~~~~~iViD  146 (414)
T 3oiy_A          137 QKRFDFVFVD  146 (414)
T ss_dssp             TCCCSEEEES
T ss_pred             cccccEEEEe
Confidence            5677877753

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=95.98  E-value=0.078  Score=48.24  Aligned_cols=74  Identities=9%  Similarity=0.104  Sum_probs=50.6

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec--CccccccCCC-----CCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT--SVAARGLDVK-----HLN   92 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT--~~~~~Gldip-----~v~   92 (231)
                      ...++||.++.  ...+.+++.   .+..+..=..+++.   ...++.|+...-.||+||  ..+.+|||+|     .++
T Consensus       393 ~g~~lvlF~Sy--~~l~~v~~~---~~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~d~~g~~l~  464 (551)
T 3crv_A          393 KANVLVVFPSY--EIMDRVMSR---ISLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLIS  464 (551)
T ss_dssp             SSEEEEEESCH--HHHHHHHTT---CCSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCEETTEESEE
T ss_pred             CCCEEEEecCH--HHHHHHHHh---cCCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceecccccccccCCccee
Confidence            45677788877  567777762   34444443335553   456777854344899998  6999999999     477


Q ss_pred             EEEEecCCC
Q psy17587         93 LVVNYDCPN  101 (231)
Q Consensus        93 ~VI~~d~P~  101 (231)
                      .||...+|.
T Consensus       465 ~viI~~lPf  473 (551)
T 3crv_A          465 DVVIVGIPY  473 (551)
T ss_dssp             EEEEESCCC
T ss_pred             EEEEEcCCC
Confidence            888877664

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=95.52  E-value=0.09  Score=41.29  Aligned_cols=73  Identities=15%  Similarity=0.253  Sum_probs=52.8

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc------ccccC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA------ARGLD   87 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~------~~Gld   87 (231)
                      ...++||.|+++  ..++++.+.+...     ++++..++|+.+..+...   .+..+..+|+|+|.-.      ...++
T Consensus        81 ~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~~~~~~~~i~v~T~~~l~~~~~~~~~~  155 (220)
T 1t6n_A           81 GQVSVLVMCHTR--ELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALARNKSLN  155 (220)
T ss_dssp             TCCCEEEECSCH--HHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHH---HHHHSCCSEEEECHHHHHHHHHTTSSC
T ss_pred             CCEEEEEEeCCH--HHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHH---HHhcCCCCEEEeCHHHHHHHHHhCCCC
Confidence            345888899987  7788888887654     789999999998766543   3455678999999631      22356


Q ss_pred             CCCCcEEEE
Q psy17587         88 VKHLNLVVN   96 (231)
Q Consensus        88 ip~v~~VI~   96 (231)
                      +..+++||.
T Consensus       156 ~~~~~~lVi  164 (220)
T 1t6n_A          156 LKHIKHFIL  164 (220)
T ss_dssp             CTTCCEEEE
T ss_pred             cccCCEEEE
Confidence            667776664

>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=95.09  E-value=0.058  Score=53.55  Aligned_cols=78  Identities=14%  Similarity=0.176  Sum_probs=63.8

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-ccccccCCCCC
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-VAARGLDVKHL   91 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-~~~~Gldip~v   91 (231)
                      ...+.+++|.|+++  ..+.++++.+..    .++.+..++|..+..++...++.+.+|+.+|+|+|. .+...+.+.++
T Consensus       649 ~~~g~~vlvlvPt~--~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l  726 (1151)
T 2eyq_A          649 VDNHKQVAVLVPTT--LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDL  726 (1151)
T ss_dssp             HTTTCEEEEECSSH--HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSE
T ss_pred             HHhCCeEEEEechH--HHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCcccccc
Confidence            34567889899987  778888888764    367899999999999999999999999999999995 44455778888


Q ss_pred             cEEEE
Q psy17587         92 NLVVN   96 (231)
Q Consensus        92 ~~VI~   96 (231)
                      .+||.
T Consensus       727 ~lvIi  731 (1151)
T 2eyq_A          727 GLLIV  731 (1151)
T ss_dssp             EEEEE
T ss_pred             ceEEE
Confidence            87774

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

Probab=94.89  E-value=0.034  Score=54.98  Aligned_cols=78  Identities=12%  Similarity=0.139  Sum_probs=64.5

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHH---CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc----cccCCCC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMK---AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA----RGLDVKH   90 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~----~Gldip~   90 (231)
                      ..+.++||.++++  +.+.++++.+..   .++++..+||+++..+|....+.+.+|..+|+|+|+-.-    .-+++.+
T Consensus       119 ~~~~~~Lil~Ptr--eLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~  196 (1104)
T 4ddu_A          119 RKGKKSALVFPTV--TLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKR  196 (1104)
T ss_dssp             TTTCCEEEEESSH--HHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSC
T ss_pred             hcCCeEEEEechH--HHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccC
Confidence            4567888899988  889999999987   578999999999999999999999999999999996322    1155678


Q ss_pred             CcEEEEe
Q psy17587         91 LNLVVNY   97 (231)
Q Consensus        91 v~~VI~~   97 (231)
                      +++||.-
T Consensus       197 l~~lViD  203 (1104)
T 4ddu_A          197 FDFVFVD  203 (1104)
T ss_dssp             CSEEEES
T ss_pred             cCEEEEe
Confidence            8888763

>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=94.37  E-value=0.21  Score=40.39  Aligned_cols=76  Identities=18%  Similarity=0.279  Sum_probs=53.0

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----cc--
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AA--   83 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~--   83 (231)
                      .....+.++||.++++  ..+.++.+.+...    ++.+..++|+.+..+....+    .+..+|+|+|+-     +.  
T Consensus       106 ~~~~~~~~~lil~Ptr--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~  179 (249)
T 3ber_A          106 LETPQRLFALVLTPTR--ELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENT  179 (249)
T ss_dssp             HHSCCSSCEEEECSSH--HHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHS
T ss_pred             hcCCCCceEEEEeCCH--HHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcC
Confidence            3333456788899987  7788888877654    78999999998866544332    246899999963     11  


Q ss_pred             cccCCCCCcEEEE
Q psy17587         84 RGLDVKHLNLVVN   96 (231)
Q Consensus        84 ~Gldip~v~~VI~   96 (231)
                      .++++..+++||.
T Consensus       180 ~~~~l~~~~~lVi  192 (249)
T 3ber_A          180 KGFNLRALKYLVM  192 (249)
T ss_dssp             TTCCCTTCCEEEE
T ss_pred             CCcCccccCEEEE
Confidence            3466777777665

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=94.30  E-value=0.15  Score=40.42  Aligned_cols=78  Identities=12%  Similarity=0.183  Sum_probs=53.4

Q ss_pred             ccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc----
Q psy17587         12 GGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA----   82 (231)
Q Consensus        12 ~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~----   82 (231)
                      ..+.....+.++||.|+++  ..+.++.+.+...     ++.+..++|+.+..++...+     ...+|+|+|+--    
T Consensus        84 ~~l~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~  156 (230)
T 2oxc_A           84 DSLVLENLSTQILILAPTR--EIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQL  156 (230)
T ss_dssp             HHCCTTSCSCCEEEECSSH--HHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHH
T ss_pred             HHHHhcCCCceEEEEeCCH--HHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHH
Confidence            3333334467888899987  7789988888653     67889999999876654433     257899999732    


Q ss_pred             --ccccCCCCCcEEEE
Q psy17587         83 --ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 --~~Gldip~v~~VI~   96 (231)
                        ...+++..+++||.
T Consensus       157 ~~~~~~~~~~~~~lVi  172 (230)
T 2oxc_A          157 IELDYLNPGSIRLFIL  172 (230)
T ss_dssp             HHTTSSCGGGCCEEEE
T ss_pred             HhcCCcccccCCEEEe
Confidence              12345566666654

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=94.13  E-value=0.25  Score=38.08  Aligned_cols=74  Identities=16%  Similarity=0.228  Sum_probs=50.3

Q ss_pred             cCCCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----ccc-c
Q psy17587         17 YDRDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AAR-G   85 (231)
Q Consensus        17 ~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~~-G   85 (231)
                      ...+.++||.|+++  ..+.++.+.+...     +..+..++|+.+..+....   + .+..+|+|+|+-     ... .
T Consensus        68 ~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~i~v~T~~~l~~~~~~~~  141 (206)
T 1vec_A           68 KKDNIQAMVIVPTR--ELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR---L-DDTVHVVIATPGRILDLIKKGV  141 (206)
T ss_dssp             TSCSCCEEEECSCH--HHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH---T-TSCCSEEEECHHHHHHHHHTTC
T ss_pred             cCCCeeEEEEeCcH--HHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHh---c-CCCCCEEEeCHHHHHHHHHcCC
Confidence            33456788899987  7788888887643     6788999999886654322   2 356789999972     222 3


Q ss_pred             cCCCCCcEEEE
Q psy17587         86 LDVKHLNLVVN   96 (231)
Q Consensus        86 ldip~v~~VI~   96 (231)
                      +++..+++||.
T Consensus       142 ~~~~~~~~lVi  152 (206)
T 1vec_A          142 AKVDHVQMIVL  152 (206)
T ss_dssp             SCCTTCCEEEE
T ss_pred             cCcccCCEEEE
Confidence            45666676664

>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=93.84  E-value=0.31  Score=41.37  Aligned_cols=79  Identities=14%  Similarity=0.260  Sum_probs=56.7

Q ss_pred             cccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc-----
Q psy17587         13 GIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA-----   82 (231)
Q Consensus        13 ~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~-----   82 (231)
                      .+.......++||.|+++  ..++++.+.+...     ++++..++|+.+..+....   +..+..+|+|+|.-.     
T Consensus        69 ~l~~~~~~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~iiv~T~~~l~~~~  143 (391)
T 1xti_A           69 QLEPVTGQVSVLVMCHTR--ELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALA  143 (391)
T ss_dssp             HCCCCTTCCCEEEECSCH--HHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHH---HHHSCCSEEEECHHHHHHHH
T ss_pred             hhcccCCCeeEEEECCCH--HHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHH---HhcCCCCEEEECHHHHHHHH
Confidence            333334466888899987  7788888887654     7899999999987665433   455778999999632     


Q ss_pred             -ccccCCCCCcEEEE
Q psy17587         83 -ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 -~~Gldip~v~~VI~   96 (231)
                       ...+++..+++||.
T Consensus       144 ~~~~~~~~~~~~vVi  158 (391)
T 1xti_A          144 RNKSLNLKHIKHFIL  158 (391)
T ss_dssp             HTTSSCCTTCSEEEE
T ss_pred             HcCCccccccCEEEE
Confidence             23356778887775

>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=93.59  E-value=0.2  Score=45.32  Aligned_cols=59  Identities=17%  Similarity=0.194  Sum_probs=53.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS   80 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~   80 (231)
                      ...+||.++.+  ..+.+..+.|...|+.+..+||+.+..++......+..|..+|+++|+
T Consensus        65 ~g~~lvi~P~~--aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           65 NGLTVVVSPLI--SLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SSEEEEECSCH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCCEEEECChH--HHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            35678789987  779999999999999999999999999999999999999999999986

>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=93.49  E-value=0.2  Score=46.06  Aligned_cols=60  Identities=15%  Similarity=0.099  Sum_probs=53.4

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHH--hCCCccEEEecCc
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDF--KNGKVRLLIATSV   81 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F--~~g~~~vLvaT~~   81 (231)
                      ...+||.++.+  ..+.+..+.|...|+.+..++|+++..++..++..+  ..+..+|+++|+-
T Consensus        84 ~g~~lVisP~~--~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe  145 (591)
T 2v1x_A           84 DGFTLVICPLI--SLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPE  145 (591)
T ss_dssp             SSEEEEECSCH--HHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHH
T ss_pred             CCcEEEEeCHH--HHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChh
Confidence            46788889987  779999999998899999999999999999999888  5789999999983

>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=93.36  E-value=0.26  Score=39.32  Aligned_cols=74  Identities=16%  Similarity=0.275  Sum_probs=44.5

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----cccc-ccC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAAR-GLD   87 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~~-Gld   87 (231)
                      ..+.++||.++++  ..+.++.+.+...    +..+..++|+.+...   ....+..+..+|+|+|+     .+.+ .++
T Consensus        96 ~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~  170 (237)
T 3bor_A           96 FKETQALVLAPTR--ELAQQIQKVILALGDYMGATCHACIGGTNVRN---EMQKLQAEAPHIVVGTPGRVFDMLNRRYLS  170 (237)
T ss_dssp             SCSCCEEEECSSH--HHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSC
T ss_pred             CCCceEEEEECcH--HHHHHHHHHHHHHhhhcCceEEEEECCCchHH---HHHHHhcCCCCEEEECHHHHHHHHHhCCcC
Confidence            3466888899987  7788888888654    577888888865433   33455667789999994     2333 355


Q ss_pred             CCCCcEEEE
Q psy17587         88 VKHLNLVVN   96 (231)
Q Consensus        88 ip~v~~VI~   96 (231)
                      +..+++||.
T Consensus       171 ~~~~~~lVi  179 (237)
T 3bor_A          171 PKWIKMFVL  179 (237)
T ss_dssp             STTCCEEEE
T ss_pred             cccCcEEEE
Confidence            666776664

>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=92.99  E-value=0.52  Score=37.53  Aligned_cols=72  Identities=11%  Similarity=0.086  Sum_probs=51.7

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----cc-cccCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AA-RGLDV   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~-~Gldi   88 (231)
                      .+.++||.|+++  ..+.++.+.+..    .++.+..++|+.+..+....+..    ..+|+|+|+-     +. ..+++
T Consensus       101 ~~~~~lil~Pt~--~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~  174 (242)
T 3fe2_A          101 DGPICLVLAPTR--ELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNL  174 (242)
T ss_dssp             CCCSEEEECSSH--HHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCC
T ss_pred             CCCEEEEEeCcH--HHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCc
Confidence            356788899987  778888776654    48899999999987766554433    4789999962     22 23567


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      .++++||.
T Consensus       175 ~~~~~lVi  182 (242)
T 3fe2_A          175 RRTTYLVL  182 (242)
T ss_dssp             TTCCEEEE
T ss_pred             ccccEEEE
Confidence            77777765

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=92.58  E-value=0.23  Score=38.91  Aligned_cols=78  Identities=13%  Similarity=0.191  Sum_probs=46.5

Q ss_pred             ccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc-----
Q psy17587         12 GGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA-----   82 (231)
Q Consensus        12 ~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~-----   82 (231)
                      ..+.....+.++||.|+++  ..+.++.+.+...    ++.+..++|+.+..+....   +.  ..+|+|+|+-.     
T Consensus        74 ~~l~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~--~~~iiv~Tp~~l~~~~  146 (224)
T 1qde_A           74 QRIDTSVKAPQALMLAPTR--ELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG---LR--DAQIVVGTPGRVFDNI  146 (224)
T ss_dssp             HHCCTTCCSCCEEEECSSH--HHHHHHHHHHHHHTTTSCCCEEEECC-------------CT--TCSEEEECHHHHHHHH
T ss_pred             HHHhccCCCceEEEEECCH--HHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhc---CC--CCCEEEECHHHHHHHH
Confidence            3333334567888899987  7788888877643    6888999998775544322   22  37899999632     


Q ss_pred             -ccccCCCCCcEEEE
Q psy17587         83 -ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 -~~Gldip~v~~VI~   96 (231)
                       ....++..+++||.
T Consensus       147 ~~~~~~~~~~~~iVi  161 (224)
T 1qde_A          147 QRRRFRTDKIKMFIL  161 (224)
T ss_dssp             HTTSSCCTTCCEEEE
T ss_pred             HhCCcchhhCcEEEE
Confidence             23455666776664

>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=92.35  E-value=0.65  Score=35.67  Aligned_cols=72  Identities=15%  Similarity=0.209  Sum_probs=50.3

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC--CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----cc-cccCCCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA--GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AA-RGLDVKH   90 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~--~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~-~Gldip~   90 (231)
                      .+.+++|.|+++  ..+.++.+.+...  ++++..++|+.+.......+.    ...+|+|+|+-     +. ..+++..
T Consensus        71 ~~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~  144 (207)
T 2gxq_A           71 RKPRALVLTPTR--ELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSR  144 (207)
T ss_dssp             CCCSEEEECSSH--HHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTT
T ss_pred             CCCcEEEEECCH--HHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhh
Confidence            467788899987  7799999988765  478889999987655443332    25789999962     12 2355667


Q ss_pred             CcEEEE
Q psy17587         91 LNLVVN   96 (231)
Q Consensus        91 v~~VI~   96 (231)
                      +++||.
T Consensus       145 ~~~iVi  150 (207)
T 2gxq_A          145 VEVAVL  150 (207)
T ss_dssp             CSEEEE
T ss_pred             ceEEEE
Confidence            776665

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=92.10  E-value=0.17  Score=35.42  Aligned_cols=47  Identities=17%  Similarity=0.380  Sum_probs=37.3

Q ss_pred             hhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCC
Q psy17587          8 LSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGI   56 (231)
Q Consensus         8 ~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~   56 (231)
                      ..|.+.+....+++.+|++|.+-.+  ....+..|...|+++..+.||+
T Consensus        44 ~~l~~~~~~l~~~~~ivv~C~~G~r--S~~aa~~L~~~G~~~~~l~GG~   90 (103)
T 3iwh_A           44 DTIPDNLNSFNKNEIYYIVCAGGVR--SAKVVEYLEANGIDAVNVEGGM   90 (103)
T ss_dssp             GGGGGCGGGCCTTSEEEEECSSSSH--HHHHHHHHHTTTCEEEEETTHH
T ss_pred             cchhhhhhhhcCCCeEEEECCCCHH--HHHHHHHHHHcCCCEEEecChH
Confidence            3455666777788999999987644  6778889999999998888885

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=91.52  E-value=0.23  Score=34.12  Aligned_cols=47  Identities=19%  Similarity=0.370  Sum_probs=37.2

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      .+.+.+....+++.+|+||.+-.+  +...+..|...|+++..+.||+.
T Consensus        45 ~l~~~~~~l~~~~~ivvyC~~g~r--s~~a~~~L~~~G~~v~~l~GG~~   91 (100)
T 3foj_A           45 SIPDNLNYFNDNETYYIICKAGGR--SAQVVQYLEQNGVNAVNVEGGMD   91 (100)
T ss_dssp             GGGGCGGGSCTTSEEEEECSSSHH--HHHHHHHHHTTTCEEEEETTHHH
T ss_pred             HHHHHHHhCCCCCcEEEEcCCCch--HHHHHHHHHHCCCCEEEecccHH
Confidence            445556666778999999988633  78888999999999999999863

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=91.28  E-value=1.8  Score=30.61  Aligned_cols=53  Identities=21%  Similarity=0.324  Sum_probs=45.1

Q ss_pred             eEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEE
Q psy17587         22 TIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLL   76 (231)
Q Consensus        22 ~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vL   76 (231)
                      -.++|++..  +....+...+...|..+..++++.....|...++.|.....++-
T Consensus         4 ifvvfssdp--eilkeivreikrqgvrvvllysdqdekrrrerleefekqgvdvr   56 (162)
T 2l82_A            4 IFVVFSSDP--EILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVR   56 (162)
T ss_dssp             EEEEEESCH--HHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTCEEE
T ss_pred             EEEEecCCH--HHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCCcee
Confidence            356788877  67999999999999999999999999999999999987655443

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=91.24  E-value=0.23  Score=34.81  Aligned_cols=47  Identities=23%  Similarity=0.273  Sum_probs=37.1

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      .|.+.+....+++.||+||.+-.+  +...+..|...|+++..+.||+.
T Consensus        44 ~l~~~~~~l~~~~~ivvyC~~G~r--s~~aa~~L~~~G~~v~~l~GG~~   90 (108)
T 3gk5_A           44 ELREKWKILERDKKYAVICAHGNR--SAAAVEFLSQLGLNIVDVEGGIQ   90 (108)
T ss_dssp             HHHHHGGGSCTTSCEEEECSSSHH--HHHHHHHHHTTTCCEEEETTHHH
T ss_pred             HHHHHHHhCCCCCeEEEEcCCCcH--HHHHHHHHHHcCCCEEEEcCcHH
Confidence            344555666678899999988634  78888999999999999999864

>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=90.99  E-value=0.6  Score=36.65  Aligned_cols=72  Identities=15%  Similarity=0.257  Sum_probs=46.4

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH---CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------cccccCCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK---AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------AARGLDVK   89 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~---~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~~~Gldip   89 (231)
                      .+.++||.++++  ..+.++.+.+..   .++.+..++|+.+..++...   +. ...+|+|+|+-      ....+++.
T Consensus        93 ~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~iiv~Tp~~l~~~~~~~~~~~~  166 (228)
T 3iuy_A           93 NGPGMLVLTPTR--ELALHVEAECSKYSYKGLKSICIYGGRNRNGQIED---IS-KGVDIIIATPGRLNDLQMNNSVNLR  166 (228)
T ss_dssp             CCCSEEEECSSH--HHHHHHHHHHHHHCCTTCCEEEECC------CHHH---HH-SCCSEEEECHHHHHHHHHTTCCCCT
T ss_pred             CCCcEEEEeCCH--HHHHHHHHHHHHhcccCceEEEEECCCChHHHHHH---hc-CCCCEEEECHHHHHHHHHcCCcCcc
Confidence            467788899987  779999988876   37889999998775544332   23 34789999962      22345566


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      ++++||.
T Consensus       167 ~~~~lVi  173 (228)
T 3iuy_A          167 SITYLVI  173 (228)
T ss_dssp             TCCEEEE
T ss_pred             cceEEEE
Confidence            7776664

>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=90.00  E-value=1.3  Score=37.62  Aligned_cols=72  Identities=18%  Similarity=0.230  Sum_probs=51.0

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----cc-cccCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AA-RGLDV   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~-~Gldi   88 (231)
                      .+.++||.|+++  ..++++.+.+...    ++.+..++|+....+....    ..+..+|+|+|.-     +. ...++
T Consensus        88 ~~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~Ivv~T~~~l~~~~~~~~~~~  161 (400)
T 1s2m_A           88 NKIQALIMVPTR--ELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILR----LNETVHILVGTPGRVLDLASRKVADL  161 (400)
T ss_dssp             CSCCEEEECSSH--HHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHH----TTSCCSEEEECHHHHHHHHHTTCSCC
T ss_pred             CCccEEEEcCCH--HHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHH----hcCCCCEEEEchHHHHHHHHhCCccc
Confidence            456788899987  7788888887643    6889999999876543322    2467899999952     22 33567


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      .++++||.
T Consensus       162 ~~~~~vIi  169 (400)
T 1s2m_A          162 SDCSLFIM  169 (400)
T ss_dssp             TTCCEEEE
T ss_pred             ccCCEEEE
Confidence            77887775

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=89.98  E-value=0.42  Score=32.35  Aligned_cols=45  Identities=20%  Similarity=0.296  Sum_probs=34.3

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      +.+.+....+ +.+|++|.+-.+  ....+..|...|+++..+.||+.
T Consensus        44 l~~~~~~l~~-~~ivvyC~~g~r--s~~a~~~L~~~G~~v~~l~GG~~   88 (94)
T 1wv9_A           44 IQKGEHGLPR-RPLLLVCEKGLL--SQVAALYLEAEGYEAMSLEGGLQ   88 (94)
T ss_dssp             HTTTCCCCCS-SCEEEECSSSHH--HHHHHHHHHHHTCCEEEETTGGG
T ss_pred             HHHHHHhCCC-CCEEEEcCCCCh--HHHHHHHHHHcCCcEEEEcccHH
Confidence            3444555556 889999988633  77888889999999888999874

>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=89.00  E-value=2.1  Score=36.40  Aligned_cols=79  Identities=16%  Similarity=0.217  Sum_probs=54.1

Q ss_pred             ccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----cc
Q psy17587         12 GGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VA   82 (231)
Q Consensus        12 ~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~   82 (231)
                      ..+.....+.++||.|+++  ..+.++.+.+...    ++.+..++|+.+..+....+.    ...+|+|+|+     .+
T Consensus        97 ~~l~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~ivv~Tp~~l~~~l  170 (410)
T 2j0s_A           97 QCLDIQVRETQALILAPTR--ELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD----YGQHVVAGTPGRVFDMI  170 (410)
T ss_dssp             HTCCTTSCSCCEEEECSSH--HHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH----HCCSEEEECHHHHHHHH
T ss_pred             HHHhhccCCceEEEEcCcH--HHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhh----cCCCEEEcCHHHHHHHH
Confidence            3333334567888899987  7789888888653    578889999988766544332    2458999995     23


Q ss_pred             cc-ccCCCCCcEEEE
Q psy17587         83 AR-GLDVKHLNLVVN   96 (231)
Q Consensus        83 ~~-Gldip~v~~VI~   96 (231)
                      .+ .+++..+++||.
T Consensus       171 ~~~~~~~~~~~~vVi  185 (410)
T 2j0s_A          171 RRRSLRTRAIKMLVL  185 (410)
T ss_dssp             HTTSSCCTTCCEEEE
T ss_pred             HhCCccHhheeEEEE
Confidence            33 356667787775

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=88.93  E-value=0.35  Score=37.88  Aligned_cols=77  Identities=22%  Similarity=0.210  Sum_probs=48.7

Q ss_pred             ccccCCCCeEEEEcCChhHHHHHHHHHHHHHC--------CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc----
Q psy17587         14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA--------GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV----   81 (231)
Q Consensus        14 L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~--------~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~----   81 (231)
                      +.....+.++||.|+++  ..+.++.+.+...        ++.+..++|+.+..+...   .+ ....+|+|+|+-    
T Consensus        66 l~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~-~~~~~Iiv~Tp~~l~~  139 (219)
T 1q0u_A           66 IKPERAEVQAVITAPTR--ELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALE---KL-NVQPHIVIGTPGRIND  139 (219)
T ss_dssp             CCTTSCSCCEEEECSSH--HHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTC---CC-SSCCSEEEECHHHHHH
T ss_pred             HHhCcCCceEEEEcCcH--HHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHH---Hc-CCCCCEEEeCHHHHHH
Confidence            33333467888899987  7788888877543        678889999875443211   11 246789999952    


Q ss_pred             -ccc-ccCCCCCcEEEE
Q psy17587         82 -AAR-GLDVKHLNLVVN   96 (231)
Q Consensus        82 -~~~-Gldip~v~~VI~   96 (231)
                       +.. .+++..+++||.
T Consensus       140 ~l~~~~~~~~~~~~lVi  156 (219)
T 1q0u_A          140 FIREQALDVHTAHILVV  156 (219)
T ss_dssp             HHHTTCCCGGGCCEEEE
T ss_pred             HHHcCCCCcCcceEEEE
Confidence             222 345566666554

>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=88.65  E-value=1.3  Score=37.40  Aligned_cols=79  Identities=13%  Similarity=0.167  Sum_probs=54.5

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc----
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA----   82 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~----   82 (231)
                      +..+.....+.++||.|+++  ..+.++.+.+..    .++.+..++|+.+..+....+.     ..+|+|+|.-.    
T Consensus        80 ~~~l~~~~~~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~i~v~T~~~l~~~  152 (394)
T 1fuu_A           80 LQRIDTSVKAPQALMLAPTR--ELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-----DAQIVVGTPGRVFDN  152 (394)
T ss_dssp             HHHCCTTCCSCCEEEECSSH--HHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-----HCSEEEECHHHHHHH
T ss_pred             HHHhhccCCCCCEEEEcCCH--HHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-----CCCEEEECHHHHHHH
Confidence            33344444567888899987  778888887764    3688999999998776655444     46799999532    


Q ss_pred             --ccccCCCCCcEEEE
Q psy17587         83 --ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 --~~Gldip~v~~VI~   96 (231)
                        ...+++..+++||.
T Consensus       153 ~~~~~~~~~~~~~vIi  168 (394)
T 1fuu_A          153 IQRRRFRTDKIKMFIL  168 (394)
T ss_dssp             HHTTSSCCTTCCEEEE
T ss_pred             HHhCCcchhhCcEEEE
Confidence              22345667777765

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=88.03  E-value=0.31  Score=34.94  Aligned_cols=48  Identities=23%  Similarity=0.293  Sum_probs=35.3

Q ss_pred             hhhccccccCCC-CeEEEEc-CChhHHHHHHHHHHHHHCCCCeeeccCCCCH
Q psy17587          9 SLHGGIDQYDRD-STIVDFK-NGKVRLLVCAIVKELMKAGYPCLSLHGGIDQ   58 (231)
Q Consensus         9 ~L~~~L~~~~~~-~~iiiF~-~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~   58 (231)
                      .+...+....++ +.||++| .+-.+  +...+..|...|+++..+.||+..
T Consensus        77 ~~~~~~~~~~~~~~~ivvyC~~~G~r--s~~a~~~L~~~G~~v~~l~GG~~~  126 (134)
T 3g5j_A           77 DIYLQAAELALNYDNIVIYCARGGMR--SGSIVNLLSSLGVNVYQLEGGYKA  126 (134)
T ss_dssp             HHHHHHHHHHTTCSEEEEECSSSSHH--HHHHHHHHHHTTCCCEEETTHHHH
T ss_pred             HHHHHHHHhccCCCeEEEEECCCChH--HHHHHHHHHHcCCceEEEeCcHHH
Confidence            344444445566 8999999 46533  778888999999999999999753

>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=87.88  E-value=2.1  Score=34.10  Aligned_cols=71  Identities=17%  Similarity=0.151  Sum_probs=49.3

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc------ccccCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA------ARGLDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~------~~Gldip   89 (231)
                      +.++||.|+++  +.+.++.+.+...    ++.+..++|+.+..+....+    ....+|+|+|+--      ...+++.
T Consensus       100 ~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~  173 (253)
T 1wrb_A          100 YPKCLILAPTR--ELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLE  173 (253)
T ss_dssp             CCSEEEECSSH--HHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCT
T ss_pred             CceEEEEECCH--HHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChh
Confidence            35788899987  7788888877643    57888899998765543322    3467899999732      2235677


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      .+++||.
T Consensus       174 ~~~~lVi  180 (253)
T 1wrb_A          174 FCKYIVL  180 (253)
T ss_dssp             TCCEEEE
T ss_pred             hCCEEEE
Confidence            7777765

>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=87.77  E-value=3  Score=33.64  Aligned_cols=72  Identities=17%  Similarity=0.216  Sum_probs=50.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecC-----ccc--cccC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATS-----VAA--RGLD   87 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~-----~~~--~Gld   87 (231)
                      .+.++||.++++  ..+.++.+.+..    .+..+..++|+.+.......   +..+ .+|+|+|+     .+.  .+++
T Consensus       125 ~~~~~lil~Pt~--~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~-~~Iiv~Tp~~l~~~~~~~~~~~  198 (262)
T 3ly5_A          125 NGTGVLILSPTR--ELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQK---LGNG-INIIVATPGRLLDHMQNTPGFM  198 (262)
T ss_dssp             GCCCEEEECSSH--HHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHH---HHHC-CSEEEECHHHHHHHHHHCTTCC
T ss_pred             CCceEEEEeCCH--HHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHH---hcCC-CCEEEEcHHHHHHHHHccCCcc
Confidence            356788889987  778888888865    36778899999876654433   3333 89999995     222  2466


Q ss_pred             CCCCcEEEE
Q psy17587         88 VKHLNLVVN   96 (231)
Q Consensus        88 ip~v~~VI~   96 (231)
                      +.++.+||.
T Consensus       199 ~~~l~~lVi  207 (262)
T 3ly5_A          199 YKNLQCLVI  207 (262)
T ss_dssp             CTTCCEEEE
T ss_pred             cccCCEEEE
Confidence            777777665

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=87.72  E-value=1.1  Score=35.35  Aligned_cols=71  Identities=15%  Similarity=0.230  Sum_probs=47.4

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc-----cc--ccC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA-----AR--GLD   87 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~-----~~--Gld   87 (231)
                      .+.++||.|+++  ..+.++.+.+...    ++.+..++|+.+..+....+     +..+|+|+|.-.     .+  .++
T Consensus        96 ~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~  168 (236)
T 2pl3_A           96 DGLGVLIISPTR--ELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFH  168 (236)
T ss_dssp             GCCCEEEECSSH--HHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCC
T ss_pred             CCceEEEEeCCH--HHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCcc
Confidence            356788899987  7788888888654    47899999998755443332     467899999631     11  245


Q ss_pred             CCCCcEEEE
Q psy17587         88 VKHLNLVVN   96 (231)
Q Consensus        88 ip~v~~VI~   96 (231)
                      +.++++||.
T Consensus       169 ~~~~~~lVi  177 (236)
T 2pl3_A          169 ATDLQMLVL  177 (236)
T ss_dssp             CTTCCEEEE
T ss_pred             cccccEEEE
Confidence            556666654

>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=87.20  E-value=1.2  Score=38.33  Aligned_cols=71  Identities=14%  Similarity=0.251  Sum_probs=52.4

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC-CC---CeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc------cccCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA-GY---PCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA------RGLDV   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~---~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~------~Gldi   88 (231)
                      .+.++||.|+++  ..++++.+.+... +.   .+..+||+.+..++.....     ..+|+|+|.-.-      ..+..
T Consensus        51 ~~~~~liv~P~~--~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----~~~ivv~T~~~l~~~~~~~~~~~  123 (494)
T 1wp9_A           51 YGGKVLMLAPTK--PLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----RAKVIVATPQTIENDLLAGRISL  123 (494)
T ss_dssp             SCSCEEEECSSH--HHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----HCSEEEECHHHHHHHHHTTSCCT
T ss_pred             CCCeEEEEECCH--HHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----CCCEEEecHHHHHHHHhcCCcch
Confidence            467888899987  6788888888765 55   8999999999887655443     468999996322      23566


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      ..+++||.
T Consensus       124 ~~~~~vIi  131 (494)
T 1wp9_A          124 EDVSLIVF  131 (494)
T ss_dssp             TSCSEEEE
T ss_pred             hhceEEEE
Confidence            77777775

>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=86.89  E-value=0.76  Score=38.20  Aligned_cols=75  Identities=11%  Similarity=0.032  Sum_probs=49.5

Q ss_pred             cccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc----
Q psy17587         13 GIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA----   83 (231)
Q Consensus        13 ~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~----   83 (231)
                      .+.......++||.++++  +.+.++++.+...     ++.+..++|+.+...+.       ....+|+|+|+---    
T Consensus       155 ~l~~~~~~~~~lil~Ptr--eLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~~~~~IlV~TP~~l~~~l  225 (300)
T 3fmo_B          155 QVEPANKYPQCLCLSPTY--ELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ-------KISEQIVIGTPGTVLDWC  225 (300)
T ss_dssp             HCCTTSCSCCEEEECSSH--HHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC-------CCCCSEEEECHHHHHHHH
T ss_pred             hhhccCCCceEEEEcCcH--HHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh-------cCCCCEEEECHHHHHHHH
Confidence            333333445788899987  7788888777643     56777888876532211       35678999997431    


Q ss_pred             ---cccCCCCCcEEEE
Q psy17587         84 ---RGLDVKHLNLVVN   96 (231)
Q Consensus        84 ---~Gldip~v~~VI~   96 (231)
                         ..+++..+.++|.
T Consensus       226 ~~~~~~~l~~l~~lVl  241 (300)
T 3fmo_B          226 SKLKFIDPKKIKVFVL  241 (300)
T ss_dssp             TTTCCCCGGGCSEEEE
T ss_pred             HhcCCCChhhceEEEE
Confidence               3567778887775

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

Probab=86.63  E-value=3.3  Score=35.21  Aligned_cols=70  Identities=17%  Similarity=0.137  Sum_probs=50.0

Q ss_pred             CeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----cc-cccCCCC
Q psy17587         21 STIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AA-RGLDVKH   90 (231)
Q Consensus        21 ~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~-~Gldip~   90 (231)
                      .++||.++++  ..+.++++.+..    .++.+..++|+.+..+....   + ....+|+|+|+-     +. ..+++..
T Consensus       102 ~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~~~~~I~v~Tp~~l~~~l~~~~~~~~~  175 (417)
T 2i4i_A          102 PISLVLAPTR--ELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRD---L-ERGCHLLVATPGRLVDMMERGKIGLDF  175 (417)
T ss_dssp             CSEEEECSSH--HHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHH---H-TTCCSEEEECHHHHHHHHHTTSBCCTT
T ss_pred             ccEEEECCcH--HHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHH---h-hCCCCEEEEChHHHHHHHHcCCcChhh
Confidence            5688899987  778888888764    36889999999887654433   2 235789999972     22 2356777


Q ss_pred             CcEEEE
Q psy17587         91 LNLVVN   96 (231)
Q Consensus        91 v~~VI~   96 (231)
                      +++||.
T Consensus       176 ~~~iVi  181 (417)
T 2i4i_A          176 CKYLVL  181 (417)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            787775

>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=85.97  E-value=0.96  Score=40.21  Aligned_cols=71  Identities=11%  Similarity=0.157  Sum_probs=46.8

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc-----cc-c-CC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA-----RG-L-DV   88 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~-----~G-l-di   88 (231)
                      +.++||.|+++  ..+.++.+.+...    ++.+..+||+.+..++...+.    ...+|+|+|+-.-     .+ + ++
T Consensus        55 ~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~  128 (556)
T 4a2p_A           55 KAKVVFLATKV--PVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI----EDSDIIVVTPQILVNSFEDGTLTSL  128 (556)
T ss_dssp             CCCEEEECSSH--HHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHHHH----HHCSEEEECHHHHHHHHHSSSCCCS
T ss_pred             CCeEEEEeCCH--HHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHHhh----CCCCEEEECHHHHHHHHHhCccccc
Confidence            67788899987  6788888877654    899999999987665433222    1378999996322     22 3 57


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      ..+++||.
T Consensus       129 ~~~~~vVi  136 (556)
T 4a2p_A          129 SIFTLMIF  136 (556)
T ss_dssp             TTCSEEEE
T ss_pred             ccCCEEEE
Confidence            77887775

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

Probab=85.86  E-value=0.66  Score=41.16  Aligned_cols=71  Identities=17%  Similarity=0.237  Sum_probs=49.1

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc-----ccc-c-CC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA-----ARG-L-DV   88 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~-----~~G-l-di   88 (231)
                      +.++||.|+++  ..+.++.+.+...    ++.+..+||+.+...+...+.    +..+|+|+|+-.     ..+ + ++
T Consensus        52 ~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~  125 (555)
T 3tbk_A           52 KGKVVFFANQI--PVYEQQATVFSRYFERLGYNIASISGATSDSVSVQHII----EDNDIIILTPQILVNNLNNGAIPSL  125 (555)
T ss_dssp             CCCEEEECSSH--HHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHHHH----HHCSEEEECHHHHHHHHHTSSSCCG
T ss_pred             CCEEEEEeCCH--HHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHHHh----cCCCEEEECHHHHHHHHhcCccccc
Confidence            67788899987  6688877777654    899999999987655432222    147899999632     222 3 56


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      ..+++||.
T Consensus       126 ~~~~~vVi  133 (555)
T 3tbk_A          126 SVFTLMIF  133 (555)
T ss_dssp             GGCSEEEE
T ss_pred             ccCCEEEE
Confidence            67777775

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=85.80  E-value=0.41  Score=34.29  Aligned_cols=49  Identities=22%  Similarity=0.279  Sum_probs=35.7

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      .|...+....+++.||++|.+-.+..+...+..|...|+++..+.||+.
T Consensus        60 ~l~~~~~~l~~~~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~~  108 (124)
T 3flh_A           60 DLATRIGELDPAKTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGALE  108 (124)
T ss_dssp             HHHHHGGGSCTTSEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHHH
T ss_pred             HHHHHHhcCCCCCeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcHH
Confidence            3444555666788999999875221157788888888999889999864

>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=85.01  E-value=3  Score=35.35  Aligned_cols=81  Identities=17%  Similarity=0.202  Sum_probs=55.0

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----   81 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----   81 (231)
                      +..+.....+.+++|.++++  ..+.++.+.+...    +..+..++|+.+....   ......+..+|+|+|+-     
T Consensus        99 ~~~~~~~~~~~~~lil~P~~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~iiv~T~~~l~~~  173 (414)
T 3eiq_A           99 LQQIELDLKATQALVLAPTR--ELAQQIQKVVMALGDYMGASCHACIGGTNVRAE---VQKLQMEAPHIIVGTPGRVFDM  173 (414)
T ss_dssp             HHHCCTTSCSCCEEEECSSH--HHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHH---HHHHTTTCCSEEEECHHHHHHH
T ss_pred             HHHHhhcCCceeEEEEeChH--HHHHHHHHHHHHHhcccCceEEEEECCcchHHH---HHHHhcCCCCEEEECHHHHHHH
Confidence            33343333567888899987  7788888887653    6788888888765443   45566678899999952     


Q ss_pred             cc-cccCCCCCcEEEE
Q psy17587         82 AA-RGLDVKHLNLVVN   96 (231)
Q Consensus        82 ~~-~Gldip~v~~VI~   96 (231)
                      +. ..+++..+++||.
T Consensus       174 l~~~~~~~~~~~~vVi  189 (414)
T 3eiq_A          174 LNRRYLSPKYIKMFVL  189 (414)
T ss_dssp             HHHTSSCSTTCCEEEE
T ss_pred             HHcCCcccccCcEEEE
Confidence            22 2355666777765

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=84.94  E-value=0.63  Score=32.28  Aligned_cols=46  Identities=20%  Similarity=0.296  Sum_probs=34.6

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      +.+.+....+++.+|++|.+-.+  ....+..|...|++ +..+.||+.
T Consensus        48 l~~~~~~l~~~~~ivvyc~~g~r--s~~a~~~L~~~G~~~v~~l~GG~~   94 (108)
T 1gmx_A           48 LGAFMRDNDFDTPVMVMCYHGNS--SKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHSCTTSCEEEECSSSSH--HHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             HHHHHHhcCCCCCEEEEcCCCch--HHHHHHHHHHcCCceEEEecCCHH
Confidence            33344445678899999988633  78888889888995 888999864

>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=84.93  E-value=0.6  Score=37.13  Aligned_cols=73  Identities=18%  Similarity=0.250  Sum_probs=47.6

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----ccc---cc
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AAR---GL   86 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~~---Gl   86 (231)
                      .+.++||.++++  ..+.++.+.+...    ++.+..++|+.....   .......+..+|+|+|+-     +..   .+
T Consensus        97 ~~~~~lil~Pt~--~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~  171 (245)
T 3dkp_A           97 KGFRALIISPTR--ELASQIHRELIKISEGTGFRIHMIHKAAVAAK---KFGPKSSKKFDILVTTPNRLIYLLKQDPPGI  171 (245)
T ss_dssp             SSCCEEEECSSH--HHHHHHHHHHHHHTTTSCCCEECCCHHHHHHT---TTSTTSCCCCCEEEECHHHHHHHHHSSSCSC
T ss_pred             CCceEEEEeCCH--HHHHHHHHHHHHHhcccCceEEEEecCccHHH---HhhhhhcCCCCEEEECHHHHHHHHHhCCCCc
Confidence            456788899987  7789998888754    677777776532211   111223567789999952     112   46


Q ss_pred             CCCCCcEEEE
Q psy17587         87 DVKHLNLVVN   96 (231)
Q Consensus        87 dip~v~~VI~   96 (231)
                      ++.++++||.
T Consensus       172 ~~~~~~~lVi  181 (245)
T 3dkp_A          172 DLASVEWLVV  181 (245)
T ss_dssp             CCTTCCEEEE
T ss_pred             ccccCcEEEE
Confidence            7777777765

>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=84.62  E-value=1.4  Score=41.68  Aligned_cols=71  Identities=11%  Similarity=0.156  Sum_probs=46.7

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----cccc-c-CC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AARG-L-DV   88 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~~G-l-di   88 (231)
                      +.++||.|+++  ..+.++.+.+...    ++++..+||+.+...+...+.    +..+|+|+|+-     +..+ + .+
T Consensus       296 ~~~~Lvl~Pt~--~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~----~~~~Ivv~Tp~~l~~~l~~~~~~~~  369 (797)
T 4a2q_A          296 KAKVVFLATKV--PVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVI----EDSDIIVVTPQILVNSFEDGTLTSL  369 (797)
T ss_dssp             CCCEEEECSSH--HHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHHHH----HTCSEEEECHHHHHHHHHSSSCCCG
T ss_pred             CCeEEEEeCCH--HHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHHhh----CCCCEEEEchHHHHHHHHhcccccc
Confidence            67888899987  6788888777654    899999999987665433222    25789999953     1222 3 56


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      .++++||.
T Consensus       370 ~~~~~iVi  377 (797)
T 4a2q_A          370 SIFTLMIF  377 (797)
T ss_dssp             GGCSEEEE
T ss_pred             ccCCEEEE
Confidence            67787775

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=83.71  E-value=1.2  Score=30.82  Aligned_cols=40  Identities=23%  Similarity=0.402  Sum_probs=31.8

Q ss_pred             ccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         16 QYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        16 ~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      ...+++.||+||.+-.  .+...+..|...|++ +..+.||+.
T Consensus        48 ~l~~~~~ivvyc~~g~--rs~~a~~~L~~~G~~~v~~l~GG~~   88 (106)
T 3hix_A           48 SLEKSRDIYVYGAGDE--QTSQAVNLLRSAGFEHVSELKGGLA   88 (106)
T ss_dssp             HSCTTSCEEEECSSHH--HHHHHHHHHHHTTCSCEEECTTHHH
T ss_pred             cCCCCCeEEEEECCCC--hHHHHHHHHHHcCCcCEEEecCCHH
Confidence            4456788999999863  378888999999995 888999864

>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=83.08  E-value=1.5  Score=43.16  Aligned_cols=74  Identities=16%  Similarity=0.286  Sum_probs=54.2

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC----CC----CeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc-ccccC-C
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA----GY----PCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA-ARGLD-V   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~----~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~-~~Gld-i   88 (231)
                      .+.++||.++++  ..+.++++.+...    ++    .+..+||+.+..++....+.+++  .+|+|+|+-. ..-+. +
T Consensus        98 ~~~~~lil~Ptr--eLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~L  173 (1054)
T 1gku_B           98 KGKRCYVIFPTS--LLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYREL  173 (1054)
T ss_dssp             TSCCEEEEESCH--HHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTTS
T ss_pred             cCCeEEEEeccH--HHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHHh
Confidence            457788899987  7788888887643    56    88999999999888877777777  8999999721 11111 4


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      ..+++||.
T Consensus       174 ~~l~~lVi  181 (1054)
T 1gku_B          174 GHFDFIFV  181 (1054)
T ss_dssp             CCCSEEEE
T ss_pred             ccCCEEEE
Confidence            46666664

>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=81.89  E-value=2.7  Score=36.62  Aligned_cols=71  Identities=20%  Similarity=0.150  Sum_probs=51.6

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----ccc-ccCCC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----AAR-GLDVK   89 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~~~-Gldip   89 (231)
                      +.++||.|+++  +.+.++.+.+.+.    ++.+..++|+.+..++...+    ....+|+|+|+-     +.+ .+++.
T Consensus       129 ~~~~lil~Ptr--eLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l----~~~~~Ivv~Tp~~l~~~l~~~~~~l~  202 (434)
T 2db3_A          129 RPQVVIVSPTR--ELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECI----TRGCHVVIATPGRLLDFVDRTFITFE  202 (434)
T ss_dssp             CCSEEEECSSH--HHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHH----TTCCSEEEECHHHHHHHHHTTSCCCT
T ss_pred             CccEEEEecCH--HHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHh----hcCCCEEEEChHHHHHHHHhCCcccc
Confidence            56888899987  7899998887653    57888999999876544332    246899999962     223 35677


Q ss_pred             CCcEEEE
Q psy17587         90 HLNLVVN   96 (231)
Q Consensus        90 ~v~~VI~   96 (231)
                      .++++|.
T Consensus       203 ~~~~lVl  209 (434)
T 2db3_A          203 DTRFVVL  209 (434)
T ss_dssp             TCCEEEE
T ss_pred             cCCeEEE
Confidence            8887775

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=80.86  E-value=1.2  Score=32.04  Aligned_cols=40  Identities=18%  Similarity=0.337  Sum_probs=31.6

Q ss_pred             ccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         16 QYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        16 ~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      ...+++.||+||.+-.+  +...+..|...|++ +..+.||+.
T Consensus        78 ~l~~~~~ivvyC~~G~r--s~~aa~~L~~~G~~~v~~l~GG~~  118 (129)
T 1tq1_A           78 HFGQSDNIIVGCQSGGR--SIKATTDLLHAGFTGVKDIVGGYS  118 (129)
T ss_dssp             TCCTTSSEEEEESSCSH--HHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             hCCCCCeEEEECCCCcH--HHHHHHHHHHcCCCCeEEeCCcHH
Confidence            34567899999988644  77888888888985 888999974

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=80.75  E-value=1.7  Score=28.52  Aligned_cols=37  Identities=22%  Similarity=0.333  Sum_probs=28.4

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      .+++.+|++|.+-.  .+...+..|...|++ +..+ |++.
T Consensus        39 ~~~~~ivv~C~~g~--rs~~aa~~L~~~G~~~v~~l-GG~~   76 (85)
T 2jtq_A           39 DKNDTVKVYCNAGR--QSGQAKEILSEMGYTHVENA-GGLK   76 (85)
T ss_dssp             CTTSEEEEEESSSH--HHHHHHHHHHHTTCSSEEEE-EETT
T ss_pred             CCCCcEEEEcCCCc--hHHHHHHHHHHcCCCCEEec-cCHH
Confidence            56789999999863  478888899999986 5555 7754

>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=80.50  E-value=2.3  Score=40.68  Aligned_cols=55  Identities=7%  Similarity=-0.061  Sum_probs=40.5

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHH----HCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELM----KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~----~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      .+..++|.|+++  ..+.+.++.+.    ..|+++.++.|+++..+|....      .++|+|+|+-
T Consensus       114 ~g~~vlVltPTr--eLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~r~~~~------~~dIvvgTpg  172 (853)
T 2fsf_A          114 TGKGVHVVTVND--YLAQRDAENNRPLFEFLGLTVGINLPGMPAPAKREAY------AADITYGTNN  172 (853)
T ss_dssp             TSSCCEEEESSH--HHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHH------HSSEEEEEHH
T ss_pred             cCCcEEEEcCCH--HHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHhc------CCCEEEECCc
Confidence            355677788876  66776666553    4589999999999987665443      3789999973

---

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	231
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	9e-25
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	6e-21
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-19
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	3e-18
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	7e-14
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	1e-13
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	3e-13
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-12
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	6e-12
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-05
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	1e-11
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	5e-11
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	7e-11
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-08
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	0.002
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	1e-08
d1gm5a4	206	c.37.1.19 (A:550-755) RecG helicase domain {Thermo	3e-08
d2p6ra4	201	c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglob	1e-06
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	1e-04
d1tf5a4	175	c.37.1.19 (A:396-570) Translocation ATPase SecA, n	7e-04

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 96.9 bits (241), Expect = 9e-25
 Identities = 26/159 (16%), Positives = 47/159 (29%), Gaps = 25/159 (15%)

Query: 8   LSLHGGIDQYDRDSTIVDFKNGKVRLLVCA-------IVKELMKAGYPCLSLHGGIDQYD 60
           LS  G I  Y +   +   K G+  L+ C        +  +L+  G   ++ + G+D   
Sbjct: 16  LSTTGEIPFYGKAIPLEVIKGGRH-LIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSV 74

Query: 61  R----------DSTIVDFKNGKVRLLIATSVAARG---LDVKHLNLVVNYDCPNHYEDYV 107
                         ++    G    +I  +          +     +     P       
Sbjct: 75  IPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRT 134

Query: 108 HRCGRTGRAGNKGFAYTFITLEQER---HAGEIIRALEA 143
            R GRTGR G  G        E+      +  +    +A
Sbjct: 135 QRRGRTGR-GKPGIYRFVAPGERPSGMFDSSVLCECYDA 172

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 86.5 bits (213), Expect = 6e-21
 Identities = 29/101 (28%), Positives = 42/101 (41%), Gaps = 9/101 (8%)

Query: 35  VCAIVKELMKAGYPCLSLHGGIDQYDR--------DSTIVDFKNGKVRLLIATSVAARGL 86
              IV EL+K G       G   + +            + +F  G+  +L+ATSV   GL
Sbjct: 174 AKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGL 233

Query: 87  DVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT 127
           DV  ++LVV Y+        + R GRTGR    G     + 
Sbjct: 234 DVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMA 273

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 78.4 bits (192), Expect = 7e-19
 Identities = 39/119 (32%), Positives = 69/119 (57%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           +  +L    +   +++  + Q +RD+ + +F++G  R+LI+T + ARG+DV+ ++LV+NY
Sbjct: 43  LTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINY 102

Query: 98  DCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMW 156
           D P + E+Y+HR GR GR G KG A  F+T E      E+ +        +P D+  + 
Sbjct: 103 DLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATLL 161

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 78.7 bits (193), Expect = 3e-18
 Identities = 23/169 (13%), Positives = 44/169 (26%), Gaps = 10/169 (5%)

Query: 51  SLHGGIDQYDRDSTIVDFKNGKVRLLIATS----VAARGLDVKH-LNLVVNYDCPNHYED 105
               GI    +      F  G++  LI T+       RGLD+   +   V   CP+    
Sbjct: 48  KFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPS---- 103

Query: 106 YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTF 165
           +            +                 ++ A+E     + E L K+  ++      
Sbjct: 104 FRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKD 163

Query: 166 CFRAGNKGFAYTFIT-LEQERHAGEIIRALEASGVPIPEDLDKILAEGL 213
                 +       T ++       +       G     + D  L    
Sbjct: 164 VVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAF 212

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

 Score = 65.6 bits (159), Expect = 7e-14
 Identities = 19/97 (19%), Positives = 34/97 (35%)

Query: 46  GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
           G     LH  I   +R   I D + GK  +L+  ++   GLD+  ++LV   D       
Sbjct: 55  GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFL 114

Query: 106 YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALE 142
              R            A   + +  +     +  A++
Sbjct: 115 RSERSLIQTIGRAARNANGHVIMYADTITKSMEIAIQ 151

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 63.8 bits (154), Expect = 1e-13
 Identities = 41/93 (44%), Positives = 55/93 (59%), Gaps = 3/93 (3%)

Query: 58  QYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAG 117
           Q  R+  I  FK  K+R+LIAT V +RG+DV  LN V+NY  P + E Y+HR GRTGRAG
Sbjct: 64  QSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAG 123

Query: 118 NKGFAYTFITLEQERHAGEIIRALEASGVPIPE 150
            KG A + I   + +    I RA+    + I +
Sbjct: 124 KKGKAISIINRREYKKLRYIERAM---KLKIKK 153

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.4 bits (153), Expect = 3e-13
 Identities = 44/115 (38%), Positives = 69/115 (60%), Gaps = 5/115 (4%)

Query: 47  YPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYEDY 106
           +   S+HG + Q +R+S + +F++G  R+LI+T V ARGLDV  ++L++NYD PN+ E Y
Sbjct: 59  FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELY 118

Query: 107 VHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLI 161
           +HR GR+GR G KG A  F+  +  R   +I +        +P ++      DLI
Sbjct: 119 IHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNV-----ADLI 168

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 62.2 bits (150), Expect = 1e-12
 Identities = 16/88 (18%), Positives = 34/88 (38%)

Query: 41  ELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCP 100
             +   +   ++     + +R+  +  F+ G+ R ++++ V   G+DV   N+ V     
Sbjct: 107 YRISKVFLIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGS 166

Query: 101 NHYEDYVHRCGRTGRAGNKGFAYTFITL 128
               +Y+ R GR  R            L
Sbjct: 167 GSAREYIQRLGRILRPSKGKKEAVLYEL 194

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 59.7 bits (143), Expect = 6e-12
 Identities = 46/148 (31%), Positives = 76/148 (51%), Gaps = 5/148 (3%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
             +   +  I+ F N   R+ + A  K++   GY C   H  + Q +R+    +F+ GKV
Sbjct: 27  FSKLQINQAII-FCNSTNRVELLA--KKITDLGYSCYYSHARMKQQERNKVFHEFRQGKV 83

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R L+ + +  RG+D++ +N+V+N+D P   E Y+HR GR+GR G+ G A   I      +
Sbjct: 84  RTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFN 143

Query: 134 AGEIIRALEASGVPIPEDLDKMW--AED 159
             +I + L      IP  +DK    AE+
Sbjct: 144 LYKIEQELGTEIAAIPATIDKSLYVAEN 171

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 41.6 bits (96), Expect = 2e-05
 Identities = 15/59 (25%), Positives = 20/59 (33%)

Query: 151 DLDKMWAEDLIVRTFCFRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKIL 209
           D  K     L       R G+ G A   I      +  +I + L      IP  +DK L
Sbjct: 108 DFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSL 166

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

 Score = 58.2 bits (140), Expect = 1e-11
 Identities = 27/131 (20%), Positives = 45/131 (34%), Gaps = 20/131 (15%)

Query: 7   CLSLHGGIDQYDRDSTIVDFKNGKVRLLVCA-------IVKELMKAGYPCLSLHGGIDQY 59
            LS  G I  Y +   +   K G+  L+ C        +  +L+  G   ++ + G+D  
Sbjct: 14  ALSTTGEIPFYGKAIPLEVIKGGRH-LIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS 72

Query: 60  DRDSTIVDFKNGKVRLLIATSVAARGLDVKH---LNLVVNYDCPNHYEDYVHRCGRTGRA 116
                          +++AT     G        ++   +   P        R GRTGR 
Sbjct: 73  V-------IPTNGDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR- 124

Query: 117 GNKGFAYTFIT 127
           G  G  Y F+ 
Sbjct: 125 GKPG-IYRFVA 134

>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 = 58.4 bits (140), Expect = 7e-11
 Identities = 16/114 (14%), Positives = 28/114 (24%), Gaps = 23/114 (20%)

Query: 35  VCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVK----- 89
              I   L K G   + L       +     +  +      ++ T ++  G + K     
Sbjct: 191 GNDIAACLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTDISEMGANFKAERVI 246

Query: 90  ----HLNLVVNYDCPNH----------YEDYVHRCGRTGRAGNKGFAYTFITLE 129
                +  V+  D              +     R GR GR             E
Sbjct: 247 DPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE 300

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (120), Expect = 1e-08
 Identities = 40/142 (28%), Positives = 76/142 (53%), Gaps = 4/142 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           +D  + +  ++ F     R +  A +       +P +++H G+ Q +R S    FK+ + 
Sbjct: 22  LDVLEFNQVVI-FVKSVQRCIALAQLLVEQN--FPAIAIHRGMPQEERLSRYQQFKDFQR 78

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           R+L+AT++  RG+D++ +N+  NYD P   + Y+HR  R GR G KG A TF++ E +  
Sbjct: 79  RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAK 138

Query: 134 -AGEIIRALEASGVPIPEDLDK 154
              ++    E +   +P+++D 
Sbjct: 139 ILNDVQDRFEVNISELPDEIDI 160

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (80), Expect = 0.002
 Identities = 25/163 (15%), Positives = 54/163 (33%), Gaps = 13/163 (7%)

Query: 55  GIDQY-------DRDSTIVDF--KNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNHYED 105
           G+ QY       +++  + D        +++I      R + +  L +  N+     +  
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 60

Query: 106 YVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKMWAEDLIVRTF 165
                  +     K F    +        G  I  +  +      D+ +     L     
Sbjct: 61  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFN---YDMPEDSDTYLHRVAR 117

Query: 166 CFRAGNKGFAYTFITLEQERH-AGEIIRALEASGVPIPEDLDK 207
             R G KG A TF++ E +     ++    E +   +P+++D 
Sbjct: 118 AGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI 160

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 51.2 bits (121), Expect = 1e-08
 Identities = 26/120 (21%), Positives = 48/120 (40%), Gaps = 3/120 (2%)

Query: 14  IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKV 73
           + +    S I+ + N + +  V      L   G    + H G++   R      F+   +
Sbjct: 25  VQEQRGKSGII-YCNSRAK--VEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDL 81

Query: 74  RLLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH 133
           ++++AT     G++  ++  VV++D P + E Y    GR GR G    A  F        
Sbjct: 82  QIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAW 141

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 49.8 bits (118), Expect = 3e-08
 Identities = 27/114 (23%), Positives = 53/114 (46%), Gaps = 3/114 (2%)

Query: 43  MKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDCPNH 102
           +   +    +HG + Q ++D  +++F  G+  +L++T+V   G+DV   N++V  +    
Sbjct: 61  VFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERF 120

Query: 103 YEDYVHR-CGRTGRAGNKGFAYTFI-TLEQERHAGEIIRALEASGVPIPE-DLD 153
               +H+  GR GR G + + +  +  + +E         L   G  I E DL 
Sbjct: 121 GLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTDGFKIAEYDLK 174

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 201

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 45.3 bits (106), Expect = 1e-06
 Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 9/112 (8%)

Query: 39  VKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV--- 95
           + E ++ G      H G+    R      F+ G +++++AT   A G+++    ++V   
Sbjct: 89  LAECVRKGAAFH--HAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSL 146

Query: 96  ----NYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEA 143
                Y       +Y    GR GR G        I + +      + R +  
Sbjct: 147 YRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIFG 198

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 23/126 (18%), Positives = 39/126 (30%), Gaps = 22/126 (17%)

Query: 37  AIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLV-- 94
            +   L KAG   + L+        +      K  K   ++AT +A  G ++    ++  
Sbjct: 51  VMAASLRKAGKSVVVLNRKT----FEREYPTIKQKKPDFILATDIAEMGANLCVERVLDC 106

Query: 95  ------VNYDCPNHYEDYV----------HRCGRTGRAGNKGFAYTFITLEQERHAGEII 138
                 V  D                    R GR GR  N+     + +     +    +
Sbjct: 107 RTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHV 166

Query: 139 RALEAS 144
             LEAS
Sbjct: 167 CWLEAS 172

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]} Length = 175

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]

 Score = 36.8 bits (85), Expect = 7e-04
 Identities = 27/115 (23%), Positives = 42/115 (36%), Gaps = 13/115 (11%)

Query: 38  IVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNY 97
           I K L   G P   L+    + +        + G   + IAT++A RG D+K    V   
Sbjct: 50  ISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKEL 107

Query: 98  D--------CPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE---RHAGEIIRAL 141
                                GR+GR G+ G    ++++E E   R   E   A+
Sbjct: 108 GGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAM 162

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	231
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	100.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.98
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.98
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.96
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.96
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.92
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.92
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.87
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.87
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.87
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.85
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.84
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.82
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.71
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.68
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.61
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.55
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	99.31
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.65
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.32
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.18
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	93.23
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	91.58
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	90.46
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	88.34
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	88.3
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	87.77
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	85.47
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	84.15
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	82.41
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	82.09
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	81.81

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=7.8e-36  Score=232.46  Aligned_cols=150  Identities=31%  Similarity=0.513  Sum_probs=132.1

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      .++|+..|.++++... ..++||||+++  ..++.+++.|...++++..+||+|++.+|..+++.|+.|+.+||||||++
T Consensus        11 ~e~K~~~L~~ll~~~~-~~k~iIF~~s~--~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~   87 (162)
T d1fuka_          11 EEYKYECLTDLYDSIS-VTQAVIFCNTR--RKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL   87 (162)
T ss_dssp             GGGHHHHHHHHHHHTT-CSCEEEEESSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGG
T ss_pred             cHHHHHHHHHHHHhCC-CCcEEEEEEEE--chHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeeccccc
Confidence            4568888888887664 56677899998  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHHHH
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLDKM  155 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~  155 (231)
                      +||+|+|+|++|||||+|++++.|+||+||+||.|+.|.|++|+++.+...+..+.+.+.....++|.++.++
T Consensus        88 ~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~~~~ip~~~~~l  160 (162)
T d1fuka_          88 ARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELEKFYSTQIEELPSDIATL  160 (162)
T ss_dssp             TTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETTTHHHHHHHHHHSSCCCEECCSCCTTT
T ss_pred             cccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHHHHHHHHHHHHHHcCcCCCCChHHHHh
Confidence            9999999999999999999999999999999999999999999999999988888888888777788765443

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.2e-34  Score=227.55  Aligned_cols=148  Identities=28%  Similarity=0.509  Sum_probs=136.6

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      .+.|+..|.++|+.. +..++||||+++  ..++.++..|...|+.+..+||+|++++|..++++|++|+.++||||+++
T Consensus        16 ~~~K~~~L~~ll~~~-~~~k~iVF~~~~--~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~   92 (171)
T d1s2ma2          16 ERQKLHCLNTLFSKL-QINQAIIFCNST--NRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLL   92 (171)
T ss_dssp             GGGHHHHHHHHHHHS-CCSEEEEECSSH--HHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCS
T ss_pred             HHHHHHHHHHHHHhC-CCCceEEEEeee--ehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchhHh
Confidence            457899999999876 456788899998  78999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchhHH
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPEDLD  153 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~  153 (231)
                      ++|+|+|++++|||||+|+++.+|+||+||+||.|+.|.|++|+++.+...+..+.+.+..+..++|..++
T Consensus        93 ~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~e~~~~~~i~~~l~~~~~~~p~~~d  163 (171)
T d1s2ma2          93 TRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATID  163 (171)
T ss_dssp             SSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGGGHHHHHHHHHHHTCCCEECCSSCC
T ss_pred             hhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHHHHHHHHHHHHHHCCCCCCCCcccc
Confidence            99999999999999999999999999999999999999999999999999999999888877777776543

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.5e-34  Score=226.38  Aligned_cols=146  Identities=34%  Similarity=0.513  Sum_probs=132.5

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ...|+..|.++|... ...++||||+++  ..++.++..|...|+++..+||+|++++|..+++.|++|+.++|||||++
T Consensus        18 ~~~K~~~L~~ll~~~-~~~k~iiF~~~~--~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~   94 (168)
T d2j0sa2          18 EEWKFDTLCDLYDTL-TITQAVIFCNTK--RKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVW   94 (168)
T ss_dssp             TTHHHHHHHHHHHHH-TSSEEEEECSSH--HHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGG
T ss_pred             hHHHHHHHHHHHHhC-CCCceEEEeeeH--HHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchh
Confidence            346888898888765 456788899998  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCCCCCchh
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASGVPIPED  151 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~  151 (231)
                      +||+|+|+|++|||||+|+++..|+||+||+||.|+.|.+++|+.+.+...++.+.+.++....++|..
T Consensus        95 ~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~d~~~~~~i~~~~~~~i~e~p~~  163 (168)
T d2j0sa2          95 ARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMN  163 (168)
T ss_dssp             SSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGGGHHHHHHHHHHTTCCCEECCSC
T ss_pred             cccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHHHHHHHHHHHHHHcCcCCCCCcC
Confidence            999999999999999999999999999999999999999999999999988888877776665555544

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=9.4e-33  Score=213.32  Aligned_cols=138  Identities=34%  Similarity=0.473  Sum_probs=126.2

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      .+.|+..|.++|+..  +.++||||+++  ..++.+++.|...|+.+..+||++++.+|..++++|++|+.+|||||+++
T Consensus        13 ~~~K~~~L~~ll~~~--~~k~IIF~~s~--~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~   88 (155)
T d1hv8a2          13 ENERFEALCRLLKNK--EFYGLVFCKTK--RDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVM   88 (155)
T ss_dssp             GGGHHHHHHHHHCST--TCCEEEECSSH--HHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTH
T ss_pred             hHHHHHHHHHHHccC--CCCEEEEECch--HHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhHH
Confidence            356888899988754  44678899998  78999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhC
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEAS  144 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~  144 (231)
                      ++|+|+|+|++||+||+|+++.+|+||+||+||.|+.|.+++++++.|...++.+.+.++.+
T Consensus        89 ~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~d~~~~~~i~~~~~~~  150 (155)
T d1hv8a2          89 SRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRREYKKLRYIERAMKLK  150 (155)
T ss_dssp             HHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTTSHHHHHHHHHHHTCC
T ss_pred             hhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchHHHHHHHHHHHHHCCC
Confidence            99999999999999999999999999999999999999999999999888777777666543

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.98  E-value=1.9e-32  Score=214.33  Aligned_cols=147  Identities=28%  Similarity=0.512  Sum_probs=129.2

Q ss_pred             CCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcc
Q psy17587          3 AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVA   82 (231)
Q Consensus         3 ~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~   82 (231)
                      ...|+..|.++|+... ..++||||+++  ..++.+++.|...|+++..+||+|++++|..++++|++|+++|||||+++
T Consensus        11 ~~~K~~~L~~ll~~~~-~~k~iIF~~~~--~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~   87 (168)
T d1t5ia_          11 DNEKNRKLFDLLDVLE-FNQVVIFVKSV--QRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLF   87 (168)
T ss_dssp             GGGHHHHHHHHHHHSC-CSSEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCC
T ss_pred             hHHHHHHHHHHHHhCC-CCeEEEEEeee--ecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccccc
Confidence            4578899999988775 45677799988  77999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEeccc-chHHHHHHHHHHHhCCCCCchhH
Q psy17587         83 ARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLE-QERHAGEIIRALEASGVPIPEDL  152 (231)
Q Consensus        83 ~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-~~~~~~~~~~~l~~~~~~~~~~l  152 (231)
                      ++|+|+|.+++||+||+|+++..|+||+||+||.|+.|.|++|+++. +...+..+.+.+.....++|+.+
T Consensus        88 ~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~  158 (168)
T d1t5ia_          88 GRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  158 (168)
T ss_dssp             STTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             cchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchh
Confidence            99999999999999999999999999999999999999999999886 45555666666766666676654

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.98  E-value=5.7e-32  Score=217.15  Aligned_cols=132  Identities=20%  Similarity=0.309  Sum_probs=121.5

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|+..|+++|+... +.++||||+++  ..++.++..|...|+.+..+||+|++++|..+++.|++|+++|||||++++
T Consensus        15 ~~k~~~L~~~l~~~~-~~~~IIF~~t~--~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~   91 (200)
T d1oywa3          15 FKPLDQLMRYVQEQR-GKSGIIYCNSR--AKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFG   91 (200)
T ss_dssp             SSHHHHHHHHHHHTT-TCCEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSC
T ss_pred             CcHHHHHHHHHHhcC-CCCEEEEEeee--hhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhh
Confidence            567888999887764 55677799998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHH
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEII  138 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~  138 (231)
                      +|+|+|+|++|||||+|+++.+|+||+||+||.|+.|.|++|+++.+...++.++
T Consensus        92 ~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~~g~ai~~~~~~d~~~l~~~i  146 (200)
T d1oywa3          92 MGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL  146 (200)
T ss_dssp             TTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSSCEEEEEEECHHHHHHHHHHH
T ss_pred             hccCCCCCCEEEECCCccchHHHHHHhhhhhcCCCCceEEEecCHHHHHHHHhhh
Confidence            9999999999999999999999999999999999999999999998877555443

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=99.96  E-value=5.5e-29  Score=196.42  Aligned_cols=121  Identities=22%  Similarity=0.309  Sum_probs=104.1

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .++..|+..+.+. ..+.+++|||+++  ..++.++..|...|+++..+||+|++.+|.+++++|++|+++|||||++++
T Consensus        15 ~qvd~ll~~i~~~~~~~~~~iif~~~~--~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~   92 (181)
T d1t5la2          15 GQIDDLIGEIRERVERNERTLVTTLTK--KMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLR   92 (181)
T ss_dssp             THHHHHHHHHHHHHHTTCEEEEECSSH--HHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCS
T ss_pred             CcHHHHHHHHHHHHhcCCeEEEEeehh--hhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHH
Confidence            3444555555443 4567899999998  779999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCC-----CHhHHHHHhcccCCCCCceeEEEEecc
Q psy17587         84 RGLDVKHLNLVVNYDCPN-----HYEDYVHRCGRTGRAGNKGFAYTFITL  128 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~-----~~~~y~qr~GR~gR~g~~g~~i~~~~~  128 (231)
                      ||+|+|+|++|||||+|.     +...|+||+||+||.|.. .++.+...
T Consensus        93 rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~-~~~~~~~~  141 (181)
T d1t5la2          93 EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANG-HVIMYADT  141 (181)
T ss_dssp             SSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTC-EEEEECSS
T ss_pred             ccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccccCc-eeEeecch
Confidence            999999999999999996     688999999999998864 44444433

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=99.96  E-value=7.4e-29  Score=193.60  Aligned_cols=125  Identities=21%  Similarity=0.313  Sum_probs=108.4

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      +.+..|++.+++. ..+.++||||+++  ..++.+++.|...|+++..+||+|++.+|.+++++|++|+++|||||++++
T Consensus        15 ~qv~dll~~i~~~~~~g~r~lvfc~t~--~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~   92 (174)
T d1c4oa2          15 NQILDLMEGIRERAARGERTLVTVLTV--RMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLR   92 (174)
T ss_dssp             THHHHHHHHHHHHHHTTCEEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCC
T ss_pred             CCHHHHHHHHHHHHhcCCcEEEEEcch--hHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeee
Confidence            3445566555443 5688999999998  789999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCC-----CHhHHHHHhcccCCCCCceeEEEEecccchH
Q psy17587         84 RGLDVKHLNLVVNYDCPN-----HYEDYVHRCGRTGRAGNKGFAYTFITLEQER  132 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~-----~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~  132 (231)
                      +|+|+|+|++||+||+|.     +..+|+||+||+||.++ |.++++.......
T Consensus        93 ~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~-g~~~~~~~~~~~~  145 (174)
T d1c4oa2          93 EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAR-GEVWLYADRVSEA  145 (174)
T ss_dssp             TTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTT-CEEEEECSSCCHH
T ss_pred             eeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhcCC-CeeEEeecCCCHH
Confidence            999999999999999776     55889999999999875 7777776554443

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.92  E-value=5.2e-26  Score=171.67  Aligned_cols=100  Identities=21%  Similarity=0.360  Sum_probs=89.9

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEec
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYD   98 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d   98 (231)
                      ..++.||||+++  ..|+.|++.|...|+++..+||+|++.       +|++|+.+||||||++++|+| |+++.|||+|
T Consensus        34 ~~~k~IVFc~t~--~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~  103 (138)
T d1jr6a_          34 KGGRHLIFCHSK--KKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCN  103 (138)
T ss_dssp             TTSCEEEECSCH--HHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECS
T ss_pred             CCCCEEEEeCcH--HHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEE
Confidence            456777799998  779999999999999999999999854       578999999999999999999 9999999865


Q ss_pred             ----CCCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         99 ----CPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        99 ----~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                          +|.++++|+||+||+|| |++|. ++|++++|
T Consensus       104 ~~~~~P~~~~~y~qr~GR~gR-g~~G~-~~~i~~~e  137 (138)
T d1jr6a_         104 TSDGKPQDAVSRTQRRGRTGR-GKPGI-YRFVAPGE  137 (138)
T ss_dssp             EETTEECCHHHHHHHHTTBCS-SSCEE-EEECCSSC
T ss_pred             ecCCCCCCHHHHHhHhccccC-CCCcE-EEEEcCCC
Confidence                69999999999999999 99995 77888765

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.92  E-value=1.5e-25  Score=188.41  Aligned_cols=123  Identities=30%  Similarity=0.411  Sum_probs=105.3

Q ss_pred             chhhhhccccc---cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccC--------CCCHHHHHHHHHHHhCCCcc
Q psy17587          6 PCLSLHGGIDQ---YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHG--------GIDQYDRDSTIVDFKNGKVR   74 (231)
Q Consensus         6 k~~~L~~~L~~---~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg--------~~~~~~R~~~~~~F~~g~~~   74 (231)
                      |+..|.+.|.+   ...+.++||||+++  ..++.+++.|...++++..+||        +|++.+|..+++.|++|+++
T Consensus       144 K~~~l~~~l~~~~~~~~~~k~iiF~~~~--~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~  221 (286)
T d1wp9a2         144 KMDKLKEIIREQLQRKQNSKIIVFTNYR--ETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFN  221 (286)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCEEEECSCH--HHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTSCS
T ss_pred             HHHHHHHHHHHHHHhCCCCcEEEEeCcH--HhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCCCc
Confidence            45555555543   24577889999988  7899999999999999988876        57777899999999999999


Q ss_pred             EEEecCccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccch
Q psy17587         75 LLIATSVAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus        75 vLvaT~~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      |||||+++++|+|+|+|++||+||+|+++..|+||+||+||.+ .|.++.|++++..
T Consensus       222 vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~~-~~~~~~l~~~~~~  277 (286)
T d1wp9a2         222 VLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM-PGRVIILMAKGTR  277 (286)
T ss_dssp             EEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC-CSEEEEEEETTSH
T ss_pred             EEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCCC-CCEEEEEEeCCCH
Confidence            9999999999999999999999999999999999999999965 6888888887743

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.87  E-value=1.7e-22  Score=161.63  Aligned_cols=112  Identities=19%  Similarity=0.309  Sum_probs=96.0

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHC------------------------------CCCeeeccCCCCHHHHHHHHHHH
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKA------------------------------GYPCLSLHGGIDQYDRDSTIVDF   68 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~------------------------------~~~~~~lhg~~~~~~R~~~~~~F   68 (231)
                      .+..+||||+++  ..|+.++..|...                              ...+.++||+|++.+|..+++.|
T Consensus        39 ~~~~~LVF~~sR--k~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f  116 (201)
T d2p6ra4          39 ENGGVLVFESTR--RGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAF  116 (201)
T ss_dssp             TTCCEEEECSSH--HHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHH
T ss_pred             cCCcEEEEeCCH--HHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHH
Confidence            356788899987  6788888776531                              12277899999999999999999


Q ss_pred             hCCCccEEEecCccccccCCCCCcEEEE-------ecCCCCHhHHHHHhcccCCCCC--ceeEEEEecccchH
Q psy17587         69 KNGKVRLLIATSVAARGLDVKHLNLVVN-------YDCPNHYEDYVHRCGRTGRAGN--KGFAYTFITLEQER  132 (231)
Q Consensus        69 ~~g~~~vLvaT~~~~~Gldip~v~~VI~-------~d~P~~~~~y~qr~GR~gR~g~--~g~~i~~~~~~~~~  132 (231)
                      ++|.++|||||+++++|+|+|..++||.       ++.|.++.+|+||+|||||.|.  .|.+++++.+.+..
T Consensus       117 ~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~~  189 (201)
T d2p6ra4         117 RRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDRE  189 (201)
T ss_dssp             HTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHH
T ss_pred             hCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCCCCCeeEEEEEeCCCChH
Confidence            9999999999999999999999999996       6788999999999999999984  79999887776543

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.87  E-value=2.7e-23  Score=166.39  Aligned_cols=139  Identities=18%  Similarity=0.242  Sum_probs=103.0

Q ss_pred             chhhhhccccc-cCCCCeEEEEcCChhH------HHHHHHHHHHHHC---CCCeeeccCCCCHHHHHHHHHHHhCCCccE
Q psy17587          6 PCLSLHGGIDQ-YDRDSTIVDFKNGKVR------LLVCAIVKELMKA---GYPCLSLHGGIDQYDRDSTIVDFKNGKVRL   75 (231)
Q Consensus         6 k~~~L~~~L~~-~~~~~~iiiF~~~~~~------~~~~~l~~~L~~~---~~~~~~lhg~~~~~~R~~~~~~F~~g~~~v   75 (231)
                      +...+.+.|++ ...+..+-+.||....      ..+....+.|.+.   ++++..+||+|++++|.+++.+|++|+++|
T Consensus        14 ~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~i   93 (206)
T d1gm5a4          14 RVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDI   93 (206)
T ss_dssp             THHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSB
T ss_pred             cHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEE
Confidence            45566666644 3456666667876411      0122333444332   678899999999999999999999999999


Q ss_pred             EEecCccccccCCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEecccchHHHHHHHHHHHhCC
Q psy17587         76 LIATSVAARGLDVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLEQERHAGEIIRALEASG  145 (231)
Q Consensus        76 LvaT~~~~~Gldip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~~~~~~~~l~~~~  145 (231)
                      ||||+++++|||+|++++||+++.|. ..+.|.|..||+||.|..|.|++++.+......+ -++.+...+
T Consensus        94 LVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~-rl~~~~~~~  163 (206)
T d1gm5a4          94 LVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAME-RLRFFTLNT  163 (206)
T ss_dssp             CCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHH-HHHHHHTCC
T ss_pred             EEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchh-hhhhccccC
Confidence            99999999999999999999999997 6777778899999999999999998776554333 334444333

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.87  E-value=3.1e-25  Score=183.05  Aligned_cols=116  Identities=15%  Similarity=0.187  Sum_probs=99.3

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEec----
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIAT----   79 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT----   79 (231)
                      +.|+..|.++|++..  ++.||||+++  ..++.|++.|..      .+||+|++.+|.+++++|++|+++|||||    
T Consensus        11 ~~~~~~l~~~l~~~~--~~~iif~~~~--~~~~~l~~~l~~------~~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~~   80 (248)
T d1gkub2          11 DESISTLSSILEKLG--TGGIIYARTG--EEAEEIYESLKN------KFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYY   80 (248)
T ss_dssp             CCCTTTTHHHHTTSC--SCEEEEESSH--HHHHHHHHTTTT------SSCEEECTTSSSHHHHHHHHTSCSEEEEECC--
T ss_pred             chHHHHHHHHHHHhC--CCEEEEECCH--HHHHHHHHHHHH------hccCCCCHHHHHHHHHHHHhCCCeEEEEecccc
Confidence            567888999998764  4677899988  789999999964      38999999999999999999999999999    


Q ss_pred             CccccccCCCC-CcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccchHH
Q psy17587         80 SVAARGLDVKH-LNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQERH  133 (231)
Q Consensus        80 ~~~~~Gldip~-v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~~~~  133 (231)
                      ++++||||+|+ |++|||||+|+    |.||+||+||.|..|.+++++...+...
T Consensus        81 ~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~g~~~~~~~~~~~~~~~~  131 (248)
T d1gkub2          81 GTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSLSPQMVKLLAYLYRNVDE  131 (248)
T ss_dssp             ----CCSCCTTTCCEEEEESCCE----EEEECSCGGGSCHHHHHHHHTTTSCHHH
T ss_pred             chhhhccCccccccEEEEeCCCc----chhhhhhhhccCcceEeeeeccHhhHHH
Confidence            88999999996 99999999995    8899999999999999988887766553

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.85  E-value=4.6e-22  Score=158.62  Aligned_cols=117  Identities=21%  Similarity=0.344  Sum_probs=101.0

Q ss_pred             CCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          4 GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         4 ~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      ..|+..|.++|+.. ++.++||||+..  ..++.|.+.|     .+..+||++++.+|..++++|++|+++|||||++++
T Consensus        78 ~~K~~~l~~ll~~~-~~~k~lvf~~~~--~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~~~~~~  149 (200)
T d2fwra1          78 KNKIRKLREILERH-RKDKIIIFTRHN--ELVYRISKVF-----LIPAITHRTSREEREEILEGFRTGRFRAIVSSQVLD  149 (200)
T ss_dssp             SHHHHHHHHHHHHT-SSSCBCCBCSCH--HHHHHHHHHT-----TCCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCC
T ss_pred             HHHHHHHHHHHHhC-CCCcEEEEeCcH--HHHHHHHhhc-----CcceeeCCCCHHHHHHHHHHhhcCCeeeeeecchhh
Confidence            45777888888765 456778899987  7788888776     456789999999999999999999999999999999


Q ss_pred             cccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc---eeEEEEecc
Q psy17587         84 RGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK---GFAYTFITL  128 (231)
Q Consensus        84 ~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~---g~~i~~~~~  128 (231)
                      +|+|+|.+++||++++|+++..|+||+||++|.|+.   ...+.|+..
T Consensus       150 ~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~~~k~~~~i~~~v~~  197 (200)
T d2fwra1         150 EGIDVPDANVGVIMSGSGSAREYIQRLGRILRPSKGKKEAVLYELISR  197 (200)
T ss_dssp             SSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCCTTTCCEEEEEEEEC
T ss_pred             cccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCCCCCcEEEEEEEecC
Confidence            999999999999999999999999999999999862   455556654

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.84  E-value=8.3e-22  Score=163.73  Aligned_cols=106  Identities=16%  Similarity=0.201  Sum_probs=92.3

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHH----------HHHHHHHhCCCccEEEecCcccc---c
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDR----------DSTIVDFKNGKVRLLIATSVAAR---G   85 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R----------~~~~~~F~~g~~~vLvaT~~~~~---G   85 (231)
                      .+.++||||+++  ..++.|++.|...|+++..+||+|+++.|          ..+++.|++|+.+++|+|+++++   |
T Consensus        35 kggk~LVFcnSR--~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~g  112 (299)
T d1a1va2          35 KGGRHLIFCHSK--KKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVD  112 (299)
T ss_dssp             HSSEEEEECSSH--HHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEE
T ss_pred             cCCCEEEECCcH--HHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCC
Confidence            367888899998  77999999999999999999999999887          46788999999999999999999   6


Q ss_pred             cCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCceeEEEEec
Q psy17587         86 LDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus        86 ldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                      +|++.+.+||++|+|.++++|+||+||+|| |+.|....+..
T Consensus       113 iDid~V~~VI~~d~P~SvesyIQRiGRTGR-Gr~G~~~~l~~  153 (299)
T d1a1va2         113 FSLDPTFTIETTTLPQDAVSRTQRRGRTGR-GKPGIYRFVAP  153 (299)
T ss_dssp             CCCSSSCEEEEEEEECBHHHHHHHHTTBCS-SSCEEEEESCS
T ss_pred             CCCCcceEEEeCCCCCCHHHHHhhccccCC-CCCceEEEEec
Confidence            777788899999999999999999999999 88887754443

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.82  E-value=1.1e-19  Score=144.66  Aligned_cols=118  Identities=15%  Similarity=0.265  Sum_probs=104.1

Q ss_pred             hhccc-cccCCCCeEEEEcCChhHHHHHHHHHHHHH--CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccccc
Q psy17587         10 LHGGI-DQYDRDSTIVDFKNGKVRLLVCAIVKELMK--AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGL   86 (231)
Q Consensus        10 L~~~L-~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~--~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gl   86 (231)
                      +.+.| .+...+..+-+.||..  +.++.+.+.+.+  .++++..+||.|+++++.+++.+|++|+++|||||++++.|+
T Consensus        20 i~~~I~~El~rGgQvy~V~p~I--~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGi   97 (211)
T d2eyqa5          20 VREAILREILRGGQVYYLYNDV--ENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGI   97 (211)
T ss_dssp             HHHHHHHHHTTTCEEEEECCCS--SCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGS
T ss_pred             HHHHHHHHHHcCCeEEEEEcCc--cchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhcc
Confidence            44444 4556688888889987  668888888865  478999999999999999999999999999999999999999


Q ss_pred             CCCCCcEEEEecCCC-CHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         87 DVKHLNLVVNYDCPN-HYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        87 dip~v~~VI~~d~P~-~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                      |+|+++++|.++.+. .++++.|..||+||.+..+.|+++..+.
T Consensus        98 DvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~  141 (211)
T d2eyqa5          98 DIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP  141 (211)
T ss_dssp             CCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCG
T ss_pred             CCCCCcEEEEecchhccccccccccceeeecCccceEEEEecCC
Confidence            999999999999986 8999999999999999999999998654

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.71  E-value=4.5e-17  Score=139.72  Aligned_cols=122  Identities=17%  Similarity=0.199  Sum_probs=104.7

Q ss_pred             chhhhhcccccc--CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCcc---EEEecC
Q psy17587          6 PCLSLHGGIDQY--DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVR---LLIATS   80 (231)
Q Consensus         6 k~~~L~~~L~~~--~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~---vLvaT~   80 (231)
                      |+..|.++|...  ..+.++|||++..  ...+.|.+.|...|+++..+||+++..+|..+++.|+++...   +|++|.
T Consensus       102 Kl~~L~~ll~~~~~~~g~KvlIFs~~~--~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~~  179 (346)
T d1z3ix1         102 KMLVLDYILAMTRTTTSDKVVLVSNYT--QTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  179 (346)
T ss_dssp             HHHHHHHHHHHHHHHCCCEEEEEESCH--HHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             HHHHHHHHHHHHHHhcCCceeEEeehh--hhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecch
Confidence            566666666543  4578999999977  779999999999999999999999999999999999987543   678899


Q ss_pred             ccccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCce--eEEEEeccc
Q psy17587         81 VAARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNKG--FAYTFITLE  129 (231)
Q Consensus        81 ~~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~g--~~i~~~~~~  129 (231)
                      +++.|+|++.++.||+||+||++..+.|++||+.|.|+..  .++.|+..+
T Consensus       180 agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R~GQ~~~V~v~rli~~~  230 (346)
T d1z3ix1         180 AGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTG  230 (346)
T ss_dssp             GSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSSTTCCSCEEEEEEEETT
T ss_pred             hhhhccccccceEEEEecCCCccchHhHhhhcccccCCCCceEEEEEEeCC
Confidence            9999999999999999999999999999999999999854  445555554

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.68  E-value=4.3e-17  Score=133.27  Aligned_cols=122  Identities=18%  Similarity=0.200  Sum_probs=90.2

Q ss_pred             chhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHC-CCCeeeccCCCCHHHHHHHHHHHhCCC-ccEEE-ecCc
Q psy17587          6 PCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKA-GYPCLSLHGGIDQYDRDSTIVDFKNGK-VRLLI-ATSV   81 (231)
Q Consensus         6 k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~-~~~~~~lhg~~~~~~R~~~~~~F~~g~-~~vLv-aT~~   81 (231)
                      |+..|.+.|... ..+.++||||+..  ...+.+...|... +.++..+||+++..+|..++++|.++. ..+++ +|.+
T Consensus        70 K~~~l~~~l~~~~~~g~kviIFs~~~--~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~~~  147 (244)
T d1z5za1          70 KMIRTMEIIEEALDEGDKIAIFTQFV--DMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKA  147 (244)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEESCH--HHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEECCT
T ss_pred             HHHHHHHHHHhhcccccceEEEeece--ehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccccc
Confidence            677788888653 4578899999977  7788888888654 889999999999999999999998764 66664 5689


Q ss_pred             cccccCCCCCcEEEEecCCCCHhHHHHHhcccCCCCCc--eeEEEEeccc
Q psy17587         82 AARGLDVKHLNLVVNYDCPNHYEDYVHRCGRTGRAGNK--GFAYTFITLE  129 (231)
Q Consensus        82 ~~~Gldip~v~~VI~~d~P~~~~~y~qr~GR~gR~g~~--g~~i~~~~~~  129 (231)
                      ++.|+|++.+++||++|+||++..+.|+.||+.|.|+.  ..++.++..+
T Consensus       148 ~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~Gq~~~v~i~~l~~~~  197 (244)
T d1z5za1         148 GGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVG  197 (244)
T ss_dssp             TCCCCCCTTCSEEEECSCCSCTTTC--------------CCEEEEEEETT
T ss_pred             cccccccchhhhhhhcCchhhhHHHhhhcceeeecCCCCceEEEEEeeCC
Confidence            99999999999999999999999999999999999974  4445555554

>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=99.61  E-value=9.2e-16  Score=127.94  Aligned_cols=104  Identities=18%  Similarity=0.148  Sum_probs=86.0

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEE---
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVV---   95 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI---   95 (231)
                      .+.+++|||+++  ..++.+++.|.+.++.+..+||++++..+    ..|++|..+++|||+++++|+|++ ++.||   
T Consensus       177 ~~~~~lvf~~~~--~~~~~l~~~L~~~~~~~~~l~~~~~~~~~----~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~  249 (305)
T d2bmfa2         177 FKGKTVWFVPSI--KAGNDIAACLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTDISEMGANFK-AERVIDPR  249 (305)
T ss_dssp             SCSCEEEECSCH--HHHHHHHHHHHHHTCCCEECCTTCHHHHG----GGGGTSCCSEEEECGGGGTTCCCC-CSEEEECC
T ss_pred             hCCCEEEEeccH--HHHHHHHHHHHhCCCCEEEeCCcChHHHH----hhhhccchhhhhhhHHHHhcCCCC-ccEEEEcC
Confidence            356788899998  77999999999999999999999976544    468999999999999999999995 34443   


Q ss_pred             -------EecC----------CCCHhHHHHHhcccCCCCCceeEEEEeccc
Q psy17587         96 -------NYDC----------PNHYEDYVHRCGRTGRAGNKGFAYTFITLE  129 (231)
Q Consensus        96 -------~~d~----------P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~  129 (231)
                             ++|.          |-+..+|+||+||+||.|+.+...+++...
T Consensus       250 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~Qr~GR~GR~~~~~~~~~~~~~~  300 (305)
T d2bmfa2         250 RCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRVGRNPKNENDQYIYMGE  300 (305)
T ss_dssp             EEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCSSSCCCEEEEECSC
T ss_pred             CceeeeEecCCCCceEEeccccCCHHHHhhhhcCcCcCCCCceEEEEECCC
Confidence                   3444          567899999999999999888777766544

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.55  E-value=9.3e-15  Score=122.44  Aligned_cols=101  Identities=19%  Similarity=0.206  Sum_probs=79.5

Q ss_pred             CCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccccccCCCCCcEEEEecC
Q psy17587         20 DSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAARGLDVKHLNLVVNYDC   99 (231)
Q Consensus        20 ~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~Gldip~v~~VI~~d~   99 (231)
                      .+++++||++.  ..++.+++.|...|.+|.++||.++..++.    .|++|+.++||||++++.|+|+ ++.+||.+.+
T Consensus        36 ~g~~~~F~~s~--~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~  108 (299)
T d1yksa2          36 KRPTAWFLPSI--RAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRT  108 (299)
T ss_dssp             CSCEEEECSCH--HHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCE
T ss_pred             CCCEEEEeCCH--HHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCc
Confidence            56788899998  779999999999999999999999977754    5789999999999999999999 4999986443


Q ss_pred             -------------------CCCHhHHHHHhcccCCCCCceeEEEEec
Q psy17587        100 -------------------PNHYEDYVHRCGRTGRAGNKGFAYTFIT  127 (231)
Q Consensus       100 -------------------P~~~~~y~qr~GR~gR~g~~g~~i~~~~  127 (231)
                                         |-+..+-.||.||+||.+..+.++.++.
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~  155 (299)
T d1yksa2         109 AFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS  155 (299)
T ss_dssp             EEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEEC
T ss_pred             eeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeC
Confidence                               3467888999999999876555555554

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.31  E-value=2.8e-12  Score=98.34  Aligned_cols=122  Identities=22%  Similarity=0.258  Sum_probs=98.0

Q ss_pred             Cchhhhhccccc-cCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCccc
Q psy17587          5 YPCLSLHGGIDQ-YDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAA   83 (231)
Q Consensus         5 ~k~~~L~~~L~~-~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~   83 (231)
                      .|..++.+.+.+ +..++.+||+|.+.  +..+.+++.|.+.+++..++++....++-  .+-...-..-.|.|||+.++
T Consensus        18 eK~~AIi~eV~~~~~~grPVLIgT~SI--e~SE~ls~~L~~~gi~h~vLnAk~~~~Ea--~II~~Ag~~g~VtIATNmAG   93 (175)
T d1tf5a4          18 GKFKAVAEDVAQRYMTGQPVLVGTVAV--ETSELISKLLKNKGIPHQVLNAKNHEREA--QIIEEAGQKGAVTIATNMAG   93 (175)
T ss_dssp             HHHHHHHHHHHHHHHHTCCEEEEESCH--HHHHHHHHHHHTTTCCCEEECSSCHHHHH--HHHTTTTSTTCEEEEETTSS
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEEeCcH--HHHHHHHHHHHHcCCCceeehhhhHHHHH--HHHHhccCCCceeehhhHHH
Confidence            455666666643 44589999999998  77999999999999999999998653332  23333233446999999999


Q ss_pred             cccCCC---CCc-----EEEEecCCCCHhHHHHHhcccCCCCCceeEEEEecccc
Q psy17587         84 RGLDVK---HLN-----LVVNYDCPNHYEDYVHRCGRTGRAGNKGFAYTFITLEQ  130 (231)
Q Consensus        84 ~Gldip---~v~-----~VI~~d~P~~~~~y~qr~GR~gR~g~~g~~i~~~~~~~  130 (231)
                      ||.|+.   .|.     +||.-..|.+..-..|..||+||.|.+|.+.+|++-+|
T Consensus        94 RGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQGdpGs~~~~~sleD  148 (175)
T d1tf5a4          94 RGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMED  148 (175)
T ss_dssp             TTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             cCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhhCCCcccEEEEEcCH
Confidence            999986   232     89999999999999999999999999999999997665

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.65  E-value=4.5e-08  Score=76.23  Aligned_cols=122  Identities=17%  Similarity=0.253  Sum_probs=94.2

Q ss_pred             Cchhhhhcccccc-CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCC-CccEEEecCcc
Q psy17587          5 YPCLSLHGGIDQY-DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNG-KVRLLIATSVA   82 (231)
Q Consensus         5 ~k~~~L~~~L~~~-~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g-~~~vLvaT~~~   82 (231)
                      .|..++.+.++.. ..++.|+|.+.+.  +..+.|++.|.+.++++.++++...  +|+..+=. ..| .-.|-|||+.+
T Consensus        18 ~K~~Avv~ei~~~h~~GqPVLVGT~SV--e~SE~lS~lL~~~gi~h~vLNAK~h--erEAeIIA-qAG~~GaVTIATNMA   92 (219)
T d1nkta4          18 AKYIAVVDDVAERYAKGQPVLIGTTSV--ERSEYLSRQFTKRRIPHNVLNAKYH--EQEATIIA-VAGRRGGVTVATNMA   92 (219)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEESCH--HHHHHHHHHHHHTTCCCEEECSSCH--HHHHHHHH-TTTSTTCEEEEETTC
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEeeCcH--HHHHHHHHHHHHhccchhccchhhH--HHHHHHHH-hcccCCcEEeecccc
Confidence            3555666666444 4589999999988  7899999999999999999999754  33332222 234 45688999999


Q ss_pred             ccccCCCC-----------------------------------------------C-----cEEEEecCCCCHhHHHHHh
Q psy17587         83 ARGLDVKH-----------------------------------------------L-----NLVVNYDCPNHYEDYVHRC  110 (231)
Q Consensus        83 ~~Gldip~-----------------------------------------------v-----~~VI~~d~P~~~~~y~qr~  110 (231)
                      +||.||-=                                               |     =+||--.-..+-.-=-|-.
T Consensus        93 GRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTErHeSrRIDnQLR  172 (219)
T d1nkta4          93 GRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLR  172 (219)
T ss_dssp             STTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHH
T ss_pred             CCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEecccccccccccccc
Confidence            99999931                                               1     1677777777777788999


Q ss_pred             cccCCCCCceeEEEEecccch
Q psy17587        111 GRTGRAGNKGFAYTFITLEQE  131 (231)
Q Consensus       111 GR~gR~g~~g~~i~~~~~~~~  131 (231)
                      ||+||.|.+|.+..|++-+|.
T Consensus       173 GRsGRQGDPGsSrFflSLeDd  193 (219)
T d1nkta4         173 GRSGRQGDPGESRFYLSLGDE  193 (219)
T ss_dssp             HTSSGGGCCEEEEEEEETTSH
T ss_pred             ccccccCCCccceeEEeccHH
Confidence            999999999999999987664

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.32  E-value=0.00026  Score=56.90  Aligned_cols=97  Identities=16%  Similarity=0.218  Sum_probs=69.2

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHH----HCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc-
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELM----KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR-   84 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~----~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~-   84 (231)
                      +.-.+.....+..+++-+++.  ..+.+.++.+.    ..|+.+..+||+++..+|..++...++|+++|+|+|-.+-. 
T Consensus       122 ~~a~~~~~~~g~q~~~m~Pt~--~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~  199 (264)
T d1gm5a3         122 QLAILDNYEAGFQTAFMVPTS--ILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE  199 (264)
T ss_dssp             HHHHHHHHHHTSCEEEECSCH--HHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH
T ss_pred             HHHHHHHHhcccceeEEeehH--hhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC
Confidence            333334445577888889986  55776666654    34789999999999999999999999999999999976554 


Q ss_pred             ccCCCCCcEEEEecCCCCHhHHHHHh
Q psy17587         85 GLDVKHLNLVVNYDCPNHYEDYVHRC  110 (231)
Q Consensus        85 Gldip~v~~VI~~d~P~~~~~y~qr~  110 (231)
                      .+.+.++.+||.-.  .+--.|.||-
T Consensus       200 ~~~f~~LglviiDE--qH~fgv~Qr~  223 (264)
T d1gm5a3         200 DVHFKNLGLVIIDE--QHRFGVKQRE  223 (264)
T ss_dssp             CCCCSCCCEEEEES--CCCC-----C
T ss_pred             CCCccccceeeecc--ccccchhhHH
Confidence            68888888877533  2233566654

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.18  E-value=0.00089  Score=52.67  Aligned_cols=84  Identities=13%  Similarity=0.147  Sum_probs=69.2

Q ss_pred             hccccccCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCcccc-c
Q psy17587         11 HGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSVAAR-G   85 (231)
Q Consensus        11 ~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~~~~-G   85 (231)
                      .-.......+..+++-+++.  ..+.+..+.+..    .+..+..+||.++..+|..++..+.+|+++|+|.|-.+-. .
T Consensus        95 ~a~~~~~~~g~qv~~l~Pt~--~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~  172 (233)
T d2eyqa3          95 RAAFLAVDNHKQVAVLVPTT--LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSD  172 (233)
T ss_dssp             HHHHHHHTTTCEEEEECSSH--HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSC
T ss_pred             HHHHHHHHcCCceEEEccHH--HhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccC
Confidence            33334456688999899987  778888888875    4788999999999999999999999999999999986554 6


Q ss_pred             cCCCCCcEEEE
Q psy17587         86 LDVKHLNLVVN   96 (231)
Q Consensus        86 ldip~v~~VI~   96 (231)
                      +.+++..+||.
T Consensus       173 ~~f~~LgLiIi  183 (233)
T d2eyqa3         173 VKFKDLGLLIV  183 (233)
T ss_dssp             CCCSSEEEEEE
T ss_pred             Cccccccceee
Confidence            88888887765

>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=93.23  E-value=0.29  Score=37.19  Aligned_cols=81  Identities=16%  Similarity=0.205  Sum_probs=55.7

Q ss_pred             hhccccccCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc----
Q psy17587         10 LHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV----   81 (231)
Q Consensus        10 L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~----   81 (231)
                      ++..|.......+.+|+|+++  +.+.++.+.+..    .++.+..+.|+.+..+....+.   . ..+|+|+|+-    
T Consensus        75 il~~l~~~~~~~~~lil~Ptr--eLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~---~-~~~Ilv~TPgrl~~  148 (222)
T d2j0sa1          75 VLQCLDIQVRETQALILAPTR--ELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD---Y-GQHVVAGTPGRVFD  148 (222)
T ss_dssp             HHHTCCTTSCSCCEEEECSSH--HHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH---H-CCSEEEECHHHHHH
T ss_pred             ccccccccccCceeEEecchH--HHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc---c-CCeEEeCCCCcHHh
Confidence            344444444556778899988  889998887754    3578889999988766554443   2 3589999962    


Q ss_pred             --cccccCCCCCcEEEE
Q psy17587         82 --AARGLDVKHLNLVVN   96 (231)
Q Consensus        82 --~~~Gldip~v~~VI~   96 (231)
                        -...+++.++.++|.
T Consensus       149 ~~~~~~~~~~~l~~lVl  165 (222)
T d2j0sa1         149 MIRRRSLRTRAIKMLVL  165 (222)
T ss_dssp             HHHTTSSCCTTCCEEEE
T ss_pred             cccccccccccceeeee
Confidence              245566777777664

>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=91.58  E-value=0.14  Score=35.09  Aligned_cols=79  Identities=14%  Similarity=0.086  Sum_probs=57.0

Q ss_pred             CCCCchhhhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc
Q psy17587          2 KAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV   81 (231)
Q Consensus         2 ~~~~k~~~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~   81 (231)
                      ++.+.+..|..+|++.  +.+|||+|.+.  -..+.|.+.|...++.+..+.+ .+         +|.++.  +.++...
T Consensus        18 ~~~~p~~~L~~~i~~~--~~~Vli~a~s~--g~~erl~e~L~~~~i~~~~~~~-~~---------~~~~~~--~~i~~~~   81 (117)
T d2eyqa2          18 QQKAPLDALRKFLETF--DGPVVFSVESE--GRREALGELLARIKIAPQRIMR-LD---------EASDRG--RYLMIGA   81 (117)
T ss_dssp             SSSSTTHHHHHHHTTC--CSCCCEEESSH--HHHHHHHHHHGGGTCCCEECSS-GG---------GCCTTC--CEEEECC
T ss_pred             chhcHHHHHHHHHHhC--CCeEEEEECCc--cHHHHHHHHHHHcCCCceEecC-hh---------hhcCce--EEEEEec
Confidence            3456677777777653  46788888988  4599999999999988765543 22         344444  5556677


Q ss_pred             cccccCCCCCcEEEE
Q psy17587         82 AARGLDVKHLNLVVN   96 (231)
Q Consensus        82 ~~~Gldip~v~~VI~   96 (231)
                      +..|.-+|+..++|.
T Consensus        82 l~~GF~~~~~~l~vI   96 (117)
T d2eyqa2          82 AEHGFVDTVRNLALI   96 (117)
T ss_dssp             CCSCEEETTTTEEEE
T ss_pred             CccccccCCCCEEEE
Confidence            899998898888776

>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=90.46  E-value=0.69  Score=34.35  Aligned_cols=71  Identities=13%  Similarity=0.222  Sum_probs=51.0

Q ss_pred             CCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-----c-ccccCC
Q psy17587         19 RDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-----A-ARGLDV   88 (231)
Q Consensus        19 ~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-----~-~~Gldi   88 (231)
                      .+.+++|.|+++  +.+.++.+.+..    .+..+...+|+.+..+..+.+   +  ..+|+|+|+-     + ...+++
T Consensus        71 ~~~~~lil~pt~--~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~--~~~IlV~TP~~l~~~l~~~~~~~  143 (208)
T d1hv8a1          71 NGIEAIILTPTR--ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKAL---K--NANIVVGTPGRILDHINRGTLNL  143 (208)
T ss_dssp             SSCCEEEECSCH--HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHH---H--TCSEEEECHHHHHHHHHTTCSCT
T ss_pred             cCcceEEEeecc--ccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhc---C--CCCEEEEChHHHHHHHHcCCCCc
Confidence            456788899987  778888777654    367888999998877665544   2  3689999952     2 334677


Q ss_pred             CCCcEEEE
Q psy17587         89 KHLNLVVN   96 (231)
Q Consensus        89 p~v~~VI~   96 (231)
                      .++.++|.
T Consensus       144 ~~l~~lVi  151 (208)
T d1hv8a1         144 KNVKYFIL  151 (208)
T ss_dssp             TSCCEEEE
T ss_pred             ccCcEEEE
Confidence            77777665

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=88.34  E-value=0.15  Score=34.65  Aligned_cols=41  Identities=17%  Similarity=0.319  Sum_probs=32.4

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHCCC-CeeeccCCCC
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGY-PCLSLHGGID   57 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~-~~~~lhg~~~   57 (231)
                      ....++++||++|++-.+  +...+..|...|+ ++..+.||+.
T Consensus        67 ~~~~~~~~iv~~C~~G~r--s~~a~~~L~~~G~~nv~~l~GG~~  108 (119)
T d1tq1a_          67 SHFGQSDNIIVGCQSGGR--SIKATTDLLHAGFTGVKDIVGGYS  108 (119)
T ss_dssp             TTCCTTSSEEEEESSCSH--HHHHHHHHHHHHCCSEEEEECCHH
T ss_pred             HhcCCCcEEEEEcCCcCc--HHHHHHHHHhcccCCeEEecChHH
Confidence            344568899999987644  7778888988898 4888999974

>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=88.30  E-value=1.7  Score=32.01  Aligned_cols=78  Identities=14%  Similarity=0.255  Sum_probs=49.5

Q ss_pred             ccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------c
Q psy17587         14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------A   82 (231)
Q Consensus        14 L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~   82 (231)
                      +.......+++|.|+++  +.+.++.+.+...     ...+..++|+.+......   .+.....+|+|+|+-      -
T Consensus        63 ~~~~~~~~~~lil~Ptr--eL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~ilI~TP~rl~~~~~  137 (207)
T d1t6na_          63 LEPVTGQVSVLVMCHTR--ELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE---VLKKNCPHIVVGTPGRILALAR  137 (207)
T ss_dssp             CCCCTTCCCEEEECSCH--HHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHH---HHHHSCCSEEEECHHHHHHHHH
T ss_pred             ecccCCCceEEEEeccc--hhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHH---HHHhcCCCEEEeCcchhhhhcc
Confidence            33333455778899987  7788888887643     345778888887665433   334566889999973      1


Q ss_pred             ccccCCCCCcEEEE
Q psy17587         83 ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 ~~Gldip~v~~VI~   96 (231)
                      ...+++.++.++|.
T Consensus       138 ~~~~~l~~l~~lVl  151 (207)
T d1t6na_         138 NKSLNLKHIKHFIL  151 (207)
T ss_dssp             TTSSCCTTCCEEEE
T ss_pred             CCceeccccceeeh
Confidence            12345555555543

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=87.77  E-value=0.18  Score=33.70  Aligned_cols=47  Identities=19%  Similarity=0.300  Sum_probs=36.8

Q ss_pred             hhhccccccCCCCeEEEEcCChhHHHHHHHHHHHHHCCCC-eeeccCCCC
Q psy17587          9 SLHGGIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKAGYP-CLSLHGGID   57 (231)
Q Consensus         9 ~L~~~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~-~~~lhg~~~   57 (231)
                      .|...+....++..+|++|.+-.+  +...+..|...|++ +..+.||+.
T Consensus        47 ~l~~~~~~~~~~~~ivv~c~~g~r--s~~~a~~L~~~G~~~v~~l~GG~~   94 (108)
T d1gmxa_          47 TLGAFMRDNDFDTPVMVMCYHGNS--SKGAAQYLLQQGYDVVYSIDGGFE   94 (108)
T ss_dssp             HHHHHHHHSCTTSCEEEECSSSSH--HHHHHHHHHHHTCSSEEEETTHHH
T ss_pred             hHHHHhhhccccCcccccCCCChH--HHHHHHHHHHcCCCCEEEEcChHH
Confidence            445556666788999999987644  78889999999985 888999864

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.47  E-value=0.5  Score=32.48  Aligned_cols=38  Identities=21%  Similarity=0.234  Sum_probs=32.0

Q ss_pred             CCCCeEEEEcCChhHHHHHHHHHHHHHCCCCeeeccCCCC
Q psy17587         18 DRDSTIVDFKNGKVRLLVCAIVKELMKAGYPCLSLHGGID   57 (231)
Q Consensus        18 ~~~~~iiiF~~~~~~~~~~~l~~~L~~~~~~~~~lhg~~~   57 (231)
                      .+++.+|+||.+-.+  +...+..|...|+.+..+.||+.
T Consensus        78 ~~~~~ivl~C~~G~r--S~~aa~~L~~~G~~v~~l~GG~~  115 (130)
T d1yt8a4          78 VRGARLVLVDDDGVR--ANMSASWLAQMGWQVAVLDGLSE  115 (130)
T ss_dssp             SBTCEEEEECSSSSH--HHHHHHHHHHTTCEEEEECSCCG
T ss_pred             CccceEEeecCCCcc--HHHHHHHHHHcCCCeEEEcCchH
Confidence            457899999988644  78889999999999999999974

>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=84.15  E-value=2.7  Score=30.86  Aligned_cols=77  Identities=17%  Similarity=0.234  Sum_probs=48.9

Q ss_pred             ccccCCCCeEEEEcCChhHHHHHHHHHHHHHC-----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------c
Q psy17587         14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA-----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------A   82 (231)
Q Consensus        14 L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~   82 (231)
                      +........++|.|+++  +.+.++.+.+...     +..+...+|+.+..+....+    ....+|+|+|+-      -
T Consensus        65 ~~~~~~~~~~lil~pt~--el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~ivv~TPgrl~~~~~  138 (206)
T d1veca_          65 LDLKKDNIQAMVIVPTR--ELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL----DDTVHVVIATPGRILDLIK  138 (206)
T ss_dssp             CCTTSCSCCEEEECSCH--HHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHH
T ss_pred             ccccccCcceEEEeecc--hhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHH----HhccCeEEeCCcccccccc
Confidence            33344566788899987  7788887776532     46677888887766544333    456789999863      2


Q ss_pred             ccccCCCCCcEEEE
Q psy17587         83 ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 ~~Gldip~v~~VI~   96 (231)
                      ...+++.++.++|.
T Consensus       139 ~~~~~~~~l~~lVl  152 (206)
T d1veca_         139 KGVAKVDHVQMIVL  152 (206)
T ss_dssp             TTCSCCTTCCEEEE
T ss_pred             chhccccccceEEE
Confidence            22345555555553

>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=82.41  E-value=1.3  Score=33.09  Aligned_cols=78  Identities=14%  Similarity=0.217  Sum_probs=49.2

Q ss_pred             cccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCC----eeeccCCCCHHHHHHHHHHHhCCCccEEEecCc-cccc
Q psy17587         15 DQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYP----CLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV-AARG   85 (231)
Q Consensus        15 ~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~----~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~-~~~G   85 (231)
                      ....++++++|.++++  ..++++.+.+.+.    ++.    +..++++.+..++...+....  ..+|+|+|+- +.+.
T Consensus        81 ~~~~~~~rvliv~Pt~--~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~--~~~Ilv~Tp~~l~~~  156 (237)
T d1gkub1          81 FLALKGKRCYVIFPTS--LLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLR--NFKIVITTTQFLSKH  156 (237)
T ss_dssp             HHHTTSCCEEEEESCH--HHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGG--GCSEEEEEHHHHHHC
T ss_pred             HHHHhcCeEEEEeccH--HHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhcccc--ccceeccChHHHHHh
Confidence            3334567888889987  7788888887642    333    446677777777766655443  4679999863 2222


Q ss_pred             -cCCCCCcEEEE
Q psy17587         86 -LDVKHLNLVVN   96 (231)
Q Consensus        86 -ldip~v~~VI~   96 (231)
                       .++.++++||.
T Consensus       157 ~~~~~~~~~vVv  168 (237)
T d1gkub1         157 YRELGHFDFIFV  168 (237)
T ss_dssp             STTSCCCSEEEE
T ss_pred             hhhcCCCCEEEE
Confidence             34455666554

>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=82.09  E-value=3.7  Score=29.91  Aligned_cols=77  Identities=16%  Similarity=0.219  Sum_probs=50.1

Q ss_pred             ccccCCCCeEEEEcCChhHHHHHHHHHHHHH----CCCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------cc
Q psy17587         14 IDQYDRDSTIVDFKNGKVRLLVCAIVKELMK----AGYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------AA   83 (231)
Q Consensus        14 L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~----~~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~~   83 (231)
                      +.........++.++..  ..+......+..    .++.+...+|+.+.......+    ....+|+|+|+.      -.
T Consensus        63 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~  136 (206)
T d1s2ma1          63 VKPKLNKIQALIMVPTR--ELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRL----NETVHILVGTPGRVLDLASR  136 (206)
T ss_dssp             CCTTSCSCCEEEECSSH--HHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHT
T ss_pred             cccccccccceeeccch--hhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHh----cccceEEEECCccccccccc
Confidence            33344556667678876  556665555543    378999999998877654333    456899999963      23


Q ss_pred             cccCCCCCcEEEE
Q psy17587         84 RGLDVKHLNLVVN   96 (231)
Q Consensus        84 ~Gldip~v~~VI~   96 (231)
                      ..+++.++.++|.
T Consensus       137 ~~~~l~~l~~lV~  149 (206)
T d1s2ma1         137 KVADLSDCSLFIM  149 (206)
T ss_dssp             TCSCCTTCCEEEE
T ss_pred             ceeecccceEEEe
Confidence            3466777777664

>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=81.81  E-value=1.8  Score=32.03  Aligned_cols=77  Identities=13%  Similarity=0.162  Sum_probs=44.8

Q ss_pred             cccccCCCCeEEEEcCChhHHHHHHHHHHHHHC----CCCeeeccCCCCHHHHHHHHHHHhCCCccEEEecCc------c
Q psy17587         13 GIDQYDRDSTIVDFKNGKVRLLVCAIVKELMKA----GYPCLSLHGGIDQYDRDSTIVDFKNGKVRLLIATSV------A   82 (231)
Q Consensus        13 ~L~~~~~~~~iiiF~~~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~~~~F~~g~~~vLvaT~~------~   82 (231)
                      .|........++|.|+++  +.+.++...+...    ...+...+++-+..++...     -...+|+|+|+-      -
T Consensus        71 ~l~~~~~~~~~lil~pt~--el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~IvI~TP~~l~~~~~  143 (212)
T d1qdea_          71 RIDTSVKAPQALMLAPTR--ELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEG-----LRDAQIVVGTPGRVFDNIQ  143 (212)
T ss_dssp             HCCTTCCSCCEEEECSSH--HHHHHHHHHHHHHTTTSCCCEEEECC---------------CTTCSEEEECHHHHHHHHH
T ss_pred             hhhccCCCcceEEEcccH--HHhhhhhhhhcccccccccceeeEeeccchhHHHHH-----hcCCcEEEECCCccccccc
Confidence            344444567788899987  7788888877543    4566677776554443322     124689999963      3


Q ss_pred             ccccCCCCCcEEEE
Q psy17587         83 ARGLDVKHLNLVVN   96 (231)
Q Consensus        83 ~~Gldip~v~~VI~   96 (231)
                      ..++++..+.++|.
T Consensus       144 ~~~~~l~~l~~lVl  157 (212)
T d1qdea_         144 RRRFRTDKIKMFIL  157 (212)
T ss_dssp             TTSSCCTTCCEEEE
T ss_pred             cCceecCcceEEee
Confidence            44567777777665