Psyllid ID: psy4698

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------26
Protein Sequence
MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHccccccccEEEEEcccHHHHHHHHHHHHHHccccccEEEEEEccccHHHHHHHHcccccEEEccccHHHHHHcccccccccccEEEEEcHHHHcccccHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHcccccEEEEEccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHcccHHHHHHHHcccccEEEEEcEEccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEccccccccc
Coil and Loop (DISEMBL)
maeqrgdnwedpkngpaeneaeqpayngppgmavdglietnwdhvaenfddmELSEELLRGIYAygfekpsaiqqraiipcvrgndviaqaqsgtgktatFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDfmsvschaciggtivrdDIRKLEAGaqvvvgtpgrvfdMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE
Flexible Loop (DISEMBL)
maeqrgdnwedpkngpAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGaqvvvgtpgrvfdMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE
Low Complexity Region (SEG)
MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE
Disordered region (IsUnstruct)
********************************AVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV********
Disordered Region (DISOPRED)
*************************************IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTL*
Disordered Region (DISEMBL)
*********************EQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE
Disordered Region (DISPRO)
MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE
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	258	2.2.26 [Sep-21-2011]
Q4R8K5	406	Eukaryotic initiation fac	N/A	N/A	0.899	0.571	0.733	1e-100
A5A6N4	406	Eukaryotic initiation fac	yes	N/A	0.899	0.571	0.733	1e-100
Q5RKI1	407	Eukaryotic initiation fac	yes	N/A	0.903	0.572	0.735	1e-100
Q5R4X1	407	Eukaryotic initiation fac	yes	N/A	0.903	0.572	0.735	1e-100
P10630	407	Eukaryotic initiation fac	no	N/A	0.903	0.572	0.735	1e-100
Q14240	407	Eukaryotic initiation fac	no	N/A	0.903	0.572	0.735	1e-100
Q3SZ65	407	Eukaryotic initiation fac	no	N/A	0.903	0.572	0.735	1e-100
P60843	406	Eukaryotic initiation fac	no	N/A	0.899	0.571	0.733	1e-100
P60842	406	Eukaryotic initiation fac	yes	N/A	0.899	0.571	0.733	1e-100
Q3SZ54	406	Eukaryotic initiation fac	yes	N/A	0.899	0.571	0.733	1e-100

>sp|Q4R8K5|IF4A1_MACFA Eukaryotic initiation factor 4A-I OS=Macaca fascicularis GN=EIF4A1 PE=2 SV=1

 Score =  366 bits (939), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 171/233 (73%), Positives = 207/233 (88%), Gaps = 1/233 (0%)

Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct: 12  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 71

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct: 72  VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 131

Query: 147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
           HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct: 132 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 191

Query: 206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 244

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.
Macaca fascicularis (taxid: 9541)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|A5A6N4|IF4A1_PANTR Eukaryotic initiation factor 4A-I OS=Pan troglodytes GN=EIF4A1 PE=2 SV=1

 Score =  366 bits (939), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 171/233 (73%), Positives = 207/233 (88%), Gaps = 1/233 (0%)

Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct: 12  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 71

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct: 72  VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 131

Query: 147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
           HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct: 132 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 191

Query: 206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 244

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RKI1|IF4A2_RAT Eukaryotic initiation factor 4A-II OS=Rattus norvegicus GN=Eif4a2 PE=1 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 172/234 (73%), Positives = 205/234 (87%), Gaps = 1/234 (0%)

Query: 26  YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
           + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct: 12  HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query: 86  DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
           DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct: 72  DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query: 146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
           CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct: 132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query: 205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5R4X1|IF4A2_PONAB Eukaryotic initiation factor 4A-II OS=Pongo abelii GN=EIF4A2 PE=2 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 172/234 (73%), Positives = 205/234 (87%), Gaps = 1/234 (0%)

Query: 26  YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
           + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct: 12  HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query: 86  DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
           DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct: 72  DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query: 146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
           CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct: 132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query: 205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P10630|IF4A2_MOUSE Eukaryotic initiation factor 4A-II OS=Mus musculus GN=Eif4a2 PE=2 SV=2

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 172/234 (73%), Positives = 205/234 (87%), Gaps = 1/234 (0%)

Query: 26  YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
           + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct: 12  HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query: 86  DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
           DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct: 72  DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query: 146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
           CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct: 132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query: 205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q14240|IF4A2_HUMAN Eukaryotic initiation factor 4A-II OS=Homo sapiens GN=EIF4A2 PE=1 SV=2

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 172/234 (73%), Positives = 205/234 (87%), Gaps = 1/234 (0%)

Query: 26  YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
           + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct: 12  HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query: 86  DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
           DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct: 72  DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query: 146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
           CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct: 132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query: 205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3SZ65|IF4A2_BOVIN Eukaryotic initiation factor 4A-II OS=Bos taurus GN=EIF4A2 PE=2 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 172/234 (73%), Positives = 205/234 (87%), Gaps = 1/234 (0%)

Query: 26  YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
           + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct: 12  HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query: 86  DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
           DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct: 72  DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query: 146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
           CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct: 132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query: 205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P60843|IF4A1_MOUSE Eukaryotic initiation factor 4A-I OS=Mus musculus GN=Eif4a1 PE=2 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 171/233 (73%), Positives = 207/233 (88%), Gaps = 1/233 (0%)

Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct: 12  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 71

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct: 72  VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 131

Query: 147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
           HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct: 132 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 191

Query: 206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 244

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P60842|IF4A1_HUMAN Eukaryotic initiation factor 4A-I OS=Homo sapiens GN=EIF4A1 PE=1 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 171/233 (73%), Positives = 207/233 (88%), Gaps = 1/233 (0%)

Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct: 12  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 71

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct: 72  VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 131

Query: 147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
           HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct: 132 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 191

Query: 206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 244

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3SZ54|IF4A1_BOVIN Eukaryotic initiation factor 4A-I OS=Bos taurus GN=EIF4A1 PE=2 SV=1

 Score =  365 bits (938), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 171/233 (73%), Positives = 207/233 (88%), Gaps = 1/233 (0%)

Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct: 12  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 71

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct: 72  VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 131

Query: 147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
           HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct: 132 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 191

Query: 206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 192 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 244

ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

Bos taurus (taxid: 9913)

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	258
410810331	420	eukaryotic initiation factor 4A [Phaedon	0.992	0.609	0.767	1e-114
332372808	423	unknown [Dendroctonus ponderosae]	0.992	0.605	0.778	1e-114
322799953	423	hypothetical protein SINV_07394 [Solenop	0.988	0.602	0.787	1e-113
307194191	423	Eukaryotic initiation factor 4A-II [Harp	0.988	0.602	0.783	1e-113
332026541	423	Eukaryotic initiation factor 4A-II [Acro	0.988	0.602	0.787	1e-113
307189936	423	Eukaryotic initiation factor 4A-II [Camp	0.988	0.602	0.787	1e-113
299758408	419	eukaryotic initiation factor 4a [Triboli	0.980	0.603	0.769	1e-113
350421455	423	PREDICTED: eukaryotic initiation factor	0.988	0.602	0.772	1e-112
270007520	482	hypothetical protein TcasGA2_TC014113 [T	0.972	0.520	0.775	1e-112
383860102	423	PREDICTED: eukaryotic initiation factor	0.988	0.602	0.768	1e-112

>gi|410810331|emb|CCJ09440.1| eukaryotic initiation factor 4A [Phaedon cochleariae]

 Score =  418 bits (1075), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 198/258 (76%), Positives = 226/258 (87%), Gaps = 2/258 (0%)

Query: 1   MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLR 60
           + + R + W+  KNGPA +E E   Y+GPPGM  DG+IE+NW+ V +NFDDM L EELLR
Sbjct: 3   VTDSRTEEWD--KNGPANDEKEPQVYDGPPGMEPDGIIESNWEEVTDNFDDMNLKEELLR 60

Query: 61  GIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALI 120
           GIYAYGFEKPSAIQQRAIIPCV+G+DVIAQAQSGTGKTATFSISILQQ+D +++ECQALI
Sbjct: 61  GIYAYGFEKPSAIQQRAIIPCVKGHDVIAQAQSGTGKTATFSISILQQIDTSVRECQALI 120

Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
           LAPTRELAQQIQKVVIALGDFMS  CHACIGGT VR+D+RKLE G  VVVGTPGRV+DMI
Sbjct: 121 LAPTRELAQQIQKVVIALGDFMSAQCHACIGGTNVREDMRKLETGMHVVVGTPGRVYDMI 180

Query: 181 SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK 240
           +R AL T  I+MFVLDEADEMLSRGFKDQI+DVFK L++DVQVILLSATMP DVLDV+  
Sbjct: 181 TRRALRTSNIKMFVLDEADEMLSRGFKDQIHDVFKMLSSDVQVILLSATMPTDVLDVTKS 240

Query: 241 FMRDPIKILVKKEELTLE 258
           FMR+P++ILVKKEELTLE
Sbjct: 241 FMRNPVRILVKKEELTLE 258

Source: Phaedon cochleariae

Species: Phaedon cochleariae

Genus: Phaedon

Family: Chrysomelidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332372808|gb|AEE61546.1| unknown [Dendroctonus ponderosae]

 Score =  416 bits (1068), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 200/257 (77%), Positives = 222/257 (86%), Gaps = 1/257 (0%)

Query: 3   EQRGDNWE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRG 61
           E+R + W+ + K G    E EQPAY+GPPGM  DG+IE+NW+ V  NFDDM L EELLRG
Sbjct: 5   ERRNEEWDKNGKTGSFSEEKEQPAYDGPPGMDPDGIIESNWEQVVTNFDDMSLKEELLRG 64

Query: 62  IYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL 121
           IYAYGFEKPSAIQQRAIIPCV+G+DVIAQAQSGTGKTATFSISILQQ+D  ++ECQALIL
Sbjct: 65  IYAYGFEKPSAIQQRAIIPCVKGHDVIAQAQSGTGKTATFSISILQQIDTTVRECQALIL 124

Query: 122 APTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMIS 181
           APTRELAQQIQKVVIALGDFMS  CHACIGGT VR+D+RKL+ G  VVVGTPGRVFDMI+
Sbjct: 125 APTRELAQQIQKVVIALGDFMSAQCHACIGGTNVREDMRKLDTGVHVVVGTPGRVFDMIN 184

Query: 182 RGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF 241
           R AL  + I+MFVLDEADEMLSRGFKDQI+DVFK LN DVQVILLSATMP DVLDV+  F
Sbjct: 185 RRALRPQHIKMFVLDEADEMLSRGFKDQIHDVFKTLNADVQVILLSATMPPDVLDVTKSF 244

Query: 242 MRDPIKILVKKEELTLE 258
           MR PI+ILVKKEELTLE
Sbjct: 245 MRAPIRILVKKEELTLE 261

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322799953|gb|EFZ21079.1| hypothetical protein SINV_07394 [Solenopsis invicta]

 Score =  414 bits (1065), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 204/259 (78%), Positives = 226/259 (87%), Gaps = 4/259 (1%)

Query: 2   AEQRGDN-WE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELL 59
           AE+R D+ W  D KNGP+E  +EQP Y+GPPGM  DG+IE+NWD V ENFD+M L EELL
Sbjct: 5   AERRNDDQWSGDSKNGPSE--SEQPTYDGPPGMDPDGIIESNWDVVVENFDEMNLKEELL 62

Query: 60  RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL 119
           RGIYAYGFEKPSAIQQRAI+PC+RG DVIAQAQSGTGKTATFSISILQQ+D  IKECQAL
Sbjct: 63  RGIYAYGFEKPSAIQQRAILPCIRGLDVIAQAQSGTGKTATFSISILQQIDTTIKECQAL 122

Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM 179
           ILAPTRELAQQIQKVVIALGDFM   CHACIGGT VR+D+RKL+ G  VVVGTPGRV+DM
Sbjct: 123 ILAPTRELAQQIQKVVIALGDFMHAECHACIGGTNVREDMRKLDQGVHVVVGTPGRVYDM 182

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           ISR AL    I++FVLDEADEMLSRGFKDQI+DVFK L N+VQVILLSATMP+DVLDVS 
Sbjct: 183 ISRRALRASSIKLFVLDEADEMLSRGFKDQIHDVFKLLPNEVQVILLSATMPSDVLDVSK 242

Query: 240 KFMRDPIKILVKKEELTLE 258
            FMR+PI+ILVKKEELTLE
Sbjct: 243 CFMRNPIRILVKKEELTLE 261

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307194191|gb|EFN76608.1| Eukaryotic initiation factor 4A-II [Harpegnathos saltator]

 Score =  414 bits (1063), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 203/259 (78%), Positives = 227/259 (87%), Gaps = 4/259 (1%)

Query: 2   AEQRGDN-WE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELL 59
           +E+R D+ W  D KNGP+E  +EQP Y+GPPGM  DG+IE+NWD V ENFD+M L EELL
Sbjct: 5   SERRNDDQWSGDSKNGPSE--SEQPTYDGPPGMDPDGIIESNWDVVVENFDEMNLKEELL 62

Query: 60  RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL 119
           RGIYAYGFEKPSAIQQRAI+PC+RG DVIAQAQSGTGKTATFSISILQQ+D +IKECQAL
Sbjct: 63  RGIYAYGFEKPSAIQQRAILPCIRGLDVIAQAQSGTGKTATFSISILQQIDTSIKECQAL 122

Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM 179
           ILAPTRELAQQIQKVVIALGDFM   CHACIGGT VR+D+RKL+ G  VVVGTPGRV+DM
Sbjct: 123 ILAPTRELAQQIQKVVIALGDFMHAECHACIGGTNVREDMRKLDQGVHVVVGTPGRVYDM 182

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           ISR AL    I++FVLDEADEMLSRGFKDQI+DVFK L N+VQVILLSATMP+DVLDVS 
Sbjct: 183 ISRRALRASSIKLFVLDEADEMLSRGFKDQIHDVFKLLPNEVQVILLSATMPSDVLDVSK 242

Query: 240 KFMRDPIKILVKKEELTLE 258
            FMR+PI+ILVKKEELTLE
Sbjct: 243 CFMRNPIRILVKKEELTLE 261

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026541|gb|EGI66659.1| Eukaryotic initiation factor 4A-II [Acromyrmex echinatior]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 204/259 (78%), Positives = 227/259 (87%), Gaps = 4/259 (1%)

Query: 2   AEQRGDN-WE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELL 59
           AE+R D+ W  D KNGP+E  +EQP Y+GPPGM  DG+IE+NWD V ENFD+M L EELL
Sbjct: 5   AERRNDDQWPGDSKNGPSE--SEQPTYDGPPGMDPDGVIESNWDVVVENFDEMNLKEELL 62

Query: 60  RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL 119
           RGIYAYGFEKPSAIQQRAI+PC+RG DVIAQAQSGTGKTATFSISILQQ+D +IKECQAL
Sbjct: 63  RGIYAYGFEKPSAIQQRAILPCIRGLDVIAQAQSGTGKTATFSISILQQIDTSIKECQAL 122

Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM 179
           ILAPTRELAQQIQKVVIALGDFM   CHACIGGT VR+D+RKL+ G  VVVGTPGRV+DM
Sbjct: 123 ILAPTRELAQQIQKVVIALGDFMHAECHACIGGTNVREDMRKLDQGVHVVVGTPGRVYDM 182

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           ISR AL    I++FVLDEADEMLSRGFKDQI+DVFK L N+VQVILLSATMP+DVLDVS 
Sbjct: 183 ISRRALRASSIKLFVLDEADEMLSRGFKDQIHDVFKLLPNEVQVILLSATMPSDVLDVSK 242

Query: 240 KFMRDPIKILVKKEELTLE 258
            FMR+PI+ILVKKEELTLE
Sbjct: 243 CFMRNPIRILVKKEELTLE 261

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189936|gb|EFN74172.1| Eukaryotic initiation factor 4A-II [Camponotus floridanus]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 204/259 (78%), Positives = 227/259 (87%), Gaps = 4/259 (1%)

Query: 2   AEQRGDN-WE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELL 59
           AE+R D+ W  D KNGP+E  +EQP Y+GPPGM  DG+IE+NWD V ENFD+M L EELL
Sbjct: 5   AERRNDDQWPGDSKNGPSE--SEQPTYDGPPGMDPDGIIESNWDVVVENFDEMNLKEELL 62

Query: 60  RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL 119
           RGIYAYGFEKPSAIQQRAI+PC+RG DVIAQAQSGTGKTATFSISILQQ+D +IKECQAL
Sbjct: 63  RGIYAYGFEKPSAIQQRAILPCIRGLDVIAQAQSGTGKTATFSISILQQIDTSIKECQAL 122

Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM 179
           ILAPTRELAQQIQKVVIALGDFM   CHACIGGT VR+D+RKL+ G  VVVGTPGRV+DM
Sbjct: 123 ILAPTRELAQQIQKVVIALGDFMHAECHACIGGTNVREDMRKLDQGVHVVVGTPGRVYDM 182

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           ISR AL    I++FVLDEADEMLSRGFKDQI+DVFK L N+VQVILLSATMP+DVLDVS 
Sbjct: 183 ISRRALRANSIKLFVLDEADEMLSRGFKDQIHDVFKLLPNEVQVILLSATMPSDVLDVSK 242

Query: 240 KFMRDPIKILVKKEELTLE 258
            FMR+PI+ILVKKEELTLE
Sbjct: 243 CFMRNPIRILVKKEELTLE 261

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|299758408|ref|NP_001177648.1| eukaryotic initiation factor 4a [Tribolium castaneum]

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 197/256 (76%), Positives = 227/256 (88%), Gaps = 3/256 (1%)

Query: 3   EQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGI 62
           ++R + W+  KNGPA ++  Q AY+GPPGM  DG+I++NWD V +NFDDM L EELLRGI
Sbjct: 5   DRRNEEWD--KNGPASDKESQ-AYDGPPGMDPDGVIDSNWDEVVDNFDDMNLKEELLRGI 61

Query: 63  YAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA 122
           YAYGFEKPSAIQQRAIIPCV+G+DVIAQAQSGTGKTATFSISILQQ+D +++ECQALILA
Sbjct: 62  YAYGFEKPSAIQQRAIIPCVKGHDVIAQAQSGTGKTATFSISILQQIDTSLRECQALILA 121

Query: 123 PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR 182
           PTRELAQQIQKVVIALGDFMS  CHACIGGT VR+D+RKLE G  VVVGTPGRV+DMI+R
Sbjct: 122 PTRELAQQIQKVVIALGDFMSAQCHACIGGTNVREDMRKLETGVHVVVGTPGRVYDMINR 181

Query: 183 GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFM 242
            +L    I+MFVLDEADEMLSRGFKDQI+DVF+ LN+DVQVILLSATMPADVLDV+  FM
Sbjct: 182 RSLRANFIKMFVLDEADEMLSRGFKDQIHDVFRMLNSDVQVILLSATMPADVLDVTKSFM 241

Query: 243 RDPIKILVKKEELTLE 258
           R+P++ILVKKEELTLE
Sbjct: 242 RNPVRILVKKEELTLE 257

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350421455|ref|XP_003492849.1| PREDICTED: eukaryotic initiation factor 4A-like isoform 1 [Bombus impatiens]

 Score =  410 bits (1054), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 200/259 (77%), Positives = 226/259 (87%), Gaps = 4/259 (1%)

Query: 2   AEQRGDN-WE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELL 59
           +E+R D+ W  D KNGP+E  ++Q  Y+GPPGM  DG+IE+NWD V +NFD+M L EELL
Sbjct: 5   SERRNDDQWAGDSKNGPSE--SDQQTYDGPPGMEPDGIIESNWDVVVDNFDEMNLKEELL 62

Query: 60  RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL 119
           RGIYAYGFEKPSAIQQRAI+PC+RG+DVIAQAQSGTGKTATFSISILQQ+D NIKECQAL
Sbjct: 63  RGIYAYGFEKPSAIQQRAILPCIRGHDVIAQAQSGTGKTATFSISILQQIDTNIKECQAL 122

Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM 179
           ILAPTRELAQQIQKVVIALGDFM   CHACIGGT VR+D+RKLE G  +VVGTPGRV+DM
Sbjct: 123 ILAPTRELAQQIQKVVIALGDFMHAECHACIGGTNVREDMRKLEQGVHIVVGTPGRVYDM 182

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           ISR AL    I++FVLDEADEMLSRGFKDQI+DVFK L ++VQVILLSATMP DVLDVS 
Sbjct: 183 ISRRALRASSIKLFVLDEADEMLSRGFKDQIHDVFKLLPHEVQVILLSATMPTDVLDVST 242

Query: 240 KFMRDPIKILVKKEELTLE 258
            FMR+PI+ILVKKEELTLE
Sbjct: 243 CFMRNPIRILVKKEELTLE 261

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270007520|gb|EFA03968.1| hypothetical protein TcasGA2_TC014113 [Tribolium castaneum]

 Score =  409 bits (1051), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 197/254 (77%), Positives = 225/254 (88%), Gaps = 3/254 (1%)

Query: 5   RGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYA 64
           R + W+  KNGPA ++  Q AY+GPPGM  DG+I++NWD V +NFDDM L EELLRGIYA
Sbjct: 70  RNEEWD--KNGPASDKESQ-AYDGPPGMDPDGVIDSNWDEVVDNFDDMNLKEELLRGIYA 126

Query: 65  YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT 124
           YGFEKPSAIQQRAIIPCV+G+DVIAQAQSGTGKTATFSISILQQ+D +++ECQALILAPT
Sbjct: 127 YGFEKPSAIQQRAIIPCVKGHDVIAQAQSGTGKTATFSISILQQIDTSLRECQALILAPT 186

Query: 125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA 184
           RELAQQIQKVVIALGDFMS  CHACIGGT VR+D+RKLE G  VVVGTPGRV+DMI+R +
Sbjct: 187 RELAQQIQKVVIALGDFMSAQCHACIGGTNVREDMRKLETGVHVVVGTPGRVYDMINRRS 246

Query: 185 LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRD 244
           L    I+MFVLDEADEMLSRGFKDQI+DVF+ LN+DVQVILLSATMPADVLDV+  FMR+
Sbjct: 247 LRANFIKMFVLDEADEMLSRGFKDQIHDVFRMLNSDVQVILLSATMPADVLDVTKSFMRN 306

Query: 245 PIKILVKKEELTLE 258
           P++ILVKKEELTLE
Sbjct: 307 PVRILVKKEELTLE 320

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383860102|ref|XP_003705530.1| PREDICTED: eukaryotic initiation factor 4A-II-like isoform 1 [Megachile rotundata]

 Score =  409 bits (1050), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 199/259 (76%), Positives = 227/259 (87%), Gaps = 4/259 (1%)

Query: 2   AEQRGDN-WE-DPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELL 59
           +E+R D+ W  D KNGP+E  +EQ  YNGPPGM  DG+IE+NWD V +NFD+M L EELL
Sbjct: 5   SERRNDDQWAGDSKNGPSE--SEQQTYNGPPGMDPDGIIESNWDVVVDNFDEMNLKEELL 62

Query: 60  RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL 119
           RGIYAYGFEKPSAIQQRAI+PC+RG+DVIAQAQSGTGKTATFSISILQQ+D N+KECQAL
Sbjct: 63  RGIYAYGFEKPSAIQQRAILPCIRGHDVIAQAQSGTGKTATFSISILQQIDTNLKECQAL 122

Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM 179
           ILAPTRELAQQIQKVVIALGDFM   CHACIGGT VR+D+RKL+ G  +VVGTPGRV+DM
Sbjct: 123 ILAPTRELAQQIQKVVIALGDFMHAECHACIGGTNVREDMRKLDQGVHIVVGTPGRVYDM 182

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           ISR AL    I++FVLDEADEMLSRGFKDQI+DVFK L ++VQVILLSATMP+DVLDVS 
Sbjct: 183 ISRRALRANSIKLFVLDEADEMLSRGFKDQIHDVFKLLPHEVQVILLSATMPSDVLDVSK 242

Query: 240 KFMRDPIKILVKKEELTLE 258
            FMR+PI+ILVK+EELTLE
Sbjct: 243 CFMRNPIRILVKREELTLE 261

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	258
UNIPROTKB|F8WFX2	408	Eif4a2 "Eukaryotic initiation	0.937	0.593	0.710	1.9e-90
ZFIN|ZDB-GENE-040426-2802	411	eif4a2 "eukaryotic translation	0.949	0.596	0.704	1.9e-90
UNIPROTKB|Q3SZ65	407	EIF4A2 "Eukaryotic initiation	0.903	0.572	0.735	2.5e-90
UNIPROTKB|E2R3J1	407	EIF4A2 "Uncharacterized protei	0.903	0.572	0.735	2.5e-90
UNIPROTKB|E7EQG2	362	EIF4A2 "Eukaryotic initiation	0.903	0.643	0.735	2.5e-90
UNIPROTKB|Q14240	407	EIF4A2 "Eukaryotic initiation	0.903	0.572	0.735	2.5e-90
UNIPROTKB|A6M930	407	EIF4A2 "Eukaryotic translation	0.903	0.572	0.735	2.5e-90
MGI|MGI:106906	407	Eif4a2 "eukaryotic translation	0.903	0.572	0.735	2.5e-90
RGD|1309225	407	Eif4a2 "eukaryotic translation	0.903	0.572	0.735	2.5e-90
UNIPROTKB|Q3SZ54	406	EIF4A1 "Eukaryotic initiation	0.899	0.571	0.733	3.1e-90

UNIPROTKB|F8WFX2 Eif4a2 "Eukaryotic initiation factor 4A-II" [Rattus norvegicus (taxid:10116)]

 Score = 902 (322.6 bits), Expect = 1.9e-90, P = 1.9e-90
 Identities = 174/245 (71%), Positives = 210/245 (85%)

Query:    15 GPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQ 74
             G A+  + +  + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQ
Sbjct:     4 GSADYNSRE--HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQ 61

Query:    75 QRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV 134
             QRAIIPC++G DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV
Sbjct:    62 QRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKV 121

Query:   135 VIALGDFMSVSCHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMF 193
             ++ALGD+M  +CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MF
Sbjct:   122 ILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMF 181

Query:   194 VLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
             VLDEADEMLSRGFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKE
Sbjct:   182 VLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 241

Query:   254 ELTLE 258
             ELTLE
Sbjct:   242 ELTLE 246

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

ZFIN|ZDB-GENE-040426-2802 eif4a2 "eukaryotic translation initiation factor 4A, isoform 2" [Danio rerio (taxid:7955)]

 Score = 902 (322.6 bits), Expect = 1.9e-90, P = 1.9e-90
 Identities = 174/247 (70%), Positives = 213/247 (86%)

Query:    14 NGPAE-NEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSA 72
             +G A+ N +    + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSA
Sbjct:     3 SGSADYNSSRDRDHGGPEGMEPDGVIESNWNEITDNFDDMNLKETLLRGIYAYGFEKPSA 62

Query:    73 IQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ 132
             IQQRAIIPC++G DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQ
Sbjct:    63 IQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEQKETQALVLAPTRELAQQIQ 122

Query:   133 KVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIR 191
             KV++ALGD+M  SCHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+
Sbjct:   123 KVILALGDYMGASCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIK 182

Query:   192 MFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK 251
             MFVLDEADEMLSRGFKDQIY++F+ L+ ++QV+LLSATMPADVL+V+ KFMR+P++ILVK
Sbjct:   183 MFVLDEADEMLSRGFKDQIYEIFQKLSTNIQVVLLSATMPADVLEVTTKFMREPVRILVK 242

Query:   252 KEELTLE 258
             KEELTLE
Sbjct:   243 KEELTLE 249

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

UNIPROTKB|Q3SZ65 EIF4A2 "Eukaryotic initiation factor 4A-II" [Bos taurus (taxid:9913)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

GO:0005524 "ATP binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

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

UNIPROTKB|E2R3J1 EIF4A2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E7EQG2 EIF4A2 "Eukaryotic initiation factor 4A-II" [Homo sapiens (taxid:9606)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q14240 EIF4A2 "Eukaryotic initiation factor 4A-II" [Homo sapiens (taxid:9606)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

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

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0004386 "helicase activity" evidence=TAS

GO:0006446 "regulation of translational initiation" evidence=TAS

GO:0016281 "eukaryotic translation initiation factor 4F complex" evidence=TAS

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0000289 "nuclear-transcribed mRNA poly(A) tail shortening" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019221 "cytokine-mediated signaling pathway" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|A6M930 EIF4A2 "Eukaryotic translation initiation factor 4A isoform 2" [Sus scrofa (taxid:9823)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

GO:0005524 "ATP binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

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

MGI|MGI:106906 Eif4a2 "eukaryotic translation initiation factor 4A2" [Mus musculus (taxid:10090)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

RGD|1309225 Eif4a2 "eukaryotic translation initiation factor 4A2" [Rattus norvegicus (taxid:10116)]

 Score = 901 (322.2 bits), Expect = 2.5e-90, P = 2.5e-90
 Identities = 172/234 (73%), Positives = 205/234 (87%)

Query:    26 YNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN 85
             + GP GM  DG+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G 
Sbjct:    12 HGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGY 71

Query:    86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS 145
             DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +
Sbjct:    72 DVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGAT 131

Query:   146 CHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
             CHACIGGT VR++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSR
Sbjct:   132 CHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR 191

Query:   205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             GFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLE 245

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q3SZ54 EIF4A1 "Eukaryotic initiation factor 4A-I" [Bos taurus (taxid:9913)]

 Score = 900 (321.9 bits), Expect = 3.1e-90, P = 3.1e-90
 Identities = 171/233 (73%), Positives = 207/233 (88%)

Query:    27 NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
             NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct:    12 NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 71

Query:    87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
             VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct:    72 VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 131

Query:   147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
             HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct:   132 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 191

Query:   206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct:   192 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 244

GO:0005524 "ATP binding" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" 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)
Q6Z2Z4	IF4A3_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6621	0.8488	0.5289	yes	N/A
P0CQ70	IF4A_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.7030	0.8837	0.5685	yes	N/A
P35683	IF4A1_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6666	0.8488	0.5289	yes	N/A
Q3SZ54	IF4A1_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7339	0.8992	0.5714	yes	N/A
P47943	IF4A_SCHPO	3, ., 6, ., 4, ., 1, 3	0.7410	0.8682	0.5714	yes	N/A
Q2UPY3	IF4A_ASPOR	3, ., 6, ., 4, ., 1, 3	0.7085	0.8643	0.5296	yes	N/A
Q5R4X1	IF4A2_PONAB	3, ., 6, ., 4, ., 1, 3	0.7350	0.9031	0.5724	yes	N/A
P29562	IF4A1_RABIT	3, ., 6, ., 4, ., 1, 3	0.7339	0.8992	0.5829	yes	N/A
Q4WX43	IF4A_ASPFU	3, ., 6, ., 4, ., 1, 3	0.7098	0.8682	0.5517	yes	N/A
Q6BRN4	IF4A_DEBHA	3, ., 6, ., 4, ., 1, 3	0.6278	0.8643	0.5617	yes	N/A
O02494	IF4A_CRYPV	3, ., 6, ., 4, ., 1, 3	0.6	0.9302	0.5925	yes	N/A
A5A6N4	IF4A1_PANTR	3, ., 6, ., 4, ., 1, 3	0.7339	0.8992	0.5714	yes	N/A
Q02748	IF4A_DROME	3, ., 6, ., 4, ., 1, 3	0.7586	0.8992	0.5756	yes	N/A
Q5RKI1	IF4A2_RAT	3, ., 6, ., 4, ., 1, 3	0.7350	0.9031	0.5724	yes	N/A
Q6CDV4	IF4A_YARLI	3, ., 6, ., 4, ., 1, 3	0.6742	0.8565	0.5594	yes	N/A
Q5R5F5	IF4A1_PONAB	3, ., 6, ., 4, ., 1, 3	0.7253	0.8992	0.5714	yes	N/A
A2QEN5	IF4A_ASPNC	3, ., 6, ., 4, ., 1, 3	0.7187	0.8682	0.5628	yes	N/A
P27639	IF4A_CAEEL	3, ., 6, ., 4, ., 1, 3	0.7321	0.8682	0.5572	yes	N/A
Q5B948	IF4A_EMENI	3, ., 6, ., 4, ., 1, 3	0.7187	0.8682	0.5628	yes	N/A
Q8JFP1	IF4A2_CHICK	3, ., 6, ., 4, ., 1, 3	0.7264	0.9031	0.5724	yes	N/A
P60842	IF4A1_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7339	0.8992	0.5714	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.914
3rd Layer	3.6.4	0.921

---

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	258
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-123
cd00268	203	cd00268, DEADc, DEAD-box helicases	1e-106
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-80
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-58
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	9e-54
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	7e-49
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-45
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	1e-43
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-39
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-37
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	8e-34
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	8e-32
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-29
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	3e-29
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	6e-28
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	2e-07
COG1205	851	COG1205, COG1205, Distinct helicase family with a	0.003

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

 Score =  357 bits (917), Expect = e-123
 Identities = 152/232 (65%), Positives = 188/232 (81%)

Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           N    +A  G IE+N+D + ++FD ++L+E+LLRGIY+YGFEKPSAIQQR I P + G D
Sbjct: 8   NQSEQVASTGTIESNYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYD 67

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
            I QAQSGTGKTATF I+ LQ +D ++  CQALILAPTRELAQQIQKVV+ALGD++ V C
Sbjct: 68  TIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRC 127

Query: 147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF 206
           HAC+GGT+VRDDI KL+AG  +VVGTPGRV+DMI +  L    +++F+LDEADEMLSRGF
Sbjct: 128 HACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGF 187

Query: 207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           K QIYDVFK L  DVQV L SATMP ++L+++ KFMRDP +ILVKK+ELTLE
Sbjct: 188 KGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLE 239

Length = 401

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

 Score =  304 bits (782), Expect = e-106
 Identities = 105/203 (51%), Positives = 138/203 (67%), Gaps = 2/203 (0%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F+++ LS ELLRGIYA GFEKP+ IQ RAI P + G DVI QAQ+G+GKTA F I IL++
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 109 VD--QNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
           +D        QALILAPTRELA QI +V   LG   ++      GGT +   IRKL+ G 
Sbjct: 61  LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
            +VV TPGR+ D++ RG L   +++  VLDEAD ML  GF+DQI ++ K L  D Q +L 
Sbjct: 121 HIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLF 180

Query: 227 SATMPADVLDVSMKFMRDPIKIL 249
           SATMP +V D++ KF+R+P++IL
Sbjct: 181 SATMPKEVRDLARKFLRNPVRIL 203

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

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

 Score =  250 bits (639), Expect = 3e-80
 Identities = 91/223 (40%), Positives = 128/223 (57%), Gaps = 3/223 (1%)

Query: 38  IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
           +    +     F  + LS ELL+ +   GFE+P+ IQ  AI   + G DV+ QAQ+GTGK
Sbjct: 20  LSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGK 79

Query: 98  TATFSISILQQVDQ--NIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTI 154
           TA F + +LQ++ +    K   ALILAPTRELA QI + +  LG  +  +      GG  
Sbjct: 80  TAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVS 139

Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
           +R  I  L+ G  +VV TPGR+ D+I RG L    +   VLDEAD ML  GF D I  + 
Sbjct: 140 IRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKIL 199

Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTL 257
           K L  D Q +L SATMP D+ +++ +++ DP++I V  E+L  
Sbjct: 200 KALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLER 242

Length = 513

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

 Score =  182 bits (465), Expect = 2e-58
 Identities = 68/169 (40%), Positives = 105/169 (62%), Gaps = 2/169 (1%)

Query: 71  SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ 130
           + IQ +AI   + G DV+ QA +G+GKT  F + ILQ +       QAL+LAPTRELA+Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 131 IQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQ 189
           I + +  L   + +      GGT +++  RKL+ G A ++VGTPGR+ D++ RG L   +
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120

Query: 190 -IRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDV 237
            +++ VLDEA  +L  GF D + ++   L  D Q++LLSAT+P ++ D+
Sbjct: 121 NLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 169

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

 Score =  172 bits (437), Expect = 9e-54
 Identities = 70/196 (35%), Positives = 109/196 (55%), Gaps = 3/196 (1%)

Query: 62  IYAYGFEKPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALI 120
           I  +GFE     Q+ AI   + G  DVI  A +G+GKT    +  L+ + +  K  + L+
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG-KGGRVLV 59

Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDM 179
           L PTRELA+Q  + +  LG  + +      GG   R+ +RKLE+G   ++V TPGR+ D+
Sbjct: 60  LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
           +    LS   + + +LDEA  +L  GF DQ+  + K L  +VQ++LLSAT P ++ ++  
Sbjct: 120 LENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLE 179

Query: 240 KFMRDPIKILVKKEEL 255
            F+ DP+ I V    L
Sbjct: 180 LFLNDPVFIDVGFTPL 195

Length = 201

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

 Score =  166 bits (424), Expect = 7e-49
 Identities = 78/207 (37%), Positives = 115/207 (55%), Gaps = 9/207 (4%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F  + L   LL  +   G+ + + IQ +++   + G DVIAQA++G+GKTA F + +LQ+
Sbjct: 6   FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQK 65

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-----VSCHACIGGTIVRDDIRKLE 163
           +D      QAL+L PTRELA Q+ K +  L  F+        C    GG  +   I  LE
Sbjct: 66  LDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLC----GGVPMGPQIDSLE 121

Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
            GA ++VGTPGR+ D + +G L    +   VLDEAD ML  GF+D I  + +      Q 
Sbjct: 122 HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQT 181

Query: 224 ILLSATMPADVLDVSMKFMRDPIKILV 250
           +L SAT P  +  +S +F RDP+++ V
Sbjct: 182 LLFSATYPEGIAAISQRFQRDPVEVKV 208

Length = 460

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

 Score =  160 bits (406), Expect = 3e-45
 Identities = 81/201 (40%), Positives = 114/201 (56%), Gaps = 7/201 (3%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F D+ L   +L  +   G+EKPS IQ   I   + G DV+  AQ+G+GKTA FS+ +L  
Sbjct: 8   FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFM----SVSCHACIGGTIVRDDIRKLEA 164
           +D  +K  Q L+LAPTRELA Q+ +   A+ DF      V+  A  GG      +R L  
Sbjct: 68  LDPELKAPQILVLAPTRELAVQVAE---AMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ 124

Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           G Q+VVGTPGR+ D + RG L   ++   VLDEADEML  GF + +  +   +    Q  
Sbjct: 125 GPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTA 184

Query: 225 LLSATMPADVLDVSMKFMRDP 245
           L SATMP  +  ++ +FM++P
Sbjct: 185 LFSATMPEAIRRITRRFMKEP 205

Length = 629

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

 Score =  144 bits (364), Expect = 1e-43
 Identities = 56/146 (38%), Positives = 82/146 (56%), Gaps = 2/146 (1%)

Query: 85  NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV 144
            DV+  A +G+GKT    + IL+ +D   K  Q L+LAPTRELA Q+ + +  L     +
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE-GI 58

Query: 145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR 204
                IGGT ++   + L     +VVGTPGR+ D + R  LS K++ + +LDEA  +L++
Sbjct: 59  KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQ 118

Query: 205 GFKDQIYDVFKHLNNDVQVILLSATM 230
           GF      +   L  D QV+LLSAT 
Sbjct: 119 GFGLLGLKILLKLPKDRQVLLLSATP 144

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

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

 Score =  142 bits (360), Expect = 1e-39
 Identities = 77/209 (36%), Positives = 118/209 (56%), Gaps = 6/209 (2%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
           +FD + LS ++LR +   G+ +P+ IQQ+AI   + G D++A AQ+GTGKTA F++ +LQ
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 108 QVDQNI------KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
            +          +  +ALIL PTRELA QI + V     ++++      GG  +   + K
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121

Query: 162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV 221
           L  G  V+V TPGR+ D+  + A+   Q+ + VLDEAD ML  GF   I  V   L    
Sbjct: 122 LRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKR 181

Query: 222 QVILLSATMPADVLDVSMKFMRDPIKILV 250
           Q +L SAT   D+  ++ K + +P++I V
Sbjct: 182 QNLLFSATFSDDIKALAEKLLHNPLEIEV 210

Length = 456

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

 Score =  135 bits (342), Expect = 4e-37
 Identities = 76/218 (34%), Positives = 119/218 (54%), Gaps = 10/218 (4%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F D  L+ EL+  I+  GF   + IQ + +   + G+D I +AQ+GTGKTA F ISI+ Q
Sbjct: 89  FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148

Query: 109 VDQN-------IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
           + Q        + E +ALI+APTREL  QI K   AL  +  ++    +GG      +++
Sbjct: 149 LLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQ 208

Query: 162 LEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL--N 218
           LEA    ++V TPGR+ D   RG +    + + VLDEAD ML  GF  Q+  + +     
Sbjct: 209 LEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRK 268

Query: 219 NDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
            + Q +L SAT   DV++++ ++  DP  + ++ E + 
Sbjct: 269 EERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVA 306

Length = 475

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

 Score =  127 bits (321), Expect = 8e-34
 Identities = 66/207 (31%), Positives = 113/207 (54%), Gaps = 8/207 (3%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F    L  +LL  +   G+E P+ IQ +AI   + G  ++  A +G+GKTA+F + I+ +
Sbjct: 123 FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISR 182

Query: 109 V----DQNIKECQ---ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
                  +  E +   A++L PTREL  Q++     LG  +       +GG  +   + +
Sbjct: 183 CCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYR 242

Query: 162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV 221
           ++ G +++VGTPGR+ D++S+  +    + + VLDE D ML RGF+DQ+  +F+ L+   
Sbjct: 243 IQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQP- 301

Query: 222 QVILLSATMPADVLDVSMKFMRDPIKI 248
           QV+L SAT+  +V   +    +D I I
Sbjct: 302 QVLLFSATVSPEVEKFASSLAKDIILI 328

Length = 518

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

 Score =  120 bits (304), Expect = 8e-32
 Identities = 68/206 (33%), Positives = 96/206 (46%), Gaps = 5/206 (2%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F ++EL E LL  +   G+ +P+AIQ  AI P + G DV+  A +GTGKTA F +  LQ
Sbjct: 2   TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61

Query: 108 QVDQ--NIKECQA--LILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE 163
            +      K      LIL PTRELA Q+      L     +      GG    +      
Sbjct: 62  HLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS 121

Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
               +VV TPGR+   I       + +   +LDEAD ML  GF   I  +        Q 
Sbjct: 122 ENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQT 181

Query: 224 ILLSATMPAD-VLDVSMKFMRDPIKI 248
           +L SAT+  D V D + + + DP+++
Sbjct: 182 LLFSATLEGDAVQDFAERLLNDPVEV 207

Length = 434

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

 Score =  113 bits (286), Expect = 3e-29
 Identities = 73/229 (31%), Positives = 111/229 (48%), Gaps = 20/229 (8%)

Query: 43  DHVAE-NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--- 98
            H+ E  F D  L  +++  +   GF   + IQ  A+   + G DV  QAQ+GTGKT   
Sbjct: 3   THLTEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAF 62

Query: 99  --ATFSISILQQVDQNIKECQ--ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTI 154
             ATF   +     ++ K  Q  ALI+APTRELA QI      L     +      GG  
Sbjct: 63  LTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDG 122

Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
               ++ LE+G  +++GT GR+ D   +  ++   I++ VLDEAD M   GF   I  +F
Sbjct: 123 YDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLF 182

Query: 215 -------KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
                  + LN     +L SAT+   V +++ + M +P  + V+ E+ T
Sbjct: 183 RRMPPANQRLN-----MLFSATLSYRVRELAFEHMNNPEYVEVEPEQKT 226

Length = 423

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

 Score =  115 bits (288), Expect = 3e-29
 Identities = 73/220 (33%), Positives = 118/220 (53%), Gaps = 12/220 (5%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F   +L   LL G+ + GF + + IQ   +   + G DV  QAQ+GTGKT  F ++++ 
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 108 Q-------VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
           +        D+  ++ +ALILAPTRELA QI K  +  G  + +   A + G +  D  R
Sbjct: 70  RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLR-FALVYGGVDYDKQR 128

Query: 161 K-LEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL- 217
           + L+ G  V++ TPGR+ D + +   +S     + VLDEAD M   GF   I  + + + 
Sbjct: 129 ELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMP 188

Query: 218 -NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
                Q +L SAT+   VL+++ + M +P K++V+ E +T
Sbjct: 189 ERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETIT 228

Length = 572

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

 Score =  111 bits (279), Expect = 6e-28
 Identities = 65/220 (29%), Positives = 108/220 (49%), Gaps = 14/220 (6%)

Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF----S 102
            +F+     + +L+ +   GF +P+ IQ +     + G D+I  A++G+GKT  F     
Sbjct: 130 VSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAI 189

Query: 103 ISILQQV-----DQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
           + I  Q      D  I     L+LAPTRELA+QI++     G    +      GG   R 
Sbjct: 190 VHINAQPLLRYGDGPI----VLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRG 245

Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
            I  L  G ++++  PGR+ D +     + +++   VLDEAD ML  GF+ QI  +   +
Sbjct: 246 QIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQI 305

Query: 218 NNDVQVILLSATMPADVLDVSMKFMRD-PIKILVKKEELT 256
             D Q ++ SAT P +V  ++    ++ P+ + V   +LT
Sbjct: 306 RPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLT 345

Length = 545

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 51.6 bits (124), Expect = 2e-07
 Identities = 41/185 (22%), Positives = 80/185 (43%), Gaps = 39/185 (21%)

Query: 74  QQRAIIPCV-RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ 132
           QQ A+   +    +V+  A +G+GKT    ++IL  + +   +   + + P + LA++  
Sbjct: 36  QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKV--VYIVPLKALAEEKY 93

Query: 133 -----------KVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMIS 181
                      +V I+ GD+               D   +  A   V+V TP ++  +  
Sbjct: 94  EEFSRLEELGIRVGISTGDY---------------DLDDERLARYDVIVTTPEKLDSLTR 138

Query: 182 RGALSTKQIRMFVLDEADEMLS---RG-FKDQIYDVFKHLNNDVQVILLSATMP-----A 232
           +     +++ + V+DE   +L    RG   + I    + LN  ++++ LSAT+P     A
Sbjct: 139 KRPSWIEEVDLVVIDEI-HLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNAEEVA 197

Query: 233 DVLDV 237
           D L+ 
Sbjct: 198 DWLNA 202

Length = 766

>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 35/166 (21%), Positives = 66/166 (39%), Gaps = 29/166 (17%)

Query: 84  GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ-QIQKVVIALGDF- 141
           G +V+    +G+GKT +F + IL  + ++    +AL+L PT  LA  Q +++   + D  
Sbjct: 85  GRNVVVTTGTGSGKTESFLLPILDHLLRD-PSARALLLYPTNALANDQAERLRELISDLP 143

Query: 142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALS--------TKQIRMF 193
             V+     G T   +    +     +++  P    DM+    L          + ++  
Sbjct: 144 GKVTFGRYTGDTPPEERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNLKYL 199

Query: 194 VLDEAD----------EMLSRGFKDQIYDVFKHLNNDVQVILLSAT 229
           V+DE             +L R          +   + +Q+I  SAT
Sbjct: 200 VVDELHTYRGVQGSEVALLLRRLL----RRLRRYGSPLQIICTSAT 241

Length = 851

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	258
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
KOG0328|consensus	400		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0338|consensus	691		100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0346|consensus	569		100.0
PTZ00424	401	helicase 45; Provisional	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0343|consensus	758		100.0
KOG0345|consensus	567		100.0
KOG0342|consensus	543		100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0327|consensus	397		100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0348|consensus	708		100.0
KOG0339|consensus	731		100.0
KOG0326|consensus	459		100.0
KOG0335|consensus	482		100.0
KOG0336|consensus	629		100.0
KOG0341|consensus	610		100.0
KOG0340|consensus	442		100.0
KOG0333|consensus	673		100.0
KOG0337|consensus	529		100.0
KOG0329|consensus	387		100.0
KOG0334|consensus	997		100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.97
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.97
KOG4284|consensus	980		99.97
KOG0347|consensus	731		99.97
KOG0332|consensus	477		99.97
PRK00254	720	ski2-like helicase; Provisional	99.97
PRK02362	737	ski2-like helicase; Provisional	99.97
KOG0350|consensus	620		99.96
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.96
PRK01172	674	ski2-like helicase; Provisional	99.95
PRK13767	876	ATP-dependent helicase; Provisional	99.95
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.94
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.94
COG1205	851	Distinct helicase family with a unique C-terminal	99.93
PRK09401	1176	reverse gyrase; Reviewed	99.93
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.93
KOG0344|consensus	593		99.92
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.92
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.92
COG1204	766	Superfamily II helicase [General function predicti	99.92
PRK10689	1147	transcription-repair coupling factor; Provisional	99.92
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.91
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.91
PRK14701	1638	reverse gyrase; Provisional	99.9
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.9
COG1202	830	Superfamily II helicase, archaea-specific [General	99.9
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.9
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.9
KOG0952|consensus	1230		99.89
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.88
PHA02653	675	RNA helicase NPH-II; Provisional	99.88
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.87
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.87
PHA02558	501	uvsW UvsW helicase; Provisional	99.86
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.86
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.86
PRK13766	773	Hef nuclease; Provisional	99.85
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.85
KOG0354|consensus	746		99.85
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.84
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.82
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.82
KOG0947|consensus	1248		99.81
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.8
PRK05580	679	primosome assembly protein PriA; Validated	99.8
KOG0349|consensus	725		99.79
KOG0948|consensus	1041		99.78
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.78
KOG0951|consensus	1674		99.74
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.74
KOG0352|consensus	641		99.72
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.72
PRK09694	878	helicase Cas3; Provisional	99.7
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.7
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.7
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.7
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.7
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.69
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.69
KOG0351|consensus	941		99.68
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.68
KOG0353|consensus	695		99.67
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.66
KOG0920|consensus	924		99.64
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.64
KOG0950|consensus	1008		99.62
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.62
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.61
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.57
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.55
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.54
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.53
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.52
KOG0922|consensus	674		99.5
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.49
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.45
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.45
KOG0949|consensus	1330		99.44
COG4096	875	HsdR Type I site-specific restriction-modification	99.42
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.42
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.42
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.41
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.39
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.39
KOG0925|consensus	699		99.38
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.38
KOG0923|consensus	902		99.3
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.29
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.29
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.29
COG4889	1518	Predicted helicase [General function prediction on	99.23
PRK04914	956	ATP-dependent helicase HepA; Validated	99.21
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.2
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.19
KOG0385|consensus	971		99.18
KOG0926|consensus	1172		99.17
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.15
KOG0924|consensus	1042		99.11
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.09
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.09
KOG0387|consensus	923		99.07
KOG1123|consensus	776		99.06
KOG0390|consensus	776		99.05
KOG0951|consensus	1674		99.05
PRK14873	665	primosome assembly protein PriA; Provisional	99.03
KOG0384|consensus	1373		99.02
PRK15483	986	type III restriction-modification system StyLTI en	99.02
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.0
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.99
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.97
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.89
COG0610	962	Type I site-specific restriction-modification syst	98.87
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.87
KOG0921|consensus	1282		98.84
KOG0389|consensus	941		98.84
KOG4439|consensus	901		98.8
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.79
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.77
KOG0392|consensus	1549		98.76
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.76
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.73
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.71
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.69
KOG1000|consensus	689		98.58
KOG0391|consensus	1958		98.54
PRK10536	262	hypothetical protein; Provisional	98.53
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.53
KOG1002|consensus	791		98.53
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.52
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.51
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.5
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.49
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.49
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.47
KOG0952|consensus	1230		98.35
KOG1802|consensus	935		98.34
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.34
KOG4150|consensus	1034		98.26
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	98.2
PF13245	76	AAA_19: Part of AAA domain	98.19
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	98.15
PRK13889	988	conjugal transfer relaxase TraA; Provisional	98.15
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.1
KOG2340|consensus	698		98.09
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	98.07
KOG1803|consensus	649		98.06
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	98.04
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.04
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.04
PRK08181	269	transposase; Validated	98.0
PRK06526	254	transposase; Provisional	97.98
KOG0386|consensus	1157		97.94
KOG1132|consensus	945		97.91
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.9
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.9
KOG0388|consensus	1185		97.89
KOG0989|consensus	346		97.88
PRK04296	190	thymidine kinase; Provisional	97.83
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.78
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	97.78
KOG1015|consensus	1567		97.72
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.72
smart00382	148	AAA ATPases associated with a variety of cellular	97.71
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.7
PRK14974	336	cell division protein FtsY; Provisional	97.7
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.7
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.69
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.65
KOG1805|consensus	1100		97.62
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.62
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.53
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.51
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.51
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	97.47
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	97.41
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.4
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.4
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.39
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	97.39
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.39
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	97.38
KOG1001|consensus	674		97.37
KOG1016|consensus	1387		97.36
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.35
PF13173	128	AAA_14: AAA domain	97.32
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.31
PRK06893	229	DNA replication initiation factor; Validated	97.3
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.28
PRK06835	329	DNA replication protein DnaC; Validated	97.27
PRK05642	234	DNA replication initiation factor; Validated	97.26
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.25
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.25
CHL00181	287	cbbX CbbX; Provisional	97.24
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.24
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.23
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	97.23
PRK09183	259	transposase/IS protein; Provisional	97.19
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	97.19
PHA02533	534	17 large terminase protein; Provisional	97.18
PRK11054	684	helD DNA helicase IV; Provisional	97.18
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.16
PRK07952	244	DNA replication protein DnaC; Validated	97.15
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.14
KOG0298|consensus	1394		97.14
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.13
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.12
PRK08084	235	DNA replication initiation factor; Provisional	97.12
PRK08727	233	hypothetical protein; Validated	97.11
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.1
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.1
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.09
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.05
PLN03025	319	replication factor C subunit; Provisional	97.04
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.03
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.03
PRK06921	266	hypothetical protein; Provisional	97.01
KOG0953|consensus	700		97.01
KOG1131|consensus	755		97.01
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.01
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.0
PF00004	132	AAA: ATPase family associated with various cellula	96.98
PRK12402	337	replication factor C small subunit 2; Reviewed	96.98
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.95
PRK08116	268	hypothetical protein; Validated	96.95
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.95
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.94
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.93
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.92
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.91
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.91
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.91
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	96.91
PF05729	166	NACHT: NACHT domain	96.91
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.9
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.88
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.88
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.88
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.86
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.85
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.85
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.84
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.83
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	96.8
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.8
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.78
PRK12377	248	putative replication protein; Provisional	96.78
PHA02544	316	44 clamp loader, small subunit; Provisional	96.73
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.72
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	96.71
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.7
PRK12422	445	chromosomal replication initiation protein; Provis	96.69
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.68
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	96.67
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	96.66
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	96.66
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.65
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.64
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.61
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	96.6
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.59
KOG0991|consensus	333		96.58
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.56
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.56
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.56
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.56
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.52
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.51
PHA00729	226	NTP-binding motif containing protein	96.51
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	96.5
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.5
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.48
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.48
PRK13341	725	recombination factor protein RarA/unknown domain f	96.46
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	96.45
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.43
PRK11823	446	DNA repair protein RadA; Provisional	96.41
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.39
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.39
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.38
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.38
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	96.37
PTZ00293	211	thymidine kinase; Provisional	96.37
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.36
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.36
PRK13342	413	recombination factor protein RarA; Reviewed	96.36
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	96.35
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.33
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.32
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.31
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.31
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	96.3
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	96.3
COG4626	546	Phage terminase-like protein, large subunit [Gener	96.3
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.28
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.27
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	96.27
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	96.23
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.23
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.22
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.2
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	96.2
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.19
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.17
PHA03372	668	DNA packaging terminase subunit 1; Provisional	96.16
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.12
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.11
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.1
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	96.09
KOG0741|consensus	744		96.09
PRK06904	472	replicative DNA helicase; Validated	96.08
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.05
KOG2028|consensus	554		96.03
PRK08840	464	replicative DNA helicase; Provisional	96.02
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	96.02
KOG2004|consensus	906		96.01
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	96.01
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	96.0
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.99
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.96
PRK07004	460	replicative DNA helicase; Provisional	95.95
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	95.95
PRK10867	433	signal recognition particle protein; Provisional	95.93
PRK05298	652	excinuclease ABC subunit B; Provisional	95.93
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.91
KOG1513|consensus	1300		95.91
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.89
PRK06067	234	flagellar accessory protein FlaH; Validated	95.88
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	95.87
PRK04195	482	replication factor C large subunit; Provisional	95.87
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	95.84
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.82
PRK08006	471	replicative DNA helicase; Provisional	95.82
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.81
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.75
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	95.74
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	95.72
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	95.71
KOG0738|consensus	491		95.7
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.68
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.65
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.61
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	95.56
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.56
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	95.54
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	95.53
PRK06620	214	hypothetical protein; Validated	95.52
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.51
PRK09165	497	replicative DNA helicase; Provisional	95.5
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.49
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.48
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	95.45
PRK08939	306	primosomal protein DnaI; Reviewed	95.44
PRK09087	226	hypothetical protein; Validated	95.44
TIGR00959	428	ffh signal recognition particle protein. This mode	95.39
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	95.36
PRK04841	903	transcriptional regulator MalT; Provisional	95.36
PRK05748	448	replicative DNA helicase; Provisional	95.35
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	95.34
KOG2228|consensus	408		95.32
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.32
PRK08506	472	replicative DNA helicase; Provisional	95.3
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.25
TIGR00665	434	DnaB replicative DNA helicase. This model describe	95.23
PRK04328	249	hypothetical protein; Provisional	95.22
PRK05636	505	replicative DNA helicase; Provisional	95.21
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.2
PRK08760	476	replicative DNA helicase; Provisional	95.19
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	95.18
KOG0739|consensus	439		95.17
PRK13851	344	type IV secretion system protein VirB11; Provision	95.14
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.11
PRK10416	318	signal recognition particle-docking protein FtsY;	95.07
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.07
PRK05595	444	replicative DNA helicase; Provisional	95.02
PHA00012	361	I assembly protein	95.02
KOG0058|consensus	716		95.01
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	95.01
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	94.95
PHA00350	399	putative assembly protein	94.92
PRK07399	314	DNA polymerase III subunit delta'; Validated	94.88
COG3972	660	Superfamily I DNA and RNA helicases [General funct	94.87
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.86
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.86
KOG0742|consensus	630		94.85
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.81
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	94.8
TIGR00767	415	rho transcription termination factor Rho. Members	94.76
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.73
PRK10436	462	hypothetical protein; Provisional	94.73
KOG0732|consensus	1080		94.72
PRK08058	329	DNA polymerase III subunit delta'; Validated	94.72
PRK10865	857	protein disaggregation chaperone; Provisional	94.69
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	94.68
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.67
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	94.67
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	94.67
PRK06321	472	replicative DNA helicase; Provisional	94.65
KOG1133|consensus	821		94.64
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	94.63
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	94.57
PRK05973	237	replicative DNA helicase; Provisional	94.56
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	94.52
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	94.43
KOG0734|consensus	752		94.41
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.4
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.35
PRK09354	349	recA recombinase A; Provisional	94.31
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.31
KOG0737|consensus	386		94.3
cd01128	249	rho_factor Transcription termination factor rho is	94.29
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.28
PRK09376	416	rho transcription termination factor Rho; Provisio	94.26
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	94.26
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	94.2
COG1221	403	PspF Transcriptional regulators containing an AAA-	94.2
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	94.19
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.18
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	94.18
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	94.17
PF12846	304	AAA_10: AAA-like domain	94.15
TIGR02533	486	type_II_gspE general secretory pathway protein E.	94.13
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	94.12
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	94.05
PRK13897	606	type IV secretion system component VirD4; Provisio	93.88
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	93.86
KOG0730|consensus	693		93.86
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	93.86
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	93.84
cd00983	325	recA RecA is a bacterial enzyme which has roles in	93.8
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	93.8
KOG2227|consensus	529		93.78
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	93.72
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	93.71
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	93.7
CHL00095	821	clpC Clp protease ATP binding subunit	93.65
PRK13764	602	ATPase; Provisional	93.63
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	93.61
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	93.55
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	93.54
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	93.5
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.48
KOG0741|consensus	744		93.45
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	93.43
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	93.39
CHL00176	638	ftsH cell division protein; Validated	93.36
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	93.34
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	93.32
PF14516	331	AAA_35: AAA-like domain	93.31
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	93.26
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	93.18
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	93.12
KOG0344|consensus	593		93.08
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	93.04
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.03
PF13555	62	AAA_29: P-loop containing region of AAA domain	92.96
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	92.83
PRK13850	670	type IV secretion system protein VirD4; Provisiona	92.82
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	92.78
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	92.74
PRK13700	732	conjugal transfer protein TraD; Provisional	92.74
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.72
PRK07773	886	replicative DNA helicase; Validated	92.69
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	92.69
PRK10263	1355	DNA translocase FtsK; Provisional	92.64
COG4987	573	CydC ABC-type transport system involved in cytochr	92.63
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	92.62
PHA02542	473	41 41 helicase; Provisional	92.6

>KOG0330|consensus

Probab=100.00  E-value=8.9e-41  Score=277.65  Aligned_cols=211  Identities=34%  Similarity=0.536  Sum_probs=201.2

Q ss_pred             ccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          44 HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        44 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ..-.+|.++++.+.+.+++++.|+..|+++|++++|.++.|++++..+.||||||.+|++|+++.+....+.++++|++|
T Consensus        58 e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtP  137 (476)
T KOG0330|consen   58 ESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTP  137 (476)
T ss_pred             hhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecC
Confidence            34457999999999999999999999999999999999999999999999999999999999999999888889999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHh-cCCCCCCCccEEEEccchhhh
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMIS-RGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~-~~~~~~~~l~~lVvDE~h~~~  202 (258)
                      +|+|+.|+...+..+++.+++.+.++.||.....+...+...++|+|+||++|++++. .+.+++..++++|+||||+++
T Consensus       138 tRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlL  217 (476)
T KOG0330|consen  138 TRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLL  217 (476)
T ss_pred             cHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhh
Confidence            9999999999999999999999999999999998888888899999999999999998 588999999999999999999


Q ss_pred             ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCc
Q psy4698         203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       203 ~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~  254 (258)
                      +.+|...+..+++.+|...|.+++|||||..+..+.+..+.+|+.|.++..-
T Consensus       218 d~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky  269 (476)
T KOG0330|consen  218 DMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKY  269 (476)
T ss_pred             hhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchh
Confidence            9999999999999999999999999999999999999999999999886543

>KOG0331|consensus

Probab=100.00  E-value=5.9e-40  Score=287.35  Aligned_cols=205  Identities=35%  Similarity=0.614  Sum_probs=196.4

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh------ccccceEEEE
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ------NIKECQALIL  121 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~------~~~~~~~lil  121 (258)
                      .|..+++++.+...++..||..|+++|...||.++.|+|++..+.||||||++|++|++.++..      ...++++||+
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            7999999999999999999999999999999999999999999999999999999999999986      3457899999


Q ss_pred             eccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         122 APTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       122 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      +|||+||.|+...+..++....+.+.+++|+.....+.+.+.++++|+|+||++|.++++.+...+++++++|+||||+|
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrM  251 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRM  251 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCcHHHHHHHHHhC-CCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         202 LSRGFKDQIYDVFKHL-NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      ++.+|..++.+++..+ ++..|++++|||+|..++.++..|+.+|+.|.+-.
T Consensus       252 ldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~  303 (519)
T KOG0331|consen  252 LDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGN  303 (519)
T ss_pred             hccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecc
Confidence            9999999999999999 55568999999999999999999999999998853

>KOG0328|consensus

Probab=100.00  E-value=8e-40  Score=262.02  Aligned_cols=218  Identities=64%  Similarity=1.028  Sum_probs=209.3

Q ss_pred             cccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEE
Q psy4698          41 NWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALI  120 (258)
Q Consensus        41 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~li  120 (258)
                      ........|+++++.+++++.....||.+|+.+|+.|++.++.|+|+++.+..|+|||.+|-+.+++.+.-+.+..+++|
T Consensus        21 ~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~li  100 (400)
T KOG0328|consen   21 EKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALI  100 (400)
T ss_pred             cCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEE
Confidence            33456678999999999999999999999999999999999999999999999999999999999998888777789999


Q ss_pred             EeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchh
Q psy4698         121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE  200 (258)
Q Consensus       121 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  200 (258)
                      ++|||+|+.|..+++..++..+++.+..+.|+.+..+..+.+..|.+++.+||++++++++++.+.-+.++++|+||+|.
T Consensus       101 lsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDe  180 (400)
T KOG0328|consen  101 LSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADE  180 (400)
T ss_pred             ecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccCC
Q psy4698         201 MLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE  258 (258)
Q Consensus       201 ~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  258 (258)
                      |++.++..++..+++.+|+.+|++++|||+|.++.+..++|+.||+.|.+...++|+|
T Consensus       181 mL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlE  238 (400)
T KOG0328|consen  181 MLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLE  238 (400)
T ss_pred             HHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchh
Confidence            9999999999999999999999999999999999999999999999999999999986

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

Probab=100.00  E-value=1.3e-38  Score=287.39  Aligned_cols=209  Identities=43%  Similarity=0.687  Sum_probs=196.1

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-ccccce-EEEEecc
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-NIKECQ-ALILAPT  124 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~-~lil~P~  124 (258)
                      ..|.++++++.+++.+.+.||..|+++|..++|.++.|+|+++.++||||||.+|++|+++.+.. ...... +||++||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            67999999999999999999999999999999999999999999999999999999999999874 222222 9999999


Q ss_pred             HHHHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         125 RELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      |+||.|+++.+..++... ++.+..++|+.....+...+..+++|+|+||+++++++.++.+.+++++++|+||||+|++
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd  188 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLD  188 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhc
Confidence            999999999999999988 7899999999998888888888899999999999999999999999999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         204 RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       204 ~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      .+|...+..++..++.+.|++++|||+|..+..+.+.++++|+.|.+..+..
T Consensus       189 ~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~  240 (513)
T COG0513         189 MGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKL  240 (513)
T ss_pred             CCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccc
Confidence            9999999999999999999999999999999999999999999999985544

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=4.1e-38  Score=286.34  Aligned_cols=216  Identities=28%  Similarity=0.494  Sum_probs=197.4

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-----c
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-----I  113 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-----~  113 (258)
                      ..+.++...+|+++++++.+.+.|.+.||..|+++|.+++|.++.|+|+++++|||||||++|++|++..+...     .
T Consensus       122 g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~  201 (545)
T PTZ00110        122 GENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYG  201 (545)
T ss_pred             CCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCC
Confidence            34556677899999999999999999999999999999999999999999999999999999999999887542     2


Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF  193 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~l  193 (258)
                      .++++||++||++|+.|+.+.++.++...++.+...+++.....+...+..+++|+|+||++|.+++..+...++++++|
T Consensus       202 ~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~l  281 (545)
T PTZ00110        202 DGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYL  281 (545)
T ss_pred             CCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEE
Confidence            35789999999999999999999999888888889999988888888888899999999999999999988889999999


Q ss_pred             EEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcC-CCeEEEecCCc
Q psy4698         194 VLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMR-DPIKILVKKEE  254 (258)
Q Consensus       194 VvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~v~~~~~~  254 (258)
                      |+||||++++.+|...+..++..++++.|++++|||+|++++.+.+.++. +|+.+.+...+
T Consensus       282 ViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~  343 (545)
T PTZ00110        282 VLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLD  343 (545)
T ss_pred             EeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCc
Confidence            99999999999999999999999999999999999999999999999886 68888775544

>KOG0338|consensus

Probab=100.00  E-value=4e-39  Score=275.67  Aligned_cols=210  Identities=33%  Similarity=0.573  Sum_probs=199.2

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc---cceEEEEe
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK---ECQALILA  122 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~---~~~~lil~  122 (258)
                      ..+|.+++++-.+++.+...||..|+|+|..++|..+-|++++.++.||||||.+|++|+++++....+   -.|+||+|
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~  259 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLV  259 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEe
Confidence            568999999999999999999999999999999999999999999999999999999999999976533   35899999


Q ss_pred             ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccchhh
Q psy4698         123 PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       123 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~~  201 (258)
                      |||+|+.|++.+.++++.++++.++.+.||...+.+-..++..+||+|+||++|.+++++ -.|+++++..+|+||||+|
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRM  339 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRM  339 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHH
Confidence            999999999999999999999999999999999999889999999999999999999987 4688999999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      ++.+|..++..+++..+++.|.++|||||+.++++++...++.|+.|.+++..-
T Consensus       340 LeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~  393 (691)
T KOG0338|consen  340 LEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKD  393 (691)
T ss_pred             HHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccc
Confidence            999999999999999999999999999999999999999999999999987654

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

Probab=100.00  E-value=1.7e-37  Score=281.32  Aligned_cols=214  Identities=30%  Similarity=0.544  Sum_probs=195.1

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-------
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-------  111 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-------  111 (258)
                      +.++++...+|+++++++.+.+.|.+.||..|+++|.++++.++.|+|+++++|||||||++|++|++..+..       
T Consensus       113 g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~  192 (518)
T PLN00206        113 GEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPS  192 (518)
T ss_pred             CCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcccccc
Confidence            4566677889999999999999999999999999999999999999999999999999999999999987753       


Q ss_pred             ccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCcc
Q psy4698         112 NIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIR  191 (258)
Q Consensus       112 ~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~  191 (258)
                      ...++++||++||++|+.|+.+.++.++...++.+....|+.....+...+..+++|+|+||++|.+++.++.+.+++++
T Consensus       193 ~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~  272 (518)
T PLN00206        193 EQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVS  272 (518)
T ss_pred             ccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchhee
Confidence            22457899999999999999999999988888888888888888777778888899999999999999999888999999


Q ss_pred             EEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         192 MFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       192 ~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      +||+||||+|++.+|...+..++..++ +.|++++|||++++++.+.+.++.++..|.+...
T Consensus       273 ~lViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~  333 (518)
T PLN00206        273 VLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNP  333 (518)
T ss_pred             EEEeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999999999999999999999998884 6899999999999999999999999998887543

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.3e-37  Score=273.90  Aligned_cols=208  Identities=31%  Similarity=0.486  Sum_probs=190.7

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-------cccceEE
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-------IKECQAL  119 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-------~~~~~~l  119 (258)
                      ..|+++++++.+.+.|.+.||..|+++|.+++|.++.|+|++++||||||||++|++|+++.+...       ..++++|
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~l   87 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRAL   87 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            579999999999999999999999999999999999999999999999999999999999988642       2346899


Q ss_pred             EEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       120 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                      |++|+++|+.|+++.+..++...++.+..++|+.....+...+..+++|+|+||+++.+++..+.+.++++++||+||||
T Consensus        88 il~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad  167 (423)
T PRK04837         88 IMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEAD  167 (423)
T ss_pred             EECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHH
Confidence            99999999999999999999988999999999888777777778889999999999999999988999999999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCC--CccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCc
Q psy4698         200 EMLSRGFKDQIYDVFKHLNN--DVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~  254 (258)
                      ++++.++...+..++..++.  ..+.+++|||++..+..+...++.+|..+.+.+..
T Consensus       168 ~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~  224 (423)
T PRK04837        168 RMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQ  224 (423)
T ss_pred             HHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCC
Confidence            99999999999999999874  45789999999999999999999999999886554

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=2.2e-37  Score=277.84  Aligned_cols=207  Identities=37%  Similarity=0.650  Sum_probs=193.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .+|+++++++.+.+.+.+.||..|+++|.++++.++.|+|+++++|||||||++|++|+++.+......++++|++||++
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptre   83 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE   83 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHH
Confidence            47999999999999999999999999999999999999999999999999999999999999977666678999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      |+.|+.+.++.++... ++.+..++|+.....+...+..+++|+|+||+++.+++.++.+.++++++||+||||++++.+
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g  163 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG  163 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcC
Confidence            9999999999887654 688888999988888888888889999999999999999988899999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      +...+..++..++...|++++|||+|+.+..+.+.++.+|..+.+...
T Consensus       164 ~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~  211 (460)
T PRK11776        164 FQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVEST  211 (460)
T ss_pred             cHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcC
Confidence            999999999999999999999999999999999999999999988654

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=2.1e-37  Score=284.57  Aligned_cols=209  Identities=38%  Similarity=0.647  Sum_probs=194.3

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..|.++++++.+++.|.+.||..|+++|.++++.++.|+++++.||||+|||++|.+|+++.+.....++++||++||++
T Consensus         6 ~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTre   85 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRE   85 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHH
Confidence            46999999999999999999999999999999999999999999999999999999999999877666679999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      |+.|+++.++.+.... ++.+..++++.....+...+..+++|+|+||+++++++.++.+.++++++||+||||++++.+
T Consensus        86 La~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~g  165 (629)
T PRK11634         86 LAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMG  165 (629)
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcc
Confidence            9999999999887654 688888899988888888888889999999999999999988999999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      +...+..++..++...|++++|||+|..+..+.+.|+.+|..|.+.....
T Consensus       166 f~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~  215 (629)
T PRK11634        166 FIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVT  215 (629)
T ss_pred             cHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccc
Confidence            99999999999999999999999999999999999999999998866544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=3.8e-37  Score=275.58  Aligned_cols=207  Identities=37%  Similarity=0.637  Sum_probs=190.8

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc------ccceEEEE
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI------KECQALIL  121 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~------~~~~~lil  121 (258)
                      +|+++++++.+.+.|.+.||..|+++|.++++.++.|+|+++++|||||||++|++|+++.+....      ...++||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            588999999999999999999999999999999999999999999999999999999999886532      23589999


Q ss_pred             eccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         122 APTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       122 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      +||++|+.|+.+.++.+....++.+..++|+.....+...+..+++|+|+||++|++++....+.++++++||+||||++
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~l  161 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRM  161 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHH
Confidence            99999999999999999888888888889998877777777788999999999999999988889999999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCc
Q psy4698         202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~  254 (258)
                      ++.++...+..++..++...|++++|||+++++..+...++.+|..+.+....
T Consensus       162 l~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~  214 (456)
T PRK10590        162 LDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRN  214 (456)
T ss_pred             hccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEeccc
Confidence            99999999999999999999999999999999999999999999988775543

>KOG0346|consensus

Probab=100.00  E-value=9e-38  Score=263.25  Aligned_cols=210  Identities=32%  Similarity=0.500  Sum_probs=187.8

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc------cccceEEE
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN------IKECQALI  120 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~------~~~~~~li  120 (258)
                      .+|+++++++.+++++.+.|+..|+-+|..++|.+++|+|++..|.||||||.+|++|+++.+...      ..++.++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            579999999999999999999999999999999999999999999999999999999999998653      34678999


Q ss_pred             EeccHHHHHHHHHHHHHhcCCCC--ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC-CCCCCccEEEEcc
Q psy4698         121 LAPTRELAQQIQKVVIALGDFMS--VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA-LSTKQIRMFVLDE  197 (258)
Q Consensus       121 l~P~~~l~~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~-~~~~~l~~lVvDE  197 (258)
                      ++||++||.|.+.++.++.....  +++..+.+..+.......+...++|+|+||++++.++..+. ..+..++++|+||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDE  178 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDE  178 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEech
Confidence            99999999999999988765443  34444444444445556777789999999999999998876 6788999999999


Q ss_pred             chhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         198 ADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       198 ~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      ||.++..++...+.++.+.+|+.+|.++||||++.+++.+.+.|+++|+++...++++.
T Consensus       179 ADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~  237 (569)
T KOG0346|consen  179 ADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELP  237 (569)
T ss_pred             hhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCC
Confidence            99999999999999999999999999999999999999999999999999999888874

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=2.3e-36  Score=267.03  Aligned_cols=220  Identities=67%  Similarity=1.093  Sum_probs=198.5

Q ss_pred             cccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccc
Q psy4698          37 LIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKEC  116 (258)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~  116 (258)
                      ..+.+.......|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||||||++|+++++..+.....+.
T Consensus        18 ~~~~~~~~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~   97 (401)
T PTZ00424         18 TIESNYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNAC   97 (401)
T ss_pred             ccccccccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCc
Confidence            33444445567899999999999999999999999999999999999999999999999999999999999887655667


Q ss_pred             eEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEc
Q psy4698         117 QALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLD  196 (258)
Q Consensus       117 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvD  196 (258)
                      ++||++|+++|+.|+.+.+..++...+..+..+.|+.........+..+++|+|+||+++++++.++...++++++||+|
T Consensus        98 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViD  177 (401)
T PTZ00424         98 QALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILD  177 (401)
T ss_pred             eEEEECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEe
Confidence            89999999999999999999998888888888888887777777777889999999999999999888889999999999


Q ss_pred             cchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         197 EADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       197 E~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      |+|++.+.++...+..+++.++++.|++++|||+|+++..+...++.+|..+.+...+.+
T Consensus       178 Eah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (401)
T PTZ00424        178 EADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELT  237 (401)
T ss_pred             cHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcc
Confidence            999999989999999999999999999999999999999999999999998887765544

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=3.9e-36  Score=241.84  Aligned_cols=201  Identities=52%  Similarity=0.843  Sum_probs=185.8

Q ss_pred             cCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc--cccceEEEEeccHH
Q psy4698          49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN--IKECQALILAPTRE  126 (258)
Q Consensus        49 ~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~--~~~~~~lil~P~~~  126 (258)
                      |+++++++.+.+.|.+.|+..|+++|.++++.+.+|+++++.+|||+|||++|+++++..+...  ..+++++|++|+++
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~   80 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRE   80 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHH
Confidence            6889999999999999999999999999999999999999999999999999999999998876  56679999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      |+.|+...++.+....+..+..+.|+...........++++|+|+||+.+.+++.++...+++++++|+||+|.+.+.++
T Consensus        81 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~  160 (203)
T cd00268          81 LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGF  160 (203)
T ss_pred             HHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccCh
Confidence            99999999999988778888888888877766666666799999999999999988888889999999999999988888


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEE
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKIL  249 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~  249 (258)
                      ...+..+++.++..+|++++|||+++.+.++++.++++|++|.
T Consensus       161 ~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~  203 (203)
T cd00268         161 EDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRIL  203 (203)
T ss_pred             HHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEeC
Confidence            9999999999999999999999999999999999999999873

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.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.1e-36  Score=276.23  Aligned_cols=210  Identities=33%  Similarity=0.542  Sum_probs=190.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-------cccceEE
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-------IKECQAL  119 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-------~~~~~~l  119 (258)
                      .+|+++++++.+++.|.+.||..|+++|.+++|.++.|+|+++.+|||||||++|++|+++.+...       ...+++|
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            369999999999999999999999999999999999999999999999999999999999988542       1246899


Q ss_pred             EEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccc
Q psy4698         120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEA  198 (258)
Q Consensus       120 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~  198 (258)
                      |++||++|+.|+++.+..++...++.+..++|+.....+...+..+++|+|+||++|++++... .+.++.+++||+|||
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEA  168 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEA  168 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCH
Confidence            9999999999999999999999999999999998887777777778999999999999998764 467889999999999


Q ss_pred             hhhhccCcHHHHHHHHHhCCC--CccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         199 DEMLSRGFKDQIYDVFKHLNN--DVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       199 h~~~~~~~~~~~~~~~~~l~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      |++++.++...+..+++.++.  ..|++++|||++..+..+...++.+|..+.+.....+
T Consensus       169 h~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~  228 (572)
T PRK04537        169 DRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETIT  228 (572)
T ss_pred             HHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEecccccc
Confidence            999999999999999999986  6899999999999999999999999988877665543

>KOG0343|consensus

Probab=100.00  E-value=4.4e-37  Score=265.35  Aligned_cols=206  Identities=33%  Similarity=0.546  Sum_probs=193.4

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc----ccceEEEEe
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI----KECQALILA  122 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~----~~~~~lil~  122 (258)
                      ..|++++++..+.+.|+..+|..++.+|+.++|..++|++++-.+.||||||++++.|+++.+...+    .|.-+|||+
T Consensus        69 ~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIIS  148 (758)
T KOG0343|consen   69 KKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIIS  148 (758)
T ss_pred             hhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEec
Confidence            4799999999999999999999999999999999999999999999999999999999999998753    345699999


Q ss_pred             ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccchhh
Q psy4698         123 PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       123 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h~~  201 (258)
                      |||+||.|.+.++.+.++..++......||.....+...+.+ ++|+||||++|++++..+ .++.+++.++|+||||++
T Consensus       149 PTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~~-mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~  227 (758)
T KOG0343|consen  149 PTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERISQ-MNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRM  227 (758)
T ss_pred             chHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhhc-CCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHH
Confidence            999999999999999999999999999999998888777766 899999999999999774 578899999999999999


Q ss_pred             hccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      ++.+|...+..++..+|+..|++++|||-++.++++++..++||++|.+...
T Consensus       228 LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~  279 (758)
T KOG0343|consen  228 LDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHEN  279 (758)
T ss_pred             HHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEecc
Confidence            9999999999999999999999999999999999999999999999999743

>KOG0345|consensus

Probab=100.00  E-value=3e-36  Score=255.93  Aligned_cols=207  Identities=33%  Similarity=0.598  Sum_probs=185.7

Q ss_pred             CcCCCC--CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc-----cceEEE
Q psy4698          48 NFDDME--LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK-----ECQALI  120 (258)
Q Consensus        48 ~~~~~~--~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~-----~~~~li  120 (258)
                      .|++++  +++++++.+.+.||..+||+|..++|.++.++|+++.++||||||++|++|+++.+.....     ...++|
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalI   84 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALI   84 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEE
Confidence            466665  5699999999999999999999999999999999999999999999999999999954321     236999


Q ss_pred             EeccHHHHHHHHHHHHHhcCC-CCceEEEEECCcchHHHHHHHhc-CCcEEEeChHHHHHHHhcC--CCCCCCccEEEEc
Q psy4698         121 LAPTRELAQQIQKVVIALGDF-MSVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRG--ALSTKQIRMFVLD  196 (258)
Q Consensus       121 l~P~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~Ilv~Tp~~l~~~l~~~--~~~~~~l~~lVvD  196 (258)
                      |+|||+|+.|+.+++..|... .++++.++.||.........+.+ +++|+||||++|++++++.  .+++.+++++|+|
T Consensus        85 IsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLD  164 (567)
T KOG0345|consen   85 ISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLD  164 (567)
T ss_pred             ecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEec
Confidence            999999999999999998765 67888999999888877766654 5889999999999999884  4556699999999


Q ss_pred             cchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCc
Q psy4698         197 EADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       197 E~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~  254 (258)
                      |||++++.+|...+..++..+|+..++=++|||...++.++.+..++||+.|.|..++
T Consensus       165 EADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~  222 (567)
T KOG0345|consen  165 EADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKS  222 (567)
T ss_pred             chHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccc
Confidence            9999999999999999999999999999999999999999999999999999996555

>KOG0342|consensus

Probab=100.00  E-value=2.7e-36  Score=257.49  Aligned_cols=210  Identities=32%  Similarity=0.525  Sum_probs=194.1

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc----cccceEEEE
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----IKECQALIL  121 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~----~~~~~~lil  121 (258)
                      ...|++..+++...+++..+||..++++|...++.++.|+|+++.|-||+|||+++++|+++.+...    .++..++|+
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi  160 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLII  160 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEe
Confidence            3468899999999999999999999999999999999999999999999999999999999998764    345679999


Q ss_pred             eccHHHHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccch
Q psy4698         122 APTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEAD  199 (258)
Q Consensus       122 ~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h  199 (258)
                      ||||+|+.|.+.+++.+.... +..+....|+.....+...+..+++|+|+||++|++++++ ..+...+++++|+||||
T Consensus       161 ~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEAD  240 (543)
T KOG0342|consen  161 CPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEAD  240 (543)
T ss_pred             cccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecch
Confidence            999999999999999988877 8899999999999988888888999999999999999988 45666788999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcC-CCeEEEecCCcc
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMR-DPIKILVKKEEL  255 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~-~~~~v~~~~~~~  255 (258)
                      ++++.+|...+..++..+++..|.+++|||.|.+++++++.-++ +|++|.++++.-
T Consensus       241 rlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~  297 (543)
T KOG0342|consen  241 RLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGE  297 (543)
T ss_pred             hhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCC
Confidence            99999999999999999999999999999999999999999877 699999977653

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=7.4e-35  Score=262.30  Aligned_cols=210  Identities=36%  Similarity=0.573  Sum_probs=187.5

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc-------ccceE
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI-------KECQA  118 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~-------~~~~~  118 (258)
                      ...|.++++++.+.+.|.+.|+..++++|.++++.+..|+|+++.+|||||||++|++|+++.+....       ...++
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~a  165 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRA  165 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceE
Confidence            34688999999999999999999999999999999999999999999999999999999999886542       14689


Q ss_pred             EEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEcc
Q psy4698         119 LILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDE  197 (258)
Q Consensus       119 lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE  197 (258)
                      ||++||++|+.|+++.++.+....++.+..+.|+.....+...+. ..++|+|+||++|+.++.+....++++++|||||
T Consensus       166 Lil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDE  245 (475)
T PRK01297        166 LIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDE  245 (475)
T ss_pred             EEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEech
Confidence            999999999999999999998888888888888876655555544 4589999999999999988888899999999999


Q ss_pred             chhhhccCcHHHHHHHHHhCCC--CccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         198 ADEMLSRGFKDQIYDVFKHLNN--DVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       198 ~h~~~~~~~~~~~~~~~~~l~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      +|++.+.++...+..+++.++.  +.|++++|||++.++.++.+.++.+|.++.+...+.
T Consensus       246 ah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  305 (475)
T PRK01297        246 ADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV  305 (475)
T ss_pred             HHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcC
Confidence            9999999999999999998864  579999999999999999999999999988765543

>KOG0327|consensus

Probab=100.00  E-value=9.8e-37  Score=253.58  Aligned_cols=232  Identities=74%  Similarity=1.154  Sum_probs=217.9

Q ss_pred             CCCCCCcccCcccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHH
Q psy4698          27 NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISIL  106 (258)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l  106 (258)
                      .+|.++..+..++++|.....+|+++++.+.+++.++..||.+|+++|+.|+..+..|.|+.+.+.+|+|||.++..+++
T Consensus         6 ~g~~~~e~~~~iesn~~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iL   85 (397)
T KOG0327|consen    6 NGPDGMEPEGVIESNWNEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISIL   85 (397)
T ss_pred             CCCcccCccccccccHHHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHH
Confidence            46666777999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchH-HHHHHHhcCCcEEEeChHHHHHHHhcCCC
Q psy4698         107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVR-DDIRKLEAGAQVVVGTPGRVFDMISRGAL  185 (258)
Q Consensus       107 ~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~  185 (258)
                      +.+......+++++++|+++|+.|...+...++...++.+..+.|+.... +.......+..|+++||++++.++..+.+
T Consensus        86 q~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l  165 (397)
T KOG0327|consen   86 QQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSL  165 (397)
T ss_pred             hhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccc
Confidence            99988878889999999999999999999999999999999999888776 44444555689999999999999999989


Q ss_pred             CCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccCC
Q psy4698         186 STKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE  258 (258)
Q Consensus       186 ~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  258 (258)
                      ..+.++++|+||+|.++..++..++..+++.+|++.|++++|||+|.++....+.|+++|+.|.+.++++|+|
T Consensus       166 ~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~  238 (397)
T KOG0327|consen  166 STDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLE  238 (397)
T ss_pred             cccceeEEeecchHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhh
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999975

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=2.9e-35  Score=262.44  Aligned_cols=206  Identities=32%  Similarity=0.532  Sum_probs=189.1

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc----cccceEEEEec
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----IKECQALILAP  123 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~----~~~~~~lil~P  123 (258)
                      +|+++++++.+.+.|.+.||..|+++|.++++.++.|+|+++++|||+|||++|++|+++.+...    ..+.++||++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~P   81 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTP   81 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECC
Confidence            58999999999999999999999999999999999999999999999999999999999988542    23468999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      +++|+.|+++.+..++...++.+..+.|+.........+..+++|+|+||++|++++..+.+.+.++++||+||||++++
T Consensus        82 t~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~  161 (434)
T PRK11192         82 TRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLD  161 (434)
T ss_pred             cHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhC
Confidence            99999999999999999999999999999887777777777899999999999999999988999999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCccEEEEEeeCCh-hHHHHHHHhcCCCeEEEecCC
Q psy4698         204 RGFKDQIYDVFKHLNNDVQVILLSATMPA-DVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       204 ~~~~~~~~~~~~~l~~~~~~i~~SAT~~~-~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      .++...+..+...++...|++++|||++. .+.++.+.++.+|+.+.+...
T Consensus       162 ~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~  212 (434)
T PRK11192        162 MGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPS  212 (434)
T ss_pred             CCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCC
Confidence            99999999999999888999999999985 588999999999999887543

>KOG0348|consensus

Probab=100.00  E-value=1.6e-36  Score=261.08  Aligned_cols=204  Identities=30%  Similarity=0.504  Sum_probs=184.2

Q ss_pred             cCcCCCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc------cccceEE
Q psy4698          47 ENFDDMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN------IKECQAL  119 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~------~~~~~~l  119 (258)
                      ..|.++++++.+...|.. +++..|+.+|.+++|.+++|+|++|.++||||||++|++|+++.+..-      ..|+-++
T Consensus       136 ~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~AL  215 (708)
T KOG0348|consen  136 AAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYAL  215 (708)
T ss_pred             ccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEE
Confidence            468999999999999984 799999999999999999999999999999999999999999998653      3356799


Q ss_pred             EEeccHHHHHHHHHHHHHhcCCCCceE-EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEcc
Q psy4698         120 ILAPTRELAQQIQKVVIALGDFMSVSC-HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDE  197 (258)
Q Consensus       120 il~P~~~l~~q~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE  197 (258)
                      |++|||+||.|.++.+.++.+..-..+ +.+.||.....+...++.|++|+|+||++|.+++.+ ..+.+++++|+|+||
T Consensus       216 VivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDE  295 (708)
T KOG0348|consen  216 VIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDE  295 (708)
T ss_pred             EEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecc
Confidence            999999999999999999887655444 668899888888899999999999999999999987 567889999999999


Q ss_pred             chhhhccCcHHHHHHHHHhCC-------------CCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         198 ADEMLSRGFKDQIYDVFKHLN-------------NDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       198 ~h~~~~~~~~~~~~~~~~~l~-------------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      +|++++-+|...+..++..+.             +..|.+++|||+...+.++....+.||+.|..
T Consensus       296 aDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~l  361 (708)
T KOG0348|consen  296 ADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISL  361 (708)
T ss_pred             hhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeec
Confidence            999999999999999988772             13588999999999999999999999999983

>KOG0339|consensus

Probab=100.00  E-value=8.3e-36  Score=255.27  Aligned_cols=215  Identities=30%  Similarity=0.507  Sum_probs=203.5

Q ss_pred             cccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc----
Q psy4698          37 LIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----  112 (258)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~----  112 (258)
                      ..+.+.++....|+.++++..+....++..|..|+++|.+++|..+.|++++=.+.||||||-+|+.|++.++...    
T Consensus       213 v~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~  292 (731)
T KOG0339|consen  213 VSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELK  292 (731)
T ss_pred             eccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhc
Confidence            3445667777899999999999999999999999999999999999999999999999999999999999888543    


Q ss_pred             -cccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCcc
Q psy4698         113 -IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIR  191 (258)
Q Consensus       113 -~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~  191 (258)
                       +.++-.+|++||++|+.|++.++++|++.+++++.+++|+....++...+..++.|+||||++|+++++-+..++.+++
T Consensus       293 ~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS  372 (731)
T KOG0339|consen  293 PGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVS  372 (731)
T ss_pred             CCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeee
Confidence             5678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         192 MFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       192 ~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +||+||+++|++.+|..++..|...++++.|.|++|||++..++.+++.++.+|+.|..-
T Consensus       373 ~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg  432 (731)
T KOG0339|consen  373 YLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQG  432 (731)
T ss_pred             EEEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEe
Confidence            999999999999999999999999999999999999999999999999999999998663

>KOG0326|consensus

Probab=100.00  E-value=2.2e-35  Score=240.18  Aligned_cols=206  Identities=38%  Similarity=0.642  Sum_probs=198.8

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..|+++.+...++....+.||.+|+|+|.+++|.++.|+|+++.+..|+|||.+|.+|+++.+.......+++|++|+|+
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtre  164 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRE  164 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecch
Confidence            46999999999999999999999999999999999999999999999999999999999999999988899999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      ||.|....|+++++.+++.+....|+.+.++..-.+..+.+++|+||++++++...+--.++++.++|+||||.+++..|
T Consensus       165 lALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~F  244 (459)
T KOG0326|consen  165 LALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDF  244 (459)
T ss_pred             hhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchhh
Confidence            99999999999999999999999999999999888999999999999999999999988999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      ...+..++..+|++.|++++|||+|-.++.|.+.++++|..|..-+
T Consensus       245 ~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~  290 (459)
T KOG0326|consen  245 QPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLME  290 (459)
T ss_pred             hhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhh
Confidence            9999999999999999999999999999999999999999997644

>KOG0335|consensus

Probab=100.00  E-value=1.6e-34  Score=249.52  Aligned_cols=212  Identities=35%  Similarity=0.527  Sum_probs=193.4

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc----
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK----  114 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~----  114 (258)
                      ..+.++....|.+..+.+.+..+++..++..|+|+|+.++|.+..|++++++|+||||||.+|++|++..+...+.    
T Consensus        66 G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~  145 (482)
T KOG0335|consen   66 GRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRG  145 (482)
T ss_pred             CCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCc
Confidence            3444555568888888999999999999999999999999999999999999999999999999999999876522    


Q ss_pred             ------cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCC
Q psy4698         115 ------ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTK  188 (258)
Q Consensus       115 ------~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~  188 (258)
                            .++++|++||++|+.|++++++++.-...+.....+++.....+.+.+.++|+|+|+||++|.+++..+.+.++
T Consensus       146 ~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~  225 (482)
T KOG0335|consen  146 ESGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLD  225 (482)
T ss_pred             ccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehh
Confidence                  47999999999999999999999998889999999999999999999999999999999999999999999999


Q ss_pred             CccEEEEccchhhhc-cCcHHHHHHHHHhCCC----CccEEEEEeeCChhHHHHHHHhcCC-CeEEEe
Q psy4698         189 QIRMFVLDEADEMLS-RGFKDQIYDVFKHLNN----DVQVILLSATMPADVLDVSMKFMRD-PIKILV  250 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~-~~~~~~~~~~~~~l~~----~~~~i~~SAT~~~~~~~~~~~~~~~-~~~v~~  250 (258)
                      +++++|+||||+|++ .+|..++..++.....    ..|.++||||+|.+++.++..|+.+ -+.+.|
T Consensus       226 ~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV  293 (482)
T KOG0335|consen  226 NCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAV  293 (482)
T ss_pred             hCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEE
Confidence            999999999999999 8999999999988753    6799999999999999999999997 555555

>KOG0336|consensus

Probab=100.00  E-value=6.5e-34  Score=238.36  Aligned_cols=212  Identities=32%  Similarity=0.520  Sum_probs=190.2

Q ss_pred             cccccCcCC-CCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh------cccc
Q psy4698          43 DHVAENFDD-MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ------NIKE  115 (258)
Q Consensus        43 ~~~~~~~~~-~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~------~~~~  115 (258)
                      +++.-+|++ +.-.+.+.+.+++.||.+|+|+|.++||.+++|.+++.++.||+|||++||+|.+.++..      ...+
T Consensus       215 PnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~  294 (629)
T KOG0336|consen  215 PNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNG  294 (629)
T ss_pred             CCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCC
Confidence            333345654 356789999999999999999999999999999999999999999999999998877643      2456


Q ss_pred             ceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEE
Q psy4698         116 CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVL  195 (258)
Q Consensus       116 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVv  195 (258)
                      +.+++++|+++|+.|+.-.+++. ++.++...+++|+.+...+...++.+.+|+|+||++|.++...+.+++..+.++|+
T Consensus       295 p~~lvl~ptreLalqie~e~~ky-syng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVl  373 (629)
T KOG0336|consen  295 PGVLVLTPTRELALQIEGEVKKY-SYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVL  373 (629)
T ss_pred             CceEEEeccHHHHHHHHhHHhHh-hhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEe
Confidence            78999999999999998877665 45577888899999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         196 DEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       196 DE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      ||||+|++.+|..++.+++-.++++.|+++.|||+|..+.+++..|+++|++|.+-.=++
T Consensus       374 DEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL  433 (629)
T KOG0336|consen  374 DEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDL  433 (629)
T ss_pred             cchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccce
Confidence            999999999999999999999999999999999999999999999999999998755444

>KOG0341|consensus

Probab=100.00  E-value=1.3e-34  Score=241.22  Aligned_cols=212  Identities=30%  Similarity=0.539  Sum_probs=195.6

Q ss_pred             ccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh--------
Q psy4698          40 TNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ--------  111 (258)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~--------  111 (258)
                      ...++.+.+|.++.++..+++.|++.|+.+|+|+|.+-+|.+++|++.+-.+-||||||++|.+|++.....        
T Consensus       163 d~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~  242 (610)
T KOG0341|consen  163 DDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFA  242 (610)
T ss_pred             CCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccc
Confidence            455677889999999999999999999999999999999999999999999999999999999999876543        


Q ss_pred             ccccceEEEEeccHHHHHHHHHHHHHhcCC------CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC
Q psy4698         112 NIKECQALILAPTRELAQQIQKVVIALGDF------MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL  185 (258)
Q Consensus       112 ~~~~~~~lil~P~~~l~~q~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~  185 (258)
                      .+.++-.+|+||+|+|+.|.+..+..+...      ..++...+.|+...+.+...++.|.+|+|+||++|.+++..+.+
T Consensus       243 ~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~  322 (610)
T KOG0341|consen  243 RGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIM  322 (610)
T ss_pred             cCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhc
Confidence            355788999999999999999988776532      24677888999999999999999999999999999999999999


Q ss_pred             CCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         186 STKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       186 ~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      ++.-++++++||||+|.+.+|...+..++..+....|.+++|||||+.++.|++.-+-.|+.|.|-
T Consensus       323 sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVG  388 (610)
T KOG0341|consen  323 SLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVG  388 (610)
T ss_pred             cHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecc
Confidence            999999999999999999999999999999999999999999999999999999999999999884

>KOG0340|consensus

Probab=100.00  E-value=2.3e-33  Score=231.07  Aligned_cols=215  Identities=33%  Similarity=0.466  Sum_probs=196.8

Q ss_pred             ccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          44 HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        44 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .....|+.+|+++++.+.++..|+..|+|+|..++|.++.|+|++=+|.||||||.++.+|+++++.....+.-++|++|
T Consensus         4 ~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP   83 (442)
T KOG0340|consen    4 KTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP   83 (442)
T ss_pred             cccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999888889999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC----CCCCCCccEEEEccch
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG----ALSTKQIRMFVLDEAD  199 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~----~~~~~~l~~lVvDE~h  199 (258)
                      |++|+.|+.+.+..+++.+++++...+|+...-.+...+...++++|+||+++..++..+    ...+++++++|+||||
T Consensus        84 TrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEAD  163 (442)
T KOG0340|consen   84 TRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEAD  163 (442)
T ss_pred             hHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchh
Confidence            999999999999999999999999999999888888888888999999999999998775    3457889999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCC--CeEEEecCCcccCC
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRD--PIKILVKKEELTLE  258 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~--~~~v~~~~~~~~~~  258 (258)
                      ++++..|...+..+.+.+|...|.+++|||+++.++++..-..+.  +..+.+.++..|+|
T Consensus       164 rvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstve  224 (442)
T KOG0340|consen  164 RVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVE  224 (442)
T ss_pred             hhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchh
Confidence            999999999999999999999999999999999998888766664  66677766666654

>KOG0333|consensus

Probab=100.00  E-value=4.5e-33  Score=239.33  Aligned_cols=216  Identities=31%  Similarity=0.522  Sum_probs=200.2

Q ss_pred             CcccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh----
Q psy4698          36 GLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ----  111 (258)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~----  111 (258)
                      .+.....+....+|++.+++.++++.+.+.|+..|+|+|+.++|..++.+|++..+.||||||.+|++|++..+..    
T Consensus       234 s~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~  313 (673)
T KOG0333|consen  234 SIKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPM  313 (673)
T ss_pred             eecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCc
Confidence            4555666778889999999999999999999999999999999999999999999999999999999999887633    


Q ss_pred             -----ccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCC
Q psy4698         112 -----NIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALS  186 (258)
Q Consensus       112 -----~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~  186 (258)
                           ...++.++++.||++|++|+...-.+|++..+..+..+.|+....++-..+..||.|+|+||++|.+.+.+..+-
T Consensus       314 ~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lv  393 (673)
T KOG0333|consen  314 ARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLV  393 (673)
T ss_pred             chhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHH
Confidence                 345789999999999999999999999999999999999999999888889999999999999999999999999


Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCC-----------------------C--ccEEEEEeeCChhHHHHHHHh
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-----------------------D--VQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~-----------------------~--~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      ++++.+||+||||+|.+.+|..++..++..+|.                       .  .|.++||||+|+.++.+++.|
T Consensus       394 l~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~y  473 (673)
T KOG0333|consen  394 LNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSY  473 (673)
T ss_pred             hccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHH
Confidence            999999999999999999999999999999863                       1  699999999999999999999


Q ss_pred             cCCCeEEEec
Q psy4698         242 MRDPIKILVK  251 (258)
Q Consensus       242 ~~~~~~v~~~  251 (258)
                      +++|+.|.+.
T Consensus       474 lr~pv~vtig  483 (673)
T KOG0333|consen  474 LRRPVVVTIG  483 (673)
T ss_pred             hhCCeEEEec
Confidence            9999999873

>KOG0337|consensus

Probab=100.00  E-value=8e-33  Score=232.33  Aligned_cols=206  Identities=32%  Similarity=0.553  Sum_probs=194.8

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEecc
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPT  124 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~  124 (258)
                      ...|..++++..+.+++.+.||..|+|+|++.+|.++++++++-.+-||||||.++++|+++.+... ..+.|+++++|+
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilspt   99 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPT   99 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCc
Confidence            4679999999999999999999999999999999999999999999999999999999999998764 345699999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc
Q psy4698         125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR  204 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~  204 (258)
                      ++|+.|..++.+.+++.++.++.+.+|+....+++..+..+.||+++||+++..+.-.-.+.++.+.++|+||+|+++..
T Consensus       100 reLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfem  179 (529)
T KOG0337|consen  100 RELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEM  179 (529)
T ss_pred             HHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhh
Confidence            99999999999999999999999999999999999999988999999999998877666688999999999999999999


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +|..++..++.+++.+.|.++||||+|+.+-++.+.-+.+|+.|+++
T Consensus       180 gfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRld  226 (529)
T KOG0337|consen  180 GFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLD  226 (529)
T ss_pred             hhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEee
Confidence            99999999999999999999999999999999999999999999964

>KOG0329|consensus

Probab=100.00  E-value=5.5e-32  Score=214.41  Aligned_cols=207  Identities=38%  Similarity=0.645  Sum_probs=194.1

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..|.++-+.+++++++...||.+|+.+|.+++|...-|-+++..+..|.|||.++.+.-++.+........++++|.||+
T Consensus        42 sgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtre  121 (387)
T KOG0329|consen   42 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRE  121 (387)
T ss_pred             cchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHH
Confidence            56999999999999999999999999999999999999999999999999999999999999998877788999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-  204 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-  204 (258)
                      |+-|+.+...++.+++ ++.+..++||.........+.+.++|+|+||++++.+.+++.+++++++++|+||+|.|+.+ 
T Consensus       122 lafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~l  201 (387)
T KOG0329|consen  122 LAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQL  201 (387)
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHH
Confidence            9999999999988766 68899999999988888888888999999999999999999999999999999999988765 


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      .....+..+++..|...|+.++|||+++++...++.||+||..|.|++|
T Consensus       202 DMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE  250 (387)
T KOG0329|consen  202 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDE  250 (387)
T ss_pred             HHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccch
Confidence            6778888999999999999999999999999999999999999999776

>KOG0334|consensus

Probab=100.00  E-value=2.1e-32  Score=251.65  Aligned_cols=215  Identities=33%  Similarity=0.570  Sum_probs=197.5

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-----cc
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-----NI  113 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-----~~  113 (258)
                      ....+.+...|.+.|++..+++.+++.|+.+|+++|.+|||++..|+++|.+|.||||||++|++|++.+...     .+
T Consensus       357 g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~g  436 (997)
T KOG0334|consen  357 GKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEG  436 (997)
T ss_pred             cCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhhC
Confidence            3456778889999999999999999999999999999999999999999999999999999999999977643     25


Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC---CCCCCc
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA---LSTKQI  190 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~---~~~~~l  190 (258)
                      .|+-++|++||++|+.|+.+.++.|.+.+++.+.+.+|+....+++..+.+++.|+||||++..+++-.+.   .++.++
T Consensus       437 dGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~  516 (997)
T KOG0334|consen  437 DGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRV  516 (997)
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCcccccccc
Confidence            58899999999999999999999999999999999999999999999999999999999999999885543   345566


Q ss_pred             cEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         191 RMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       191 ~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      .++|+||||+|++.+|..++..++..+++..|++++|||+|..++.+.+.-+..|+-|.|...
T Consensus       517 t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~  579 (997)
T KOG0334|consen  517 TYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGR  579 (997)
T ss_pred             ceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccc
Confidence            699999999999999999999999999999999999999999999999999999999877643

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

Probab=99.97  E-value=3.1e-30  Score=241.44  Aligned_cols=191  Identities=22%  Similarity=0.310  Sum_probs=156.0

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      +++.+.+.|++.|+..|+++|.++++.+++|+|+++.+|||||||++|++|+++.+..+ .+.++||++|+++|+.|+..
T Consensus        21 l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~l~PtraLa~q~~~   99 (742)
T TIGR03817        21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-PRATALYLAPTKALAADQLR   99 (742)
T ss_pred             CCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEEEcChHHHHHHHHH
Confidence            78999999999999999999999999999999999999999999999999999998764 45699999999999999999


Q ss_pred             HHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-C---CCCCCCccEEEEccchhhhccCcHHH
Q psy4698         134 VVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-G---ALSTKQIRMFVLDEADEMLSRGFKDQ  209 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~---~~~~~~l~~lVvDE~h~~~~~~~~~~  209 (258)
                      .++.++ ..++.+..+.|+... .+...+..+++|+|+||+.+...+.. .   ...++++++||+||+|.+.+ .|+..
T Consensus       100 ~l~~l~-~~~i~v~~~~Gdt~~-~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g-~fg~~  176 (742)
T TIGR03817       100 AVRELT-LRGVRPATYDGDTPT-EERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG-VFGSH  176 (742)
T ss_pred             HHHHhc-cCCeEEEEEeCCCCH-HHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC-ccHHH
Confidence            999987 446777777666654 44455667789999999998653321 1   12378999999999999865 46666


Q ss_pred             HHHHHHhC-------CCCccEEEEEeeCChhHHHHHHHhcCCCeEEE
Q psy4698         210 IYDVFKHL-------NNDVQVILLSATMPADVLDVSMKFMRDPIKIL  249 (258)
Q Consensus       210 ~~~~~~~l-------~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~  249 (258)
                      +..+++++       +.++|++++|||+++..+ +++.++..|+.+.
T Consensus       177 ~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~i  222 (742)
T TIGR03817       177 VALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVAV  222 (742)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEEE
Confidence            55555443       467899999999998755 6778888886654

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.

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

Probab=99.97  E-value=3e-30  Score=201.38  Aligned_cols=166  Identities=30%  Similarity=0.531  Sum_probs=144.3

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEE
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACI  150 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~  150 (258)
                      |++|.++++.+.+|+++++.+|||+|||++++++++..+.+. +..++++++|+++|+.|....+..++...+..+..++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~   79 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH   79 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccccccccccc
Confidence            689999999999999999999999999999999999988887 5568999999999999999999999888778888888


Q ss_pred             CCcchH-HHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC--CccEEEEE
Q psy4698         151 GGTIVR-DDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN--DVQVILLS  227 (258)
Q Consensus       151 ~~~~~~-~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~--~~~~i~~S  227 (258)
                      ++.... .....+.++++|+|+||+++.+++..+...+.++++||+||+|.+....+...+..+++.+..  +.|++++|
T Consensus        80 ~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i~~S  159 (169)
T PF00270_consen   80 GGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFKNIQIILLS  159 (169)
T ss_dssp             TTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTTTSEEEEEE
T ss_pred             ccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCCCCCcEEEEe
Confidence            877654 444455667999999999999999986667788999999999999887888888888888743  58999999


Q ss_pred             eeCChhHHHH
Q psy4698         228 ATMPADVLDV  237 (258)
Q Consensus       228 AT~~~~~~~~  237 (258)
                      ||++.+++++
T Consensus       160 AT~~~~~~~~  169 (169)
T PF00270_consen  160 ATLPSNVEKL  169 (169)
T ss_dssp             SSSTHHHHHH
T ss_pred             eCCChhHhhC
Confidence            9999777653

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 ....

>KOG4284|consensus

Probab=99.97  E-value=9.3e-31  Score=229.83  Aligned_cols=208  Identities=36%  Similarity=0.601  Sum_probs=194.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..|+++.+...++..|+..+|..|+++|..|+|.+..+-|+||.+..|+|||++|...+++.+......++++|++|||+
T Consensus        25 ~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTRE  104 (980)
T KOG4284|consen   25 PGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTRE  104 (980)
T ss_pred             CCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchh
Confidence            46999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhcC-CCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc-c
Q psy4698         127 LAQQIQKVVIALGD-FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-R  204 (258)
Q Consensus       127 l~~q~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-~  204 (258)
                      ++.|+.+.+..++. ..++.|..+.||.........++. ++|+||||+++.+++..+.++++.++++|+||||.+++ .
T Consensus       105 iaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~-~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~  183 (980)
T KOG4284|consen  105 IAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ-TRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTE  183 (980)
T ss_pred             hhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh-ceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchh
Confidence            99999999999876 568999999999988777666665 78999999999999999999999999999999999988 5


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      .|...+..++..+|...|++.+|||.|..+.+.+.+||+||.+|+.+..+.
T Consensus       184 sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~  234 (980)
T KOG4284|consen  184 SFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDV  234 (980)
T ss_pred             hHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCc
Confidence            688999999999999999999999999999999999999999999876654

>KOG0347|consensus

Probab=99.97  E-value=7.7e-30  Score=220.59  Aligned_cols=187  Identities=32%  Similarity=0.592  Sum_probs=168.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhc-----------cc
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQN-----------IK  114 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~-----------~~  114 (258)
                      ..|..++++..++++|...||..|+++|..++|.+..| .|++-.|.||||||++|-+|++..+...           .+
T Consensus       181 sAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k  260 (731)
T KOG0347|consen  181 SAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAK  260 (731)
T ss_pred             HHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHhc
Confidence            35899999999999999999999999999999999999 6899999999999999999999955332           23


Q ss_pred             cce--EEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC---CCCC
Q psy4698         115 ECQ--ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL---STKQ  189 (258)
Q Consensus       115 ~~~--~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~---~~~~  189 (258)
                      +++  +||++|||+|+.|+.+.+..++...++.+....||.....+.+.++..++|+|+||++||.++..+..   .+++
T Consensus       261 ~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~  340 (731)
T KOG0347|consen  261 YVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKK  340 (731)
T ss_pred             cCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhh
Confidence            345  99999999999999999999999999999999999999888888998999999999999999987544   4678


Q ss_pred             ccEEEEccchhhhccCcHHHHHHHHHhCC-----CCccEEEEEeeCChh
Q psy4698         190 IRMFVLDEADEMLSRGFKDQIYDVFKHLN-----NDVQVILLSATMPAD  233 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~~~~~~~~~~~l~-----~~~~~i~~SAT~~~~  233 (258)
                      ++++|+||+|+|+..++..++..++..++     ...|.+.+|||++-.
T Consensus       341 vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~  389 (731)
T KOG0347|consen  341 VKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLV  389 (731)
T ss_pred             ceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehh
Confidence            89999999999999999999999998886     357999999998653

>KOG0332|consensus

Probab=99.97  E-value=4.4e-30  Score=213.01  Aligned_cols=217  Identities=39%  Similarity=0.632  Sum_probs=191.6

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccc
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKEC  116 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~  116 (258)
                      +.+.--+..+|+++++.+++++.+..++|.+|+.+|..++|.++..  +|++..+..|+|||.+|.+.++.++......+
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~P  161 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVP  161 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCC
Confidence            3444455678999999999999999999999999999999999877  68999999999999999999999999988889


Q ss_pred             eEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEE
Q psy4698         117 QALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVL  195 (258)
Q Consensus       117 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVv  195 (258)
                      ++++++|+++|+.|..+++.+.|+..++.......+....... .+  ..+|+|+||+.+.+++.. ..+.+..++.+|+
T Consensus       162 Q~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG~-~i--~eqIviGTPGtv~Dlm~klk~id~~kikvfVl  238 (477)
T KOG0332|consen  162 QCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRGN-KL--TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVL  238 (477)
T ss_pred             CceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCcccccCC-cc--hhheeeCCCccHHHHHHHHHhhChhhceEEEe
Confidence            9999999999999999999999999888776666554221110 01  147999999999999887 7788899999999


Q ss_pred             ccchhhhcc-CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccCC
Q psy4698         196 DEADEMLSR-GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE  258 (258)
Q Consensus       196 DE~h~~~~~-~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  258 (258)
                      ||||.|++. +|.+.-..+.+.+++++|++++|||+...+.+|+.....+|..+.+..++++|.
T Consensus       239 DEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~  302 (477)
T KOG0332|consen  239 DEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALD  302 (477)
T ss_pred             cchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhcccc
Confidence            999999876 689999999999999999999999999999999999999999999999999873

>PRK00254 ski2-like helicase; Provisional

Probab=99.97  E-value=3e-29  Score=235.71  Aligned_cols=186  Identities=17%  Similarity=0.250  Sum_probs=161.3

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .|+++++++.+.+.+++.|+..|+++|.++++. +..|+|+++++|||||||++|.+|+++.+...  +.++||++|+++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~--~~~~l~l~P~~a   79 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GGKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc--CCeEEEEeChHH
Confidence            477889999999999999999999999999986 88999999999999999999999999887653  358999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      |+.|+++.++.+. ..++.+..+.|+......+   ...++|+|+||+++..++.++...++++++||+||+|.+.+.++
T Consensus        80 La~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~~---~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~r  155 (720)
T PRK00254         80 LAEEKYREFKDWE-KLGLRVAMTTGDYDSTDEW---LGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDR  155 (720)
T ss_pred             HHHHHHHHHHHHh-hcCCEEEEEeCCCCCchhh---hccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccc
Confidence            9999999998764 4578888888876543321   24579999999999999887777789999999999999988889


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      +..+..++.++..+.|+|++|||+++ ..++.++
T Consensus       156 g~~le~il~~l~~~~qiI~lSATl~n-~~~la~w  188 (720)
T PRK00254        156 GATLEMILTHMLGRAQILGLSATVGN-AEELAEW  188 (720)
T ss_pred             hHHHHHHHHhcCcCCcEEEEEccCCC-HHHHHHH
Confidence            99999999999989999999999986 4666654

>PRK02362 ski2-like helicase; Provisional

Probab=99.97  E-value=2.2e-29  Score=237.25  Aligned_cols=185  Identities=23%  Similarity=0.292  Sum_probs=155.7

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .|+++++++.+.+.+++.|+..|+++|.++++. +..|+|+++++|||||||++|.+++++.+..   +.+++|++|+++
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~---~~kal~i~P~ra   78 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR---GGKALYIVPLRA   78 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc---CCcEEEEeChHH
Confidence            578899999999999999999999999999998 7889999999999999999999999998863   458999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      |+.|.++.++.+.. .++.+..+.|+......   ....++|+|+||+++..+++++...++++++||+||+|.+.+.++
T Consensus        79 La~q~~~~~~~~~~-~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~r  154 (737)
T PRK02362         79 LASEKFEEFERFEE-LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANR  154 (737)
T ss_pred             HHHHHHHHHHHhhc-CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcc
Confidence            99999999988753 47788888877654332   123479999999999999887666788999999999999988788


Q ss_pred             HHHHHHHHHhC---CCCccEEEEEeeCChhHHHHHHH
Q psy4698         207 KDQIYDVFKHL---NNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       207 ~~~~~~~~~~l---~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      +..+..++.++   .++.|+|++|||+++ ..++.++
T Consensus       155 g~~le~il~rl~~~~~~~qii~lSATl~n-~~~la~w  190 (737)
T PRK02362        155 GPTLEVTLAKLRRLNPDLQVVALSATIGN-ADELADW  190 (737)
T ss_pred             hHHHHHHHHHHHhcCCCCcEEEEcccCCC-HHHHHHH
Confidence            87777665554   577899999999986 3444443

>KOG0350|consensus

Probab=99.96  E-value=4.8e-28  Score=207.40  Aligned_cols=205  Identities=24%  Similarity=0.378  Sum_probs=171.2

Q ss_pred             CcCCCCCCHHHHHH----------HHHCCCCCCcHHHHHHhhhhhc---------CCcEEEEcccCCCcchHhHHHHHHH
Q psy4698          48 NFDDMELSEELLRG----------IYAYGFEKPSAIQQRAIIPCVR---------GNDVIAQAQSGTGKTATFSISILQQ  108 (258)
Q Consensus        48 ~~~~~~~~~~l~~~----------l~~~~~~~~~~~Q~~~~~~l~~---------g~~~li~~~tGsGKT~~~l~~~l~~  108 (258)
                      -|+.++++..+...          +.++++.+.+|+|..++|.++.         ++|++|.||||||||++|.+|+++.
T Consensus       128 ~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~  207 (620)
T KOG0350|consen  128 IFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQL  207 (620)
T ss_pred             eeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHH
Confidence            35666666555444          8889999999999999999842         4789999999999999999999999


Q ss_pred             hhhc-cccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC-----CcEEEeChHHHHHHHhc
Q psy4698         109 VDQN-IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-----AQVVVGTPGRVFDMISR  182 (258)
Q Consensus       109 l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~Ilv~Tp~~l~~~l~~  182 (258)
                      +... -+.-|++|++|+++|+.|+++.+..++...++.+..+.|......+.+.+.+.     .||+|+||++|.+++.+
T Consensus       208 L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~  287 (620)
T KOG0350|consen  208 LSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNN  287 (620)
T ss_pred             HccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccC
Confidence            9876 34469999999999999999999999999999999999998888877776643     48999999999999985


Q ss_pred             -CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC----------------------------------CCccEEEEE
Q psy4698         183 -GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN----------------------------------NDVQVILLS  227 (258)
Q Consensus       183 -~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~----------------------------------~~~~~i~~S  227 (258)
                       ..+.++.++++||||||+|++..|..++..++..+.                                  +..+.+.+|
T Consensus       288 ~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~s  367 (620)
T KOG0350|consen  288 TKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFS  367 (620)
T ss_pred             CCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcc
Confidence             789999999999999999998877776665554431                                  123578889


Q ss_pred             eeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         228 ATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       228 AT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      ||++.+-..+...-++.|-...|.+
T Consensus       368 atLsqdP~Kl~~l~l~~Prl~~v~~  392 (620)
T KOG0350|consen  368 ATLSQDPSKLKDLTLHIPRLFHVSK  392 (620)
T ss_pred             hhhhcChHHHhhhhcCCCceEEeec
Confidence            9999888888888889996665543

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

Probab=99.96  E-value=2.7e-28  Score=224.88  Aligned_cols=196  Identities=18%  Similarity=0.189  Sum_probs=167.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-----cccceEEEEeccHHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-----IKECQALILAPTRELA  128 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-----~~~~~~lil~P~~~l~  128 (258)
                      +++.+.+.++.. |..||+.|.+|++.+.+|+|+++.+|||||||+++.+|++..+...     ..+..+||++|.++|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            788999999887 8899999999999999999999999999999999999999999877     2346899999999999


Q ss_pred             HHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--CCCCCccEEEEccchhhhccCc
Q psy4698         129 QQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA--LSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       129 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      +++...++..+...|+.+...+|+....+..+...+.++|+|+||++|.-++....  -.+.+++++||||+|.+.++..
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKR  166 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKR  166 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhcccc
Confidence            99999999999999999999999999888888888889999999999887776532  3578999999999999988877


Q ss_pred             HHHHHHHHHhCC---CCccEEEEEeeCChhHHHHHHHhcCCC---eEEEec
Q psy4698         207 KDQIYDVFKHLN---NDVQVILLSATMPADVLDVSMKFMRDP---IKILVK  251 (258)
Q Consensus       207 ~~~~~~~~~~l~---~~~~~i~~SAT~~~~~~~~~~~~~~~~---~~v~~~  251 (258)
                      +.++.-.+.++.   .+.|.|++|||+. +.....++.....   .+|.+.
T Consensus       167 G~~Lsl~LeRL~~l~~~~qRIGLSATV~-~~~~varfL~g~~~~~~Iv~~~  216 (814)
T COG1201         167 GVQLALSLERLRELAGDFQRIGLSATVG-PPEEVAKFLVGFGDPCEIVDVS  216 (814)
T ss_pred             chhhhhhHHHHHhhCcccEEEeehhccC-CHHHHHHHhcCCCCceEEEEcc
Confidence            777765554442   3799999999997 4566666666654   555443

>PRK01172 ski2-like helicase; Provisional

Probab=99.95  E-value=2.4e-27  Score=221.76  Aligned_cols=185  Identities=20%  Similarity=0.238  Sum_probs=152.9

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      .|+++++++.+.+.+.+.++. ++++|.++++.+..|+++++++|||||||+++.+++++.+..+   .+++|++|+++|
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~---~k~v~i~P~raL   77 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAG---LKSIYIVPLRSL   77 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhC---CcEEEEechHHH
Confidence            477899999999999998885 9999999999999999999999999999999999999887653   479999999999


Q ss_pred             HHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH
Q psy4698         128 AQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK  207 (258)
Q Consensus       128 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~  207 (258)
                      +.|.++.++++. ..+..+....|+......   ....++|+|+||+++..++.+....+.++++||+||+|.+.+.+++
T Consensus        78 a~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg  153 (674)
T PRK01172         78 AMEKYEELSRLR-SLGMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRG  153 (674)
T ss_pred             HHHHHHHHHHHh-hcCCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCcc
Confidence            999999998764 356777777776543322   1235799999999999888877667889999999999998877777


Q ss_pred             HHHHHHHH---hCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         208 DQIYDVFK---HLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       208 ~~~~~~~~---~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      ..+..++.   .++++.|+|++|||+++ ..++.+++
T Consensus       154 ~~le~ll~~~~~~~~~~riI~lSATl~n-~~~la~wl  189 (674)
T PRK01172        154 PTLETVLSSARYVNPDARILALSATVSN-ANELAQWL  189 (674)
T ss_pred             HHHHHHHHHHHhcCcCCcEEEEeCccCC-HHHHHHHh
Confidence            66666554   45678999999999975 45566543

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.95  E-value=5.2e-27  Score=223.64  Aligned_cols=178  Identities=17%  Similarity=0.244  Sum_probs=143.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc------cccceEEEEeccHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN------IKECQALILAPTREL  127 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~------~~~~~~lil~P~~~l  127 (258)
                      +++.+.+.+++ ++..|+++|.++++.+++|+|+++++|||||||++|++|+++.+...      ..+.++||++|+++|
T Consensus        18 l~~~v~~~~~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFKE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHHH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            56777777665 68899999999999999999999999999999999999999988642      235689999999999


Q ss_pred             HHHHHHHHHH-------h----cCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC--CCCCccEE
Q psy4698         128 AQQIQKVVIA-------L----GDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL--STKQIRMF  193 (258)
Q Consensus       128 ~~q~~~~~~~-------~----~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--~~~~l~~l  193 (258)
                      +.|+++.+..       +    +... ++.+....|+.......+.+...++|+|+||+++..++....+  .++++++|
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~V  176 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWV  176 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEE
Confidence            9999876542       2    2333 6677888888877777667777799999999999877765433  47899999


Q ss_pred             EEccchhhhccCcHHHHHHHHHh----CCCCccEEEEEeeCCh
Q psy4698         194 VLDEADEMLSRGFKDQIYDVFKH----LNNDVQVILLSATMPA  232 (258)
Q Consensus       194 VvDE~h~~~~~~~~~~~~~~~~~----l~~~~~~i~~SAT~~~  232 (258)
                      |+||+|.+.+..++..+...+.+    .+...|+|++|||+++
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~  219 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEP  219 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCC
Confidence            99999999877666655544433    3367899999999976

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

Probab=99.94  E-value=4.5e-26  Score=211.34  Aligned_cols=184  Identities=23%  Similarity=0.272  Sum_probs=148.6

Q ss_pred             CCCCCCcHHHHHHhhhhhcCC-cEEEEcccCCCcchHhHHHHHHHhhhccccce-EEEEeccHHHHHHHHHHHHHhcCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQ-ALILAPTRELAQQIQKVVIALGDFM  142 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~-~lil~P~~~l~~q~~~~~~~~~~~~  142 (258)
                      .||. |+++|.++++.++.|+ ++++.+|||||||.++.++++. +......++ .++++|+|+|+.|.++.++++++.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~-~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLA-VEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhcc-ccccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            4786 9999999999999998 5788899999999976555543 222233344 4557799999999999999988754


Q ss_pred             -----------------------CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC--------------
Q psy4698         143 -----------------------SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL--------------  185 (258)
Q Consensus       143 -----------------------~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--------------  185 (258)
                                             ++.+..++|+.....++..+..+++|+|+|+    +++.++.+              
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~~~pi~  165 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFKSRPLH  165 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccccccch
Confidence                                   4778889999999889999999999999996    44444443              


Q ss_pred             --CCCCccEEEEccchhhhccCcHHHHHHHHHhC--CCC---ccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         186 --STKQIRMFVLDEADEMLSRGFKDQIYDVFKHL--NND---VQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       186 --~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l--~~~---~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                        .++++++||+||||  ++.+|...+..+++.+  ++.   .|+++||||++.++.++.+.++.++..+.+....++
T Consensus       166 ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~  241 (844)
T TIGR02621       166 AGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLA  241 (844)
T ss_pred             hhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeeccccccc
Confidence              26789999999999  5788999999999975  332   699999999999999999999988888777665554

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.

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

Probab=99.94  E-value=7.8e-25  Score=206.46  Aligned_cols=185  Identities=19%  Similarity=0.287  Sum_probs=138.0

Q ss_pred             CcC--CCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          48 NFD--DMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        48 ~~~--~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|.  .+++...+...+++ +|+..++++|.++++.++.|+|+++.+|||+|||++|++|++..      ++.+|||+|+
T Consensus       436 ~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPL  509 (1195)
T PLN03137        436 KWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPL  509 (1195)
T ss_pred             cccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCH
Confidence            365  46677777777765 79999999999999999999999999999999999999999853      3479999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh------cCCcEEEeChHHHHH---HHhc--CCCCCCCccEE
Q psy4698         125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE------AGAQVVVGTPGRVFD---MISR--GALSTKQIRMF  193 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~Ilv~Tp~~l~~---~l~~--~~~~~~~l~~l  193 (258)
                      ++|+.++...+...    ++....+.++.........+.      .+++|+|+||+++..   ++..  .......+++|
T Consensus       510 iSLmqDQV~~L~~~----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslI  585 (1195)
T PLN03137        510 VSLIQDQIMNLLQA----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARF  585 (1195)
T ss_pred             HHHHHHHHHHHHhC----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcccccee
Confidence            99999777666553    466666777665544433222      458999999999752   1211  11123458899


Q ss_pred             EEccchhhhccC--cHHHHHH--HHHhCCCCccEEEEEeeCChhHHHHHHHhc
Q psy4698         194 VLDEADEMLSRG--FKDQIYD--VFKHLNNDVQVILLSATMPADVLDVSMKFM  242 (258)
Q Consensus       194 VvDE~h~~~~~~--~~~~~~~--~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~  242 (258)
                      ||||||++++++  |...+..  .++...+..+++++|||++..+++.+...+
T Consensus       586 VIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L  638 (1195)
T PLN03137        586 VIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQAL  638 (1195)
T ss_pred             ccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHc
Confidence            999999999886  5555543  244444578899999999998887555443

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

Probab=99.93  E-value=5.8e-25  Score=207.24  Aligned_cols=191  Identities=19%  Similarity=0.292  Sum_probs=153.9

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHH
Q psy4698          55 SEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV  134 (258)
Q Consensus        55 ~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~  134 (258)
                      ...+...+.+.|...++.+|.+|+..+.+|+|++|+.+||||||.+|++|+++.+...... ++|++.|+++|++++.+.
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~r  134 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAER  134 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHHH
Confidence            3445778888899999999999999999999999999999999999999999999887554 899999999999999999


Q ss_pred             HHHhcCCCC--ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC----CCCCCccEEEEccchhhhccCcHH
Q psy4698         135 VIALGDFMS--VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA----LSTKQIRMFVLDEADEMLSRGFKD  208 (258)
Q Consensus       135 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~----~~~~~l~~lVvDE~h~~~~~~~~~  208 (258)
                      ++++....+  +.+..+.|+.........+.+.++|+++||++|..++.+..    +.++++++||+||+|. +..-++.
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHt-YrGv~GS  213 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHT-YRGVQGS  213 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEeccee-ccccchh
Confidence            999988776  67777777776665556677889999999999988554422    2356799999999995 4555777


Q ss_pred             HHHHHHHhC-------CCCccEEEEEeeCChhHHHHHHHhcCCCeEE
Q psy4698         209 QIYDVFKHL-------NNDVQVILLSATMPADVLDVSMKFMRDPIKI  248 (258)
Q Consensus       209 ~~~~~~~~l-------~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v  248 (258)
                      .+.-+++++       +...|+|+.|||+.+.- ++.+.+.+....+
T Consensus       214 ~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~-e~~~~l~~~~f~~  259 (851)
T COG1205         214 EVALLLRRLLRRLRRYGSPLQIICTSATLANPG-EFAEELFGRDFEV  259 (851)
T ss_pred             HHHHHHHHHHHHHhccCCCceEEEEeccccChH-HHHHHhcCCccee
Confidence            776666665       35789999999998764 4455555444433

>PRK09401 reverse gyrase; Reviewed

Probab=99.93  E-value=3.1e-24  Score=207.96  Aligned_cols=184  Identities=19%  Similarity=0.231  Sum_probs=136.9

Q ss_pred             HHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          60 RGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        60 ~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      +.+++ .|+ .|+++|..+++.++.|+|++++||||+|||..+ +++...+..  ++.+++|++||++|+.|+++.++.+
T Consensus        71 ~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~-l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l  146 (1176)
T PRK09401         71 KFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFG-LVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKF  146 (1176)
T ss_pred             HHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHH-HHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHH
Confidence            34444 366 899999999999999999999999999999644 444444433  3568999999999999999999999


Q ss_pred             cCCCCceEEEEECCcc-----hHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc---------
Q psy4698         139 GDFMSVSCHACIGGTI-----VRDDIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS---------  203 (258)
Q Consensus       139 ~~~~~~~~~~~~~~~~-----~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~---------  203 (258)
                      +...++.+....++..     .......+. .+++|+|+||++|.+.+.  .+....+++||+||||++++         
T Consensus       147 ~~~~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l  224 (1176)
T PRK09401        147 GEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLL  224 (1176)
T ss_pred             hhhcCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHH
Confidence            9888877776665543     222333444 358999999999998876  35566799999999999986         


Q ss_pred             --cCcH-HHHHHHHHhCCC------------------------CccEEEEEeeCChh-HHHHHHHhcCCCeEEEecC
Q psy4698         204 --RGFK-DQIYDVFKHLNN------------------------DVQVILLSATMPAD-VLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       204 --~~~~-~~~~~~~~~l~~------------------------~~~~i~~SAT~~~~-~~~~~~~~~~~~~~v~~~~  252 (258)
                        .+|. ..+..++..++.                        ..|++++|||+++. +..   .++.++..+.+..
T Consensus       225 ~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~  298 (1176)
T PRK09401        225 YLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGS  298 (1176)
T ss_pred             HhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecC
Confidence              3553 566666666653                        68999999999864 432   2334444444433

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.93  E-value=1.6e-24  Score=194.77  Aligned_cols=176  Identities=18%  Similarity=0.276  Sum_probs=128.9

Q ss_pred             HCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          64 AYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        64 ~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .+|+..++++|.++++.+++|+++++.+|||+|||++|++|++..      +..+||++|+++|+.|+...++.++    
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~g----   75 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKASG----   75 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHcC----
Confidence            379999999999999999999999999999999999999998752      3479999999999999999887653    


Q ss_pred             ceEEEEECCcchHHHH---HHH-hcCCcEEEeChHHHHHHH-hcCCC-CCCCccEEEEccchhhhccC--cHHHHHH---
Q psy4698         144 VSCHACIGGTIVRDDI---RKL-EAGAQVVVGTPGRVFDMI-SRGAL-STKQIRMFVLDEADEMLSRG--FKDQIYD---  212 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~---~~~-~~~~~Ilv~Tp~~l~~~l-~~~~~-~~~~l~~lVvDE~h~~~~~~--~~~~~~~---  212 (258)
                      +....+.++....+..   ..+ ...++|+++||+.+.... ....+ ...++++|||||||++++++  +...+..   
T Consensus        76 i~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l~~  155 (470)
T TIGR00614        76 IPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGS  155 (470)
T ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHHHH
Confidence            5555555554433221   222 234899999999875321 00111 46789999999999998775  4444333   


Q ss_pred             HHHhCCCCccEEEEEeeCChhHHHHHHHh--cCCCeEEEe
Q psy4698         213 VFKHLNNDVQVILLSATMPADVLDVSMKF--MRDPIKILV  250 (258)
Q Consensus       213 ~~~~l~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~~v~~  250 (258)
                      +...+ ++.+++++|||+++.+...+...  +.+|.++..
T Consensus       156 l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~  194 (470)
T TIGR00614       156 LKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCT  194 (470)
T ss_pred             HHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeC
Confidence            33333 57889999999999876655444  346655543

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

>KOG0344|consensus

Probab=99.92  E-value=4.9e-25  Score=192.53  Aligned_cols=211  Identities=27%  Similarity=0.404  Sum_probs=173.0

Q ss_pred             cccccCcCC----CCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc-----
Q psy4698          43 DHVAENFDD----MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI-----  113 (258)
Q Consensus        43 ~~~~~~~~~----~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~-----  113 (258)
                      ++...+|.+    +..++.+++.+.+.+|..|++.|.+++|.++++++++.|+|||||||++|.+|++..+....     
T Consensus       128 ~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~  207 (593)
T KOG0344|consen  128 PPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHK  207 (593)
T ss_pred             CCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCc
Confidence            445556665    56789999999999999999999999999999999999999999999999999999986532     


Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhc--CCCCceEEEEECCcchHH-HHHHHhcCCcEEEeChHHHHHHHhcCC--CCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALG--DFMSVSCHACIGGTIVRD-DIRKLEAGAQVVVGTPGRVFDMISRGA--LSTK  188 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~-~~~~~~~~~~Ilv~Tp~~l~~~l~~~~--~~~~  188 (258)
                      .+.+++|+.|+++|+.|.+..+.++.  ...+.............+ ........++|+|+||.++..++..+.  +.+.
T Consensus       208 ~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~  287 (593)
T KOG0344|consen  208 VGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLS  287 (593)
T ss_pred             cceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhh
Confidence            35689999999999999999999998  455544443333322111 112223348999999999999998865  7789


Q ss_pred             CccEEEEccchhhhcc-CcHHHHHHHHHhCC-CCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         189 QIRMFVLDEADEMLSR-GFKDQIYDVFKHLN-NDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      .+.++|+||+|.+++. .|..++..++.... ++..+-++|||++..+++.++.-+.+++.|.+--.
T Consensus       288 ~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~  354 (593)
T KOG0344|consen  288 KVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLR  354 (593)
T ss_pred             eeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecc
Confidence            9999999999999998 88888888887654 56678899999999999999999999999988443

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.92  E-value=8.6e-24  Score=200.60  Aligned_cols=186  Identities=22%  Similarity=0.221  Sum_probs=146.8

Q ss_pred             CCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          53 ELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        53 ~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      +.+....+.+.+ ++| .||+.|..+++.+..+      .+.+++|+||||||.+|+.+++..+..+   .+++|++||+
T Consensus       435 ~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g---~qvlvLvPT~  510 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG---KQVAVLVPTT  510 (926)
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhC---CeEEEEeCcH
Confidence            445556665654 577 6999999999999875      6899999999999999999999887654   5899999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      +|+.|.++.++++....++.+..+.+.....+   ....+.. .++|+|+||.    ++ ...+.+++++++|+||+|++
T Consensus       511 ~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~----ll-~~~v~f~~L~llVIDEahrf  585 (926)
T TIGR00580       511 LLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK----LL-QKDVKFKDLGLLIIDEEQRF  585 (926)
T ss_pred             HHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH----Hh-hCCCCcccCCEEEeeccccc
Confidence            99999999999988877888877777655433   2333444 4899999994    23 34567899999999999984


Q ss_pred             hccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                           +......++.++.++++++||||+.+.........+.++.+|.+.+
T Consensus       586 -----gv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p  631 (926)
T TIGR00580       586 -----GVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPP  631 (926)
T ss_pred             -----chhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCC
Confidence                 3344566777788899999999987766666667778888887654

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.92  E-value=3.2e-23  Score=164.70  Aligned_cols=187  Identities=35%  Similarity=0.582  Sum_probs=155.1

Q ss_pred             CCCCCCcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .++..++++|.+++..+..+ +++++.++||+|||.++..+++..+.... ..+++|++|+..++.|+...+........
T Consensus         4 ~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~~   82 (201)
T smart00487        4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSLG   82 (201)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccCC
Confidence            46778999999999999998 99999999999999999999888877653 34799999999999999999988775544


Q ss_pred             ceEEEEECCcchHHHHHHHhcCC-cEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCcc
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQ  222 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~-~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~  222 (258)
                      .......++............+. +++++|++.+.+.+.........++++|+||+|++....+...+..++..+++..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~  162 (201)
T smart00487       83 LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQ  162 (201)
T ss_pred             eEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccce
Confidence            33344444444344444555555 99999999999998887667778999999999998765788888888888888899


Q ss_pred             EEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         223 VILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       223 ~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      ++++|||.++........+..+.+.+....
T Consensus       163 ~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      163 LLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             EEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            999999999999999999999887777654

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.92  E-value=1.9e-24  Score=201.29  Aligned_cols=187  Identities=18%  Similarity=0.254  Sum_probs=152.8

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHhhhh-hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHH
Q psy4698          53 ELSEELLRGIYAYGFEKPSAIQQRAIIPC-VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI  131 (258)
Q Consensus        53 ~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l-~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~  131 (258)
                      .++..+.+.+...++..+++.|+.++... ..++|++|++|||||||+++++.+++.+...  +.+++|++|+++|+.+.
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek   92 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEK   92 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHH
Confidence            36778888888888888888888888774 4569999999999999999999999998876  35899999999999999


Q ss_pred             HHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         132 QKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      ++.++ .....++++....|+......  . ..+++|+|+||+++..++++....+..+++||+||+|.+.+...+..+.
T Consensus        93 ~~~~~-~~~~~GirV~~~TgD~~~~~~--~-l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE  168 (766)
T COG1204          93 YEEFS-RLEELGIRVGISTGDYDLDDE--R-LARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLE  168 (766)
T ss_pred             HHHhh-hHHhcCCEEEEecCCcccchh--h-hccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceeh
Confidence            99998 335668999988888765442  2 2348999999999999999887788899999999999887776777777


Q ss_pred             HHHHhCC---CCccEEEEEeeCChhHHHHHHHhcCCCe
Q psy4698         212 DVFKHLN---NDVQVILLSATMPADVLDVSMKFMRDPI  246 (258)
Q Consensus       212 ~~~~~l~---~~~~~i~~SAT~~~~~~~~~~~~~~~~~  246 (258)
                      .++.+++   ..+|++++|||+|+- .+++.+.--+++
T Consensus       169 ~iv~r~~~~~~~~rivgLSATlpN~-~evA~wL~a~~~  205 (766)
T COG1204         169 SIVARMRRLNELIRIVGLSATLPNA-EEVADWLNAKLV  205 (766)
T ss_pred             hHHHHHHhhCcceEEEEEeeecCCH-HHHHHHhCCccc
Confidence            7776654   447999999999964 666666544544

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.92  E-value=2.9e-23  Score=200.86  Aligned_cols=185  Identities=21%  Similarity=0.220  Sum_probs=145.7

Q ss_pred             CHHHHH-HHHHCCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          55 SEELLR-GIYAYGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        55 ~~~l~~-~l~~~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      +....+ ....+.| .|++.|.++++.++.+      .+++++|+||+|||.+++.+++..+.   .+.+++|++||++|
T Consensus       586 ~~~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~---~g~qvlvLvPT~eL  661 (1147)
T PRK10689        586 DREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE---NHKQVAVLVPTTLL  661 (1147)
T ss_pred             CHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH---cCCeEEEEeCcHHH
Confidence            334444 4445667 8999999999999887      78999999999999999888877654   34689999999999


Q ss_pred             HHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH---Hh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         128 AQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK---LE-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       128 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      +.|+++.+++.....++.+..+.+.....++...   +. .+++|+|+||+.+    . ..+.++++++||+||+|++  
T Consensus       662 A~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~-~~v~~~~L~lLVIDEahrf--  734 (1147)
T PRK10689        662 AQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q-SDVKWKDLGLLIVDEEHRF--  734 (1147)
T ss_pred             HHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h-CCCCHhhCCEEEEechhhc--
Confidence            9999999998776667777777777665544332   33 3589999999633    2 3456789999999999986  


Q ss_pred             cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         204 RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       204 ~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                       ++  .....++.++.++|++++|||+.+...++...++.++.+|.+++.
T Consensus       735 -G~--~~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~  781 (1147)
T PRK10689        735 -GV--RHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA  781 (1147)
T ss_pred             -ch--hHHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCC
Confidence             22  234556778889999999999888888888889999999987554

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.91  E-value=7.5e-23  Score=188.87  Aligned_cols=183  Identities=16%  Similarity=0.236  Sum_probs=131.3

Q ss_pred             CHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          55 SEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        55 ~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      .....+.|++ +|+..++++|.++++.++.|+++++.+|||+|||++|++|++..      ...+||++|+++|+.|+..
T Consensus        10 ~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dqv~   83 (607)
T PRK11057         10 ESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQVD   83 (607)
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHHHH
Confidence            3344445544 79999999999999999999999999999999999999998753      2379999999999999999


Q ss_pred             HHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC--cH
Q psy4698         134 VVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG--FK  207 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~--~~  207 (258)
                      .++.++    +......+........   ..+. ...+++++||+++........+...++++|||||||++.+++  |.
T Consensus        84 ~l~~~g----i~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr  159 (607)
T PRK11057         84 QLLANG----VAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFR  159 (607)
T ss_pred             HHHHcC----CcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCccc
Confidence            887753    4454544544433222   2223 347899999999863222222344578999999999998765  43


Q ss_pred             HHH---HHHHHhCCCCccEEEEEeeCChhHHHHHHHh--cCCCeEE
Q psy4698         208 DQI---YDVFKHLNNDVQVILLSATMPADVLDVSMKF--MRDPIKI  248 (258)
Q Consensus       208 ~~~---~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~~v  248 (258)
                      ..+   ..+...+ ++.+++++|||.++.....+...  +.+|.+.
T Consensus       160 ~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~  204 (607)
T PRK11057        160 PEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQ  204 (607)
T ss_pred             HHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEE
Confidence            333   3333343 56889999999998876544333  4455544

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.91  E-value=5.8e-23  Score=189.69  Aligned_cols=172  Identities=18%  Similarity=0.267  Sum_probs=129.2

Q ss_pred             HHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          61 GIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        61 ~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .|++ +|+..++++|.++++.++.|+|+++++|||+|||++|++|++..      +..++|++|+++|+.|+...++.++
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~~g   77 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRAAG   77 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHHcC
Confidence            3443 79999999999999999999999999999999999999998742      2369999999999999999888763


Q ss_pred             CCCCceEEEEECCcchHHHH---HH-HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC--cHHH---H
Q psy4698         140 DFMSVSCHACIGGTIVRDDI---RK-LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG--FKDQ---I  210 (258)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~--~~~~---~  210 (258)
                          +.+..+.++....+..   .. .....+|+++||+++........+...++++|||||||++.+++  |...   +
T Consensus        78 ----i~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l  153 (591)
T TIGR01389        78 ----VAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRL  153 (591)
T ss_pred             ----CcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHH
Confidence                5555555555443322   12 23458999999999864333233455689999999999998765  4443   3


Q ss_pred             HHHHHhCCCCccEEEEEeeCChhHHHHHHHhcC
Q psy4698         211 YDVFKHLNNDVQVILLSATMPADVLDVSMKFMR  243 (258)
Q Consensus       211 ~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~  243 (258)
                      ..+...++. .+++++|||.+..+...+...+.
T Consensus       154 ~~l~~~~~~-~~vi~lTAT~~~~~~~~i~~~l~  185 (591)
T TIGR01389       154 GSLAERFPQ-VPRIALTATADAETRQDIRELLR  185 (591)
T ss_pred             HHHHHhCCC-CCEEEEEeCCCHHHHHHHHHHcC
Confidence            344445544 45999999999988776665553

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.90  E-value=1.2e-22  Score=201.03  Aligned_cols=193  Identities=21%  Similarity=0.240  Sum_probs=139.7

Q ss_pred             HHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHH
Q psy4698          56 EELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV  134 (258)
Q Consensus        56 ~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~  134 (258)
                      ..+.+.+++ .|+ .|+++|..+++.++.|+++++.||||+|||++++++++....   ++.+++|++||++|+.|+++.
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~---~g~~aLVl~PTreLa~Qi~~~  141 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL---KGKKCYIILPTTLLVKQTVEK  141 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh---cCCeEEEEECHHHHHHHHHHH
Confidence            344556665 788 799999999999999999999999999999976655554322   345899999999999999999


Q ss_pred             HHHhcCCC--CceEEEEECCcchHHH---HHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc-----
Q psy4698         135 VIALGDFM--SVSCHACIGGTIVRDD---IRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-----  203 (258)
Q Consensus       135 ~~~~~~~~--~~~~~~~~~~~~~~~~---~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-----  203 (258)
                      ++.++...  ++.+..++|+......   ...+..+ ++|+|+||+.|.+.+...  ...++++||+||||++++     
T Consensus       142 l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~~~i~~iVVDEAD~ml~~~kni  219 (1638)
T PRK14701        142 IESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KHLKFDFIFVDDVDAFLKASKNI  219 (1638)
T ss_pred             HHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hhCCCCEEEEECceecccccccc
Confidence            99988765  4556667777665543   3344444 899999999988766542  126799999999999986     


Q ss_pred             ------cCcHHHHHH----HHH----------------------hCCCCcc-EEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         204 ------RGFKDQIYD----VFK----------------------HLNNDVQ-VILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       204 ------~~~~~~~~~----~~~----------------------~l~~~~~-~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                            .+|..++..    +++                      .+++..| .+.+|||++.. .+. ..+++++..+.+
T Consensus       220 d~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r-~~~-~~l~~~~l~f~v  297 (1638)
T PRK14701        220 DRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAK-GDR-VKLYRELLGFEV  297 (1638)
T ss_pred             chhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCch-hHH-HHHhhcCeEEEe
Confidence                  356665543    322                      2344555 56799999863 111 234467777777


Q ss_pred             cCCccc
Q psy4698         251 KKEELT  256 (258)
Q Consensus       251 ~~~~~~  256 (258)
                      .....+
T Consensus       298 ~~~~~~  303 (1638)
T PRK14701        298 GSGRSA  303 (1638)
T ss_pred             cCCCCC
Confidence            555443

>TIGR01054 rgy reverse gyrase

Probab=99.90  E-value=2e-22  Score=195.67  Aligned_cols=191  Identities=19%  Similarity=0.258  Sum_probs=134.9

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHH
Q psy4698          56 EELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        56 ~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      ....+.+.+.....|+++|..+++.++.|++++++||||+|||. +.+++...+..  .+++++|++||++|+.|+++.+
T Consensus        65 ~~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l  141 (1171)
T TIGR01054        65 KEFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKI  141 (1171)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHH
Confidence            33445555544458999999999999999999999999999997 54566555443  3568999999999999999999


Q ss_pred             HHhcCCCCceEE---EEECCcchHHH---HHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc-----
Q psy4698         136 IALGDFMSVSCH---ACIGGTIVRDD---IRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-----  203 (258)
Q Consensus       136 ~~~~~~~~~~~~---~~~~~~~~~~~---~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-----  203 (258)
                      +.++...++...   .++|+......   ...+.+ +++|+|+||+.|.+.+..-  .. +++++|+||||+|++     
T Consensus       142 ~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l--~~-~~~~iVvDEaD~~L~~~k~v  218 (1171)
T TIGR01054       142 SSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL--GP-KFDFIFVDDVDALLKASKNV  218 (1171)
T ss_pred             HHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh--cC-CCCEEEEeChHhhhhccccH
Confidence            999876665433   45666554432   333444 4899999999998877652  12 899999999999987     


Q ss_pred             ------cCcHHH-HHHH----------------------HHhCCCCcc--EEEEEee-CChhHHHHHHHhcCCCeEEEec
Q psy4698         204 ------RGFKDQ-IYDV----------------------FKHLNNDVQ--VILLSAT-MPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       204 ------~~~~~~-~~~~----------------------~~~l~~~~~--~i~~SAT-~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                            .+|..+ +..+                      ++.+++..|  ++++||| .|..+..   .++++++.+.+.
T Consensus       219 d~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~  295 (1171)
T TIGR01054       219 DKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVG  295 (1171)
T ss_pred             HHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEec
Confidence                  345543 3332                      223445555  5678999 5765442   345566666664


Q ss_pred             CCcc
Q psy4698         252 KEEL  255 (258)
Q Consensus       252 ~~~~  255 (258)
                      +...
T Consensus       296 ~~~~  299 (1171)
T TIGR01054       296 GGSD  299 (1171)
T ss_pred             Cccc
Confidence            4433

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.

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

Probab=99.90  E-value=8.7e-23  Score=178.12  Aligned_cols=191  Identities=19%  Similarity=0.230  Sum_probs=156.9

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      ....++++++...+.|+..|+..+.|+|..++.+ +++|+|.++.++|+||||++..++-+..+..+++  +.+|++|..
T Consensus       194 ~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~--KmlfLvPLV  271 (830)
T COG1202         194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGK--KMLFLVPLV  271 (830)
T ss_pred             ccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCC--eEEEEehhH
Confidence            4678899999999999999999999999999988 8999999999999999999999999998888543  799999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH----HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI----RKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      +||+|.+..++.-.+.+++.+..-.|....+...    ......+||+|+|++.+-.+++.+ ..+.+++.+|+||+|.+
T Consensus       272 ALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL  350 (830)
T COG1202         272 ALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTL  350 (830)
T ss_pred             HhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeec
Confidence            9999999999887788888887767665443321    111234899999999988888877 67899999999999988


Q ss_pred             hccCcHHHHHHHH---HhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         202 LSRGFKDQIYDVF---KHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       202 ~~~~~~~~~~~~~---~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      -+...+..+.-++   +.+-+..|+|++|||+-+. +.+++.+
T Consensus       351 ~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l  392 (830)
T COG1202         351 EDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKL  392 (830)
T ss_pred             cchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHh
Confidence            7656665555544   4455789999999999554 4455554

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.90  E-value=4.2e-22  Score=185.91  Aligned_cols=169  Identities=19%  Similarity=0.299  Sum_probs=130.9

Q ss_pred             HHHHHHHH-HCCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH
Q psy4698          56 EELLRGIY-AYGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA  128 (258)
Q Consensus        56 ~~l~~~l~-~~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~  128 (258)
                      ..+.+.+. ..+| .||++|.++++.+..+      .+.+++|+||||||++|+++++..+..   +.+++|++||++|+
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---GYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEeccHHHH
Confidence            34444443 3456 7999999999999877      379999999999999999999988754   45899999999999


Q ss_pred             HHHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc
Q psy4698         129 QQIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR  204 (258)
Q Consensus       129 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~  204 (258)
                      .|.++.++++....++.+..+.|+....+   ....+.. .++|+||||+.+.     ....+++++++|+||+|++.  
T Consensus       324 ~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~-----~~v~~~~l~lvVIDE~Hrfg--  396 (681)
T PRK10917        324 EQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQ-----DDVEFHNLGLVIIDEQHRFG--  396 (681)
T ss_pred             HHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhc-----ccchhcccceEEEechhhhh--
Confidence            99999999998888899999999876433   3334444 4999999997653     23467899999999999862  


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHH
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~  238 (258)
                         ......+......+++++||||..+....+.
T Consensus       397 ---~~qr~~l~~~~~~~~iL~~SATp~prtl~~~  427 (681)
T PRK10917        397 ---VEQRLALREKGENPHVLVMTATPIPRTLAMT  427 (681)
T ss_pred             ---HHHHHHHHhcCCCCCEEEEeCCCCHHHHHHH
Confidence               2223344444557899999999765544443

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.90  E-value=1e-22  Score=198.77  Aligned_cols=159  Identities=18%  Similarity=0.244  Sum_probs=123.9

Q ss_pred             EEcccCCCcchHhHHHHHHHhhhc----------cccceEEEEeccHHHHHHHHHHHHHhc------------CCCCceE
Q psy4698          89 AQAQSGTGKTATFSISILQQVDQN----------IKECQALILAPTRELAQQIQKVVIALG------------DFMSVSC  146 (258)
Q Consensus        89 i~~~tGsGKT~~~l~~~l~~l~~~----------~~~~~~lil~P~~~l~~q~~~~~~~~~------------~~~~~~~  146 (258)
                      |++|||||||++|.+|++..+...          ..+.++|||+|+++|+.|+.+.++...            ...++.+
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            579999999999999999988653          135799999999999999998876411            1346788


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccchhhhccCcHHH----HHHHHHhCCCCc
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEADEMLSRGFKDQ----IYDVFKHLNNDV  221 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h~~~~~~~~~~----~~~~~~~l~~~~  221 (258)
                      ....|+....+..+.+.+.++|+|+||++|..++.++ ...++++++|||||+|.+.+..++..    +.++...++.+.
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~  160 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSA  160 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCC
Confidence            8899998888777777778999999999999887653 34689999999999999987655544    344444456778


Q ss_pred             cEEEEEeeCChhHHHHHHHhcC-CCeEE
Q psy4698         222 QVILLSATMPADVLDVSMKFMR-DPIKI  248 (258)
Q Consensus       222 ~~i~~SAT~~~~~~~~~~~~~~-~~~~v  248 (258)
                      |+|++|||+++ .+++.+++.. +|+.|
T Consensus       161 QrIgLSATI~n-~eevA~~L~g~~pv~I  187 (1490)
T PRK09751        161 QRIGLSATVRS-ASDVAAFLGGDRPVTV  187 (1490)
T ss_pred             eEEEEEeeCCC-HHHHHHHhcCCCCEEE
Confidence            99999999987 4666654443 35554

>KOG0952|consensus

Probab=99.89  E-value=8.7e-23  Score=187.94  Aligned_cols=170  Identities=21%  Similarity=0.352  Sum_probs=133.3

Q ss_pred             CCCCCCcHHHHHHhhhhh-cCCcEEEEcccCCCcchHhHHHHHHHhhhc-------cccceEEEEeccHHHHHHHHHHHH
Q psy4698          65 YGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISILQQVDQN-------IKECQALILAPTRELAQQIQKVVI  136 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~-~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-------~~~~~~lil~P~~~l~~q~~~~~~  136 (258)
                      +++..++.+|.+++|.+- ...|.+||||||||||..+++.+++.+.+.       ....+++|++|+++||.+..+.+.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHh
Confidence            577889999999999865 557999999999999999999999988752       345689999999999999998887


Q ss_pred             HhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC----CCCCccEEEEccchhhhccCcHHHHHH
Q psy4698         137 ALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL----STKQIRMFVLDEADEMLSRGFKDQIYD  212 (258)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~----~~~~l~~lVvDE~h~~~~~~~~~~~~~  212 (258)
                      +-....++.+..+.|+......  .+ ..++|+|+||++ ++++.+...    .++.++++|+||+|.+ ....+..++.
T Consensus       186 kkl~~~gi~v~ELTGD~ql~~t--ei-~~tqiiVTTPEK-wDvvTRk~~~d~~l~~~V~LviIDEVHlL-hd~RGpvlEt  260 (1230)
T KOG0952|consen  186 KKLAPLGISVRELTGDTQLTKT--EI-ADTQIIVTTPEK-WDVVTRKSVGDSALFSLVRLVIIDEVHLL-HDDRGPVLET  260 (1230)
T ss_pred             hhcccccceEEEecCcchhhHH--HH-HhcCEEEecccc-eeeeeeeeccchhhhhheeeEEeeeehhh-cCcccchHHH
Confidence            7667778999888888654332  22 238999999999 555554322    3467899999999954 5557777777


Q ss_pred             HHHhCC-------CCccEEEEEeeCChhHHHHHHH
Q psy4698         213 VFKHLN-------NDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       213 ~~~~l~-------~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      ++.++.       ...+++++|||+|+ +++++++
T Consensus       261 iVaRtlr~vessqs~IRivgLSATlPN-~eDvA~f  294 (1230)
T KOG0952|consen  261 IVARTLRLVESSQSMIRIVGLSATLPN-YEDVARF  294 (1230)
T ss_pred             HHHHHHHHHHhhhhheEEEEeeccCCC-HHHHHHH
Confidence            776653       56899999999996 3555543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.88  E-value=1.3e-21  Score=181.39  Aligned_cols=163  Identities=20%  Similarity=0.257  Sum_probs=125.6

Q ss_pred             HHHHHHHCCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHH
Q psy4698          58 LLRGIYAYGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI  131 (258)
Q Consensus        58 l~~~l~~~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~  131 (258)
                      +.+.+...+| .|++.|.++++.+..+      .+.+++|+||||||++|+++++..+..   +.+++|++||++|+.|+
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---g~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---GYQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEECCHHHHHHHH
Confidence            3344556677 7999999999999876      258999999999999999999988764   35899999999999999


Q ss_pred             HHHHHHhcCCCCceEEEEECCcchHH---HHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH
Q psy4698         132 QKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK  207 (258)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~  207 (258)
                      ++.++++....++.+..+.|+.....   ....+.. .++|+|+||+.+.+     .+.+++++++|+||+|++...   
T Consensus       301 ~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~---  372 (630)
T TIGR00643       301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVE---  372 (630)
T ss_pred             HHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHH---
Confidence            99999998888899999988876543   3334443 48999999987642     356789999999999985321   


Q ss_pred             HHHHHHHHhCC--CCccEEEEEeeCChh
Q psy4698         208 DQIYDVFKHLN--NDVQVILLSATMPAD  233 (258)
Q Consensus       208 ~~~~~~~~~l~--~~~~~i~~SAT~~~~  233 (258)
                       +...+.....  ..+++++||||..+.
T Consensus       373 -qr~~l~~~~~~~~~~~~l~~SATp~pr  399 (630)
T TIGR00643       373 -QRKKLREKGQGGFTPHVLVMSATPIPR  399 (630)
T ss_pred             -HHHHHHHhcccCCCCCEEEEeCCCCcH
Confidence             1122222222  268999999997544

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.88  E-value=5e-22  Score=182.96  Aligned_cols=172  Identities=16%  Similarity=0.158  Sum_probs=127.2

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcchH---------hHHHHHHHhhh---ccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTAT---------FSISILQQVDQ---NIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~---------~l~~~l~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      ..+|.++++.+.+|+++++.|+||||||.+         |+++.+..+..   ...+.++++++|+++++.|....+.+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~  245 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKS  245 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHH
Confidence            458999999999999999999999999998         33444444421   334568999999999999999888765


Q ss_pred             cCC---CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHH
Q psy4698         139 GDF---MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFK  215 (258)
Q Consensus       139 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~  215 (258)
                      ...   .+..+...+|+...... .....+.+|+|+|++..       ...++++++||+||||++...+  ..+..+++
T Consensus       246 vg~~~~~g~~v~v~~Gg~~~~~~-~t~~k~~~Ilv~T~~L~-------l~~L~~v~~VVIDEaHEr~~~~--DllL~llk  315 (675)
T PHA02653        246 LGFDEIDGSPISLKYGSIPDELI-NTNPKPYGLVFSTHKLT-------LNKLFDYGTVIIDEVHEHDQIG--DIIIAVAR  315 (675)
T ss_pred             hCccccCCceEEEEECCcchHHh-hcccCCCCEEEEeCccc-------ccccccCCEEEccccccCccch--hHHHHHHH
Confidence            433   34566777888663211 22223579999997521       1357889999999999986553  45555665


Q ss_pred             hCC-CCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         216 HLN-NDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       216 ~l~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      .+. +..|+++||||++.+++.+ ..|+.+|..|.+++.
T Consensus       316 ~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr  353 (675)
T PHA02653        316 KHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG  353 (675)
T ss_pred             HhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC
Confidence            543 3459999999999998877 578999999998754

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

Probab=99.87  E-value=4e-21  Score=165.97  Aligned_cols=182  Identities=16%  Similarity=0.178  Sum_probs=151.4

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      +...++.||.......+.+ |++++.|||-|||+++.+.+...+...++  ++|+++||+-|+.|....|+++..-..-.
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~   88 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIPEDE   88 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCChhh
Confidence            3447899999999877776 79999999999999999999888887654  89999999999999999999987554555


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEE
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVIL  225 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~  225 (258)
                      +..+.|..... .........+|+|+||+.+.+-+..+.+++.++.++|+||||+-..+..+..+....-...+++.+++
T Consensus        89 i~~ltGev~p~-~R~~~w~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~ilg  167 (542)
T COG1111          89 IAALTGEVRPE-EREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLILG  167 (542)
T ss_pred             eeeecCCCChH-HHHHHHhhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhccCceEEE
Confidence            55666655443 33445566799999999999999999999999999999999999888888888877767778899999


Q ss_pred             EEeeCCh---hHHHHHHHhcCCCeEEEec
Q psy4698         226 LSATMPA---DVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       226 ~SAT~~~---~~~~~~~~~~~~~~~v~~~  251 (258)
                      +|||.-.   .+++.++......++|++.
T Consensus       168 LTASPGs~~ekI~eV~~nLgIe~vevrTE  196 (542)
T COG1111         168 LTASPGSDLEKIQEVVENLGIEKVEVRTE  196 (542)
T ss_pred             EecCCCCCHHHHHHHHHhCCcceEEEecC
Confidence            9999744   5777788888889998884

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.87  E-value=6.6e-21  Score=179.27  Aligned_cols=173  Identities=18%  Similarity=0.264  Sum_probs=131.0

Q ss_pred             HHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHH-HhcCCCCceEEEEE
Q psy4698          72 AIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI-ALGDFMSVSCHACI  150 (258)
Q Consensus        72 ~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~  150 (258)
                      .+-.+.+..+..+.+++++|+||||||+++.+++++...   .+++++++.|+++++.|.++.+. .++...+..+....
T Consensus         5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~v   81 (819)
T TIGR01970         5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRV   81 (819)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEE
Confidence            444566777788899999999999999999999998763   34589999999999999999875 45555555554433


Q ss_pred             CCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchh-hhccCcHHH-HHHHHHhCCCCccEEEEEe
Q psy4698         151 GGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE-MLSRGFKDQ-IYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       151 ~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~-~~~~~~~~~-~~~~~~~l~~~~~~i~~SA  228 (258)
                      ....      ....+.+|+|+|++.|++++... ..++++++||+||+|+ .++.++... +..+...++++.|+|+|||
T Consensus        82 r~~~------~~s~~t~I~v~T~G~Llr~l~~d-~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSA  154 (819)
T TIGR01970        82 RGEN------KVSRRTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSA  154 (819)
T ss_pred             cccc------ccCCCCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeC
Confidence            3321      22344789999999999998874 5789999999999995 666555433 3455666788999999999


Q ss_pred             eCChhHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         229 TMPADVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       229 T~~~~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                      |++.+.   +..|+.++.+|.+.+...++
T Consensus       155 Tl~~~~---l~~~l~~~~vI~~~gr~~pV  180 (819)
T TIGR01970       155 TLDGER---LSSLLPDAPVVESEGRSFPV  180 (819)
T ss_pred             CCCHHH---HHHHcCCCcEEEecCcceee
Confidence            999753   45677777777776655443

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.86  E-value=3.8e-21  Score=174.03  Aligned_cols=150  Identities=19%  Similarity=0.202  Sum_probs=113.8

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      ..|+++|.++++.++.+++.++.+|||+|||+++... ...+... ...++||++|+++|+.|+.+.+++++......+.
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l-~~~~~~~-~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~  190 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLL-SRYYLEN-YEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMH  190 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHH-HHHHHhc-CCCeEEEEECcHHHHHHHHHHHHHhcccccccee
Confidence            4899999999999999999999999999999976432 2222222 3348999999999999999999988754444444


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ...++....       .+.+|+|+|++++.+...   ..++++++||+||||++...    .+..++..+++..+++++|
T Consensus       191 ~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~----~~~~il~~~~~~~~~lGLT  256 (501)
T PHA02558        191 KIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGK----SLTSIITKLDNCKFKFGLT  256 (501)
T ss_pred             EEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccch----hHHHHHHhhhccceEEEEe
Confidence            444444221       346899999999875442   24678999999999998643    4556777776678899999


Q ss_pred             eeCChh
Q psy4698         228 ATMPAD  233 (258)
Q Consensus       228 AT~~~~  233 (258)
                      ||++..
T Consensus       257 ATp~~~  262 (501)
T PHA02558        257 GSLRDG  262 (501)
T ss_pred             ccCCCc
Confidence            999754

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.86  E-value=1.8e-20  Score=176.53  Aligned_cols=173  Identities=20%  Similarity=0.312  Sum_probs=129.2

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH-hcCCCCceEEEE
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA-LGDFMSVSCHAC  149 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~  149 (258)
                      ..+-.+.+.++.+++++++.|+||||||+++.+++++....   ++++++++|+++++.|.++.+.+ ++...+..+...
T Consensus         7 ~~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~   83 (812)
T PRK11664          7 AAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYR   83 (812)
T ss_pred             HHHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEE
Confidence            34445666778888999999999999999999999876432   24899999999999999998754 566666666555


Q ss_pred             ECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh-hccCc-HHHHHHHHHhCCCCccEEEEE
Q psy4698         150 IGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM-LSRGF-KDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~-~~~~~-~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .++...      .....+|+|+||+.|++++... ..++++++||+||+|+. ++.++ ...+..+++.++++.|+|+||
T Consensus        84 vr~~~~------~~~~t~I~v~T~G~Llr~l~~d-~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmS  156 (812)
T PRK11664         84 MRAESK------VGPNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMS  156 (812)
T ss_pred             ecCccc------cCCCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEe
Confidence            544321      1234689999999999998864 47899999999999973 33332 233445667788899999999


Q ss_pred             eeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         228 ATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       228 AT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      ||++.+   .+..|+.++.+|.+.+....
T Consensus       157 ATl~~~---~l~~~~~~~~~I~~~gr~~p  182 (812)
T PRK11664        157 ATLDND---RLQQLLPDAPVIVSEGRSFP  182 (812)
T ss_pred             cCCCHH---HHHHhcCCCCEEEecCcccc
Confidence            999865   23567777777777665443

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

Probab=99.86  E-value=1.1e-20  Score=177.39  Aligned_cols=177  Identities=23%  Similarity=0.288  Sum_probs=145.6

Q ss_pred             HCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          64 AYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        64 ~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      ..+| .+-++|++++-.+..|.++++++|||+|||++...++...+..+.   +++|.+|.++|.+|.++.+........
T Consensus       115 ~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~q---rviYTsPIKALsNQKyrdl~~~fgdv~  190 (1041)
T COG4581         115 EYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQ---RVIYTSPIKALSNQKYRDLLAKFGDVA  190 (1041)
T ss_pred             hCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCC---ceEeccchhhhhhhHHHHHHHHhhhhh
Confidence            3567 899999999999999999999999999999999888877776653   699999999999999988766433222


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccE
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV  223 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~  223 (258)
                      -.+..+.|+.       .+++++.|+|.|.+.|..++.++...+.++.+||+||+|.|-+...+.-....+-.+|...|+
T Consensus       191 ~~vGL~TGDv-------~IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v~~  263 (1041)
T COG4581         191 DMVGLMTGDV-------SINPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRF  263 (1041)
T ss_pred             hhccceecce-------eeCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCCcE
Confidence            2234445554       456778999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeeCChhHHHHHHHhc---CCCeEEEecC
Q psy4698         224 ILLSATMPADVLDVSMKFM---RDPIKILVKK  252 (258)
Q Consensus       224 i~~SAT~~~~~~~~~~~~~---~~~~~v~~~~  252 (258)
                      |++|||+|+. ++|..|+.   ..|..|.+.+
T Consensus       264 v~LSATv~N~-~EF~~Wi~~~~~~~~~vv~t~  294 (1041)
T COG4581         264 VFLSATVPNA-EEFAEWIQRVHSQPIHVVSTE  294 (1041)
T ss_pred             EEEeCCCCCH-HHHHHHHHhccCCCeEEEeec
Confidence            9999999976 55666654   2455554433

>PRK13766 Hef nuclease; Provisional

Probab=99.85  E-value=5.8e-20  Score=174.86  Aligned_cols=178  Identities=19%  Similarity=0.222  Sum_probs=136.4

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      +...+++||.+++..++.+ ++++++|||+|||+++++++...+.  ..+.++||++|+++|+.|+...++.+.......
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~   88 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEK   88 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCce
Confidence            3447899999999888777 8999999999999999988887773  234589999999999999999998876543445


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEE
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVIL  225 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~  225 (258)
                      +..+.|+..... ...+..+++|+|+||+.+...+..+.+.+.++++||+||||++.....+..+...+....+.+++++
T Consensus        89 v~~~~g~~~~~~-r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~il~  167 (773)
T PRK13766         89 IVVFTGEVSPEK-RAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLVLG  167 (773)
T ss_pred             EEEEeCCCCHHH-HHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEEEE
Confidence            666666655433 3445556899999999998887777788899999999999998766566666666666666788999


Q ss_pred             EEeeCCh---hHHHHHHHhcCCCeE
Q psy4698         226 LSATMPA---DVLDVSMKFMRDPIK  247 (258)
Q Consensus       226 ~SAT~~~---~~~~~~~~~~~~~~~  247 (258)
                      +|||...   .+...++......+.
T Consensus       168 lTaTP~~~~~~i~~~~~~L~i~~v~  192 (773)
T PRK13766        168 LTASPGSDEEKIKEVCENLGIEHVE  192 (773)
T ss_pred             EEcCCCCCHHHHHHHHHhCCceEEE
Confidence            9999643   344444444333333

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.85  E-value=3.5e-20  Score=161.03  Aligned_cols=168  Identities=14%  Similarity=0.141  Sum_probs=117.6

Q ss_pred             HHHHHhhhhhcCCc--EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC----CCceE
Q psy4698          73 IQQRAIIPCVRGND--VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF----MSVSC  146 (258)
Q Consensus        73 ~Q~~~~~~l~~g~~--~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~----~~~~~  146 (258)
                      +|.++++.+.++++  +++++|||||||.+++++++..      +.+++|++|+++|++|+++.++.+...    .+..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------ENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            59999999998874  7899999999999999998742      236899999999999999998887532    24444


Q ss_pred             EEEECCcchH--HH-----------------HH-HHhcCCcEEEeChHHHHHHHhcC----C-C---CCCCccEEEEccc
Q psy4698         147 HACIGGTIVR--DD-----------------IR-KLEAGAQVVVGTPGRVFDMISRG----A-L---STKQIRMFVLDEA  198 (258)
Q Consensus       147 ~~~~~~~~~~--~~-----------------~~-~~~~~~~Ilv~Tp~~l~~~l~~~----~-~---~~~~l~~lVvDE~  198 (258)
                      ..+.|.....  ..                 .. .....+.|+++||+.+..++...    . .   .+.++++||+||+
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~  154 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEF  154 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecc
Confidence            4444432111  00                 00 11235788999999987665431    1 1   2478999999999


Q ss_pred             hhhhccCc-----HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh--cCCCe
Q psy4698         199 DEMLSRGF-----KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF--MRDPI  246 (258)
Q Consensus       199 h~~~~~~~-----~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~  246 (258)
                      |.+.....     ......+++......+++++|||++..+.+.++..  +.+++
T Consensus       155 H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~  209 (357)
T TIGR03158       155 HLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKI  209 (357)
T ss_pred             cccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCcee
Confidence            98653321     12333444444446799999999999988888765  55554

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.

>KOG0354|consensus

Probab=99.85  E-value=1.8e-20  Score=170.09  Aligned_cols=168  Identities=20%  Similarity=0.242  Sum_probs=131.5

Q ss_pred             CCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          67 FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        67 ~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      ...++.||.+.....+ |+|++|++|||+|||+++...+++.+....+ .++++++|++-|+.|+...+..++..  ..+
T Consensus        60 ~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~~~~~~~~--~~~  135 (746)
T KOG0354|consen   60 NLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIACFSIYLIP--YSV  135 (746)
T ss_pred             cccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHHHhhccCc--ccc
Confidence            4479999999998888 9999999999999999998888888777644 69999999999999999767666654  344


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCC-CCCccEEEEccchhhhccCcHHHHH-HHHHhCCCCccEE
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALS-TKQIRMFVLDEADEMLSRGFKDQIY-DVFKHLNNDVQVI  224 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~-~~~l~~lVvDE~h~~~~~~~~~~~~-~~~~~l~~~~~~i  224 (258)
                      ....++.........+....+|+|+||+.+..-+.++... ++.+.++||||||+-..+.-+..+. ..+..-....|+|
T Consensus       136 T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~qIL  215 (746)
T KOG0354|consen  136 TGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKNQGNQIL  215 (746)
T ss_pred             eeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHhhhccccEE
Confidence            4445554443333355666899999999999888775433 5889999999999998887777666 4555544555999


Q ss_pred             EEEeeCChhHHHHH
Q psy4698         225 LLSATMPADVLDVS  238 (258)
Q Consensus       225 ~~SAT~~~~~~~~~  238 (258)
                      ++|||+-++.....
T Consensus       216 gLTASpG~~~~~v~  229 (746)
T KOG0354|consen  216 GLTASPGSKLEQVQ  229 (746)
T ss_pred             EEecCCCccHHHHH
Confidence            99999977655544

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.84  E-value=3.1e-20  Score=172.45  Aligned_cols=148  Identities=17%  Similarity=0.267  Sum_probs=127.2

Q ss_pred             CCCCCCHHHHHHHH-----HCCCCCC---cHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE
Q psy4698          50 DDMELSEELLRGIY-----AYGFEKP---SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL  121 (258)
Q Consensus        50 ~~~~~~~~l~~~l~-----~~~~~~~---~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil  121 (258)
                      +.+++...+.+.+.     ..|+..|   +|+|.++++.+..+++++..++||+|||++|.+|++..+..+.   .++|+
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~IV  141 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHLV  141 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEEE
Confidence            45566667766665     4577777   9999999999999999999999999999999999998876542   48999


Q ss_pred             eccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCCCCCC-------CccEE
Q psy4698         122 APTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGALSTK-------QIRMF  193 (258)
Q Consensus       122 ~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~~~~~-------~l~~l  193 (258)
                      +|+++||.|..+.+..+....++++.++.|+.....+...+  +++|+|+||++| +++++.+.+.++       .+.++
T Consensus       142 TpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~  219 (970)
T PRK12899        142 TVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFA  219 (970)
T ss_pred             eCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEE
Confidence            99999999999999999999999999999998877665444  589999999999 999998866665       55899


Q ss_pred             EEccchhhh
Q psy4698         194 VLDEADEML  202 (258)
Q Consensus       194 VvDE~h~~~  202 (258)
                      |+||||+|+
T Consensus       220 IIDEADsmL  228 (970)
T PRK12899        220 IIDEVDSIL  228 (970)
T ss_pred             EEechhhhh
Confidence            999999886

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.82  E-value=8.8e-19  Score=131.40  Aligned_cols=144  Identities=39%  Similarity=0.555  Sum_probs=111.7

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +++++.++||+|||.+++..+....... ...+++|++|+..++.++...+...... ...+....+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-cCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            4689999999999999988887776652 3458999999999999999988887654 5666666766665555555566


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ..+|+++|++.+.+............+++|+||+|.+....................+++++|||+
T Consensus        79 ~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          79 KTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             CCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            789999999999888776655566789999999999876654444333444456778999999995

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

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.82  E-value=9.6e-20  Score=158.80  Aligned_cols=154  Identities=19%  Similarity=0.177  Sum_probs=106.3

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcch----------
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIV----------  155 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~----------  155 (258)
                      ++++.+|||||||++++++++..+... .+.+++|++|+++|+.|+++.++.+...   .+...++....          
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            479999999999999999999886543 4568999999999999999999886321   22222222210          


Q ss_pred             --HHHHHHH-h-----cCCcEEEeChHHHHHHHhcCC----CCCC--CccEEEEccchhhhccCcHHHHHHHHHhCC-CC
Q psy4698         156 --RDDIRKL-E-----AGAQVVVGTPGRVFDMISRGA----LSTK--QIRMFVLDEADEMLSRGFKDQIYDVFKHLN-ND  220 (258)
Q Consensus       156 --~~~~~~~-~-----~~~~Ilv~Tp~~l~~~l~~~~----~~~~--~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~-~~  220 (258)
                        ....... .     ...+|+|+||++++..+..+.    +.+.  ..++||+||+|.+.+.+... +..+++.+. .+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~l~~~~  155 (358)
T TIGR01587        77 EFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEVLKDND  155 (358)
T ss_pred             hHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHHHHHcC
Confidence              0000000 1     126799999999988766521    1111  23789999999987653333 555555554 47


Q ss_pred             ccEEEEEeeCChhHHHHHHHhcCC
Q psy4698         221 VQVILLSATMPADVLDVSMKFMRD  244 (258)
Q Consensus       221 ~~~i~~SAT~~~~~~~~~~~~~~~  244 (258)
                      +|+++||||+|+.+.++.+.+...
T Consensus       156 ~~~i~~SATlp~~l~~~~~~~~~~  179 (358)
T TIGR01587       156 VPILLMSATLPKFLKEYAEKIGYV  179 (358)
T ss_pred             CCEEEEecCchHHHHHHHhcCCCc
Confidence            899999999998888877665443

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.

>KOG0947|consensus

Probab=99.81  E-value=2.1e-19  Score=164.38  Aligned_cols=161  Identities=22%  Similarity=0.268  Sum_probs=136.8

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      ..| .+-.+|++|+-++..|.+++|.|+|.+|||+++..++...-.   ...|++|.+|-++|.+|.++.++......+ 
T Consensus       294 ~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~---h~TR~iYTSPIKALSNQKfRDFk~tF~Dvg-  368 (1248)
T KOG0947|consen  294 YPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQK---HMTRTIYTSPIKALSNQKFRDFKETFGDVG-  368 (1248)
T ss_pred             CCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHh---hccceEecchhhhhccchHHHHHHhccccc-
Confidence            445 789999999999999999999999999999999776643322   345899999999999999999988655544 


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                         .+.|+.       .++..+.++|.|.+.|..++.++.--..++.+||+||+|.+-+...+.-...++-.+|+++++|
T Consensus       369 ---LlTGDv-------qinPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~~I  438 (1248)
T KOG0947|consen  369 ---LLTGDV-------QINPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVNFI  438 (1248)
T ss_pred             ---eeecce-------eeCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccceEE
Confidence               445554       4456689999999999999999988889999999999999888888989999999999999999


Q ss_pred             EEEeeCChhHHHHHHHh
Q psy4698         225 LLSATMPADVLDVSMKF  241 (258)
Q Consensus       225 ~~SAT~~~~~~~~~~~~  241 (258)
                      ++|||+|+. .+|+.|-
T Consensus       439 lLSATVPN~-~EFA~WI  454 (1248)
T KOG0947|consen  439 LLSATVPNT-LEFADWI  454 (1248)
T ss_pred             EEeccCCCh-HHHHHHh
Confidence            999999986 4566664

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

Probab=99.80  E-value=9.3e-19  Score=156.92  Aligned_cols=173  Identities=21%  Similarity=0.260  Sum_probs=131.0

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      +|+..+++-|.+++..+++|+++++.+|||.||++||.+|++-.      .+-+|||+|..+|..++.+.++..+    +
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~------~G~TLVVSPLiSLM~DQV~~l~~~G----i   82 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------EGLTLVVSPLISLMKDQVDQLEAAG----I   82 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc------CCCEEEECchHHHHHHHHHHHHHcC----c
Confidence            68999999999999999999999999999999999999999765      2369999999999999999998875    4


Q ss_pred             eEEEEECCcchH---HHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC--cHHHH---HHHHH
Q psy4698         145 SCHACIGGTIVR---DDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG--FKDQI---YDVFK  215 (258)
Q Consensus       145 ~~~~~~~~~~~~---~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~--~~~~~---~~~~~  215 (258)
                      ....+.+..+..   .....+..+ .++++-+||++..--..+.+.--.+.++||||||+++.|+  |...+   -.+..
T Consensus        83 ~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~  162 (590)
T COG0514          83 RAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRA  162 (590)
T ss_pred             eeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHHHHHh
Confidence            444444443322   233344444 8999999999754221111224467899999999999986  55444   45566


Q ss_pred             hCCCCccEEEEEeeCChhHHHHHHHhc--CCCeEE
Q psy4698         216 HLNNDVQVILLSATMPADVLDVSMKFM--RDPIKI  248 (258)
Q Consensus       216 ~l~~~~~~i~~SAT~~~~~~~~~~~~~--~~~~~v  248 (258)
                      .++ +++++.+|||-+..+++-+...+  ++++++
T Consensus       163 ~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~  196 (590)
T COG0514         163 GLP-NPPVLALTATATPRVRDDIREQLGLQDANIF  196 (590)
T ss_pred             hCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceE
Confidence            665 78899999999999888766644  455343

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.80  E-value=5e-18  Score=158.26  Aligned_cols=156  Identities=22%  Similarity=0.264  Sum_probs=116.6

Q ss_pred             CCcHHHHHHhhhhhcC---CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          69 KPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g---~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      .+++.|.++++.+..+   +++++.|+||||||.+|+.++...+..   +.++||++|+++|+.|+.+.+++..   +..
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---g~~vLvLvPt~~L~~Q~~~~l~~~f---g~~  217 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---GKQALVLVPEIALTPQMLARFRARF---GAP  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh---CCC
Confidence            5899999999999874   789999999999999998877766654   3489999999999999999998753   356


Q ss_pred             EEEEECCcchHH---HHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc-----HHHHHHHHHh
Q psy4698         146 CHACIGGTIVRD---DIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF-----KDQIYDVFKH  216 (258)
Q Consensus       146 ~~~~~~~~~~~~---~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~-----~~~~~~~~~~  216 (258)
                      +..++++....+   .+..+. +..+|+|+|++.++       ..++++++||+||+|.....+.     ...-...++.
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra  290 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRA  290 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHh
Confidence            777777755432   233333 44899999998765       4678999999999997643221     1112233444


Q ss_pred             CCCCccEEEEEeeCChhHHHH
Q psy4698         217 LNNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       217 l~~~~~~i~~SAT~~~~~~~~  237 (258)
                      ...+.+++++|||.+.+....
T Consensus       291 ~~~~~~~il~SATps~~s~~~  311 (679)
T PRK05580        291 KLENIPVVLGSATPSLESLAN  311 (679)
T ss_pred             hccCCCEEEEcCCCCHHHHHH
Confidence            457889999999987554433

>KOG0349|consensus

Probab=99.79  E-value=6.1e-19  Score=149.78  Aligned_cols=140  Identities=34%  Similarity=0.558  Sum_probs=122.0

Q ss_pred             EEEEeccHHHHHHHHHHHHHhc---CCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEE
Q psy4698         118 ALILAPTRELAQQIQKVVIALG---DFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV  194 (258)
Q Consensus       118 ~lil~P~~~l~~q~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lV  194 (258)
                      ++|+-|+++|++|..+.+++|.   ++..++...+.|+...+.+...++++.+|+|+||+++.+++..+.+.+..++++|
T Consensus       289 avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crFlv  368 (725)
T KOG0349|consen  289 AVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFLV  368 (725)
T ss_pred             eeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEEEE
Confidence            8999999999999999666654   3445566677888888999999999999999999999999999999999999999


Q ss_pred             EccchhhhccCcHHHHHHHHHhCCC------CccEEEEEeeCCh-hHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         195 LDEADEMLSRGFKDQIYDVFKHLNN------DVQVILLSATMPA-DVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       195 vDE~h~~~~~~~~~~~~~~~~~l~~------~~~~i~~SAT~~~-~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                      +||++-++..++...+.++...++.      ..|.+..|||+.- +++......|.-|.-|...++++-+
T Consensus       369 lDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vp  438 (725)
T KOG0349|consen  369 LDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVP  438 (725)
T ss_pred             ecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccc
Confidence            9999999998899999988888763      5799999999965 7888888899999999988888744

>KOG0948|consensus

Probab=99.78  E-value=5.9e-19  Score=158.13  Aligned_cols=173  Identities=19%  Similarity=0.246  Sum_probs=144.2

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .+-|+|..++.-+-.+.++++.|.|.+|||.++..++...+..+.   |+||.+|-++|.+|.++.+..-.+.    +..
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ---RVIYTSPIKALSNQKYREl~~EF~D----VGL  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ---RVIYTSPIKALSNQKYRELLEEFKD----VGL  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC---eEEeeChhhhhcchhHHHHHHHhcc----cce
Confidence            678999999998999999999999999999999999988887754   8999999999999999887664433    334


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      ..|+.       .++..+.++|.|.+.|..++.++.--+..+.|+|+||+|.|-+...+--+..-+-.+|++.+.+++||
T Consensus       202 MTGDV-------TInP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  202 MTGDV-------TINPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             eecce-------eeCCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence            44544       45566899999999999999999888999999999999999888888777777778899999999999


Q ss_pred             eCChhHHHHHHHhc---CCCeEEEecCCccc
Q psy4698         229 TMPADVLDVSMKFM---RDPIKILVKKEELT  256 (258)
Q Consensus       229 T~~~~~~~~~~~~~---~~~~~v~~~~~~~~  256 (258)
                      |+|+. .+|++|-.   +.|.+|.-.+.-.|
T Consensus       275 TiPNA-~qFAeWI~~ihkQPcHVVYTdyRPT  304 (1041)
T KOG0948|consen  275 TIPNA-RQFAEWICHIHKQPCHVVYTDYRPT  304 (1041)
T ss_pred             cCCCH-HHHHHHHHHHhcCCceEEeecCCCC
Confidence            99976 55776633   37777765555544

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

Probab=99.78  E-value=3.4e-18  Score=134.73  Aligned_cols=153  Identities=20%  Similarity=0.179  Sum_probs=101.9

Q ss_pred             CCcHHHHHHhhhhhc-------CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          69 KPSAIQQRAIIPCVR-------GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~-------g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      +++++|.+++..+..       .+++++.+|||||||.+++..+.....      ++++++|+..++.|+...+..+...
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~~~~~~   76 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFDDFGSE   76 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHHHhhhh
Confidence            589999999998873       588999999999999998755544433      7999999999999999999766543


Q ss_pred             CCceEEEE-----------ECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC-----------CCCCCccEEEEccch
Q psy4698         142 MSVSCHAC-----------IGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA-----------LSTKQIRMFVLDEAD  199 (258)
Q Consensus       142 ~~~~~~~~-----------~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~-----------~~~~~l~~lVvDE~h  199 (258)
                      ........           .................+++++|.+.+........           ......++||+||+|
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH  156 (184)
T PF04851_consen   77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAH  156 (184)
T ss_dssp             SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGG
T ss_pred             hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhh
Confidence            22111110           01111112222334457999999999987765321           223467899999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      ++.....   ...++.  .+...+|+||||.++
T Consensus       157 ~~~~~~~---~~~i~~--~~~~~~l~lTATp~r  184 (184)
T PF04851_consen  157 HYPSDSS---YREIIE--FKAAFILGLTATPFR  184 (184)
T ss_dssp             CTHHHHH---HHHHHH--SSCCEEEEEESS-S-
T ss_pred             hcCCHHH---HHHHHc--CCCCeEEEEEeCccC
Confidence            8754432   333444  456779999999763

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

>KOG0951|consensus

Probab=99.74  E-value=1.3e-17  Score=156.28  Aligned_cols=180  Identities=22%  Similarity=0.372  Sum_probs=136.5

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhccc--------cceEEEEec
Q psy4698          53 ELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQNIK--------ECQALILAP  123 (258)
Q Consensus        53 ~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~--------~~~~lil~P  123 (258)
                      .++.+-..++  .|...++++|..+..+.+.+ .|+++|||||+|||-++++.+++.+....+        ..+++|++|
T Consensus       295 elP~Wnq~aF--~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAP  372 (1674)
T KOG0951|consen  295 ELPKWNQPAF--FGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAP  372 (1674)
T ss_pred             CCcchhhhhc--ccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEee
Confidence            3445555555  46667999999999998877 589999999999999999999999866422        348999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCC---CCCccEEEEccchh
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALS---TKQIRMFVLDEADE  200 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~---~~~l~~lVvDE~h~  200 (258)
                      .++|++.+...+.+.....++.+....|+......  .+. +.+|+||||+. ++.+.++.-.   .+-++++|+||+|.
T Consensus       373 mKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~--qie-eTqVIV~TPEK-~DiITRk~gdraY~qlvrLlIIDEIHL  448 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKE--QIE-ETQVIVTTPEK-WDIITRKSGDRAYEQLVRLLIIDEIHL  448 (1674)
T ss_pred             HHHHHHHHHHHHHhhccccCcEEEEecccccchhh--hhh-cceeEEeccch-hhhhhcccCchhHHHHHHHHhhhhhhh
Confidence            99999999998888888889999888887653322  222 37999999999 5566654322   23578999999995


Q ss_pred             hhccCcHHHHHHHHHhC-------CCCccEEEEEeeCCh--hHHHHHH
Q psy4698         201 MLSRGFKDQIYDVFKHL-------NNDVQVILLSATMPA--DVLDVSM  239 (258)
Q Consensus       201 ~~~~~~~~~~~~~~~~l-------~~~~~~i~~SAT~~~--~~~~~~~  239 (258)
                      + ....+..+..+..+.       ...++++++|||+|+  ++..|++
T Consensus       449 L-hDdRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy~DV~~Fl~  495 (1674)
T KOG0951|consen  449 L-HDDRGPVLESIVARTFRRSESTEEGSRLVGLSATLPNYEDVASFLR  495 (1674)
T ss_pred             c-ccccchHHHHHHHHHHHHhhhcccCceeeeecccCCchhhhHHHhc
Confidence            4 445676666655543       246899999999997  4454444

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.74  E-value=7.4e-17  Score=155.82  Aligned_cols=170  Identities=21%  Similarity=0.225  Sum_probs=111.4

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc----HHHHHHHHHHHHH-hcCCCCce
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT----RELAQQIQKVVIA-LGDFMSVS  145 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~----~~l~~q~~~~~~~-~~~~~~~~  145 (258)
                      ..+..+.+..+..++.++|+|+||||||+.  +|.+-.-...+..+++++..|.    ++++.++.+.+.. ++...++.
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTTq--lPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~  153 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTTQ--LPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYK  153 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHHH--HHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceecee
Confidence            455566777777788899999999999995  4532221111222345556685    4566666665543 44433332


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccch-hhhccCcHHH-HHHHHHhCCCCccE
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEAD-EMLSRGFKDQ-IYDVFKHLNNDVQV  223 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h-~~~~~~~~~~-~~~~~~~l~~~~~~  223 (258)
                      +..  ..        ....+++|+|+||+.|++.+.... .++++++||+|||| ++++.++... +..++.. +++.|+
T Consensus       154 vrf--~~--------~~s~~t~I~v~TpG~LL~~l~~d~-~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~-rpdlKv  221 (1294)
T PRK11131        154 VRF--ND--------QVSDNTMVKLMTDGILLAEIQQDR-LLMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPDLKV  221 (1294)
T ss_pred             ecC--cc--------ccCCCCCEEEEChHHHHHHHhcCC-ccccCcEEEecCccccccccchHHHHHHHhhhc-CCCceE
Confidence            211  00        113458999999999999998765 48999999999999 4677666543 3333322 357899


Q ss_pred             EEEEeeCChhHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         224 ILLSATMPADVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       224 i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                      |+||||++.  +.+.+.|.+.| +|.+++...++
T Consensus       222 ILmSATid~--e~fs~~F~~ap-vI~V~Gr~~pV  252 (1294)
T PRK11131        222 IITSATIDP--ERFSRHFNNAP-IIEVSGRTYPV  252 (1294)
T ss_pred             EEeeCCCCH--HHHHHHcCCCC-EEEEcCccccc
Confidence            999999974  56777777666 46776655543

>KOG0352|consensus

Probab=99.72  E-value=1.4e-16  Score=135.36  Aligned_cols=182  Identities=21%  Similarity=0.311  Sum_probs=127.3

Q ss_pred             HHHHHHHH-CCCCC-CcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          57 ELLRGIYA-YGFEK-PSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        57 ~l~~~l~~-~~~~~-~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      .+.+.|++ +|+.+ -++.|..++..+..+ +++.+++|||+||++||.+|.+..     . ..+|+++|..+|+.++.+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-----~-gITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-----G-GITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-----C-CeEEEehHHHHHHHHHHH
Confidence            34556665 46554 388999999987665 689999999999999999999764     2 279999999999999999


Q ss_pred             HHHHhcCCCCceEEEEECCcchHH------HHHHHhcCCcEEEeChHHHHH----HHhcCCCCCCCccEEEEccchhhhc
Q psy4698         134 VVIALGDFMSVSCHACIGGTIVRD------DIRKLEAGAQVVVGTPGRVFD----MISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~Ilv~Tp~~l~~----~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      .+.++.    +.+..+....+..+      ....-+....+++.||++...    -+-++...-.-++++||||||+...
T Consensus        80 HL~~LK----Vp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQ  155 (641)
T KOG0352|consen   80 HLKRLK----VPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQ  155 (641)
T ss_pred             HHHhcC----CchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhh
Confidence            987763    33333333332222      122223447899999997432    2222223334578999999999988


Q ss_pred             cC--cHHHHHH---HHHhCCCCccEEEEEeeCChhHHH--HHHHhcCCCeEEE
Q psy4698         204 RG--FKDQIYD---VFKHLNNDVQVILLSATMPADVLD--VSMKFMRDPIKIL  249 (258)
Q Consensus       204 ~~--~~~~~~~---~~~~l~~~~~~i~~SAT~~~~~~~--~~~~~~~~~~~v~  249 (258)
                      |+  |...+.+   +...+ ++...+.++||-+.++++  +....+++||-+.
T Consensus       156 WGHDFRPDYL~LG~LRS~~-~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiF  207 (641)
T KOG0352|consen  156 WGHDFRPDYLTLGSLRSVC-PGVPWVALTATANAKVQEDIAFQLKLRNPVAIF  207 (641)
T ss_pred             hccccCcchhhhhhHHhhC-CCCceEEeecccChhHHHHHHHHHhhcCcHHhc
Confidence            75  5555443   33333 567899999999999887  4455677887653

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.72  E-value=8.6e-17  Score=147.79  Aligned_cols=131  Identities=20%  Similarity=0.293  Sum_probs=110.7

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|++.|......+..|+  +..++||+|||+++.+|++.....+   .++.|++|+..||.|.+..+..+...+++
T Consensus        53 lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G---~~V~VvTpt~~LA~qdae~~~~l~~~LGL  126 (745)
T TIGR00963        53 LGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTG---KGVHVVTVNDYLAQRDAEWMGQVYRFLGL  126 (745)
T ss_pred             hCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhC---CCEEEEcCCHHHHHHHHHHHHHHhccCCC
Confidence            355 89999999999998887  9999999999999999996544443   36999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhhc
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~~  203 (258)
                      .+.+..++.........  ..++|+|+||+.| +++++.+      ...++++.++|+||+|+++-
T Consensus       127 sv~~i~g~~~~~~r~~~--y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LI  190 (745)
T TIGR00963       127 SVGLILSGMSPEERREA--YACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILI  190 (745)
T ss_pred             eEEEEeCCCCHHHHHHh--cCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhH
Confidence            99999988775544333  3479999999999 8888776      34678899999999998863

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.

>PRK09694 helicase Cas3; Provisional

Probab=99.70  E-value=2.2e-16  Score=149.17  Aligned_cols=170  Identities=19%  Similarity=0.148  Sum_probs=111.2

Q ss_pred             CCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCC--Cc
Q psy4698          67 FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM--SV  144 (258)
Q Consensus        67 ~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~--~~  144 (258)
                      ...|+++|..+.........+++.+|||+|||.+++.++...+. .+...+++|..||++++++.+.+++++....  ..
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~-~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~  362 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLID-QGLADSIIFALPTQATANAMLSRLEALASKLFPSP  362 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHH-hCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCC
Confidence            34799999988655444567999999999999999877665443 3334589999999999999999987643211  23


Q ss_pred             eEEEEECCcchH------------------------HHHHHHhcC---CcEEEeChHHHHHHHhc-CCCCCCC----ccE
Q psy4698         145 SCHACIGGTIVR------------------------DDIRKLEAG---AQVVVGTPGRVFDMISR-GALSTKQ----IRM  192 (258)
Q Consensus       145 ~~~~~~~~~~~~------------------------~~~~~~~~~---~~Ilv~Tp~~l~~~l~~-~~~~~~~----l~~  192 (258)
                      .+...+|.....                        .+.......   .+|+|||+++++...-. +...+..    -++
T Consensus       363 ~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~La~sv  442 (878)
T PRK09694        363 NLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFGLGRSV  442 (878)
T ss_pred             ceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHhhccCe
Confidence            445555543211                        111101111   68999999998754322 1111111    258


Q ss_pred             EEEccchhhhccCcHHHHHHHHHhCC-CCccEEEEEeeCChhHHHHH
Q psy4698         193 FVLDEADEMLSRGFKDQIYDVFKHLN-NDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       193 lVvDE~h~~~~~~~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~~~~  238 (258)
                      |||||+|.+ +......+..+++.+. ...++|+||||+|...++.+
T Consensus       443 vIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L  488 (878)
T PRK09694        443 LIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKL  488 (878)
T ss_pred             EEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHH
Confidence            999999965 4434445555555542 35789999999999876543

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.70  E-value=2.7e-16  Score=145.16  Aligned_cols=148  Identities=17%  Similarity=0.140  Sum_probs=104.4

Q ss_pred             CCcHHHHHHhhhhhc-C--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          69 KPSAIQQRAIIPCVR-G--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~-g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      .+++||.+++..+.. |  ++.++++|||+|||++.+..+...      +.++||+||+..|+.||.+.+.++.......
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l------~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~  328 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV------KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQ  328 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh------CCCEEEEeCcHHHHHHHHHHHHHhcCCCCce
Confidence            689999999998763 3  478999999999999987655432      2369999999999999999999886444445


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--------CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR--------GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~--------~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      +..+.++....     .....+|+|+|++.+.....+        ..+.-..+++||+||+|++..    .....++..+
T Consensus       329 I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA----~~fr~il~~l  399 (732)
T TIGR00603       329 ICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA----AMFRRVLTIV  399 (732)
T ss_pred             EEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH----HHHHHHHHhc
Confidence            55555543221     112368999999876432211        112234678999999998743    3444566666


Q ss_pred             CCCccEEEEEeeCCh
Q psy4698         218 NNDVQVILLSATMPA  232 (258)
Q Consensus       218 ~~~~~~i~~SAT~~~  232 (258)
                      .. ...+++|||+.+
T Consensus       400 ~a-~~RLGLTATP~R  413 (732)
T TIGR00603       400 QA-HCKLGLTATLVR  413 (732)
T ss_pred             Cc-CcEEEEeecCcc
Confidence            43 457999999864

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).

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

Probab=99.70  E-value=1.2e-16  Score=142.49  Aligned_cols=146  Identities=20%  Similarity=0.231  Sum_probs=99.1

Q ss_pred             CCcHHHHHHhhhhhc----CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCVR----GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~----g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .++++|.+++.++..    ++..++++|||+|||.+++..+... .     .+++||||+++|+.||.+.+....... -
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~-~-----~~~Lvlv~~~~L~~Qw~~~~~~~~~~~-~  108 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL-K-----RSTLVLVPTKELLDQWAEALKKFLLLN-D  108 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh-c-----CCEEEEECcHHHHHHHHHHHHHhcCCc-c
Confidence            699999999999888    8889999999999999886555433 1     249999999999999987776654322 1


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                      .+..+.++. ..     ... ..|.|+|.+.+........+..+.+++||+||+|++....+.    .+...+.....++
T Consensus       109 ~~g~~~~~~-~~-----~~~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~----~~~~~~~~~~~~L  177 (442)
T COG1061         109 EIGIYGGGE-KE-----LEP-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYR----RILELLSAAYPRL  177 (442)
T ss_pred             ccceecCce-ec-----cCC-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHH----HHHHhhhccccee
Confidence            122222222 11     011 369999999887642112233447899999999998554332    2333332222289


Q ss_pred             EEEeeCCh
Q psy4698         225 LLSATMPA  232 (258)
Q Consensus       225 ~~SAT~~~  232 (258)
                      ++|||.++
T Consensus       178 GLTATp~R  185 (442)
T COG1061         178 GLTATPER  185 (442)
T ss_pred             eeccCcee
Confidence            99999764

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.70  E-value=1.4e-16  Score=147.09  Aligned_cols=131  Identities=18%  Similarity=0.251  Sum_probs=100.2

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .|+++|......+..|  .++.++||+|||++|.+|++.....+   ..++|++|++.|+.|..+.+..+....++.
T Consensus        68 gl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g---~~V~VVTpn~yLA~Rdae~m~~l~~~LGLs  141 (762)
T TIGR03714        68 GM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTG---KGAMLVTTNDYLAKRDAEEMGPVYEWLGLT  141 (762)
T ss_pred             CC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcC---CceEEeCCCHHHHHHHHHHHHHHHhhcCCc
Confidence            44 5666666665555555  69999999999999999987666543   369999999999999999999999999999


Q ss_pred             EEEEECCcc---hHHHHHHHhcCCcEEEeChHHH-HHHHhc------CCCCCCCccEEEEccchhhh
Q psy4698         146 CHACIGGTI---VRDDIRKLEAGAQVVVGTPGRV-FDMISR------GALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       146 ~~~~~~~~~---~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~------~~~~~~~l~~lVvDE~h~~~  202 (258)
                      +....++..   .....+....+++|++|||+.| ++++..      ....+.++.++|+||||+++
T Consensus       142 v~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsIL  208 (762)
T TIGR03714       142 VSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVL  208 (762)
T ss_pred             EEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHh
Confidence            887665421   2222333345699999999999 566643      23456789999999999985

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.70  E-value=7.8e-16  Score=149.20  Aligned_cols=172  Identities=18%  Similarity=0.184  Sum_probs=116.1

Q ss_pred             HHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH-hcCCCCceEEEEEC
Q psy4698          73 IQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA-LGDFMSVSCHACIG  151 (258)
Q Consensus        73 ~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~  151 (258)
                      +..+.+..+..+..++|+|+||||||+.....++.  ...+..+++++..|.+..+...+..+.+ ++...+-.+.....
T Consensus        71 ~~~~Il~~l~~~~vvii~g~TGSGKTTqlPq~lle--~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR  148 (1283)
T TIGR01967        71 KREDIAEAIAENQVVIIAGETGSGKTTQLPKICLE--LGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVR  148 (1283)
T ss_pred             HHHHHHHHHHhCceEEEeCCCCCCcHHHHHHHHHH--cCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEc
Confidence            33566677777788999999999999964333322  1112234677788999988888766544 55444444432111


Q ss_pred             CcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchh-hhccCcHHH-HHHHHHhCCCCccEEEEEee
Q psy4698         152 GTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE-MLSRGFKDQ-IYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       152 ~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~-~~~~~~~~~-~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ...      .....+.|.|+|++.|++.+.... .++++++||+||+|+ .++.++... +..++.. .++.|+|+||||
T Consensus       149 ~~~------~~s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~-rpdLKlIlmSAT  220 (1283)
T TIGR01967       149 FHD------QVSSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPR-RPDLKIIITSAT  220 (1283)
T ss_pred             CCc------ccCCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhh-CCCCeEEEEeCC
Confidence            111      113457899999999999987764 488999999999994 777666654 4444433 467899999999


Q ss_pred             CChhHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         230 MPADVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                      ++.  +.+.+.|.+.| +|.+++...++
T Consensus       221 ld~--~~fa~~F~~ap-vI~V~Gr~~PV  245 (1283)
T TIGR01967       221 IDP--ERFSRHFNNAP-IIEVSGRTYPV  245 (1283)
T ss_pred             cCH--HHHHHHhcCCC-EEEECCCcccc
Confidence            974  56777776666 46676655443

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=3.1e-16  Score=145.99  Aligned_cols=131  Identities=18%  Similarity=0.274  Sum_probs=109.4

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|+++|..+...+.+|+  ++.+.||+|||+++.+|++.....   +.++.|++|++.||.|.+..+..+....++
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~---G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl  148 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE---GKGVHLITVNDYLAKRDAEEMGQVYEFLGL  148 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc---CCCeEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            366 89999999999998887  999999999999999999866664   347999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEEccchhhh
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTKQIRMFVLDEADEML  202 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~~~  202 (258)
                      .+.+..++.....+.+. ..+++|+|+||+.+ ++++..+.      ..+.++.++|+||+|+++
T Consensus       149 ~v~~i~g~~~~~~~r~~-~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        149 TVGLNFSDIDDASEKKA-IYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             eEEEEeCCCCcHHHHHH-hcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            99999988773333333 34589999999998 66665432      345789999999999875

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=3e-16  Score=146.22  Aligned_cols=129  Identities=20%  Similarity=0.303  Sum_probs=110.0

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .++++|...--.+.+|+  +..++||+|||+++.+|++..+..+   ..+.|++|++.||.|.+..+..+...+++.
T Consensus        80 g~-~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G---~~V~VvTpn~yLA~qd~e~m~~l~~~lGLt  153 (896)
T PRK13104         80 GL-RHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISG---RGVHIVTVNDYLAKRDSQWMKPIYEFLGLT  153 (896)
T ss_pred             CC-CcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcC---CCEEEEcCCHHHHHHHHHHHHHHhcccCce
Confidence            44 78999988888888888  8999999999999999999777654   359999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC-CCCC-----CCccEEEEccchhhh
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG-ALST-----KQIRMFVLDEADEML  202 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~-~~~~-----~~l~~lVvDE~h~~~  202 (258)
                      +.+..++..........  .++|+|+||+.| +++++.+ .+++     ..+.++|+||+|+++
T Consensus       154 v~~i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        154 VGVIYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             EEEEeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            99999887665553333  589999999999 9999876 3444     589999999999885

>KOG0351|consensus

Probab=99.68  E-value=6e-16  Score=146.22  Aligned_cols=182  Identities=19%  Similarity=0.221  Sum_probs=131.2

Q ss_pred             HHHHH-HHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHH
Q psy4698          58 LLRGI-YAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI  136 (258)
Q Consensus        58 l~~~l-~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  136 (258)
                      ....+ ..+|...+++-|.+++...+.|+++++.+|||.||++||.+|++..      ++-+++|.|..+|+.++...+.
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L~  325 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHLS  325 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhhh
Confidence            44444 3579999999999999999999999999999999999999998643      2379999999999999988774


Q ss_pred             HhcCCCCceEEEEECCcchH---HHHHHHhc---CCcEEEeChHHHHHH--HhcCCCCCCC---ccEEEEccchhhhccC
Q psy4698         137 ALGDFMSVSCHACIGGTIVR---DDIRKLEA---GAQVVVGTPGRVFDM--ISRGALSTKQ---IRMFVLDEADEMLSRG  205 (258)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~---~~~Ilv~Tp~~l~~~--l~~~~~~~~~---l~~lVvDE~h~~~~~~  205 (258)
                      ..    ++....+.++....   .....+.+   .++|++-||+++...  +.+....+..   +.++||||||+...|+
T Consensus       326 ~~----~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWg  401 (941)
T KOG0351|consen  326 KK----GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWG  401 (941)
T ss_pred             hc----CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhc
Confidence            43    45556666665553   22333443   489999999987542  2222233444   8899999999998874


Q ss_pred             --cHH---HHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh--cCCCeEEEe
Q psy4698         206 --FKD---QIYDVFKHLNNDVQVILLSATMPADVLDVSMKF--MRDPIKILV  250 (258)
Q Consensus       206 --~~~---~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~--~~~~~~v~~  250 (258)
                        |..   .+..+..+.+. ..+|++|||.+..++.-+-..  +.+|++...
T Consensus       402 HdFRp~Yk~l~~l~~~~~~-vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~  452 (941)
T KOG0351|consen  402 HDFRPSYKRLGLLRIRFPG-VPFIALTATATERVREDVIRSLGLRNPELFKS  452 (941)
T ss_pred             ccccHHHHHHHHHHhhCCC-CCeEEeehhccHHHHHHHHHHhCCCCcceecc
Confidence              443   44444555544 789999999988776654443  335555443

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.68  E-value=4.8e-16  Score=141.97  Aligned_cols=129  Identities=19%  Similarity=0.264  Sum_probs=107.6

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .|+++|..+++.++.|+  +..+.||+|||+++.+|++.....   +.+++|++|+++||.|.+..+..+....++.
T Consensus       101 g~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~---G~~v~VvTptreLA~qdae~~~~l~~~lGls  174 (656)
T PRK12898        101 GQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA---GLPVHVITVNDYLAERDAELMRPLYEALGLT  174 (656)
T ss_pred             CC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc---CCeEEEEcCcHHHHHHHHHHHHHHHhhcCCE
Confidence            55 89999999999999999  999999999999999999987654   3579999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC-------------------------CCCCCccEEEEccch
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA-------------------------LSTKQIRMFVLDEAD  199 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~-------------------------~~~~~l~~lVvDE~h  199 (258)
                      +.+..++....  .+....+++|+|+|...+ +++++.+.                         .-...+.+.||||+|
T Consensus       175 v~~i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvD  252 (656)
T PRK12898        175 VGCVVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIVDEAD  252 (656)
T ss_pred             EEEEeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEeeccc
Confidence            99999986543  334456789999999887 55654431                         113567899999999


Q ss_pred             hhh
Q psy4698         200 EML  202 (258)
Q Consensus       200 ~~~  202 (258)
                      .++
T Consensus       253 SiL  255 (656)
T PRK12898        253 SVL  255 (656)
T ss_pred             cee
Confidence            764

>KOG0353|consensus

Probab=99.67  E-value=1.7e-15  Score=127.13  Aligned_cols=181  Identities=20%  Similarity=0.278  Sum_probs=132.8

Q ss_pred             CCCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH
Q psy4698          50 DDMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA  128 (258)
Q Consensus        50 ~~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~  128 (258)
                      ++++++....+.|++ +.+.+++|.|..++++...|++.++..|||-||++||.+|++-.      .+-++++||.++|+
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a------dg~alvi~plislm  147 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA------DGFALVICPLISLM  147 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc------CCceEeechhHHHH
Confidence            578889888888875 67889999999999999999999999999999999999998643      23699999999999


Q ss_pred             HHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHh---cCCcEEEeChHHHHH---HHhc--CCCCCCCccEEEEcc
Q psy4698         129 QQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLE---AGAQVVVGTPGRVFD---MISR--GALSTKQIRMFVLDE  197 (258)
Q Consensus       129 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~~Ilv~Tp~~l~~---~l~~--~~~~~~~l~~lVvDE  197 (258)
                      +++.-.++.++-..    ..+.......+.   -..+.   ....+++.||+.+.+   ++.+  ..+....+.+|.+||
T Consensus       148 edqil~lkqlgi~a----s~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaide  223 (695)
T KOG0353|consen  148 EDQILQLKQLGIDA----SMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDE  223 (695)
T ss_pred             HHHHHHHHHhCcch----hhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecc
Confidence            99999998886432    222222221111   11122   236899999999864   2221  334556788999999


Q ss_pred             chhhhccC--cHHHH--HHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         198 ADEMLSRG--FKDQI--YDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       198 ~h~~~~~~--~~~~~--~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      +|+...|+  |...+  ..++++--+...+|+++||-++++.+-++.
T Consensus       224 vhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~  270 (695)
T KOG0353|consen  224 VHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKD  270 (695)
T ss_pred             eeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHH
Confidence            99988774  33333  244555456788999999998887665544

>TIGR00595 priA primosomal protein N'

Probab=99.66  E-value=1.2e-15  Score=137.86  Aligned_cols=135  Identities=21%  Similarity=0.284  Sum_probs=94.6

Q ss_pred             EEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchH---HHHHHHhc
Q psy4698          88 IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVR---DDIRKLEA  164 (258)
Q Consensus        88 li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~  164 (258)
                      ++.|+||||||.+|+..+...+..   +.+++|++|+++|+.|+++.+++..   +..+..++++....   ..+..+.+
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~---g~~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~~~~~~   74 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL---GKSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVKN   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHHc
Confidence            468999999999997665555433   3479999999999999999998753   24456666665433   23334443


Q ss_pred             -CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-----cH-HHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         165 -GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-----FK-DQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       165 -~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-----~~-~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                       .++|+|+|+..++       ..++++++|||||+|+....+     +. ..+ ..++....+.++|++|||.+.+...
T Consensus        75 g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~-a~~ra~~~~~~vil~SATPsles~~  145 (505)
T TIGR00595        75 GEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDV-AVYRAKKFNCPVVLGSATPSLESYH  145 (505)
T ss_pred             CCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHH-HHHHHHhcCCCEEEEeCCCCHHHHH
Confidence             4799999998765       467899999999999865322     11 223 3333334678999999997754333

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).

>KOG0920|consensus

Probab=99.64  E-value=6.1e-15  Score=137.75  Aligned_cols=198  Identities=17%  Similarity=0.168  Sum_probs=141.7

Q ss_pred             cCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH
Q psy4698          49 FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA  128 (258)
Q Consensus        49 ~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~  128 (258)
                      +.....++...+.+..+.-...+..+...+.++.+...++|.|.||+|||+.....+++.....+..+++++..|.|-.|
T Consensus       153 ~~~~~~s~~~~~~~~~R~~LPa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsA  232 (924)
T KOG0920|consen  153 QSEPKKSESYKEMLRFRESLPAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISA  232 (924)
T ss_pred             hchhhhhhHHHHHHHHHHhCccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHH
Confidence            33334445555555544444568889999999999999999999999999999999999887777788999999999988


Q ss_pred             HHHHHHHHH-hcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh-ccCc
Q psy4698         129 QQIQKVVIA-LGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGF  206 (258)
Q Consensus       129 ~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~-~~~~  206 (258)
                      ..+++++.. .+...+-.+..     ..+.+..... ...+++||.+.|++.+.. .-.+.+++++|+||+|+-. +.++
T Consensus       233 IsvAeRVa~ER~~~~g~~VGY-----qvrl~~~~s~-~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~Df  305 (924)
T KOG0920|consen  233 ISVAERVAKERGESLGEEVGY-----QVRLESKRSR-ETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDF  305 (924)
T ss_pred             HHHHHHHHHHhccccCCeeeE-----EEeeecccCC-ceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCccc
Confidence            888866543 44434433321     1221211222 268999999999999988 3478899999999999643 3356


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      .-.+.+.+-..+++.++|+||||+.  .+.|...|. ..-++.+++.++.
T Consensus       306 lLi~lk~lL~~~p~LkvILMSAT~d--ae~fs~YF~-~~pvi~i~grtfp  352 (924)
T KOG0920|consen  306 LLILLKDLLPRNPDLKVILMSATLD--AELFSDYFG-GCPVITIPGRTFP  352 (924)
T ss_pred             HHHHHHHHhhhCCCceEEEeeeecc--hHHHHHHhC-CCceEeecCCCcc
Confidence            6555665555678999999999998  445555555 4445666666554

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

Probab=99.64  E-value=3.1e-15  Score=145.13  Aligned_cols=160  Identities=19%  Similarity=0.145  Sum_probs=107.4

Q ss_pred             CCcHHHHHHhhhhh----cC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          69 KPSAIQQRAIIPCV----RG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .++++|.+|+..+.    .| +..+++++||||||.+++. ++..+.......++||++|+.+|+.|....++.+.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~-li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIA-LMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHH-HHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            58999999998765    33 5799999999999998644 444555444456999999999999999999888643222


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-----CCCCCCccEEEEccchhhhcc--------------
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-----ALSTKQIRMFVLDEADEMLSR--------------  204 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-----~~~~~~l~~lVvDE~h~~~~~--------------  204 (258)
                      ..+...++......  .......+|+|+|.+++...+...     .+.+..+++||+||||+-...              
T Consensus       492 ~~~~~i~~i~~L~~--~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~  569 (1123)
T PRK11448        492 QTFASIYDIKGLED--KFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQ  569 (1123)
T ss_pred             cchhhhhchhhhhh--hcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchh
Confidence            11111111110011  112234789999999987765321     245678899999999985310              


Q ss_pred             -CcHHHHHHHHHhCCCCccEEEEEeeCChh
Q psy4698         205 -GFKDQIYDVFKHLNNDVQVILLSATMPAD  233 (258)
Q Consensus       205 -~~~~~~~~~~~~l~~~~~~i~~SAT~~~~  233 (258)
                       .++..+..++..+  +...|+||||....
T Consensus       570 ~~~~~~yr~iL~yF--dA~~IGLTATP~r~  597 (1123)
T PRK11448        570 LDYVSKYRRVLDYF--DAVKIGLTATPALH  597 (1123)
T ss_pred             hhHHHHHHHHHhhc--CccEEEEecCCccc
Confidence             1245666777655  35689999998643

>KOG0950|consensus

Probab=99.62  E-value=1.9e-15  Score=139.27  Aligned_cols=185  Identities=17%  Similarity=0.154  Sum_probs=140.3

Q ss_pred             cCCCCCCHHHHHHHHHCCCCCCcHHHHHHh--hhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          49 FDDMELSEELLRGIYAYGFEKPSAIQQRAI--IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        49 ~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~--~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      +.+.+.+....-..+..|..+++.+|.+++  +.+++++|++...||+.|||+++.+-++..+....+  .++.+.|..+
T Consensus       203 ~a~~~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr--~~llilp~vs  280 (1008)
T KOG0950|consen  203 FAKRLPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR--NVLLILPYVS  280 (1008)
T ss_pred             hhhcCchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh--ceeEecceee
Confidence            333333333334445678889999999998  457899999999999999999999888887766543  6999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--CCCCCCCccEEEEccchhhhcc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR--GALSTKQIRMFVLDEADEMLSR  204 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~--~~~~~~~l~~lVvDE~h~~~~~  204 (258)
                      .+......+..+....|+.+..+.|.....    .......+.|||.++-..++..  ..-.+..+++|||||.|.+.+.
T Consensus       281 iv~Ek~~~l~~~~~~~G~~ve~y~g~~~p~----~~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~  356 (1008)
T KOG0950|consen  281 IVQEKISALSPFSIDLGFPVEEYAGRFPPE----KRRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDK  356 (1008)
T ss_pred             hhHHHHhhhhhhccccCCcchhhcccCCCC----CcccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeecc
Confidence            999999999999999999988877654332    1223368999999987665543  1224667899999999999998


Q ss_pred             CcHHHHHHHHHhC-----CCCccEEEEEeeCChh--HHHHHH
Q psy4698         205 GFKDQIYDVFKHL-----NNDVQVILLSATMPAD--VLDVSM  239 (258)
Q Consensus       205 ~~~~~~~~~~~~l-----~~~~~~i~~SAT~~~~--~~~~~~  239 (258)
                      +.+..+..++..+     ....|+|+||||+|+.  +++.++
T Consensus       357 ~rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~~lL~~~L~  398 (1008)
T KOG0950|consen  357 GRGAILELLLAKILYENLETSVQIIGMSATIPNNSLLQDWLD  398 (1008)
T ss_pred             ccchHHHHHHHHHHHhccccceeEeeeecccCChHHHHHHhh
Confidence            8888877766553     2346799999999873  444444

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

Probab=99.62  E-value=2e-14  Score=135.99  Aligned_cols=191  Identities=24%  Similarity=0.236  Sum_probs=148.9

Q ss_pred             CCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          51 DMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        51 ~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .++.+......+.....-.-|+-|..|+..+...      -|=+|||.-|-|||.+++-++...+..+   .++.+++||
T Consensus       576 af~~d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~G---KQVAvLVPT  652 (1139)
T COG1197         576 AFPPDTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDG---KQVAVLVPT  652 (1139)
T ss_pred             CCCCChHHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCC---CeEEEEccc
Confidence            3445555666665532226799999999998643      3689999999999999999998888765   489999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchh
Q psy4698         125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE  200 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  200 (258)
                      .-||+|.++.+++...+..+++..++.-.+..++   .+.+.+| .||+|||.    +++. +.+.+++++++||||-|+
T Consensus       653 TlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH----rLL~-kdv~FkdLGLlIIDEEqR  727 (1139)
T COG1197         653 TLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH----RLLS-KDVKFKDLGLLIIDEEQR  727 (1139)
T ss_pred             HHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEech----HhhC-CCcEEecCCeEEEechhh
Confidence            9999999999999888888888877766555444   3344444 89999997    4444 456889999999999998


Q ss_pred             hhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCc
Q psy4698         201 MLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       201 ~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~  254 (258)
                           |+-.-+.-++.++.++-++-||||.=+.-.+....-++|-.+|.+++++
T Consensus       728 -----FGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~  776 (1139)
T COG1197         728 -----FGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPED  776 (1139)
T ss_pred             -----cCccHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCC
Confidence                 4666777888888999999999997555555666778887777776543

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

Probab=99.61  E-value=2e-14  Score=129.40  Aligned_cols=167  Identities=22%  Similarity=0.320  Sum_probs=130.7

Q ss_pred             CCCHHHHHHH-HHCCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          53 ELSEELLRGI-YAYGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        53 ~~~~~l~~~l-~~~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      +....+.+.+ ....| ++|..|+.++..+...      .+=++.|.-|||||++++++++..+.++.   ++...+||-
T Consensus       246 ~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~---Q~ALMAPTE  321 (677)
T COG1200         246 PANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGY---QAALMAPTE  321 (677)
T ss_pred             CccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCC---eeEEeccHH
Confidence            3444545444 44566 8999999999998755      25699999999999999999998887754   799999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchH---HHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVR---DDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      -||.|.+..+.++....++.+..+.|.....   .....+.+| .+|+|||.     .+-.....++++.++|+||=|++
T Consensus       322 ILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTH-----ALiQd~V~F~~LgLVIiDEQHRF  396 (677)
T COG1200         322 ILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH-----ALIQDKVEFHNLGLVIIDEQHRF  396 (677)
T ss_pred             HHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcc-----hhhhcceeecceeEEEEeccccc
Confidence            9999999999999998899998888876544   334445556 99999996     33445568899999999999984


Q ss_pred             hccCcHHHHHHHHHhCCC-CccEEEEEeeC-Chh
Q psy4698         202 LSRGFKDQIYDVFKHLNN-DVQVILLSATM-PAD  233 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l~~-~~~~i~~SAT~-~~~  233 (258)
                           +-.-...++.... .+-.+.||||. |+.
T Consensus       397 -----GV~QR~~L~~KG~~~Ph~LvMTATPIPRT  425 (677)
T COG1200         397 -----GVHQRLALREKGEQNPHVLVMTATPIPRT  425 (677)
T ss_pred             -----cHHHHHHHHHhCCCCCcEEEEeCCCchHH
Confidence                 5555555555555 57799999995 554

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

Probab=99.57  E-value=4.7e-14  Score=132.04  Aligned_cols=178  Identities=19%  Similarity=0.230  Sum_probs=127.6

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH-hcCCCCceEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA-LGDFMSVSCH  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~  147 (258)
                      ..+....+.+.++.+...++|.|+||||||+.....+++.-.  ..+.++.+.-|.|--|...+.++.+ ++...+-.|.
T Consensus        50 Pv~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VG  127 (845)
T COG1643          50 PVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVG  127 (845)
T ss_pred             CcHHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceee
Confidence            446667777788888899999999999999987777766654  3345788889999888888866654 6655554442


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh-ccCcH-HHHHHHHHhCCCCccEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFK-DQIYDVFKHLNNDVQVIL  225 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~-~~~~~-~~~~~~~~~l~~~~~~i~  225 (258)
                      ...-.     +. .......|-+.|.+.|++.+.... .++.+++||+||+|+-. +.++. ..+..++...+++.++|.
T Consensus       128 Y~iRf-----e~-~~s~~Trik~mTdGiLlrei~~D~-~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIi  200 (845)
T COG1643         128 YSIRF-----ES-KVSPRTRIKVMTDGILLREIQNDP-LLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLII  200 (845)
T ss_pred             EEEEe-----ec-cCCCCceeEEeccHHHHHHHhhCc-ccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEE
Confidence            21111     10 123347899999999999998876 48999999999999743 22333 334455666777899999


Q ss_pred             EEeeCChhHHHHHHHhcCCCeEEEecCCcccCC
Q psy4698         226 LSATMPADVLDVSMKFMRDPIKILVKKEELTLE  258 (258)
Q Consensus       226 ~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  258 (258)
                      ||||+..  + .+..|+.+.-++.+++..++||
T Consensus       201 mSATld~--~-rfs~~f~~apvi~i~GR~fPVe  230 (845)
T COG1643         201 MSATLDA--E-RFSAYFGNAPVIEIEGRTYPVE  230 (845)
T ss_pred             EecccCH--H-HHHHHcCCCCEEEecCCccceE
Confidence            9999984  3 4456667677778887777654

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.55  E-value=3.9e-14  Score=131.99  Aligned_cols=130  Identities=18%  Similarity=0.271  Sum_probs=108.8

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|++.|....-.+.+|+  +..+.||+|||+++.+|++.....+.   .+-|++|+..||.|.++.+..+...+++
T Consensus        78 lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~---~V~IvTpn~yLA~rd~e~~~~l~~~LGl  151 (830)
T PRK12904         78 LGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGK---GVHVVTVNDYLAKRDAEWMGPLYEFLGL  151 (830)
T ss_pred             hCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCC---CEEEEecCHHHHHHHHHHHHHHHhhcCC
Confidence            355 89999999988888887  89999999999999999974444432   4779999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEEccchhhh
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTKQIRMFVLDEADEML  202 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~~~  202 (258)
                      .+.+..++..........  .++|+++|++.| +++++.+.      .....+.++||||||+++
T Consensus       152 sv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiL  214 (830)
T PRK12904        152 SVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSIL  214 (830)
T ss_pred             eEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhhe
Confidence            999999887766554443  489999999999 88887654      236788999999999875

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

Probab=99.54  E-value=1.5e-13  Score=126.88  Aligned_cols=152  Identities=23%  Similarity=0.272  Sum_probs=113.1

Q ss_pred             CCcHHHHHHhhhhhcC----CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCVRG----NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g----~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .++.-|..++..+...    +..++.|.||||||.+|+-.+-+.+..+   .++|+++|.++|-.|...+++....   .
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~G---kqvLvLVPEI~Ltpq~~~rf~~rFg---~  271 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQG---KQVLVLVPEIALTPQLLARFKARFG---A  271 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcC---CEEEEEeccccchHHHHHHHHHHhC---C
Confidence            6788999999998665    5699999999999999977666666554   3799999999999999999888442   3


Q ss_pred             eEEEEECCc----chHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-----CcHHHHHHHHH
Q psy4698         145 SCHACIGGT----IVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-----GFKDQIYDVFK  215 (258)
Q Consensus       145 ~~~~~~~~~----~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-----~~~~~~~~~~~  215 (258)
                      .+..++++-    ....|.+.......|+|||...++       ..++++++|||||-|.-...     .+...-.++++
T Consensus       272 ~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~R  344 (730)
T COG1198         272 KVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLR  344 (730)
T ss_pred             ChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCHHHHHHHH
Confidence            344444443    333444444455999999998877       68899999999999965311     23344445555


Q ss_pred             hCCCCccEEEEEeeCChh
Q psy4698         216 HLNNDVQVILLSATMPAD  233 (258)
Q Consensus       216 ~l~~~~~~i~~SAT~~~~  233 (258)
                      .-..++++|+-|||.+-+
T Consensus       345 a~~~~~pvvLgSATPSLE  362 (730)
T COG1198         345 AKKENAPVVLGSATPSLE  362 (730)
T ss_pred             HHHhCCCEEEecCCCCHH
Confidence            555789999999997744

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

Probab=99.53  E-value=1.3e-13  Score=128.67  Aligned_cols=152  Identities=17%  Similarity=0.171  Sum_probs=99.8

Q ss_pred             CCcHHHHHHhhhhh----c------CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQRAIIPCV----R------GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~------g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      -++.+|.+++..+.    .      .+..++.++||||||++++..+...+ ......++||++|+.+|..|+.+.+..+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~  316 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSL  316 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhh
Confidence            37889999997753    2      24699999999999999866654444 4445568999999999999999999887


Q ss_pred             cCCCCceEEEEECCcchHHHHHHHhc-CCcEEEeChHHHHHHHhcC--CCCCCCc-cEEEEccchhhhccCcHHHHHHHH
Q psy4698         139 GDFMSVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRG--ALSTKQI-RMFVLDEADEMLSRGFKDQIYDVF  214 (258)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~Ilv~Tp~~l~~~l~~~--~~~~~~l-~~lVvDE~h~~~~~~~~~~~~~~~  214 (258)
                      +....      ....+.......+.. ..+|+|+|.+++...+...  .+....- -+||+||||+...    ..+...+
T Consensus       317 ~~~~~------~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~----~~~~~~l  386 (667)
T TIGR00348       317 QKDCA------ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQY----GELAKNL  386 (667)
T ss_pred             CCCCC------cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccc----hHHHHHH
Confidence            63210      111122222223332 3689999999997644321  1111111 2899999998532    2333444


Q ss_pred             HhCCCCccEEEEEeeCC
Q psy4698         215 KHLNNDVQVILLSATMP  231 (258)
Q Consensus       215 ~~l~~~~~~i~~SAT~~  231 (258)
                      +..-++..++++|||.-
T Consensus       387 ~~~~p~a~~lGfTaTP~  403 (667)
T TIGR00348       387 KKALKNASFFGFTGTPI  403 (667)
T ss_pred             HhhCCCCcEEEEeCCCc
Confidence            33224578999999974

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

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

Probab=99.52  E-value=3.4e-13  Score=129.38  Aligned_cols=81  Identities=21%  Similarity=0.217  Sum_probs=64.8

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHhh----hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHH
Q psy4698          55 SEELLRGIYAYGFEKPSAIQQRAII----PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ  130 (258)
Q Consensus        55 ~~~l~~~l~~~~~~~~~~~Q~~~~~----~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q  130 (258)
                      ++...+.+...|+ .+++.|.+.+.    .+..++++++.||||+|||++|++|++....   .+.+++|.+||++|..|
T Consensus       232 ~~~~~~~~~~~~~-~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq~Q  307 (850)
T TIGR01407       232 SSLFSKNIDRLGL-EYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQSQ  307 (850)
T ss_pred             cHHHHHhhhhcCC-ccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHHHH
Confidence            3466667777788 58999998665    5667899999999999999999999988766   23489999999999999


Q ss_pred             HHH-HHHHhc
Q psy4698         131 IQK-VVIALG  139 (258)
Q Consensus       131 ~~~-~~~~~~  139 (258)
                      +.. .+..+.
T Consensus       308 l~~~~~~~l~  317 (850)
T TIGR01407       308 LLEKDIPLLN  317 (850)
T ss_pred             HHHHHHHHHH
Confidence            864 444443

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.

>KOG0922|consensus

Probab=99.50  E-value=4.9e-13  Score=119.66  Aligned_cols=177  Identities=15%  Similarity=0.181  Sum_probs=121.8

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHH-HHhcCCCCceEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVV-IALGDFMSVSCH  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~-~~~~~~~~~~~~  147 (258)
                      ....+-.+.+..+..++.++|.|+||||||+.....+.+.-....  +++-+..|.|--|...+++. .+.+..+|-.+.
T Consensus        51 PI~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~--g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VG  128 (674)
T KOG0922|consen   51 PIYKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASS--GKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVG  128 (674)
T ss_pred             CHHHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccC--CcEEeecCchHHHHHHHHHHHHHhCCCcCceee
Confidence            456677788888888999999999999999987666655444332  24888889999888887554 446555554443


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-C-cHHHHHHHHHhCCCCccEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-G-FKDQIYDVFKHLNNDVQVIL  225 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~-~~~~~~~~~~~l~~~~~~i~  225 (258)
                      ....-..      .-.....|.+.|-+.|++-+..+. .++.++.||+||||+-.-. + ....++++++. +++.++|+
T Consensus       129 Y~IRFed------~ts~~TrikymTDG~LLRE~l~Dp-~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~-R~~LklIi  200 (674)
T KOG0922|consen  129 YTIRFED------STSKDTRIKYMTDGMLLREILKDP-LLSKYSVIILDEAHERSLHTDILLGLLKKILKK-RPDLKLII  200 (674)
T ss_pred             eEEEecc------cCCCceeEEEecchHHHHHHhcCC-ccccccEEEEechhhhhhHHHHHHHHHHHHHhc-CCCceEEE
Confidence            2211110      011236899999999998776654 6789999999999963211 1 22222333332 45689999


Q ss_pred             EEeeCChhHHHHHHHhcCCCeEEEecCCcccCC
Q psy4698         226 LSATMPADVLDVSMKFMRDPIKILVKKEELTLE  258 (258)
Q Consensus       226 ~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  258 (258)
                      ||||+.   .+....|+.+..++.+++..+++|
T Consensus       201 mSATld---a~kfS~yF~~a~i~~i~GR~fPVe  230 (674)
T KOG0922|consen  201 MSATLD---AEKFSEYFNNAPILTIPGRTFPVE  230 (674)
T ss_pred             Eeeeec---HHHHHHHhcCCceEeecCCCCcee
Confidence            999998   346667777788888888887764

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.49  E-value=1.5e-13  Score=128.11  Aligned_cols=130  Identities=19%  Similarity=0.256  Sum_probs=107.6

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .++++|...--.+.+|+  +..++||.|||+++.+|++.....+.   .+.|++|+..||.+-.+++..+....+++
T Consensus        80 gm-~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g~---~VhIvT~ndyLA~RD~e~m~~l~~~lGls  153 (908)
T PRK13107         80 EM-RHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTGK---GVHVITVNDYLARRDAENNRPLFEFLGLT  153 (908)
T ss_pred             CC-CcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcCC---CEEEEeCCHHHHHHHHHHHHHHHHhcCCe
Confidence            44 78899988887777777  89999999999999999987776543   49999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC-CCCC-----CCccEEEEccchhhhc
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG-ALST-----KQIRMFVLDEADEMLS  203 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~-~~~~-----~~l~~lVvDE~h~~~~  203 (258)
                      +.+..++......  .-.-+++|+++||+.| +++++.+ .+..     ..+.++||||+|.++-
T Consensus       154 v~~i~~~~~~~~r--~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLi  216 (908)
T PRK13107        154 VGINVAGLGQQEK--KAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILI  216 (908)
T ss_pred             EEEecCCCCHHHH--HhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhcc
Confidence            9988877665322  2223589999999999 8888876 3333     6789999999998863

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

Probab=99.45  E-value=2.1e-12  Score=120.22  Aligned_cols=142  Identities=17%  Similarity=0.183  Sum_probs=101.2

Q ss_pred             HHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          59 LRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        59 ~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .+.+++.....|+..|+-....+..|+++-+.||||.|||+-.++..   +.-..++.+++|++||..|+.|.++.++++
T Consensus        72 ~~fF~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~s---l~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~  148 (1187)
T COG1110          72 EEFFKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMS---LYLAKKGKRVYIIVPTTTLVRQVYERLKKF  148 (1187)
T ss_pred             HHHHHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHH---HHHHhcCCeEEEEecCHHHHHHHHHHHHHH
Confidence            34445443339999999999999999999999999999998554333   333334469999999999999999999999


Q ss_pred             cCCCC-ceEEE-EECCcch---HHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         139 GDFMS-VSCHA-CIGGTIV---RDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       139 ~~~~~-~~~~~-~~~~~~~---~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +...+ ..+.. +++....   ......+.+| .+|+|+|.+-|.+-...  +.-.+++++++|++|.++..+
T Consensus       149 ~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA~Lkas  219 (1187)
T COG1110         149 AEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDAILKAS  219 (1187)
T ss_pred             HhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHHHHhcc
Confidence            86655 33322 4444332   3334455554 89999999666544433  112468899999999887543

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

Probab=99.45  E-value=2.7e-12  Score=106.81  Aligned_cols=153  Identities=20%  Similarity=0.183  Sum_probs=113.2

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+++.|+.+-..+.    +.++.++.|-||+|||......+-+.+.+   |.++.+.+|....+.+.+.++++-..+.+ 
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~---G~~vciASPRvDVclEl~~Rlk~aF~~~~-  172 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQ---GGRVCIASPRVDVCLELYPRLKQAFSNCD-  172 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhc---CCeEEEecCcccchHHHHHHHHHhhccCC-
Confidence            68999988876654    55789999999999999864444444433   34899999999999999999988665444 


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                       +..++|+......       ..++|+|..+|+++-+.       ++++|+||+|.+.-........++-+.......+|
T Consensus       173 -I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk~a-------FD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~I  237 (441)
T COG4098         173 -IDLLYGDSDSYFR-------APLVVATTHQLLRFKQA-------FDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATI  237 (441)
T ss_pred             -eeeEecCCchhcc-------ccEEEEehHHHHHHHhh-------ccEEEEeccccccccCCHHHHHHHHHhhcccCceE
Confidence             4556666543221       57999999998876554       67999999998754433444445555556677899


Q ss_pred             EEEeeCChhHHHHHHH
Q psy4698         225 LLSATMPADVLDVSMK  240 (258)
Q Consensus       225 ~~SAT~~~~~~~~~~~  240 (258)
                      ++|||.++.+++.+..
T Consensus       238 ylTATp~k~l~r~~~~  253 (441)
T COG4098         238 YLTATPTKKLERKILK  253 (441)
T ss_pred             EEecCChHHHHHHhhh
Confidence            9999999887776644

>KOG0949|consensus

Probab=99.44  E-value=7.4e-13  Score=122.41  Aligned_cols=159  Identities=18%  Similarity=0.158  Sum_probs=111.4

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE-E
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC-H  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~-~  147 (258)
                      .|..+|.+.+..+-.+++.+|++||.+|||.+-...+ +.+.+.....-+|++.|+++|++|....+........+.- .
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~i-EKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~  589 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAI-EKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGV  589 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHH-HHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccch
Confidence            6889999999999999999999999999999875444 4444444445799999999999999876655432221111 1


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc---CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR---GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~---~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                      ...|.....-.  ...-.|+|+|+-|+.+..++-.   ...+.+.++++|+||+|.+....-......++-.+  .|.++
T Consensus       590 sl~g~ltqEYs--inp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L  665 (1330)
T KOG0949|consen  590 SLLGDLTQEYS--INPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFL  665 (1330)
T ss_pred             hhHhhhhHHhc--CCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCee
Confidence            12222211111  1112489999999999888865   45577899999999999875544333333344333  48899


Q ss_pred             EEEeeCCh
Q psy4698         225 LLSATMPA  232 (258)
Q Consensus       225 ~~SAT~~~  232 (258)
                      ++|||+-+
T Consensus       666 ~LSATigN  673 (1330)
T KOG0949|consen  666 VLSATIGN  673 (1330)
T ss_pred             EEecccCC
Confidence            99999954

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

Probab=99.42  E-value=7.3e-13  Score=121.22  Aligned_cols=165  Identities=18%  Similarity=0.184  Sum_probs=114.1

Q ss_pred             CCCcHHHHHHhhhhh----cCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCC
Q psy4698          68 EKPSAIQQRAIIPCV----RGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM  142 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~----~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  142 (258)
                      ..++.+|..|+..+.    .|+ -+++++.||+|||.++ +.++.+|.+.+...|+|+|+-+++|+.|.+..+..+...-
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~  242 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG  242 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCc
Confidence            368999999997754    443 4999999999999987 5667777777677799999999999999998887765432


Q ss_pred             CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-----CCCCCCccEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-----ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-----~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      .. +....+..        ..+.++|.|+|.+.+...+...     .+....+++||+||||+-    .......++..+
T Consensus       243 ~~-~n~i~~~~--------~~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRg----i~~~~~~I~dYF  309 (875)
T COG4096         243 TK-MNKIEDKK--------GDTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRG----IYSEWSSILDYF  309 (875)
T ss_pred             cc-eeeeeccc--------CCcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhh----HHhhhHHHHHHH
Confidence            22 11212111        1124799999999998877653     345566899999999964    344444666665


Q ss_pred             CCCccEEEEEeeCChhHHHHHHHhc-CCCeEE
Q psy4698         218 NNDVQVILLSATMPADVLDVSMKFM-RDPIKI  248 (258)
Q Consensus       218 ~~~~~~i~~SAT~~~~~~~~~~~~~-~~~~~v  248 (258)
                      ..-  +++++||....+..-.-.|+ .+|+..
T Consensus       310 dA~--~~gLTATP~~~~d~~T~~~F~g~Pt~~  339 (875)
T COG4096         310 DAA--TQGLTATPKETIDRSTYGFFNGEPTYA  339 (875)
T ss_pred             HHH--HHhhccCcccccccccccccCCCccee
Confidence            322  34559997765444333334 666654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.42  E-value=1.3e-12  Score=123.32  Aligned_cols=182  Identities=17%  Similarity=0.178  Sum_probs=120.8

Q ss_pred             CCcHHHHHHhhhhhcC---C-cEEEEcccCCCcchHhHHHHHHHhhh-ccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          69 KPSAIQQRAIIPCVRG---N-DVIAQAQSGTGKTATFSISILQQVDQ-NIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g---~-~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      ..++.|..++..+..+   . .+++.+|||+|||.+.+.++...+.. .....|++++.|++++.++.++.++......+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            4488999999887655   3 68999999999999999999888877 34566999999999999999999988655443


Q ss_pred             ceEEEEECCcchHHHHHH--------------HhcCCcEEEeChHHHHHHHh-cCCCC-CC--CccEEEEccchhhhccC
Q psy4698         144 VSCHACIGGTIVRDDIRK--------------LEAGAQVVVGTPGRVFDMIS-RGALS-TK--QIRMFVLDEADEMLSRG  205 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~--------------~~~~~~Ilv~Tp~~l~~~l~-~~~~~-~~--~l~~lVvDE~h~~~~~~  205 (258)
                      ......++..........              ......+.++||........ ...+. +.  ..+.+|+||+|.+.+..
T Consensus       275 ~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~  354 (733)
T COG1203         275 VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET  354 (733)
T ss_pred             cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc
Confidence            332212222221110000              00113455556555443211 11111 11  23689999999775553


Q ss_pred             cHHHHHHHHHhCC-CCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         206 FKDQIYDVFKHLN-NDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       206 ~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      ....+.+++..+. .+..+|+||||+|...++.+...+.+...+..
T Consensus       355 ~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~  400 (733)
T COG1203         355 MLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVE  400 (733)
T ss_pred             hHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceec
Confidence            4455555555543 46789999999999999999888876666654

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.42  E-value=9e-12  Score=119.56  Aligned_cols=163  Identities=13%  Similarity=0.108  Sum_probs=109.5

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+++||.+.+.++.    .|.+.|+.-.+|.|||+..+..+.......+....+|||||. ++..+|.+.+++++..  .
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~--l  245 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPV--L  245 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCC--C
Confidence            68999999999875    567899999999999998754443322223333479999995 6678899999888743  4


Q ss_pred             eEEEEECCcchHHHHHH---HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCc
Q psy4698         145 SCHACIGGTIVRDDIRK---LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV  221 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~---~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~  221 (258)
                      .+..++|....+.....   ....++|+|+|++.+......  +.--+.++||+||||++-  +........++.+... 
T Consensus       246 ~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~--L~k~~W~~VIvDEAHrIK--N~~Sklskalr~L~a~-  320 (1033)
T PLN03142        246 RAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTA--LKRFSWRYIIIDEAHRIK--NENSLLSKTMRLFSTN-  320 (1033)
T ss_pred             ceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHH--hccCCCCEEEEcCccccC--CHHHHHHHHHHHhhcC-
Confidence            45555665443322211   123589999999987653321  222346799999999873  3345556666666544 


Q ss_pred             cEEEEEeeC-ChhHHHHHH
Q psy4698         222 QVILLSATM-PADVLDVSM  239 (258)
Q Consensus       222 ~~i~~SAT~-~~~~~~~~~  239 (258)
                      ..+++|+|. .+.+.++..
T Consensus       321 ~RLLLTGTPlqNnl~ELws  339 (1033)
T PLN03142        321 YRLLITGTPLQNNLHELWA  339 (1033)
T ss_pred             cEEEEecCCCCCCHHHHHH
Confidence            467889995 555555443

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

Probab=99.41  E-value=1.9e-12  Score=109.77  Aligned_cols=143  Identities=20%  Similarity=0.178  Sum_probs=87.4

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhcccc---ceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKE---CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~---~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      .+.+++...+|+|||...+..+. .+....+.   ..+||+||. .+..+|...+.++.......+..+.+.........
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~  102 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSK  102 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTS
T ss_pred             CCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhccccccccccccccccccccccccc
Confidence            35699999999999988765554 33332221   259999999 88899999999988654556666555552222222


Q ss_pred             HHhcCCcEEEeChHHHH--------HHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC-C
Q psy4698         161 KLEAGAQVVVGTPGRVF--------DMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM-P  231 (258)
Q Consensus       161 ~~~~~~~Ilv~Tp~~l~--------~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~-~  231 (258)
                      ......+++|+|++.+.        ..+..     -+.++||+||+|.+  .+........+..+. ...++++|||. +
T Consensus       103 ~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~-----~~~~~vIvDEaH~~--k~~~s~~~~~l~~l~-~~~~~lLSgTP~~  174 (299)
T PF00176_consen  103 NQLPKYDVVITTYETLRKARKKKDKEDLKQ-----IKWDRVIVDEAHRL--KNKDSKRYKALRKLR-ARYRWLLSGTPIQ  174 (299)
T ss_dssp             SSCCCSSEEEEEHHHHH--TSTHTTHHHHT-----SEEEEEEETTGGGG--TTTTSHHHHHHHCCC-ECEEEEE-SS-SS
T ss_pred             cccccceeeecccccccccccccccccccc-----ccceeEEEeccccc--ccccccccccccccc-cceEEeecccccc
Confidence            33345899999999988        12222     23789999999987  333444444455565 56678899995 4


Q ss_pred             hhHHH
Q psy4698         232 ADVLD  236 (258)
Q Consensus       232 ~~~~~  236 (258)
                      +...+
T Consensus       175 n~~~d  179 (299)
T PF00176_consen  175 NSLED  179 (299)
T ss_dssp             SGSHH
T ss_pred             ccccc
Confidence            44343

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

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

Probab=99.39  E-value=7.1e-12  Score=119.27  Aligned_cols=132  Identities=21%  Similarity=0.343  Sum_probs=94.6

Q ss_pred             CCCCCCcHHHHHHhhh----hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHH-HHHHHhc
Q psy4698          65 YGFEKPSAIQQRAIIP----CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ-KVVIALG  139 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~----l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~-~~~~~~~  139 (258)
                      .|+ ..|+-|.+....    +..++.+++.|+||+|||++|++|++...    .+.+++|++||++|++|.. +.+..+.
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~l~  316 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAIQ  316 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHHH
Confidence            455 789999985544    45678899999999999999999988754    2468999999999999994 6677776


Q ss_pred             CCCCceEEEEECCcchH-----------------------------------------------HHHHHH----------
Q psy4698         140 DFMSVSCHACIGGTIVR-----------------------------------------------DDIRKL----------  162 (258)
Q Consensus       140 ~~~~~~~~~~~~~~~~~-----------------------------------------------~~~~~~----------  162 (258)
                      +..++.+..+.|+...-                                               ..|..+          
T Consensus       317 ~~~~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~~c  396 (820)
T PRK07246        317 EVFHIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQSS  396 (820)
T ss_pred             HhcCCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCCCC
Confidence            66666555544443210                                               000110          


Q ss_pred             --------------hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh
Q psy4698         163 --------------EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       163 --------------~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~  202 (258)
                                    ...++|+|+...-|+..+..+. .+...+.+||||||++.
T Consensus       397 p~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~-~~p~~~~lIiDEAH~l~  449 (820)
T PRK07246        397 LFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDK-DFARNKVLVFDEAQKLM  449 (820)
T ss_pred             CcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc-CCCCCCEEEEECcchhH
Confidence                          1125899999988777664443 35778999999999875

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

Probab=99.39  E-value=4.8e-12  Score=93.84  Aligned_cols=136  Identities=20%  Similarity=0.284  Sum_probs=81.5

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|+-.++...+|+|||.-.+.-++......  +.|+|+|.|||.++....+.++..    .+.+..   .....    ..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~--~~rvLvL~PTRvva~em~~aL~~~----~~~~~t---~~~~~----~~   69 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKR--RLRVLVLAPTRVVAEEMYEALKGL----PVRFHT---NARMR----TH   69 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHT--T--EEEEESSHHHHHHHHHHTTTS----SEEEES---TTSS-------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHc--cCeEEEecccHHHHHHHHHHHhcC----CcccCc---eeeec----cc
Confidence            455578999999999998766666555543  348999999999999988877432    333321   11111    22


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC--CCccEEEEEeeCChhH
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN--NDVQVILLSATMPADV  234 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~--~~~~~i~~SAT~~~~~  234 (258)
                      ..+.-|-+.|...+.+.+.+ .....++++||+||+|.. |.... ...-.+..+.  ..+.+|+||||.|...
T Consensus        70 ~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~-Dp~sI-A~rg~l~~~~~~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   70 FGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFT-DPTSI-AARGYLRELAESGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT---SHHHH-HHHHHHHHHHHTTS-EEEEEESS-TT--
T ss_pred             cCCCcccccccHHHHHHhcC-cccccCccEEEEeccccC-CHHHH-hhheeHHHhhhccCeeEEEEeCCCCCCC
Confidence            34456788888888777665 566789999999999964 33211 1111222221  3468999999998764

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

>KOG0925|consensus

Probab=99.38  E-value=4.6e-12  Score=109.69  Aligned_cols=200  Identities=15%  Similarity=0.155  Sum_probs=130.9

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .++.|...+.++...+.|+++--...+..+.+.+..+.++.-+++.|.||||||.....+.+.......  ..+....|.
T Consensus        23 ~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQpr  100 (699)
T KOG0925|consen   23 AINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQPR  100 (699)
T ss_pred             hcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCch
Confidence            377899999999999999987665678888888888888899999999999999998888877766654  357788899


Q ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh-c
Q psy4698         125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-S  203 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~-~  203 (258)
                      +.-+.+.+.+...   .+++...-..|..-..+.. . .+..-+-+||-+.|++-.... -.+...+.||+||||+-. .
T Consensus       101 rvaamsva~RVad---EMDv~lG~EVGysIrfEdC-~-~~~T~Lky~tDgmLlrEams~-p~l~~y~viiLDeahERtlA  174 (699)
T KOG0925|consen  101 RVAAMSVAQRVAD---EMDVTLGEEVGYSIRFEDC-T-SPNTLLKYCTDGMLLREAMSD-PLLGRYGVIILDEAHERTLA  174 (699)
T ss_pred             HHHHHHHHHHHHH---Hhccccchhcccccccccc-C-ChhHHHHHhcchHHHHHHhhC-cccccccEEEechhhhhhHH
Confidence            8888777654432   2233332222211111110 0 000112234555544433322 246788999999999632 1


Q ss_pred             -cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         204 -RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       204 -~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                       +-....++.++..- ++.++|.||||+.   ....+.|..++-++.|++ .-++
T Consensus       175 TDiLmGllk~v~~~r-pdLk~vvmSatl~---a~Kfq~yf~n~Pll~vpg-~~Pv  224 (699)
T KOG0925|consen  175 TDILMGLLKEVVRNR-PDLKLVVMSATLD---AEKFQRYFGNAPLLAVPG-THPV  224 (699)
T ss_pred             HHHHHHHHHHHHhhC-CCceEEEeecccc---hHHHHHHhCCCCeeecCC-CCce
Confidence             11223333444443 6899999999987   446777888888888876 4433

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

Probab=99.38  E-value=8.6e-12  Score=114.40  Aligned_cols=62  Identities=19%  Similarity=0.234  Sum_probs=51.9

Q ss_pred             HhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          77 AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        77 ~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      +...+.+++.+++.++||+|||++|++|++..+... .+.+++|++||++|..|+.+.+..+.
T Consensus         9 i~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117         9 CLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             HHHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            334456778899999999999999999998877632 23589999999999999999887776

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.

>KOG0923|consensus

Probab=99.30  E-value=4e-11  Score=107.28  Aligned_cols=182  Identities=13%  Similarity=0.091  Sum_probs=121.5

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHH-HHHhcCCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV-VIALGDFMS  143 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~-~~~~~~~~~  143 (258)
                      +.....+++-.+.+.++.....++|.|.||||||......+.+.=+.. .+.++-+..|.|..|..++.+ .+.++..++
T Consensus       261 RksLPVy~ykdell~av~e~QVLiI~GeTGSGKTTQiPQyL~EaGytk-~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG  339 (902)
T KOG0923|consen  261 RKSLPVYPYKDELLKAVKEHQVLIIVGETGSGKTTQIPQYLYEAGYTK-GGKKIGCTQPRRVAAMSVAARVAEEMGVKLG  339 (902)
T ss_pred             HhcCCchhhHHHHHHHHHhCcEEEEEcCCCCCccccccHHHHhccccc-CCceEeecCcchHHHHHHHHHHHHHhCcccc
Confidence            344567888899999999999999999999999998766555443333 333588888999988887644 444554444


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh-ccCcHHHHHHHHHhCCCCcc
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNNDVQ  222 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~-~~~~~~~~~~~~~~l~~~~~  222 (258)
                      ..|..     +.+.+. ...+..-|=+.|-+.|++-+... ..+..++.+||||||.-. ..+..--+.+-+.+.+++.+
T Consensus       340 ~eVGY-----sIRFEd-cTSekTvlKYMTDGmLlREfL~e-pdLasYSViiiDEAHERTL~TDILfgLvKDIar~RpdLK  412 (902)
T KOG0923|consen  340 HEVGY-----SIRFED-CTSEKTVLKYMTDGMLLREFLSE-PDLASYSVIIVDEAHERTLHTDILFGLVKDIARFRPDLK  412 (902)
T ss_pred             cccce-----EEEecc-ccCcceeeeeecchhHHHHHhcc-ccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcce
Confidence            33321     111110 11123567789999988765543 468899999999999631 12222233344555678999


Q ss_pred             EEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         223 VILLSATMPADVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       223 ~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                      ++++|||+..+   ....|+.+.-+-.+++.-.+|
T Consensus       413 llIsSAT~DAe---kFS~fFDdapIF~iPGRRyPV  444 (902)
T KOG0923|consen  413 LLISSATMDAE---KFSAFFDDAPIFRIPGRRYPV  444 (902)
T ss_pred             EEeeccccCHH---HHHHhccCCcEEeccCcccce
Confidence            99999999843   555777776666777665543

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.29  E-value=2e-11  Score=114.20  Aligned_cols=129  Identities=19%  Similarity=0.251  Sum_probs=103.5

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .++++|...--.+.+|+  +..+.||+|||+++.+|++.....+.   .+-+++|+..||.+-+..+..+....++.
T Consensus        80 Gm-~~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~G~---~VhvvT~ndyLA~RD~e~m~~l~~~lGl~  153 (913)
T PRK13103         80 GM-RHFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALSGK---GVHVVTVNDYLARRDANWMRPLYEFLGLS  153 (913)
T ss_pred             CC-CcchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHcCC---CEEEEeCCHHHHHHHHHHHHHHhcccCCE
Confidence            54 88999998888888887  89999999999999999987766553   69999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEEccchhhh
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTKQIRMFVLDEADEML  202 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~~~  202 (258)
                      +.+..++....+.... .. ++|++||..-+ +++|+.+-      .-..++.+.||||+|.++
T Consensus       154 v~~i~~~~~~~err~~-Y~-~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        154 VGIVTPFQPPEEKRAA-YA-ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             EEEECCCCCHHHHHHH-hc-CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            9987766554443332 22 89999998876 45555431      123788999999999875

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.29  E-value=6e-11  Score=100.23  Aligned_cols=70  Identities=21%  Similarity=0.165  Sum_probs=56.4

Q ss_pred             CCcHHHHH----HhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc---cceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQR----AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK---ECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~----~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .+++.|.+    +...+..|.++++.+|||+|||++++.|++..+.....   +.+++|.++|.++..|....+++.
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            46999999    44556678999999999999999999999877655332   248999999999988877666654

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.29  E-value=6e-11  Score=100.23  Aligned_cols=70  Identities=21%  Similarity=0.165  Sum_probs=56.4

Q ss_pred             CCcHHHHH----HhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc---cceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQR----AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK---ECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~----~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~---~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .+++.|.+    +...+..|.++++.+|||+|||++++.|++..+.....   +.+++|.++|.++..|....+++.
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            46999999    44556678999999999999999999999877655332   248999999999988877666654

>COG4889 Predicted helicase [General function prediction only]

Probab=99.23  E-value=2.4e-11  Score=111.72  Aligned_cols=177  Identities=20%  Similarity=0.195  Sum_probs=109.3

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCc----EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND----VIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~----~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ..|+.+.. .++..++.-..-.+|+++|+.|+++..+|..    -=+.+.+|+|||++.+ -+.+.+..    .++|+++
T Consensus       140 IDW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL-kisEala~----~~iL~Lv  213 (1518)
T COG4889         140 IDWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSL-KISEALAA----ARILFLV  213 (1518)
T ss_pred             CChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHH-HHHHHHhh----hheEeec
Confidence            45555543 3444444445667999999999999887621    2334456999999974 33444443    4899999


Q ss_pred             ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchH-----------------------HHHH--HHhcCCcEEEeChHHHH
Q psy4698         123 PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVR-----------------------DDIR--KLEAGAQVVVGTPGRVF  177 (258)
Q Consensus       123 P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~~~--~~~~~~~Ilv~Tp~~l~  177 (258)
                      |+++|..|..+.+..-. ...+.....+......                       ..+.  .-.++--|+++|++++.
T Consensus       214 PSIsLLsQTlrew~~~~-~l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~  292 (1518)
T COG4889         214 PSISLLSQTLREWTAQK-ELDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLP  292 (1518)
T ss_pred             chHHHHHHHHHHHhhcc-CccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchH
Confidence            99999999988775532 2233222222221111                       1111  11234679999999998


Q ss_pred             HHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC-----CccEEEEEeeC
Q psy4698         178 DMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-----DVQVILLSATM  230 (258)
Q Consensus       178 ~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~-----~~~~i~~SAT~  230 (258)
                      ..-......+..+++||+||||+...-.....-..-+.+.+.     ..+.+.|+||.
T Consensus       293 ~i~eAQe~G~~~fDliicDEAHRTtGa~~a~dd~saFt~vHs~~niKa~kRlYmTATP  350 (1518)
T COG4889         293 RIKEAQEAGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKAAKRLYMTATP  350 (1518)
T ss_pred             HHHHHHHcCCCCccEEEecchhccccceecccCcccceeecCcchhHHHHhhhcccCc
Confidence            877766677889999999999986433222222222222221     23567889984

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.21  E-value=2.3e-10  Score=109.55  Aligned_cols=163  Identities=18%  Similarity=0.111  Sum_probs=99.0

Q ss_pred             CCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      .|.|||.++...+...  ..+++.-.+|.|||+.+.+.+...+..+ ...++||+||. .|..||...+.+..   ++.+
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~kF---~l~~  226 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRRF---NLRF  226 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHHh---CCCe
Confidence            5899999998776543  3689999999999998866655544443 44589999997 89999998886533   2333


Q ss_pred             EEEECCcchHHH--HHHHhcCCcEEEeChHHHHHHHh-cCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCC-CCc
Q psy4698         147 HACIGGTIVRDD--IRKLEAGAQVVVGTPGRVFDMIS-RGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLN-NDV  221 (258)
Q Consensus       147 ~~~~~~~~~~~~--~~~~~~~~~Ilv~Tp~~l~~~l~-~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~-~~~  221 (258)
                      ..+.+.......  ........+++|++.+.+..--. ...+.-..++++||||||++-.. +........+..+. ...
T Consensus       227 ~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~~  306 (956)
T PRK04914        227 SLFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIP  306 (956)
T ss_pred             EEEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhccC
Confidence            333222211100  00111236899999987653111 01122246789999999998521 11111123333332 334


Q ss_pred             cEEEEEeeCCh-hHHH
Q psy4698         222 QVILLSATMPA-DVLD  236 (258)
Q Consensus       222 ~~i~~SAT~~~-~~~~  236 (258)
                      .++++|||.-. ..++
T Consensus       307 ~~LLLTATP~q~~~~e  322 (956)
T PRK04914        307 GVLLLTATPEQLGQES  322 (956)
T ss_pred             CEEEEEcCcccCCcHH
Confidence            68999999753 4443

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.20  E-value=1.4e-10  Score=106.47  Aligned_cols=130  Identities=17%  Similarity=0.237  Sum_probs=104.0

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|++.|....-.+++|+  ++.+.||+|||+++.+|++.....+.   .+-+++|+..||.+-+..+..+...+++
T Consensus        75 lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G~---~VhvvT~NdyLA~RDae~m~~ly~~LGL  148 (764)
T PRK12326         75 LGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQGR---RVHVITVNDYLARRDAEWMGPLYEALGL  148 (764)
T ss_pred             cCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCC---CeEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            355 89999999999999987  88999999999999999987776543   6999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~  202 (258)
                      .+.+..++....+.. ... .|||.++|...+ +++++.+      ......+.+.||||+|.++
T Consensus       149 svg~i~~~~~~~err-~aY-~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        149 TVGWITEESTPEERR-AAY-ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             EEEEECCCCCHHHHH-HHH-cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            999887766544333 333 489999998765 3444432      2234568899999999875

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

Probab=99.19  E-value=4.3e-10  Score=108.85  Aligned_cols=65  Identities=20%  Similarity=0.244  Sum_probs=54.0

Q ss_pred             CCCCCcHHHHHHhhh----hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          66 GFEKPSAIQQRAIIP----CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~----l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      |+ .+|+-|.+....    +..++.+++.||||+|||++|++|++......  +.+++|-++|+.|.+|...
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~--~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKK--EEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhcc--CCeEEEEcCCHHHHHHHHH
Confidence            55 789999986655    44678899999999999999999998765543  3479999999999999865

>KOG0385|consensus

Probab=99.18  E-value=6.8e-10  Score=101.00  Aligned_cols=162  Identities=17%  Similarity=0.202  Sum_probs=110.2

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+++||.+-++++.    .|-+.|+.-.+|-|||+..+..+.......+..+.-+|+||...| ..|.+.+++|+.  ++
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL-~NW~~Ef~rf~P--~l  243 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTL-DNWMNEFKRFTP--SL  243 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhH-HHHHHHHHHhCC--Cc
Confidence            68999999999875    456899999999999987743333333323334468999997665 456777888875  46


Q ss_pred             eEEEEECCcchHHHH-HHH--hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCc
Q psy4698         145 SCHACIGGTIVRDDI-RKL--EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV  221 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~-~~~--~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~  221 (258)
                      .+.+++|....+... +.+  ..+.+|+|+|++..++-  ...+.--+.+++||||||++  .+-...+..+++.+....
T Consensus       244 ~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W~ylvIDEaHRi--KN~~s~L~~~lr~f~~~n  319 (971)
T KOG0385|consen  244 NVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNWRYLVIDEAHRI--KNEKSKLSKILREFKTDN  319 (971)
T ss_pred             ceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCceEEEechhhhh--cchhhHHHHHHHHhcccc
Confidence            667778877554332 222  23589999999987643  11112234679999999998  445667778888887666


Q ss_pred             cEEEEEee-CChhHHHHH
Q psy4698         222 QVILLSAT-MPADVLDVS  238 (258)
Q Consensus       222 ~~i~~SAT-~~~~~~~~~  238 (258)
                      + +++|.| +-+++.++.
T Consensus       320 r-LLlTGTPLQNNL~ELW  336 (971)
T KOG0385|consen  320 R-LLLTGTPLQNNLHELW  336 (971)
T ss_pred             e-eEeeCCcccccHHHHH
Confidence            4 455666 466655544

>KOG0926|consensus

Probab=99.17  E-value=2.6e-10  Score=104.10  Aligned_cols=173  Identities=23%  Similarity=0.253  Sum_probs=110.6

Q ss_pred             HHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc---ccceEEEEeccHHHHHHHHHHH-HHhcC-CCCceEEE
Q psy4698          74 QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI---KECQALILAPTRELAQQIQKVV-IALGD-FMSVSCHA  148 (258)
Q Consensus        74 Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~---~~~~~lil~P~~~l~~q~~~~~-~~~~~-~~~~~~~~  148 (258)
                      ..+.++++..+.-++|||.||||||+.....+++.=+...   .+..+=|..|.|.-+...+++. .+++. ...+....
T Consensus       261 Eq~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqI  340 (1172)
T KOG0926|consen  261 EQRIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQI  340 (1172)
T ss_pred             HHHHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEE
Confidence            3566777888888999999999999987666655433322   1336677789988877776544 33544 22233333


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-----CcHHHHHHHHHhCCC----
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-----GFKDQIYDVFKHLNN----  219 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-----~~~~~~~~~~~~l~~----  219 (258)
                      -+.+        .+.....|.+.|-+.|++-+.+. +-+..++.||+||||.-.-+     |....+..+...+.+    
T Consensus       341 Rfd~--------ti~e~T~IkFMTDGVLLrEi~~D-flL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~  411 (1172)
T KOG0926|consen  341 RFDG--------TIGEDTSIKFMTDGVLLREIEND-FLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQ  411 (1172)
T ss_pred             Eecc--------ccCCCceeEEecchHHHHHHHHh-HhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcc
Confidence            3333        23344789999999999877764 56788999999999964211     112222222222222    


Q ss_pred             --CccEEEEEeeCChhHHHHH---HHhcCCCeEEEecCCcccC
Q psy4698         220 --DVQVILLSATMPADVLDVS---MKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       220 --~~~~i~~SAT~~~~~~~~~---~~~~~~~~~v~~~~~~~~~  257 (258)
                        ..++|+||||+.  +.+|.   +.|-.-|-+|.|+-..++|
T Consensus       412 ~kpLKLIIMSATLR--VsDFtenk~LFpi~pPlikVdARQfPV  452 (1172)
T KOG0926|consen  412 IKPLKLIIMSATLR--VSDFTENKRLFPIPPPLIKVDARQFPV  452 (1172)
T ss_pred             cCceeEEEEeeeEE--ecccccCceecCCCCceeeeecccCce
Confidence              468999999985  44444   3355566677777666543

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.15  E-value=3.1e-10  Score=105.83  Aligned_cols=130  Identities=17%  Similarity=0.266  Sum_probs=103.8

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|++.|....-.+.+|+  +..+.||+|||+++.+|++.....+.   .+-+++|+.-||.+-+..+..+...+++
T Consensus        77 ~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~---~v~vvT~neyLA~Rd~e~~~~~~~~LGl  150 (796)
T PRK12906         77 LGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGK---GVHVVTVNEYLSSRDATEMGELYRWLGL  150 (796)
T ss_pred             hCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC---CeEEEeccHHHHHhhHHHHHHHHHhcCC
Confidence            355 89999999988888888  99999999999999999988777654   6999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~  202 (258)
                      .+.+..++....... .. -.|||.++|...+ +++++.+      ..-...+.+.||||+|.++
T Consensus       151 ~vg~i~~~~~~~~r~-~~-y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        151 TVGLNLNSMSPDEKR-AA-YNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             eEEEeCCCCCHHHHH-HH-hcCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            998887765544432 22 3479999998876 3455442      1123567899999999875

>KOG0924|consensus

Probab=99.11  E-value=3.3e-09  Score=95.63  Aligned_cols=179  Identities=16%  Similarity=0.159  Sum_probs=110.0

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH-hcCCCCc
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA-LGDFMSV  144 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~  144 (258)
                      .+...+..+.+.+..+..++.++|.|.||||||......+++.=+.  ..+.+-+..|.|.-|...++...+ ++..++-
T Consensus       353 q~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~--~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~  430 (1042)
T KOG0924|consen  353 QYLPVFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYA--DNGMIGCTQPRRVAAISVAKRVAEEMGVTLGD  430 (1042)
T ss_pred             hhcchHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcccc--cCCeeeecCchHHHHHHHHHHHHHHhCCcccc
Confidence            3445677888888888888999999999999999864444333222  223555666999988888766544 5333332


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-C-cHHHHHHHHHhCCCCcc
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-G-FKDQIYDVFKHLNNDVQ  222 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~-~~~~~~~~~~~l~~~~~  222 (258)
                      .+...     .+.+--. ....-|-+.|-+.|++-.-.. -.+..++.||+||||.-.-+ + ....+..++++ +.+.+
T Consensus       431 ~VGYs-----IRFEdvT-~~~T~IkymTDGiLLrEsL~d-~~L~kYSviImDEAHERslNtDilfGllk~~lar-RrdlK  502 (1042)
T KOG0924|consen  431 TVGYS-----IRFEDVT-SEDTKIKYMTDGILLRESLKD-RDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDLK  502 (1042)
T ss_pred             ccceE-----EEeeecC-CCceeEEEeccchHHHHHhhh-hhhhheeEEEechhhhcccchHHHHHHHHHHHHh-hccce
Confidence            22111     1100000 122568889999887643322 24678899999999974322 1 11222223332 45789


Q ss_pred             EEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccC
Q psy4698         223 VILLSATMPADVLDVSMKFMRDPIKILVKKEELTL  257 (258)
Q Consensus       223 ~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~  257 (258)
                      +|.+||||.  .+.|...|.++|.+ .+++.+++|
T Consensus       503 liVtSATm~--a~kf~nfFgn~p~f-~IpGRTyPV  534 (1042)
T KOG0924|consen  503 LIVTSATMD--AQKFSNFFGNCPQF-TIPGRTYPV  534 (1042)
T ss_pred             EEEeecccc--HHHHHHHhCCCcee-eecCCccce
Confidence            999999997  56677666656654 455555544

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

Probab=99.09  E-value=2.1e-09  Score=88.95  Aligned_cols=130  Identities=18%  Similarity=0.272  Sum_probs=96.6

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|+ .|++.|..+.-.+..|+  ++...||-|||++..++++-....+   ..+=|++.+..|+..-+..+..+....++
T Consensus        74 ~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G---~~V~vvT~NdyLA~RD~~~~~~~y~~LGl  147 (266)
T PF07517_consen   74 LGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQG---KGVHVVTSNDYLAKRDAEEMRPFYEFLGL  147 (266)
T ss_dssp             TS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTS---S-EEEEESSHHHHHHHHHHHHHHHHHTT-
T ss_pred             cCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhc---CCcEEEeccHHHhhccHHHHHHHHHHhhh
Confidence            455 89999999998887777  9999999999999888776666654   36889999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHH-HHHhcCC------CCCCCccEEEEccchhhh
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVF-DMISRGA------LSTKQIRMFVLDEADEML  202 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~-~~l~~~~------~~~~~l~~lVvDE~h~~~  202 (258)
                      .+....++..........  .++|+++|...+. ++++.+.      .....+.++||||+|.++
T Consensus       148 sv~~~~~~~~~~~r~~~Y--~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  148 SVGIITSDMSSEERREAY--AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             -EEEEETTTEHHHHHHHH--HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             ccccCccccCHHHHHHHH--hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            999888877654433322  2689999998874 4554321      124678899999999875

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.09  E-value=1.4e-09  Score=103.25  Aligned_cols=176  Identities=19%  Similarity=0.189  Sum_probs=106.5

Q ss_pred             HHHHHHCCCCCCcHHHHHHhhhhhc--------CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHH
Q psy4698          59 LRGIYAYGFEKPSAIQQRAIIPCVR--------GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ  130 (258)
Q Consensus        59 ~~~l~~~~~~~~~~~Q~~~~~~l~~--------g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q  130 (258)
                      .+.+++..-..-+.+|.+|++.+..        |.-++=.|.||+|||++= .-++..+.....++|..|..-.|+|--|
T Consensus       398 hk~~~~r~~~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aN-ARImyaLsd~~~g~RfsiALGLRTLTLQ  476 (1110)
T TIGR02562       398 HKYFCQRSAHPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLAN-ARAMYALRDDKQGARFAIALGLRSLTLQ  476 (1110)
T ss_pred             hhhhccCCCCCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHH-HHHHHHhCCCCCCceEEEEccccceecc
Confidence            3445444444568899999988753        334677899999999985 3444556666677788888888877777


Q ss_pred             HHHHHHHhcCCCCceEEEEECCcchHHHH-------------------------------------------HHHh----
Q psy4698         131 IQKVVIALGDFMSVSCHACIGGTIVRDDI-------------------------------------------RKLE----  163 (258)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~~----  163 (258)
                      .-+.+++.....+-...++.|+....+..                                           ..+.    
T Consensus       477 TGda~r~rL~L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k  556 (1110)
T TIGR02562       477 TGHALKTRLNLSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDK  556 (1110)
T ss_pred             chHHHHHhcCCCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChh
Confidence            66666554332222233333332211100                                           0000    


Q ss_pred             ----cCCcEEEeChHHHHHHHh--cCCCC---CCC--ccEEEEccchhhhccCcHHHHHHHHHhCC-CCccEEEEEeeCC
Q psy4698         164 ----AGAQVVVGTPGRVFDMIS--RGALS---TKQ--IRMFVLDEADEMLSRGFKDQIYDVFKHLN-NDVQVILLSATMP  231 (258)
Q Consensus       164 ----~~~~Ilv~Tp~~l~~~l~--~~~~~---~~~--l~~lVvDE~h~~~~~~~~~~~~~~~~~l~-~~~~~i~~SAT~~  231 (258)
                          -...++|||+++++....  ++...   +-.  =+.||+||+|.+ +......+.+++.-.. -..++++||||+|
T Consensus       557 ~~rll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaY-D~~~~~~L~rlL~w~~~lG~~VlLmSATLP  635 (1110)
T TIGR02562       557 EKTLLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDY-EPEDLPALLRLVQLAGLLGSRVLLSSATLP  635 (1110)
T ss_pred             hhhhhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccC-CHHHHHHHHHHHHHHHHcCCCEEEEeCCCC
Confidence                015799999999987762  21111   112  258999999964 3333344444444221 3578999999999


Q ss_pred             hhHHH
Q psy4698         232 ADVLD  236 (258)
Q Consensus       232 ~~~~~  236 (258)
                      ..+.+
T Consensus       636 ~~l~~  640 (1110)
T TIGR02562       636 PALVK  640 (1110)
T ss_pred             HHHHH
Confidence            97655

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.

>KOG0387|consensus

Probab=99.07  E-value=2.5e-09  Score=97.67  Aligned_cols=164  Identities=18%  Similarity=0.135  Sum_probs=105.1

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .+++||++.+.++-    ++..-|+.-.+|-|||+..+ ..+..+... .-...+||||| ..+..||.+.+..+...  
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQii-sFLaaL~~S~k~~~paLIVCP-~Tii~qW~~E~~~w~p~--  280 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQII-SFLAALHHSGKLTKPALIVCP-ATIIHQWMKEFQTWWPP--  280 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHH-HHHHHHhhcccccCceEEEcc-HHHHHHHHHHHHHhCcc--
Confidence            57899999998863    45668999999999997653 222333322 22357999999 57888999999888654  


Q ss_pred             ceEEEEECCcch--------HHHHH-----HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHH
Q psy4698         144 VSCHACIGGTIV--------RDDIR-----KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQI  210 (258)
Q Consensus       144 ~~~~~~~~~~~~--------~~~~~-----~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~  210 (258)
                      +.+..+++....        ...+.     ....+..|+|+|++.+.  +....+.-...+++|+||.|++-+  -..++
T Consensus       281 ~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r--~~~d~l~~~~W~y~ILDEGH~IrN--pns~i  356 (923)
T KOG0387|consen  281 FRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFR--IQGDDLLGILWDYVILDEGHRIRN--PNSKI  356 (923)
T ss_pred             eEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhc--ccCcccccccccEEEecCcccccC--CccHH
Confidence            455555554431        11111     11223579999997754  122222233457999999998833  34555


Q ss_pred             HHHHHhCCCCccEEEEEee-CChhHHHHHHHh
Q psy4698         211 YDVFKHLNNDVQVILLSAT-MPADVLDVSMKF  241 (258)
Q Consensus       211 ~~~~~~l~~~~~~i~~SAT-~~~~~~~~~~~~  241 (258)
                      ......++... .|++|.| +-+++.++...|
T Consensus       357 slackki~T~~-RiILSGTPiQNnL~ELwsLf  387 (923)
T KOG0387|consen  357 SLACKKIRTVH-RIILSGTPIQNNLTELWSLF  387 (923)
T ss_pred             HHHHHhccccc-eEEeeCccccchHHHHHHHh
Confidence            56666665544 4555666 577777777654

>KOG1123|consensus

Probab=99.06  E-value=1.4e-10  Score=101.04  Aligned_cols=148  Identities=18%  Similarity=0.154  Sum_probs=99.1

Q ss_pred             CCcHHHHHHhhhhhcC---CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          69 KPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g---~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      .++|||..++.....+   ++-+|+.|.|+|||++-+.+++.      -+.++|++|.+-..+.||...++.+.---+-.
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t------ikK~clvLcts~VSVeQWkqQfk~wsti~d~~  375 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT------IKKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQ  375 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee------ecccEEEEecCccCHHHHHHHHHhhcccCccc
Confidence            5699999999887644   57899999999999987655432      12379999999999999999998886443333


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc--------CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR--------GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~--------~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      +..+......     ....+++|+|+|+..+..--++        ..+.-...+++++||+|.+...-|    .+++...
T Consensus       376 i~rFTsd~Ke-----~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MF----RRVlsiv  446 (776)
T KOG1123|consen  376 ICRFTSDAKE-----RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMF----RRVLSIV  446 (776)
T ss_pred             eEEeeccccc-----cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHH----HHHHHHH
Confidence            4333333221     2345689999999765421111        012234578999999997743322    2333333


Q ss_pred             CCCccEEEEEeeCCh
Q psy4698         218 NNDVQVILLSATMPA  232 (258)
Q Consensus       218 ~~~~~~i~~SAT~~~  232 (258)
                      ...| .++++||+=+
T Consensus       447 ~aHc-KLGLTATLvR  460 (776)
T KOG1123|consen  447 QAHC-KLGLTATLVR  460 (776)
T ss_pred             HHHh-hccceeEEee
Confidence            3344 6799999854

>KOG0390|consensus

Probab=99.05  E-value=6.4e-09  Score=96.45  Aligned_cols=173  Identities=14%  Similarity=0.127  Sum_probs=114.9

Q ss_pred             CCcHHHHHHhhhhhc---C-------CcEEEEcccCCCcchHhHHHHHHHhhhcccc-----ceEEEEeccHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVR---G-------NDVIAQAQSGTGKTATFSISILQQVDQNIKE-----CQALILAPTRELAQQIQK  133 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~---g-------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~-----~~~lil~P~~~l~~q~~~  133 (258)
                      .++|+|++.+.-+-.   |       ..+++.-.+|+|||+..+ +++..+.....+     .++||++| ..|+..|.+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~I-sflwtlLrq~P~~~~~~~k~lVV~P-~sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCI-SFIWTLLRQFPQAKPLINKPLVVAP-SSLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHH-HHHHHHHHhCcCccccccccEEEcc-HHHHHHHHH
Confidence            579999999977532   2       248888899999998864 444445444444     58999999 578888999


Q ss_pred             HHHHhcCCCCceEEEEECCcch-HHHHHHHh------cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         134 VVIALGDFMSVSCHACIGGTIV-RDDIRKLE------AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~------~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      .+.++.....+....+++.... ......+.      -..-|++.+.+.+.+....  +....++++|+||.|++  .+-
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrl--kN~  391 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRL--KNS  391 (776)
T ss_pred             HHHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCc--cch
Confidence            8888765545555555555543 11111111      1246788889888766554  44567889999999987  334


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeC-ChhHHHHHHHh-cCCCeEE
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATM-PADVLDVSMKF-MRDPIKI  248 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~-~~~~~~~~~~~-~~~~~~v  248 (258)
                      ...+...+..+. -.+.|++|.|+ -+++.++.+.. +-+|.++
T Consensus       392 ~s~~~kaL~~l~-t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~L  434 (776)
T KOG0390|consen  392 DSLTLKALSSLK-TPRRVLLTGTPIQNDLKEYFNLLDFVRPGFL  434 (776)
T ss_pred             hhHHHHHHHhcC-CCceEEeeCCcccccHHHHHHHHhhcChhhc
Confidence            555566666663 45678889996 66676665542 3345444

>KOG0951|consensus

Probab=99.05  E-value=4.1e-10  Score=106.91  Aligned_cols=152  Identities=20%  Similarity=0.324  Sum_probs=111.7

Q ss_pred             CCcHHHHHHhhhhhc-CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH-hcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVR-GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA-LGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~-g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~  146 (258)
                      ..+++|.++++.+-+ ++++++.+|+|||||.++-++++.    .....+++++.|..+.+..++..+.+ +....|..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~ 1218 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRI 1218 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCceE
Confidence            448899999988654 467999999999999999888876    23345899999999999888876654 666777777


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH------HHHHHHHHhCCCC
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK------DQIYDVFKHLNND  220 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~------~~~~~~~~~l~~~  220 (258)
                      ..+.|.......  . ....+|+|+||++. +.++    ....+++.|+||+|.+.+. .+      ..+..+-..+.++
T Consensus      1219 ~~l~ge~s~~lk--l-~~~~~vii~tpe~~-d~lq----~iQ~v~l~i~d~lh~igg~-~g~v~evi~S~r~ia~q~~k~ 1289 (1674)
T KOG0951|consen 1219 VKLTGETSLDLK--L-LQKGQVIISTPEQW-DLLQ----SIQQVDLFIVDELHLIGGV-YGAVYEVICSMRYIASQLEKK 1289 (1674)
T ss_pred             EecCCccccchH--H-hhhcceEEechhHH-HHHh----hhhhcceEeeehhhhhccc-CCceEEEEeeHHHHHHHHHhh
Confidence            776666554433  2 23358999999994 4443    5678899999999977522 11      1244455556678


Q ss_pred             ccEEEEEeeCChh
Q psy4698         221 VQVILLSATMPAD  233 (258)
Q Consensus       221 ~~~i~~SAT~~~~  233 (258)
                      .+++++|..+.+.
T Consensus      1290 ir~v~ls~~lana 1302 (1674)
T KOG0951|consen 1290 IRVVALSSSLANA 1302 (1674)
T ss_pred             eeEEEeehhhccc
Confidence            8999999888653

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.03  E-value=1.2e-09  Score=101.47  Aligned_cols=137  Identities=15%  Similarity=0.156  Sum_probs=95.5

Q ss_pred             EEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchH---HHHHHHhc
Q psy4698          88 IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVR---DDIRKLEA  164 (258)
Q Consensus        88 li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~  164 (258)
                      +..+.+|||||.+|+-.+-..+..+   .++|+++|.+.+..|....++.....  ..+..++++.+..   ..+..+..
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~G---k~vLvLvPEi~lt~q~~~rl~~~f~~--~~v~~lhS~l~~~~R~~~w~~~~~  238 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRAG---RGALVVVPDQRDVDRLEAALRALLGA--GDVAVLSAGLGPADRYRRWLAVLR  238 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHcC---CeEEEEecchhhHHHHHHHHHHHcCC--CcEEEECCCCCHHHHHHHHHHHhC
Confidence            3344469999999976665555543   36999999999999999999876531  3455566554433   34444555


Q ss_pred             C-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-C----cHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         165 G-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-G----FKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       165 ~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~----~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      | .+|+|||...++       ..++++++|||||-|.-... .    +...-..+++.-..++.+|+.|||.+-+...
T Consensus       239 G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~  309 (665)
T PRK14873        239 GQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQA  309 (665)
T ss_pred             CCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHH
Confidence            5 899999998877       68899999999999964321 1    2223233444444678999999998865443

>KOG0384|consensus

Probab=99.02  E-value=8.5e-10  Score=104.64  Aligned_cols=188  Identities=13%  Similarity=0.170  Sum_probs=126.6

Q ss_pred             cccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhc
Q psy4698          37 LIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQN  112 (258)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~  112 (258)
                      -....+.++...|..+...+..+.     | ..+++||.+-+++++    .+.++|+.-.+|-|||+..+..+-......
T Consensus       344 ~~~~~~~~~rp~~~Kle~qp~~~~-----g-~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~  417 (1373)
T KOG0384|consen  344 NKGCKYRPQRPRFRKLEKQPEYKG-----G-NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSL  417 (1373)
T ss_pred             CCccccCccchhHHHhhcCccccc-----c-chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhh
Confidence            344455566666777766655443     3 589999999999876    457899999999999976543332222222


Q ss_pred             cccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh----c-----CCcEEEeChHHHHHHHhcC
Q psy4698         113 IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE----A-----GAQVVVGTPGRVFDMISRG  183 (258)
Q Consensus       113 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~-----~~~Ilv~Tp~~l~~~l~~~  183 (258)
                      ...+-.||++|...+ ..|.+.+..+.   ++++.+++|....++..+...    .     ..+++++|++.++.--.  
T Consensus       418 ~~~gpflvvvplst~-~~W~~ef~~w~---~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~--  491 (1373)
T KOG0384|consen  418 QIHGPFLVVVPLSTI-TAWEREFETWT---DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA--  491 (1373)
T ss_pred             hccCCeEEEeehhhh-HHHHHHHHHHh---hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh--
Confidence            233468999996554 44555565555   678888999887776655543    1     37899999988763221  


Q ss_pred             CCCCC--CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         184 ALSTK--QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       184 ~~~~~--~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                        .++  ...+++|||||++  .+....+...+..+.-+.+++++.-.+-+.++++...
T Consensus       492 --~L~~i~w~~~~vDeahrL--kN~~~~l~~~l~~f~~~~rllitgTPlQNsikEL~sL  546 (1373)
T KOG0384|consen  492 --ELSKIPWRYLLVDEAHRL--KNDESKLYESLNQFKMNHRLLITGTPLQNSLKELWSL  546 (1373)
T ss_pred             --hhccCCcceeeecHHhhc--CchHHHHHHHHHHhcccceeeecCCCccccHHHHHHH
Confidence              222  3468999999998  4456667777777777776666555567778877643

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

Probab=99.02  E-value=6.6e-09  Score=98.67  Aligned_cols=143  Identities=14%  Similarity=0.250  Sum_probs=86.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHH---------HhcCCCCceEEEEECCc--
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI---------ALGDFMSVSCHACIGGT--  153 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~---------~~~~~~~~~~~~~~~~~--  153 (258)
                      .++.+.++||+|||.+|+-.++...... +..+.||+||+.++.....+.+.         .......+....+.++.  
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~-~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~  138 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKY-GLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK  138 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHc-CCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence            4799999999999999988877654443 34589999999988766654443         22222234444444332  


Q ss_pred             -----chHHHHHHH-------hcCCcEEEeChHHHHHHHh-c--------CC--CCCCCc----cEEEEccchhhhccCc
Q psy4698         154 -----IVRDDIRKL-------EAGAQVVVGTPGRVFDMIS-R--------GA--LSTKQI----RMFVLDEADEMLSRGF  206 (258)
Q Consensus       154 -----~~~~~~~~~-------~~~~~Ilv~Tp~~l~~~l~-~--------~~--~~~~~l----~~lVvDE~h~~~~~~~  206 (258)
                           .........       .+...|+|.|.+.|..-.. +        +.  ..+..+    -+||+||+|++-..  
T Consensus       139 k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~--  216 (986)
T PRK15483        139 KSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD--  216 (986)
T ss_pred             ccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc--
Confidence                 001111111       1147899999988764211 0        00  111111    28999999998432  


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      .... .-+..+++.+ ++.+|||.+.
T Consensus       217 ~k~~-~~i~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 NKFY-QAIEALKPQM-IIRFGATFPD  240 (986)
T ss_pred             hHHH-HHHHhcCccc-EEEEeeecCC
Confidence            2222 4446776655 6679999986

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.00  E-value=5.6e-09  Score=98.29  Aligned_cols=64  Identities=25%  Similarity=0.357  Sum_probs=52.4

Q ss_pred             CCCCCcHHHHHHhhhhh----c-----CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHH
Q psy4698          66 GFEKPSAIQQRAIIPCV----R-----GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ  132 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~----~-----g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~  132 (258)
                      || ..|+-|.+....+.    .     ++.++|.||||+|||++|++|++......+  .+++|-+.|++|-+|..
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~--k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEK--KKLVISTATVALQEQLV   95 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcC--CeEEEEcCCHHHHHHHH
Confidence            55 78999998766543    3     367999999999999999999987665443  47999999999999985

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.99  E-value=2.6e-09  Score=99.91  Aligned_cols=130  Identities=17%  Similarity=0.227  Sum_probs=99.6

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|++.|....-.+..|+  ++.+.||.|||+++.+|++-....+   ..+-|++++..||.+-+.++..+...+++
T Consensus        73 lG~-r~ydvQlig~l~L~~G~--IaEm~TGEGKTL~a~l~ayl~aL~G---~~VhVvT~NdyLA~RD~e~m~pvy~~LGL  146 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLNDGK--IAEMKTGEGKTLVATLPAYLNALTG---KGVHIVTVNDYLAKRDQEWMGQIYRFLGL  146 (870)
T ss_pred             hCC-CCCchHhhhhHhhcCCc--cccccCCCCchHHHHHHHHHHHhcC---CceEEEeCCHHHHHHHHHHHHHHHHHcCC
Confidence            355 78999998887776665  9999999999999999886544433   36999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~  202 (258)
                      .+.+..++....+...  .-.|||.++|...+ +++++.+      ......+.+.||||+|.++
T Consensus       147 svg~i~~~~~~~err~--aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        147 TVGLIQEGMSSEERKK--NYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             ceeeeCCCCChHHHHH--hcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            9988766655544322  23379999998755 3444432      1234568899999999875

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.97  E-value=4.5e-09  Score=98.37  Aligned_cols=129  Identities=17%  Similarity=0.233  Sum_probs=102.1

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .|+++|...--.+.+|+  +..+.||.|||+++.+|++.....+.   .+-|++++..||..-+.++..+....++.
T Consensus        83 G~-r~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~Gk---gVhVVTvNdYLA~RDae~m~~vy~~LGLt  156 (939)
T PRK12902         83 GM-RHFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTGK---GVHVVTVNDYLARRDAEWMGQVHRFLGLS  156 (939)
T ss_pred             CC-CcchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcCC---CeEEEeCCHHHHHhHHHHHHHHHHHhCCe
Confidence            55 78999998888888887  89999999999999999887666553   59999999999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhc------CCCCCCCccEEEEccchhhh
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISR------GALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~------~~~~~~~l~~lVvDE~h~~~  202 (258)
                      +.+..++....+.  ...-.|||++||...+ +++|+.      .......+.+.||||+|.++
T Consensus       157 vg~i~~~~~~~er--r~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        157 VGLIQQDMSPEER--KKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             EEEECCCCChHHH--HHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            9887665544333  3334589999999887 334332      22334678899999999875

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.89  E-value=2.5e-08  Score=94.30  Aligned_cols=73  Identities=23%  Similarity=0.235  Sum_probs=60.7

Q ss_pred             CCCCCcHHHHHHhhh----hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          66 GFEKPSAIQQRAIIP----CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~----l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      -|..+++.|.+.+..    +..|+++++.+|||+|||++.+.+++..........+++|.+.|.+-..|..+.+++.
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~   83 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKL   83 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhh
Confidence            455669999887765    4577899999999999999999999987765544468999999999999998888874

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).

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.87  E-value=2.2e-08  Score=96.97  Aligned_cols=136  Identities=18%  Similarity=0.184  Sum_probs=94.4

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +..+|.--+|||||++....+-..+.. ...+.++||+-++.|-.|..+.+..++.......    ...+..+..+.+..
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~-~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLEL-PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLED  348 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhc-cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHhc
Confidence            458999999999999976555444444 5667999999999999999999988875433222    33444555555554


Q ss_pred             C-CcEEEeChHHHHHHHhcC-C--CCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         165 G-AQVVVGTPGRVFDMISRG-A--LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       165 ~-~~Ilv~Tp~~l~~~l~~~-~--~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      + ..|+|+|.++|-...... .  ..-+++ .||+||||+-   .++..-..+-..+ ++...+++|+|.
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~~~~~~~~~~i-vvI~DEaHRS---Q~G~~~~~~~~~~-~~a~~~gFTGTP  413 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKEDELELLKRKNV-VVIIDEAHRS---QYGELAKLLKKAL-KKAIFIGFTGTP  413 (962)
T ss_pred             CCCcEEEEEecccchhhhcccccccCCCcE-EEEEechhhc---cccHHHHHHHHHh-ccceEEEeeCCc
Confidence            4 489999999998877654 1  122333 7999999973   2333333333334 447899999995

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

Probab=98.87  E-value=2.6e-08  Score=79.36  Aligned_cols=149  Identities=13%  Similarity=0.217  Sum_probs=76.7

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHH---H-HHhcCCCC
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV---V-IALGDFMS  143 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~---~-~~~~~~~~  143 (258)
                      ...+..|..++.++...+-+++.||.|+|||+.++..+++.+.. +...+++|+-|..+..++.-..   + .++..+..
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~-g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~   81 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE-GEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLR   81 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT-TS-SEEEEEE-S--TT----SS---------TTTH
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCcEEEEEecCCCCccccccCCCCHHHHHHHHHH
Confidence            35688999999999988889999999999999999999988877 4445888888876532221100   0 00000000


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccE
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV  223 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~  223 (258)
                      - +.-.............+.....|-+..+..    ++..  .+++ .+||+|||+.+    ...++..++.++..++++
T Consensus        82 p-~~d~l~~~~~~~~~~~~~~~~~Ie~~~~~~----iRGr--t~~~-~~iIvDEaQN~----t~~~~k~ilTR~g~~ski  149 (205)
T PF02562_consen   82 P-IYDALEELFGKEKLEELIQNGKIEIEPLAF----IRGR--TFDN-AFIIVDEAQNL----TPEELKMILTRIGEGSKI  149 (205)
T ss_dssp             H-HHHHHTTTS-TTCHHHHHHTTSEEEEEGGG----GTT----B-S-EEEEE-SGGG------HHHHHHHHTTB-TT-EE
T ss_pred             H-HHHHHHHHhChHhHHHHhhcCeEEEEehhh----hcCc--cccc-eEEEEecccCC----CHHHHHHHHcccCCCcEE
Confidence            0 000000000001111222223455555422    2221  2222 69999999976    577889999999999999


Q ss_pred             EEEEee
Q psy4698         224 ILLSAT  229 (258)
Q Consensus       224 i~~SAT  229 (258)
                      |++.-.
T Consensus       150 i~~GD~  155 (205)
T PF02562_consen  150 IITGDP  155 (205)
T ss_dssp             EEEE--
T ss_pred             EEecCc
Confidence            988654

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

>KOG0921|consensus

Probab=98.84  E-value=2.5e-08  Score=92.33  Aligned_cols=235  Identities=18%  Similarity=0.218  Sum_probs=139.8

Q ss_pred             CCCCCCCCCCCCCCCccCCCCCCCCCCCcccCcccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC
Q psy4698           5 RGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG   84 (258)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g   84 (258)
                      +-.+|.+|.-.+....+..-.+..........+-.+.+.+.     .....+.....+....-...-.+-...+.++...
T Consensus       319 s~i~wapP~anwn~w~A~nide~~la~~~~~s~~q~~~~~~-----~~~~d~e~~~~~a~re~lpva~~~~~i~q~v~dn  393 (1282)
T KOG0921|consen  319 SNISWAPPLQNWNPWRASNIDEEPLAFMSMESISQRIMEKE-----RFKRDEALDKITAQREELPVAQYRSEILQAVAEN  393 (1282)
T ss_pred             CCCCCCCccccccccccccCcccccccccccCcccchhhhh-----hhhcccchhhhhhhhhhCcHHHHHHHHHHHHhcC
Confidence            44588888888887777666444443111111111111111     1112223333333333334445556677777788


Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhcccc--ceEEEEeccHHHHHHHHHHHHH-hcCCCCceEEEEECCcchHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKE--CQALILAPTRELAQQIQKVVIA-LGDFMSVSCHACIGGTIVRDDIRK  161 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~--~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  161 (258)
                      +.++|.+.||.|||..+...+++.+..+..+  ..+.+-.|++..+..+.+.+.+ .+...+-.|     +++.+.....
T Consensus       394 ~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~tv-----gy~vRf~Sa~  468 (1282)
T KOG0921|consen  394 RVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGETC-----GYNVRFDSAT  468 (1282)
T ss_pred             ceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhcccc-----cccccccccc
Confidence            8899999999999999999999988776443  3466677888877776654422 222211111     1111111111


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh-ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       162 ~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~-~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      ...--.|++||-+-+++++...   +..+.++++||+|+.. +..|...+.+-+...-++..+++||||+..+   ++..
T Consensus       469 prpyg~i~fctvgvllr~~e~g---lrg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~lmsatIdTd---~f~~  542 (1282)
T KOG0921|consen  469 PRPYGSIMFCTVGVLLRMMENG---LRGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLMSATIDTD---LFTN  542 (1282)
T ss_pred             cccccceeeeccchhhhhhhhc---ccccccccchhhhhhccchHHHHHHHHhhhccchhhhhhhhhcccchh---hhhh
Confidence            1122469999999999988874   4567899999999753 2245555555555556778889999999865   5555


Q ss_pred             hcCCCeEEEecCCcc
Q psy4698         241 FMRDPIKILVKKEEL  255 (258)
Q Consensus       241 ~~~~~~~v~~~~~~~  255 (258)
                      |+.+-+.+.+.+..+
T Consensus       543 ~f~~~p~~~~~grt~  557 (1282)
T KOG0921|consen  543 FFSSIPDVTVHGRTF  557 (1282)
T ss_pred             hhccccceeeccccc
Confidence            666544445555544

>KOG0389|consensus

Probab=98.84  E-value=7.5e-08  Score=88.22  Aligned_cols=165  Identities=15%  Similarity=0.176  Sum_probs=105.0

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+-+||.--++++.    .+-+.|+.-.+|-|||...+ +.+..+.+.+..+.=||+||+..|-+ |.+.+.+|+.  .+
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvI-aFlayLkq~g~~gpHLVVvPsSTleN-WlrEf~kwCP--sl  474 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVI-AFLAYLKQIGNPGPHLVVVPSSTLEN-WLREFAKWCP--SL  474 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHHH-HHHHHHHHcCCCCCcEEEecchhHHH-HHHHHHHhCC--ce
Confidence            47889999888853    34468999999999998764 34444554444557899999877654 4555666764  46


Q ss_pred             eEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHH-hcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC
Q psy4698         145 SCHACIGGTIVRDDIRKLE----AGAQVVVGTPGRVFDMI-SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN  219 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l-~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~  219 (258)
                      .+..++|....+...+...    .+++|+++|+..+..-- .+.-+.-.++.++|+||.|.+ .+.....+.. +-.++.
T Consensus       475 ~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmL-KN~~SeRy~~-LM~I~A  552 (941)
T KOG0389|consen  475 KVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHML-KNRTSERYKH-LMSINA  552 (941)
T ss_pred             EEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhh-hccchHHHHH-hccccc
Confidence            7788888876655543322    24899999986543100 011122245779999999965 3323333333 333444


Q ss_pred             CccEEEEEee-CChhHHHHHHH
Q psy4698         220 DVQVILLSAT-MPADVLDVSMK  240 (258)
Q Consensus       220 ~~~~i~~SAT-~~~~~~~~~~~  240 (258)
                      +. .|+++.| +-+++++++..
T Consensus       553 n~-RlLLTGTPLQNNL~ELiSL  573 (941)
T KOG0389|consen  553 NF-RLLLTGTPLQNNLKELISL  573 (941)
T ss_pred             cc-eEEeeCCcccccHHHHHHH
Confidence            44 5566776 57777776654

>KOG4439|consensus

Probab=98.80  E-value=2.1e-08  Score=90.68  Aligned_cols=174  Identities=22%  Similarity=0.198  Sum_probs=109.8

Q ss_pred             CCcHHHHHHhhhhhcC-----CcEEEEcccCCCcchHhHHHHHHHhhh----ccc---cceEEEEeccHHHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVRG-----NDVIAQAQSGTGKTATFSISILQQVDQ----NIK---ECQALILAPTRELAQQIQKVVI  136 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g-----~~~li~~~tGsGKT~~~l~~~l~~l~~----~~~---~~~~lil~P~~~l~~q~~~~~~  136 (258)
                      .+.++|..++.++.-.     ...|+....|-|||++.+-.++..-..    ++.   ...+||||| -.|..||...+.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~P-aSli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICP-ASLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCc-HHHHHHHHHHHH
Confidence            5688999999887633     347889999999999876555543321    111   114899999 567888888887


Q ss_pred             HhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHH----HHhc--CCCCCCCc--cEEEEccchhhhccCcHH
Q psy4698         137 ALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFD----MISR--GALSTKQI--RMFVLDEADEMLSRGFKD  208 (258)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~----~l~~--~~~~~~~l--~~lVvDE~h~~~~~~~~~  208 (258)
                      .......+.+..++|.....-..+.+ ..+||+|+|+.-+..    -...  +.-.+.++  .-||+||||.+-+  ...
T Consensus       404 ~rl~~n~LsV~~~HG~n~r~i~~~~L-~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN--~~t  480 (901)
T KOG4439|consen  404 RRLEQNALSVYLYHGPNKREISAKEL-RKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRN--SNT  480 (901)
T ss_pred             HHHhhcceEEEEecCCccccCCHHHH-hhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhcc--cch
Confidence            76666678888888887533333333 349999999966544    1111  11123333  4699999998733  344


Q ss_pred             HHHHHHHhCCCCccEEEEEee-CChhHHHHHH--HhcCCCeE
Q psy4698         209 QIYDVFKHLNNDVQVILLSAT-MPADVLDVSM--KFMRDPIK  247 (258)
Q Consensus       209 ~~~~~~~~l~~~~~~i~~SAT-~~~~~~~~~~--~~~~~~~~  247 (258)
                      +.-.-++.+...+ ..++|+| +.+...++..  .|+++|-+
T Consensus       481 q~S~AVC~L~a~~-RWclTGTPiqNn~~DvysLlrFLr~~pF  521 (901)
T KOG4439|consen  481 QCSKAVCKLSAKS-RWCLTGTPIQNNLWDVYSLLRFLRCPPF  521 (901)
T ss_pred             hHHHHHHHHhhcc-eeecccCccccchhHHHHHHHHhcCCCc
Confidence            4445555665555 4566776 4554333322  36666644

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

Probab=98.79  E-value=5.3e-08  Score=91.62  Aligned_cols=71  Identities=20%  Similarity=0.278  Sum_probs=57.8

Q ss_pred             CCCCCCcHHHHHHhhhh----hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          65 YGFEKPSAIQQRAIIPC----VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l----~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      +....+++.|.+.+..+    ..++.+++.||||+|||++|+.|++......+  .+++|.++|+.+.+|..+....
T Consensus        11 ~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~--~~viist~t~~lq~q~~~~~~~   85 (654)
T COG1199          11 FPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG--KKVIISTRTKALQEQLLEEDLP   85 (654)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC--CcEEEECCCHHHHHHHHHhhcc
Confidence            44558999999988654    45566999999999999999999998876654  4799999999999888765433

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=98.77  E-value=2.2e-07  Score=77.49  Aligned_cols=174  Identities=18%  Similarity=0.196  Sum_probs=112.9

Q ss_pred             CCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhc----------CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEE
Q psy4698          50 DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVR----------GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL  119 (258)
Q Consensus        50 ~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~----------g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~l  119 (258)
                      ..+.+++.++.    .|  .++..|.+++-...+          +.-+++--.||.||--..--.+++.+.++.+  |+|
T Consensus        24 y~~~lp~~~~~----~g--~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~--r~v   95 (303)
T PF13872_consen   24 YRLHLPEEVID----SG--LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGRK--RAV   95 (303)
T ss_pred             cccCCCHHHHh----cc--cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCCC--ceE
Confidence            44456665554    34  578999999877652          3458999999999998776667777776543  799


Q ss_pred             EEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC---CCCC--------C
Q psy4698         120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG---ALST--------K  188 (258)
Q Consensus       120 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~---~~~~--------~  188 (258)
                      +++.+..|..+..+.++.++.. .+.+..+..-...  .  ...-+..|+++|+..|..--..+   .-++        .
T Consensus        96 wvS~s~dL~~Da~RDl~DIG~~-~i~v~~l~~~~~~--~--~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~  170 (303)
T PF13872_consen   96 WVSVSNDLKYDAERDLRDIGAD-NIPVHPLNKFKYG--D--IIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGE  170 (303)
T ss_pred             EEECChhhhhHHHHHHHHhCCC-cccceechhhccC--c--CCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhc
Confidence            9999999999999999988754 2222221111000  0  11223569999999887654321   1111        1


Q ss_pred             C-ccEEEEccchhhhccCc--------HHHHHHHHHhCCCCccEEEEEeeCChhHHHH
Q psy4698         189 Q-IRMFVLDEADEMLSRGF--------KDQIYDVFKHLNNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       189 ~-l~~lVvDE~h~~~~~~~--------~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~  237 (258)
                      + =.+||+||+|..-+...        ...+..+...+ ++.+++.+|||--.+.+++
T Consensus       171 dfdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~L-P~ARvvY~SATgasep~Nm  227 (303)
T PF13872_consen  171 DFDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRL-PNARVVYASATGASEPRNM  227 (303)
T ss_pred             CCCceEEeccchhcCCCCccCccccHHHHHHHHHHHhC-CCCcEEEecccccCCCcee
Confidence            1 24899999998754322        23444555666 4567999999987665554

>KOG0392|consensus

Probab=98.76  E-value=6.1e-08  Score=92.37  Aligned_cols=165  Identities=21%  Similarity=0.236  Sum_probs=114.2

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhc------cccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQN------IKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~------~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .+|.||++-++++.    .+=+-|+|-.+|-|||+..+-.+....+..      ....-.+|+||+ .|+--|...+.++
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf 1053 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKF 1053 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHh
Confidence            46889999998864    234789999999999998865555544443      122348999994 6778888888888


Q ss_pred             cCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC
Q psy4698         139 GDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN  218 (258)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~  218 (258)
                      +..  +++..+.|....+...+.-.+..+|+|+.++.+.+-+..  +.-...-++|+||-|.+  .+....+.+..+.+.
T Consensus      1054 ~pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVi--kN~ktkl~kavkqL~ 1127 (1549)
T KOG0392|consen 1054 FPF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVI--KNSKTKLTKAVKQLR 1127 (1549)
T ss_pred             cch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCccee--cchHHHHHHHHHHHh
Confidence            776  455556666665555555555579999999887632211  01113448999999977  445677777888887


Q ss_pred             CCccEEEEEee-CChhHHHHHHHh
Q psy4698         219 NDVQVILLSAT-MPADVLDVSMKF  241 (258)
Q Consensus       219 ~~~~~i~~SAT-~~~~~~~~~~~~  241 (258)
                      .+.++| +|.| +-+++.+++..|
T Consensus      1128 a~hRLI-LSGTPIQNnvleLWSLF 1150 (1549)
T KOG0392|consen 1128 ANHRLI-LSGTPIQNNVLELWSLF 1150 (1549)
T ss_pred             hcceEE-eeCCCcccCHHHHHHHH
Confidence            666555 5777 577777776654

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

Probab=98.76  E-value=1.7e-07  Score=76.38  Aligned_cols=69  Identities=25%  Similarity=0.327  Sum_probs=50.1

Q ss_pred             CCcHHHHHHhhhhhcCCc-EEEEcccCCCcchHhHHHHHHHh-----hhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVRGND-VIAQAQSGTGKTATFSISILQQV-----DQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~-~li~~~tGsGKT~~~l~~~l~~l-----~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      ++++.|.+|+..++.... .+|.||+|+|||.+..-.+...+     .....+.++++++|+...++.....+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            367899999999988888 99999999999966543333331     1234556899999999999999888766

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.73  E-value=1e-07  Score=89.19  Aligned_cols=129  Identities=16%  Similarity=0.194  Sum_probs=99.6

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. .|++.|...--.+..|+  +..+.||-|||+++.+|++-....+.   .+-|++...-||..-..++..+...+|+.
T Consensus        76 G~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~Gk---gVhVVTvNdYLA~RDae~mg~vy~fLGLs  149 (925)
T PRK12903         76 GK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGK---GVIVSTVNEYLAERDAEEMGKVFNFLGLS  149 (925)
T ss_pred             CC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCC---ceEEEecchhhhhhhHHHHHHHHHHhCCc
Confidence            55 89999999988888887  89999999999999998876655543   47788888899999899999998999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEEccchhhh
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTKQIRMFVLDEADEML  202 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~~~  202 (258)
                      +.+...+.........  -.|||.+||...| +++|+.+-      .-...+.+.||||+|.++
T Consensus       150 vG~i~~~~~~~~rr~a--Y~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        150 VGINKANMDPNLKREA--YACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             eeeeCCCCChHHHHHh--ccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            9877665444433322  3489999998776 45565432      224678899999999875

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

Probab=98.71  E-value=1.3e-07  Score=75.45  Aligned_cols=123  Identities=19%  Similarity=0.283  Sum_probs=74.3

Q ss_pred             CCcHHHHHHhhhhhcCC--cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVRGN--DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~--~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      ++++-|.+++..++...  -+++.|+.|+|||.+. ..+...+...  +.++++++||...+....+..   +       
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~---~-------   67 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAA--GKRVIGLAPTNKAAKELREKT---G-------   67 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHT--T--EEEEESSHHHHHHHHHHH---T-------
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhC--CCeEEEECCcHHHHHHHHHhh---C-------
Confidence            36889999999986543  4788899999999863 4455555543  358999999998888766642   0       


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC----CCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC-Cc
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA----LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-DV  221 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~----~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~-~~  221 (258)
                                           +-..|..+++.......    ..+...++|||||+..+    ....+..++...+. ..
T Consensus        68 ---------------------~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv----~~~~~~~ll~~~~~~~~  122 (196)
T PF13604_consen   68 ---------------------IEAQTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMV----DSRQLARLLRLAKKSGA  122 (196)
T ss_dssp             ---------------------S-EEEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-----BHHHHHHHHHHS-T-T-
T ss_pred             ---------------------cchhhHHHHHhcCCcccccccccCCcccEEEEeccccc----CHHHHHHHHHHHHhcCC
Confidence                                 11223332222111111    11456679999999976    34556667777665 67


Q ss_pred             cEEEEEee
Q psy4698         222 QVILLSAT  229 (258)
Q Consensus       222 ~~i~~SAT  229 (258)
                      ++|++.-+
T Consensus       123 klilvGD~  130 (196)
T PF13604_consen  123 KLILVGDP  130 (196)
T ss_dssp             EEEEEE-T
T ss_pred             EEEEECCc
Confidence            77877654

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=98.69  E-value=3.7e-07  Score=84.99  Aligned_cols=156  Identities=13%  Similarity=0.185  Sum_probs=102.4

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      .-.+|.+|+|||||.+..-++-+.+.+  +..++++++..++|+.+....++..+- .++....-.++....      ..
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~~--~~~~VLvVShRrSL~~sL~~rf~~~~l-~gFv~Y~d~~~~~i~------~~  120 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALKN--PDKSVLVVSHRRSLTKSLAERFKKAGL-SGFVNYLDSDDYIID------GR  120 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhccC--CCCeEEEEEhHHHHHHHHHHHHhhcCC-Ccceeeecccccccc------cc
Confidence            348999999999999876665554433  334899999999999999998866431 123222211111110      11


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHH------HHH-HHHHhCCCCccEEEEEeeCChhHHHH
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKD------QIY-DVFKHLNNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~------~~~-~~~~~l~~~~~~i~~SAT~~~~~~~~  237 (258)
                      ..+-+++..++|.++..   -.+.++++||+||+-..+..-+..      ... .+...+.....+|++-|++....-+|
T Consensus       121 ~~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdF  197 (824)
T PF02399_consen  121 PYDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDF  197 (824)
T ss_pred             ccCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHH
Confidence            25677778877765542   246678999999998776542211      122 23333456678999999999999999


Q ss_pred             HHHhcC-CCeEEEecC
Q psy4698         238 SMKFMR-DPIKILVKK  252 (258)
Q Consensus       238 ~~~~~~-~~~~v~~~~  252 (258)
                      +..+.. +++.+.++.
T Consensus       198 l~~~Rp~~~i~vI~n~  213 (824)
T PF02399_consen  198 LASCRPDENIHVIVNT  213 (824)
T ss_pred             HHHhCCCCcEEEEEee
Confidence            988755 555555443

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

>KOG1000|consensus

Probab=98.58  E-value=4.5e-07  Score=79.42  Aligned_cols=151  Identities=16%  Similarity=0.143  Sum_probs=96.1

Q ss_pred             CCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          68 EKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        68 ~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      ..+.|+|++-+.. +..|..+++.-.+|-|||+.++..+ ..+..+   --.+|+||. .+...|.+.+.+|...... +
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA-~yyraE---wplliVcPA-svrftWa~al~r~lps~~p-i  270 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIA-RYYRAE---WPLLIVCPA-SVRFTWAKALNRFLPSIHP-I  270 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHH-HHHhhc---CcEEEEecH-HHhHHHHHHHHHhcccccc-e
Confidence            3678999999987 5566779999999999999875332 222222   248999995 4556677777776543322 3


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEE
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL  226 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~  226 (258)
                      ....++.....   .+.....|.|.+++.+..+-.  .+.-...+++|+||.|++ ..........++..+..-..+|++
T Consensus       271 ~vv~~~~D~~~---~~~t~~~v~ivSye~ls~l~~--~l~~~~~~vvI~DEsH~L-k~sktkr~Ka~~dllk~akhvILL  344 (689)
T KOG1000|consen  271 FVVDKSSDPLP---DVCTSNTVAIVSYEQLSLLHD--ILKKEKYRVVIFDESHML-KDSKTKRTKAATDLLKVAKHVILL  344 (689)
T ss_pred             EEEecccCCcc---ccccCCeEEEEEHHHHHHHHH--HHhcccceEEEEechhhh-hccchhhhhhhhhHHHHhhheEEe
Confidence            33333332111   111224688888877653322  122344789999999965 444555566666666666678999


Q ss_pred             EeeC
Q psy4698         227 SATM  230 (258)
Q Consensus       227 SAT~  230 (258)
                      |.|.
T Consensus       345 SGTP  348 (689)
T KOG1000|consen  345 SGTP  348 (689)
T ss_pred             cCCc
Confidence            9984

>KOG0391|consensus

Probab=98.54  E-value=7.2e-07  Score=84.98  Aligned_cols=162  Identities=17%  Similarity=0.163  Sum_probs=107.9

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .++.||..-++++.    .+-|-|+.-.+|-|||+..+-.+.+...++++=+--||++||-.+. .|.-.+++|+-  ++
T Consensus       615 qLReYQkiGLdWLatLYeknlNGILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviL-nWEMElKRwcP--gl  691 (1958)
T KOG0391|consen  615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVIL-NWEMELKRWCP--GL  691 (1958)
T ss_pred             HHHHHHHhhHHHHHHHHHhcccceehhhhcccchhHHHHHHHHHHhcccCCCCceEEeechhhh-hhhHHHhhhCC--cc
Confidence            56899999998864    2336899999999999887555555555544434568888876544 45666888874  57


Q ss_pred             eEEEEECCcchHHHHHHHhcC---CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCc
Q psy4698         145 SCHACIGGTIVRDDIRKLEAG---AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV  221 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~---~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~  221 (258)
                      ++..++|....+..++.-+.+   .+|.|+++..+++-+..  |.-++.+++|+||||++-++ ....+.+++. ++. -
T Consensus       692 KILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A--FkrkrWqyLvLDEaqnIKnf-ksqrWQAlln-fns-q  766 (1958)
T KOG0391|consen  692 KILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA--FKRKRWQYLVLDEAQNIKNF-KSQRWQALLN-FNS-Q  766 (1958)
T ss_pred             eEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH--HHhhccceeehhhhhhhcch-hHHHHHHHhc-cch-h
Confidence            778888888766665555443   67888888777654433  44566789999999988433 3334444443 223 4


Q ss_pred             cEEEEEee-CChhHHHHH
Q psy4698         222 QVILLSAT-MPADVLDVS  238 (258)
Q Consensus       222 ~~i~~SAT-~~~~~~~~~  238 (258)
                      |.++++.| +-+.+.+++
T Consensus       767 rRLLLtgTPLqNslmELW  784 (1958)
T KOG0391|consen  767 RRLLLTGTPLQNSLMELW  784 (1958)
T ss_pred             heeeecCCchhhHHHHHH
Confidence            56666776 455544443

>PRK10536 hypothetical protein; Provisional

Probab=98.53  E-value=1.5e-06  Score=71.36  Aligned_cols=161  Identities=14%  Similarity=0.165  Sum_probs=94.9

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHH-----------HHHH
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ-----------QIQK  133 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~-----------q~~~  133 (258)
                      .++...+..|...+.++.++..+++.|++|+|||+.+...+++.+..+ ...++++.=|.....+           ....
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p  133 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQADEDLGFLPGDIAEKFAP  133 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCCchhhhCcCCCCHHHHHHH
Confidence            355567889999999998888899999999999999887777666543 2335666656644221           1112


Q ss_pred             HHHHhcCCCCceEEEEECCcchHHHHHHH-h-cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         134 VVIALGDFMSVSCHACIGGTIVRDDIRKL-E-AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      .+..+.+.+...    .+.    ...... . ....|-|...    .+++...+  . -++||+|||+.+    ....+.
T Consensus       134 ~~~pi~D~L~~~----~~~----~~~~~~~~~~~~~Iei~~l----~ymRGrtl--~-~~~vIvDEaqn~----~~~~~k  194 (262)
T PRK10536        134 YFRPVYDVLVRR----LGA----SFMQYCLRPEIGKVEIAPF----AYMRGRTF--E-NAVVILDEAQNV----TAAQMK  194 (262)
T ss_pred             HHHHHHHHHHHH----hCh----HHHHHHHHhccCcEEEecH----HHhcCCcc--c-CCEEEEechhcC----CHHHHH
Confidence            222221111100    011    111111 1 1123444443    34443332  2 269999999976    357888


Q ss_pred             HHHHhCCCCccEEEEEee----C----ChhHHHHHHHhcCCC
Q psy4698         212 DVFKHLNNDVQVILLSAT----M----PADVLDVSMKFMRDP  245 (258)
Q Consensus       212 ~~~~~l~~~~~~i~~SAT----~----~~~~~~~~~~~~~~~  245 (258)
                      .++.++..+.++|+..-.    +    ++.+......|-..+
T Consensus       195 ~~ltR~g~~sk~v~~GD~~QiD~p~~~~sGL~~~~~~~k~~~  236 (262)
T PRK10536        195 MFLTRLGENVTVIVNGDITQCDLPRGVKSGLSDALERFEEDE  236 (262)
T ss_pred             HHHhhcCCCCEEEEeCChhhccCCCCCCCCHHHHHHHhCCCC
Confidence            999999999988886543    1    234555555555444

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.53  E-value=4e-07  Score=84.36  Aligned_cols=146  Identities=15%  Similarity=0.181  Sum_probs=85.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH---HHHH-h-cCCCC-ceEEEEECCcchHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK---VVIA-L-GDFMS-VSCHACIGGTIVRDD  158 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~---~~~~-~-~~~~~-~~~~~~~~~~~~~~~  158 (258)
                      -++=|.+.||+|||.||+-.++..-..-+ -.+.||++|+.+.-.-++.   .+.+ | .+.+. .+...+.-.......
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLhk~YG-~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~~  153 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELHKKYG-LFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEKF  153 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHHHHhC-ceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHHH
Confidence            46888999999999999888776544443 3489999999887554322   2222 2 22222 222222221222222


Q ss_pred             HHHHhcCCcEEEeChHHHHHH------HhcCCCCCCC--------------c-cEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         159 IRKLEAGAQVVVGTPGRVFDM------ISRGALSTKQ--------------I-RMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       159 ~~~~~~~~~Ilv~Tp~~l~~~------l~~~~~~~~~--------------l-~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      .....+++.+++.|.+.+.+-      +........+              + -++|+||.|++...   .....-+..+
T Consensus       154 ~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~---~k~~~~i~~l  230 (985)
T COG3587         154 KFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGD---DKTYGAIKQL  230 (985)
T ss_pred             hhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccc---hHHHHHHHhh
Confidence            223345578888887665432      2111111111              1 28999999998653   3333445555


Q ss_pred             CCCccEEEEEeeCChhHH
Q psy4698         218 NNDVQVILLSATMPADVL  235 (258)
Q Consensus       218 ~~~~~~i~~SAT~~~~~~  235 (258)
                      ++-+ ++-++||.+.+..
T Consensus       231 ~pl~-ilRfgATfkd~y~  247 (985)
T COG3587         231 NPLL-ILRFGATFKDEYN  247 (985)
T ss_pred             CceE-EEEecccchhhhc
Confidence            4433 7789999998766

>KOG1002|consensus

Probab=98.53  E-value=9.8e-07  Score=77.40  Aligned_cols=151  Identities=23%  Similarity=0.216  Sum_probs=97.4

Q ss_pred             CCcHHHHHHhhhhhcCC-----cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          69 KPSAIQQRAIIPCVRGN-----DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~-----~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .+-++|++.+-++....     .-++.-.+|.|||+..+..++..+    .+...++++|+.++ .||.+.+.++.. -.
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~----~ra~tLVvaP~VAl-mQW~nEI~~~T~-gs  257 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEV----DRAPTLVVAPTVAL-MQWKNEIERHTS-GS  257 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhcc----ccCCeeEEccHHHH-HHHHHHHHHhcc-Cc
Confidence            56789999998876442     357788999999998765555433    33369999999886 567777877765 34


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-------------CCCCcc--EEEEccchhhhccCcHH
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-------------STKQIR--MFVLDEADEMLSRGFKD  208 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-------------~~~~l~--~lVvDE~h~~~~~~~~~  208 (258)
                      ..+..++|.... ...+.+.+ +|++.+|+..+....+++..             .+.+++  -||+||||.+-+.. .+
T Consensus       258 lkv~~YhG~~R~-~nikel~~-YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~-sn  334 (791)
T KOG1002|consen  258 LKVYIYHGAKRD-KNIKELMN-YDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQ-SN  334 (791)
T ss_pred             eEEEEEeccccc-CCHHHhhc-CcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhccccccc-cc
Confidence            666777766533 23334444 89999999988877654211             123333  59999999874432 22


Q ss_pred             HHHHHHHhCCCCccEEEEEeeC
Q psy4698         209 QIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       209 ~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ...++. .+ .....+++|.|.
T Consensus       335 TArAV~-~L-~tt~rw~LSGTP  354 (791)
T KOG1002|consen  335 TARAVF-AL-ETTYRWCLSGTP  354 (791)
T ss_pred             HHHHHH-hh-HhhhhhhccCCc
Confidence            222222 12 123456778874

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.52  E-value=2.6e-07  Score=87.66  Aligned_cols=127  Identities=17%  Similarity=0.236  Sum_probs=96.8

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .++++|...--.+.+|+  +..+.||-|||+++.+|++-....+.   .+=+++-.--||..=..++..+....|+.+.+
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~G~---gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~  212 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALTGR---GVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGV  212 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHcCC---CcEEEeechHhhhhhHHHHHHHHHHhCCeeee
Confidence            58889988888888888  89999999999999999987777653   36677777888888888999988899999988


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEEccchhhh
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTKQIRMFVLDEADEML  202 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~~~  202 (258)
                      ...+......  ...-.|||.+||..-| +++|+.+-      .-...+.+.||||+|.++
T Consensus       213 i~~~~~~~~R--r~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        213 ILNTMRPEER--REQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             eCCCCCHHHH--HHhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            7554333322  3344589999998765 45554431      223567899999999874

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.51  E-value=1.3e-06  Score=80.82  Aligned_cols=140  Identities=19%  Similarity=0.208  Sum_probs=87.3

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh--ccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ--NIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~--~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .++|+.|+.....++-++|.|++|+|||.+.. .++..+..  .....++++..||..-+....+.+.......+..   
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~-~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~---  229 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVA-KLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLT---  229 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHH-HHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccc---
Confidence            58999999998888899999999999998753 22222222  1233578889999888887777664432222110   


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHh------cCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCcc
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMIS------RGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQ  222 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~------~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~  222 (258)
                             ...    ......-..|..+++....      ++.-+.-.+++|||||+.++    -...+..+++.+++.++
T Consensus       230 -------~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv----d~~lm~~ll~al~~~~r  294 (615)
T PRK10875        230 -------DEQ----KKRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV----DLPMMARLIDALPPHAR  294 (615)
T ss_pred             -------hhh----hhcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc----cHHHHHHHHHhcccCCE
Confidence                   000    0001112234444433211      11122335689999999965    35666778888999999


Q ss_pred             EEEEEee
Q psy4698         223 VILLSAT  229 (258)
Q Consensus       223 ~i~~SAT  229 (258)
                      +|++.-.
T Consensus       295 lIlvGD~  301 (615)
T PRK10875        295 VIFLGDR  301 (615)
T ss_pred             EEEecch
Confidence            9988644

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.50  E-value=7.1e-07  Score=77.75  Aligned_cols=108  Identities=15%  Similarity=0.213  Sum_probs=68.0

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      .++|.|.+|||||++++-.+. .+.....+.+++++++...+.......+.....                      ...
T Consensus         3 v~~I~G~aGTGKTvla~~l~~-~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~----------------------~~~   59 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAK-ELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYN----------------------PKL   59 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHH-HhhccccCCceEEEEecchHHHHHHHHHhhhcc----------------------cch
Confidence            479999999999998754443 332233455899999999999988876644320                      000


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-------cHHHHHHHHHh
Q psy4698         166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-------FKDQIYDVFKH  216 (258)
Q Consensus       166 ~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-------~~~~~~~~~~~  216 (258)
                      ....+..+..+...+.........+++|||||||++....       ....+..+++.
T Consensus        60 ~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   60 KKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             hhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence            1233334444333332223455678999999999997631       23566666665

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.49  E-value=1.9e-06  Score=79.44  Aligned_cols=140  Identities=19%  Similarity=0.222  Sum_probs=86.3

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh---ccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ---NIKECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~---~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      .+.|+.++...+.++-++|.|+.|+|||.+.. .++..+..   ...+.++++.+||.--+....+............  
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~-~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~~--  223 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVA-RLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNLAAA--  223 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHH-HHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhcccccc--
Confidence            37899999999999999999999999998753 22222222   1113579999999887777766554432211110  


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc------CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCc
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR------GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDV  221 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~------~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~  221 (258)
                              .    .......+-..|..+++.....      ..-+...+++|||||+-++    -...+..+++.+++..
T Consensus       224 --------~----~~~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMv----d~~l~~~ll~al~~~~  287 (586)
T TIGR01447       224 --------E----ALIAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMV----DLPLMAKLLKALPPNT  287 (586)
T ss_pred             --------h----hhhhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccC----CHHHHHHHHHhcCCCC
Confidence                    0    0000111223454444433211      1112335789999999965    2446667888888889


Q ss_pred             cEEEEEee
Q psy4698         222 QVILLSAT  229 (258)
Q Consensus       222 ~~i~~SAT  229 (258)
                      ++|++.-.
T Consensus       288 rlIlvGD~  295 (586)
T TIGR01447       288 KLILLGDK  295 (586)
T ss_pred             EEEEECCh
Confidence            99988543

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

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.49  E-value=3.1e-07  Score=87.38  Aligned_cols=128  Identities=18%  Similarity=0.208  Sum_probs=95.8

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .++++|...--.+.+|+  +..+.||-|||+++.+|++.....+.   .+-+++..--||..=..++..+...+|+.+.+
T Consensus       169 ~~yDVQliGgivLh~G~--IAEM~TGEGKTLvAtlp~yLnAL~Gk---gVHvVTVNDYLA~RDaewmgply~fLGLsvg~  243 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQGK--IAEMATGEGKTLVATLPVYLNALTGN---GVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDC  243 (1112)
T ss_pred             cccchHHhhhhhhcCCc--eeeecCCCCchhHHHHHHHHHHHcCC---CcEEEEechhhhhccHHHHHHHHHHhCCceee
Confidence            67888888887888888  89999999999999999987777653   36777777889888888888888888999987


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~  202 (258)
                      ........... .-.-.|||.++|..-| +++|+.+      ..-...+.+.||||+|.++
T Consensus       244 i~~~~~~~~~r-r~aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        244 IDKHQPNSEAR-RKAYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             cCCCCCCHHHH-HHhCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            65433223332 3334589999997765 4455433      1223567899999999874

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.47  E-value=3.3e-06  Score=79.97  Aligned_cols=126  Identities=19%  Similarity=0.218  Sum_probs=80.9

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      ..+++.|++|+..+..++.+++.|+.|+|||.+. -.++..+...+...++++++||..-+....+..       +..  
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~-------g~~--  391 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT-------GLT--  391 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc-------CCc--
Confidence            3799999999999988889999999999999864 444444444332246888899977776443311       110  


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-----CCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCcc
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-----ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQ  222 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-----~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~  222 (258)
                                            -.|..+++.+....     .-.....++|||||++++.    ...+..+++.++...+
T Consensus       392 ----------------------a~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd----~~~~~~Ll~~~~~~~r  445 (720)
T TIGR01448       392 ----------------------ASTIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMD----TWLALSLLAALPDHAR  445 (720)
T ss_pred             ----------------------cccHHHHhhccCCccchhhhhccccCCEEEEeccccCC----HHHHHHHHHhCCCCCE
Confidence                                  01222222111000     0112356799999999762    3445677778888888


Q ss_pred             EEEEEee
Q psy4698         223 VILLSAT  229 (258)
Q Consensus       223 ~i~~SAT  229 (258)
                      +|++.-.
T Consensus       446 lilvGD~  452 (720)
T TIGR01448       446 LLLVGDT  452 (720)
T ss_pred             EEEECcc
Confidence            8887544

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

>KOG0952|consensus

Probab=98.35  E-value=3.5e-07  Score=86.28  Aligned_cols=135  Identities=15%  Similarity=0.202  Sum_probs=97.1

Q ss_pred             CCcHHHHHHhhhhhc-CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          69 KPSAIQQRAIIPCVR-GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~-g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      ...+.|...+-.+.. ..++++.+|||+|||.++.+.+...+... .+.+++|+.|.++|+....+.+.......++.+.
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~-p~~kvvyIap~kalvker~~Dw~~r~~~~g~k~i 1005 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYY-PGSKVVYIAPDKALVKERSDDWSKRDELPGIKVI 1005 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccC-CCccEEEEcCCchhhcccccchhhhcccCCceeE
Confidence            445566665533322 24689999999999999999988776655 4479999999999999988877665544477777


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHh--cCCCCCCCccEEEEccchhhhccCcHH
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMIS--RGALSTKQIRMFVLDEADEMLSRGFKD  208 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~--~~~~~~~~l~~lVvDE~h~~~~~~~~~  208 (258)
                      ...|+....  .... ...+++|+||++.....+  .+.-.+.+++.+|+||.|.+. .+++.
T Consensus      1006 e~tgd~~pd--~~~v-~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg-~~rgP 1064 (1230)
T KOG0952|consen 1006 ELTGDVTPD--VKAV-READIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLG-EDRGP 1064 (1230)
T ss_pred             eccCccCCC--hhhe-ecCceEEcccccccCccccccchhhhccccceeeccccccc-CCCcc
Confidence            777665544  1222 337999999999766655  244467889999999999653 33343

>KOG1802|consensus

Probab=98.34  E-value=2.7e-06  Score=77.07  Aligned_cols=77  Identities=22%  Similarity=0.242  Sum_probs=63.9

Q ss_pred             HHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          61 GIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        61 ~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .+-..++++++.-|..|+.++++..-.+|.||+|+|||.+....+++.+..  ....+|+.+|+..-++|+...+.+.+
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLaeKIh~tg  478 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAEKIHKTG  478 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHHHHHhcC
Confidence            444567889999999999999999999999999999999876666655554  33479999999999999998886654

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=98.34  E-value=1.3e-05  Score=64.69  Aligned_cols=151  Identities=21%  Similarity=0.299  Sum_probs=92.5

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhc---CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVR---GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~---g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|.-...+..++=.+. .++ -+++.|.+......+   |+|.+....+|.|||.+. .|++..+..++.. -+.+++| 
T Consensus         4 ~w~p~~~P~wLl~E~e-~~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg~~-LvrviVp-   78 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIE-SNI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADGSR-LVRVIVP-   78 (229)
T ss_pred             CCCchhChHHHHHHHH-cCc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCCCc-EEEEEcC-
Confidence            4555555666654443 344 689999999888764   578999999999999985 6777666665432 4666666 


Q ss_pred             HHHHHHHHHHHHH-hcCCCCceEEE--EECCcchH--------HHHHHHhcCCcEEEeChHHHHHHHh-------cCCC-
Q psy4698         125 RELAQQIQKVVIA-LGDFMSVSCHA--CIGGTIVR--------DDIRKLEAGAQVVVGTPGRVFDMIS-------RGAL-  185 (258)
Q Consensus       125 ~~l~~q~~~~~~~-~~~~~~~~~~~--~~~~~~~~--------~~~~~~~~~~~Ilv~Tp~~l~~~l~-------~~~~-  185 (258)
                      ++|..|.+..++. ++.-.+-.+..  +.......        ...+.......|+++||+.++.+.-       .+.. 
T Consensus        79 k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~  158 (229)
T PF12340_consen   79 KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPE  158 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHH
Confidence            6788888888766 44433433322  22222111        1112223345799999998865321       1110 


Q ss_pred             ----------CCCCccEEEEccchhhhc
Q psy4698         186 ----------STKQIRMFVLDEADEMLS  203 (258)
Q Consensus       186 ----------~~~~l~~lVvDE~h~~~~  203 (258)
                                .+.+-..=|+||+|..+.
T Consensus       159 ~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  159 EARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             HHHHHHHHHHHHHhcCCeEeECchhccC
Confidence                      122334569999997753

There are two conserved sequence motifs: LLE and NMG.

>KOG4150|consensus

Probab=98.26  E-value=4e-06  Score=74.90  Aligned_cols=194  Identities=8%  Similarity=-0.094  Sum_probs=131.8

Q ss_pred             HHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          61 GIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        61 ~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .+.++...+...+|.+++..+.+|++..+.-.|.+||.++|.+.....+.... ....+++.|+.+++....+...-...
T Consensus       278 ~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~~V~~~  356 (1034)
T KOG4150|consen  278 LLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH-ATNSLLPSEMVEHLRNGSKGQVVHVE  356 (1034)
T ss_pred             HHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc-ccceecchhHHHHhhccCCceEEEEE
Confidence            34455566789999999999999999999999999999999888877665442 34689999999988876553322211


Q ss_pred             C---CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC----CCCCccEEEEccchhhhccCcHHHHHHH
Q psy4698         141 F---MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL----STKQIRMFVLDEADEMLSRGFKDQIYDV  213 (258)
Q Consensus       141 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~----~~~~l~~lVvDE~h~~~~~~~~~~~~~~  213 (258)
                      .   ....+.-.+++.....+...++.+.+++++.|..+...+--+..    .+-...++++||+|.+ ...+.......
T Consensus       357 ~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y-~~~~~~~~~~~  435 (1034)
T KOG4150|consen  357 VIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALY-LFPTKALAQDQ  435 (1034)
T ss_pred             ehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeee-ecchhhHHHHH
Confidence            1   12233344555555555556667789999999877654432222    2234568999999954 34344444433


Q ss_pred             HHhC---------CCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         214 FKHL---------NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       214 ~~~l---------~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      ++++         +.+.|++--|||+-...+.....+.-+-+-+...+++.|
T Consensus       436 ~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs  487 (1034)
T KOG4150|consen  436 LRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPS  487 (1034)
T ss_pred             HHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCC
Confidence            3333         246799999999988877777677666666666666654

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=98.20  E-value=6.5e-06  Score=70.07  Aligned_cols=144  Identities=17%  Similarity=0.261  Sum_probs=91.5

Q ss_pred             CCCCCCcHHHHHHhhhhhcCC--cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGN--DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM  142 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~--~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~  142 (258)
                      .|+..-+..|..|+..++...  -+.+.|..|+|||+.++.+.++.....+...++|+.=|+..+.+++-          
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIG----------  293 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIG----------  293 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccC----------
Confidence            477677889999999988764  38889999999999999999988887766668888878766543321          


Q ss_pred             CceEEEEECCc--chHHHHHHHhcCCcEEE----eChHHHHHHHhcCCCCCC--------Cc--cEEEEccchhhhccCc
Q psy4698         143 SVSCHACIGGT--IVRDDIRKLEAGAQVVV----GTPGRVFDMISRGALSTK--------QI--RMFVLDEADEMLSRGF  206 (258)
Q Consensus       143 ~~~~~~~~~~~--~~~~~~~~~~~~~~Ilv----~Tp~~l~~~l~~~~~~~~--------~l--~~lVvDE~h~~~~~~~  206 (258)
                       +    +-|..  +...|...+...-..++    |+-+.+-..+.++.+.+.        .+  +++|+|||+.+    -
T Consensus       294 -f----LPG~eEeKm~PWmq~i~DnLE~L~~~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNL----T  364 (436)
T COG1875         294 -F----LPGTEEEKMGPWMQAIFDNLEVLFSPNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNL----T  364 (436)
T ss_pred             -c----CCCchhhhccchHHHHHhHHHHHhcccccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhcc----C
Confidence             0    00110  00111111111111111    123334444443332221        11  48999999987    5


Q ss_pred             HHHHHHHHHhCCCCccEEEEE
Q psy4698         207 KDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      -.+++.++.+..+..+++++.
T Consensus       365 pheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         365 PHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             HHHHHHHHHhccCCCEEEEcC
Confidence            678899999999988888874

>PF13245 AAA_19: Part of AAA domain

Probab=98.19  E-value=6e-06  Score=55.26  Aligned_cols=52  Identities=29%  Similarity=0.410  Sum_probs=39.3

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhh-ccccceEEEEeccHHHHHHHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQ-NIKECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      +.-++|.||+|||||.+..-.+...+.. ...+.++++++|++..++...+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            3446669999999998776666655532 222568999999999999988877

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.15  E-value=5.7e-05  Score=66.27  Aligned_cols=131  Identities=18%  Similarity=0.193  Sum_probs=75.8

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhh-ccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQ-NIKECQALILA--PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK  161 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (258)
                      +.+++.||||+|||++..-.+...... ...+.++.++.  +++.-+..+   ++.++...++.+..             
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~lgvpv~~-------------  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQ---IQTYGDIMGIPVKA-------------  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHH---HHHHhhcCCcceEe-------------
Confidence            468999999999998874333222222 12334555555  334444333   33444433443311             


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCCCC-ccEEEEEeeC-ChhHHHHH
Q psy4698         162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNND-VQVILLSATM-PADVLDVS  238 (258)
Q Consensus       162 ~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~~~-~~~i~~SAT~-~~~~~~~~  238 (258)
                              +-+++.+...+..    +.+.++|+||++.+..... ....+..++...... -.++.+|||. .+++.+..
T Consensus       239 --------~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~~~  306 (388)
T PRK12723        239 --------IESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVKEIF  306 (388)
T ss_pred             --------eCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHHHH
Confidence                    1234444444443    3568899999999765321 234566666665433 3678889998 45778888


Q ss_pred             HHhcC
Q psy4698         239 MKFMR  243 (258)
Q Consensus       239 ~~~~~  243 (258)
                      +.|..
T Consensus       307 ~~~~~  311 (388)
T PRK12723        307 HQFSP  311 (388)
T ss_pred             HHhcC
Confidence            88843

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=98.15  E-value=5.3e-05  Score=73.54  Aligned_cols=126  Identities=18%  Similarity=0.138  Sum_probs=78.1

Q ss_pred             CCCCCCcHHHHHHhhhhhcCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .|+ .+++-|.+++..++.++ -+++.|+.|+|||.+ +-.+...+...  +.+++.++||-.-+.....       ..+
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~--G~~V~~~ApTGkAA~~L~e-------~tG  411 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEAA--GYEVRGAALSGIAAENLEG-------GSG  411 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHc--CCeEEEecCcHHHHHHHhh-------ccC
Confidence            344 79999999999988865 489999999999986 34454444433  4579999998765544432       111


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC-CCCcc
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL-NNDVQ  222 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~~~~~  222 (258)
                      +.                        -.|..+++.-...+...+...++|||||+-++.    ...+..+++.. +..++
T Consensus       412 i~------------------------a~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~----~~~m~~LL~~a~~~gar  463 (988)
T PRK13889        412 IA------------------------SRTIASLEHGWGQGRDLLTSRDVLVIDEAGMVG----TRQLERVLSHAADAGAK  463 (988)
T ss_pred             cc------------------------hhhHHHHHhhhcccccccccCcEEEEECcccCC----HHHHHHHHHhhhhCCCE
Confidence            11                        113333322122223345567899999999653    22344555433 45677


Q ss_pred             EEEEEee
Q psy4698         223 VILLSAT  229 (258)
Q Consensus       223 ~i~~SAT  229 (258)
                      +|++.-+
T Consensus       464 vVLVGD~  470 (988)
T PRK13889        464 VVLVGDP  470 (988)
T ss_pred             EEEECCH
Confidence            7777544

>TIGR00376 DNA helicase, putative

Probab=98.10  E-value=4.7e-05  Score=71.21  Aligned_cols=67  Identities=21%  Similarity=0.246  Sum_probs=52.9

Q ss_pred             CCCcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          68 EKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      +.+++.|..|+..++.. ..++|.||+|+|||.+..-.+.+.+..   +.++++++||...+..+.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~---g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR---GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEEcCcHHHHHHHHHHHHh
Confidence            35789999999998766 678999999999998765444443332   33899999999999998887765

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

>KOG2340|consensus

Probab=98.09  E-value=1.6e-05  Score=70.53  Aligned_cols=176  Identities=18%  Similarity=0.224  Sum_probs=112.7

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEE-cccCCCc--chHhHHHHHHHhhh----------------------------ccccc
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQ-AQSGTGK--TATFSISILQQVDQ----------------------------NIKEC  116 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~-~~tGsGK--T~~~l~~~l~~l~~----------------------------~~~~~  116 (258)
                      ..+++.|.+.+....+.++++.. ...+.|+  +-+|-+.+++++..                            +...+
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            36899999999998899986553 2233455  35566677776622                            11236


Q ss_pred             eEEEEeccHHHHHHHHHHHHHhcCCCCc---------eEEEEECCcc--------hHHH---------------------
Q psy4698         117 QALILAPTRELAQQIQKVVIALGDFMSV---------SCHACIGGTI--------VRDD---------------------  158 (258)
Q Consensus       117 ~~lil~P~~~l~~q~~~~~~~~~~~~~~---------~~~~~~~~~~--------~~~~---------------------  158 (258)
                      ++||+||+|+.|-.+.+.+..+....+-         +...-+++..        ....                     
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftk  374 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTK  374 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHH
Confidence            8999999999999999988776332211         0111111100        0000                     


Q ss_pred             ----HHHHhcCCcEEEeChHHHHHHHhcC------CCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC---------
Q psy4698         159 ----IRKLEAGAQVVVGTPGRVFDMISRG------ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN---------  219 (258)
Q Consensus       159 ----~~~~~~~~~Ilv~Tp~~l~~~l~~~------~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~---------  219 (258)
                          ...-....||+||+|=.|.-++.+.      .-.++.+.++|||.+|.++. +.+..+..++..|+.         
T Consensus       375 KtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~-QNwEhl~~ifdHLn~~P~k~h~~D  453 (698)
T KOG2340|consen  375 KTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLM-QNWEHLLHIFDHLNLQPSKQHDVD  453 (698)
T ss_pred             HHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHH-hhHHHHHHHHHHhhcCcccccCCC
Confidence                1111234799999999988777632      22367889999999997653 356666666666542         


Q ss_pred             ---------------CccEEEEEeeCChhHHHHHHHhcCC
Q psy4698         220 ---------------DVQVILLSATMPADVLDVSMKFMRD  244 (258)
Q Consensus       220 ---------------~~~~i~~SAT~~~~~~~~~~~~~~~  244 (258)
                                     -.|++++|+--....-.+...++++
T Consensus       454 fSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N  493 (698)
T KOG2340|consen  454 FSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQN  493 (698)
T ss_pred             hhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhh
Confidence                           1478888888777777777776653

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=98.07  E-value=0.00011  Score=70.17  Aligned_cols=121  Identities=18%  Similarity=0.177  Sum_probs=74.4

Q ss_pred             CCcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          69 KPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      .+++-|+.++..+..+ +-++|.|+.|+|||.+. -.+...+...  +.++++++||.-.+......       .+..  
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~~--g~~V~~~ApTg~Aa~~L~~~-------~g~~--  419 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAA--GYRVIGAALSGKAAEGLQAE-------SGIE--  419 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHhC--CCeEEEEeCcHHHHHHHHhc-------cCCc--
Confidence            6899999999998774 66899999999999764 3444444432  45799999997666554431       1111  


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHh-CCCCccEEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH-LNNDVQVILL  226 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~-l~~~~~~i~~  226 (258)
                                            -.|..+++.-...+...+...++|||||+.++..    ..+..++.. .....++|++
T Consensus       420 ----------------------a~Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~~----~~~~~Ll~~~~~~~~kliLV  473 (744)
T TIGR02768       420 ----------------------SRTLASLEYAWANGRDLLSDKDVLVIDEAGMVGS----RQMARVLKEAEEAGAKVVLV  473 (744)
T ss_pred             ----------------------eeeHHHHHhhhccCcccCCCCcEEEEECcccCCH----HHHHHHHHHHHhcCCEEEEE
Confidence                                  0122222211122223456778999999996532    223344442 2346677776


Q ss_pred             E
Q psy4698         227 S  227 (258)
Q Consensus       227 S  227 (258)
                      .
T Consensus       474 G  474 (744)
T TIGR02768       474 G  474 (744)
T ss_pred             C
Confidence            5

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

>KOG1803|consensus

Probab=98.06  E-value=2e-05  Score=70.99  Aligned_cols=64  Identities=27%  Similarity=0.307  Sum_probs=52.6

Q ss_pred             CCcHHHHHHhhhhhcCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      .+.+-|+.|+......+ -.+|.||+|+|||.+....+.+.+.++   .++++..||...++.+.+++
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~---k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQK---KRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcC---CeEEEEcCchHHHHHHHHHh
Confidence            57888999998887774 489999999999998766666666654   38999999999988888753

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

Probab=98.04  E-value=3.4e-05  Score=74.89  Aligned_cols=168  Identities=17%  Similarity=0.105  Sum_probs=105.2

Q ss_pred             CCCcHHHHHHhhhhh-----cCCcEEEEcccCCCcchHhHHHHHHHhhhccc-cceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          68 EKPSAIQQRAIIPCV-----RGNDVIAQAQSGTGKTATFSISILQQVDQNIK-ECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~-----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~-~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      ..++++|.+.++++.     .+.+.++...+|.|||+..+..+...+..... .+.++++||+ ++...|.+.+.++...
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~-s~~~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPA-SLLSNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecH-HHHHHHHHHHhhhCcc
Confidence            467899999998765     25677888999999998876666553333322 3479999995 5666677777777655


Q ss_pred             CCceEEEEECCcch----HHHHHHHhcC-----CcEEEeChHHHHHHH-hcCCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         142 MSVSCHACIGGTIV----RDDIRKLEAG-----AQVVVGTPGRVFDMI-SRGALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       142 ~~~~~~~~~~~~~~----~~~~~~~~~~-----~~Ilv~Tp~~l~~~l-~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      ... +...+|....    ..........     .+++++|.+.+.+.. .+..+.-.....+|+||+|.+-+. ......
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~-~s~~~~  493 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKND-QSSEGK  493 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhh-hhHHHH
Confidence            443 5555665531    3333333332     689999999887632 122233445679999999986433 222223


Q ss_pred             HHHHhCCCCccEEEEEeeC-ChhHHHHHHH
Q psy4698         212 DVFKHLNNDVQVILLSATM-PADVLDVSMK  240 (258)
Q Consensus       212 ~~~~~l~~~~~~i~~SAT~-~~~~~~~~~~  240 (258)
                      .+. .++...+ +.+|.|. .+.+.++...
T Consensus       494 ~l~-~~~~~~~-~~LtgTPlen~l~eL~sl  521 (866)
T COG0553         494 ALQ-FLKALNR-LDLTGTPLENRLGELWSL  521 (866)
T ss_pred             HHH-HHhhcce-eeCCCChHhhhHHHHHHH
Confidence            333 4444443 7778886 5555554443

>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=98.04  E-value=6.1e-05  Score=66.66  Aligned_cols=139  Identities=22%  Similarity=0.269  Sum_probs=91.8

Q ss_pred             hccccceEEEEeccHHHHHHHHHHHHHhcCC-CCce----EEEEEC--------------CcchHHHHHHHh--------
Q psy4698         111 QNIKECQALILAPTRELAQQIQKVVIALGDF-MSVS----CHACIG--------------GTIVRDDIRKLE--------  163 (258)
Q Consensus       111 ~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~-~~~~----~~~~~~--------------~~~~~~~~~~~~--------  163 (258)
                      ++...+++|||+|+|..|-.+.+.+-.+... ..+.    ...-+|              ......+++.+.        
T Consensus        33 QGftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~F  112 (442)
T PF06862_consen   33 QGFTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCF  112 (442)
T ss_pred             cCCCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceE
Confidence            3445679999999999999999888776543 1100    000011              001111122211        


Q ss_pred             -----------------cCCcEEEeChHHHHHHHhc------CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC-
Q psy4698         164 -----------------AGAQVVVGTPGRVFDMISR------GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-  219 (258)
Q Consensus       164 -----------------~~~~Ilv~Tp~~l~~~l~~------~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~-  219 (258)
                                       ..+||||++|=.|...+..      ....++.+.++|+|.+|.++ .+.+..+..++..++. 
T Consensus       113 rlGik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~-MQNW~Hv~~v~~~lN~~  191 (442)
T PF06862_consen  113 RLGIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLL-MQNWEHVLHVFEHLNLQ  191 (442)
T ss_pred             EEeEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHH-HhhHHHHHHHHHHhccC
Confidence                             1369999999999888874      33457899999999999664 4566666666666542 


Q ss_pred             -----------------------CccEEEEEeeCChhHHHHHHHhcC-CCeEEEe
Q psy4698         220 -----------------------DVQVILLSATMPADVLDVSMKFMR-DPIKILV  250 (258)
Q Consensus       220 -----------------------~~~~i~~SAT~~~~~~~~~~~~~~-~~~~v~~  250 (258)
                                             -.|+|++|+...+++..+.+..+. -.-.|++
T Consensus       192 P~~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~  246 (442)
T PF06862_consen  192 PKKSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRL  246 (442)
T ss_pred             CCCCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEE
Confidence                                   259999999999999999988544 3444444

; GO: 0005634 nucleus

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

Probab=98.04  E-value=1.7e-05  Score=67.60  Aligned_cols=68  Identities=24%  Similarity=0.264  Sum_probs=54.2

Q ss_pred             CcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      +++-|.+++..  ...+++|.|+.|||||.+.+--+...+... ....++++++.|+..+.+...++....
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l   69 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELL   69 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhc
Confidence            46789999977  677799999999999999887777777665 455689999999999999988887753

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

>PRK08181 transposase; Validated

Probab=98.00  E-value=0.00016  Score=60.37  Aligned_cols=141  Identities=13%  Similarity=0.133  Sum_probs=77.1

Q ss_pred             CcHHHHHHhh----hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          70 PSAIQQRAII----PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        70 ~~~~Q~~~~~----~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      +...|..++.    .+..++++++.||+|+|||..+.... ..+...  +.+++|+. ...|..+.....          
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia-~~a~~~--g~~v~f~~-~~~L~~~l~~a~----------  153 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIG-LALIEN--GWRVLFTR-TTDLVQKLQVAR----------  153 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHH-HHHHHc--CCceeeee-HHHHHHHHHHHH----------
Confidence            3456665553    34577899999999999997654333 233322  23455553 344444432210          


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc-HHHHHHHHHhCCCCccEE
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF-KDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~-~~~~~~~~~~l~~~~~~i  224 (258)
                                       ..      .+.+.+++.       +.+.++||+||++....... ...+..++........+|
T Consensus       154 -----------------~~------~~~~~~l~~-------l~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~I  203 (269)
T PRK08181        154 -----------------RE------LQLESAIAK-------LDKFDLLILDDLAYVTKDQAETSVLFELISARYERRSIL  203 (269)
T ss_pred             -----------------hC------CcHHHHHHH-------HhcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEE
Confidence                             00      122222222       23567999999996543322 234555555433345566


Q ss_pred             EEEeeCChhHHHH----------HHHhcCCCeEEEecCCc
Q psy4698         225 LLSATMPADVLDV----------SMKFMRDPIKILVKKEE  254 (258)
Q Consensus       225 ~~SAT~~~~~~~~----------~~~~~~~~~~v~~~~~~  254 (258)
                      +.|..-+.++...          +...+.+..+|.+.+++
T Consensus       204 iTSN~~~~~w~~~~~D~~~a~aildRL~h~~~~i~~~g~s  243 (269)
T PRK08181        204 ITANQPFGEWNRVFPDPAMTLAAVDRLVHHATIFEMNVES  243 (269)
T ss_pred             EEcCCCHHHHHHhcCCccchhhHHHhhhcCceEEecCCcc
Confidence            6666666665543          24455667777776654

>PRK06526 transposase; Provisional

Probab=97.98  E-value=4.2e-05  Score=63.48  Aligned_cols=132  Identities=12%  Similarity=0.083  Sum_probs=70.7

Q ss_pred             hhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH
Q psy4698          79 IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD  158 (258)
Q Consensus        79 ~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (258)
                      ..+..+.++++.||+|+|||..+....... ...  +.++++... ..+..+...    -                    
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~al~~~a-~~~--g~~v~f~t~-~~l~~~l~~----~--------------------  144 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAIGLGIRA-CQA--GHRVLFATA-AQWVARLAA----A--------------------  144 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHHHHHHHH-HHC--CCchhhhhH-HHHHHHHHH----H--------------------
Confidence            445667899999999999998764333333 322  234555322 222222211    0                    


Q ss_pred             HHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc-HHHHHHHHHhCCCCccEEEEEeeCChhHHH-
Q psy4698         159 IRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF-KDQIYDVFKHLNNDVQVILLSATMPADVLD-  236 (258)
Q Consensus       159 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~-~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~-  236 (258)
                         ...      ++....+   .    .+.+.++||+||+|....... ...+..++........+|+.|..-+.++.+ 
T Consensus       145 ---~~~------~~~~~~l---~----~l~~~dlLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~~~~w~~~  208 (254)
T PRK06526        145 ---HHA------GRLQAEL---V----KLGRYPLLIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKPFGRWGEV  208 (254)
T ss_pred             ---Hhc------CcHHHHH---H----HhccCCEEEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCCHHHHHHH
Confidence               000      1211111   1    134467999999996532222 233445554332334577777776665443 


Q ss_pred             ---------HHHHhcCCCeEEEecCCc
Q psy4698         237 ---------VSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       237 ---------~~~~~~~~~~~v~~~~~~  254 (258)
                               ++....+...+|.+.+++
T Consensus       209 ~~d~~~a~ai~dRl~~~~~~i~~~g~s  235 (254)
T PRK06526        209 FGDDVVAAAMIDRLVHHAEVISLKGDS  235 (254)
T ss_pred             cCChHHHHHHHHHHhcCceEEeecCCC
Confidence                     234556677777777664

>KOG0386|consensus

Probab=97.94  E-value=7.7e-06  Score=77.13  Aligned_cols=153  Identities=16%  Similarity=0.131  Sum_probs=94.2

Q ss_pred             CCcHHHHHHhhhhhcC----CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCVRG----NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g----~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+.+||...+.+..+=    -|-++.-.+|-|||...+--+...+......+--+|++|+-.|.+-.. .+..++.  .+
T Consensus       394 ~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~NW~~-Ef~kWaP--Sv  470 (1157)
T KOG0386|consen  394 ELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLVNWSS-EFPKWAP--SV  470 (1157)
T ss_pred             CCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccCCchh-hcccccc--ce
Confidence            7899999999885432    357889999999998876666666655544456899999888766543 3334432  23


Q ss_pred             eEEEEECCcchHHHH--HHHhcCCcEEEeChHHHHHHHhcCCCCCCC--ccEEEEccchhhhccCcHHHHHHHHHhCCCC
Q psy4698         145 SCHACIGGTIVRDDI--RKLEAGAQVVVGTPGRVFDMISRGALSTKQ--IRMFVLDEADEMLSRGFKDQIYDVFKHLNND  220 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~--~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~--l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~  220 (258)
                      ....+.|....+...  .......+|+++|++.+.+    ..-.++.  ..++||||-|+|  .+....+...+.---..
T Consensus       471 ~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik----dk~lLsKI~W~yMIIDEGHRm--KNa~~KLt~~L~t~y~~  544 (1157)
T KOG0386|consen  471 QKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK----DKALLSKISWKYMIIDEGHRM--KNAICKLTDTLNTHYRA  544 (1157)
T ss_pred             eeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC----CHHHHhccCCcceeecccccc--cchhhHHHHHhhccccc
Confidence            333444443333221  1222458999999977653    2112333  357999999998  33445554444422233


Q ss_pred             ccEEEEEeeC
Q psy4698         221 VQVILLSATM  230 (258)
Q Consensus       221 ~~~i~~SAT~  230 (258)
                      ...++++.|.
T Consensus       545 q~RLLLTGTP  554 (1157)
T KOG0386|consen  545 QRRLLLTGTP  554 (1157)
T ss_pred             hhhhhhcCCh
Confidence            4456667773

>KOG1132|consensus

Probab=97.91  E-value=9.8e-05  Score=69.18  Aligned_cols=71  Identities=15%  Similarity=0.192  Sum_probs=47.5

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHH---HHHHHhhhc---------c-------------------
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSI---SILQQVDQN---------I-------------------  113 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~---~~l~~l~~~---------~-------------------  113 (258)
                      .|++.|...+..++    .+.+.++..|||+|||++.+-   +..+.+..+         .                   
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            67888887776654    446799999999999987653   333333200         0                   


Q ss_pred             --------ccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698         114 --------KECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus       114 --------~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                              .-++++|-+-|..-..|+.+.+++.+
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence                    01356666677777778877777654

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.90  E-value=0.00031  Score=68.83  Aligned_cols=138  Identities=17%  Similarity=0.156  Sum_probs=82.7

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHhhhhhc-CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHH
Q psy4698          53 ELSEELLRGIYAYGFEKPSAIQQRAIIPCVR-GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI  131 (258)
Q Consensus        53 ~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~-g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~  131 (258)
                      ++++.........++ .+++-|..++..+.. ++-+++.|+.|+|||.+. -.+...+...  +.+++-++||-.-+...
T Consensus       366 ~v~~~~l~a~~~~~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~~--G~~V~g~ApTgkAA~~L  441 (1102)
T PRK13826        366 GVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEAA--GYRVVGGALAGKAAEGL  441 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHHc--CCeEEEEcCcHHHHHHH
Confidence            344444444333343 799999999998754 456999999999999874 3444444433  45799999987666554


Q ss_pred             HHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         132 QKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      .+.       .++.                        -.|..+++.....+...+..-++|||||+.++.    ...+.
T Consensus       442 ~e~-------~Gi~------------------------a~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~----~~~m~  486 (1102)
T PRK13826        442 EKE-------AGIQ------------------------SRTLSSWELRWNQGRDQLDNKTVFVLDEAGMVA----SRQMA  486 (1102)
T ss_pred             HHh-------hCCC------------------------eeeHHHHHhhhccCccCCCCCcEEEEECcccCC----HHHHH
Confidence            331       1111                        112222211111122345556799999999652    33444


Q ss_pred             HHHHhCC-CCccEEEEEee
Q psy4698         212 DVFKHLN-NDVQVILLSAT  229 (258)
Q Consensus       212 ~~~~~l~-~~~~~i~~SAT  229 (258)
                      .+++... ..+++|++.-+
T Consensus       487 ~Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        487 LFVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             HHHHHHHhcCCEEEEECCH
Confidence            5555553 46777777544

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.90  E-value=0.00018  Score=53.56  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.8

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ++.+++.|++|+|||...
T Consensus        19 ~~~v~i~G~~G~GKT~l~   36 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLA   36 (151)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            678999999999999754

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>KOG0388|consensus

Probab=97.89  E-value=4.9e-05  Score=69.68  Aligned_cols=159  Identities=17%  Similarity=0.173  Sum_probs=103.6

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      ++-.||.+-++++.    +|-|-|+.-.+|-|||...+-.+.+......--+-.||++|...| ..|++.+.+|+.  .+
T Consensus       567 tLKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaStL-~NWaqEisrFlP--~~  643 (1185)
T KOG0388|consen  567 TLKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPASTL-HNWAQEISRFLP--SF  643 (1185)
T ss_pred             hhHHHhhccHHHHHHHHHccccceehhhhccchhHHHHHHHHHHHHhccCCCceEEeehHHHH-hHHHHHHHHhCc--cc
Confidence            45678888888764    567889999999999998855554444443333468999997665 345555656653  46


Q ss_pred             eEEEEECCcchHHHHHHH---------hcCCcEEEeChHHHH---HHHhcCCCCCCCccEEEEccchhhhccCcHHHHHH
Q psy4698         145 SCHACIGGTIVRDDIRKL---------EAGAQVVVGTPGRVF---DMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD  212 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~---------~~~~~Ilv~Tp~~l~---~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~  212 (258)
                      .+.-+.|+...+...+..         ..+.+|+|++++.+.   +++++-     ...+.|+|||+.+- +........
T Consensus       644 k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qkv-----KWQYMILDEAQAIK-SSsS~RWKt  717 (1185)
T KOG0388|consen  644 KVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQKV-----KWQYMILDEAQAIK-SSSSSRWKT  717 (1185)
T ss_pred             eeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHHhh-----hhhheehhHHHHhh-hhhhhHHHH
Confidence            777788888776655552         234789999987653   233221     24589999999763 334555555


Q ss_pred             HHHhCCCCccEEEEEeeC-ChhHHHHH
Q psy4698         213 VFKHLNNDVQVILLSATM-PADVLDVS  238 (258)
Q Consensus       213 ~~~~l~~~~~~i~~SAT~-~~~~~~~~  238 (258)
                      ++..  +....++++.|. -+.+++++
T Consensus       718 LLsF--~cRNRLLLTGTPIQNsMqELW  742 (1185)
T KOG0388|consen  718 LLSF--KCRNRLLLTGTPIQNSMQELW  742 (1185)
T ss_pred             Hhhh--hccceeeecCCccchHHHHHH
Confidence            6554  233456777774 55555544

>KOG0989|consensus

Probab=97.88  E-value=2e-05  Score=65.62  Aligned_cols=48  Identities=17%  Similarity=0.360  Sum_probs=35.4

Q ss_pred             CCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         184 ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       184 ~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      ....+.++.||+||+|.|.. .-...+.+.+.......++++...-+++
T Consensus       124 ~~~~~~fKiiIlDEcdsmts-daq~aLrr~mE~~s~~trFiLIcnylsr  171 (346)
T KOG0989|consen  124 GYPCPPFKIIILDECDSMTS-DAQAALRRTMEDFSRTTRFILICNYLSR  171 (346)
T ss_pred             CCCCCcceEEEEechhhhhH-HHHHHHHHHHhccccceEEEEEcCChhh
Confidence            34567789999999998753 3667777788877777788877766543

>PRK04296 thymidine kinase; Provisional

Probab=97.83  E-value=4.5e-05  Score=60.54  Aligned_cols=113  Identities=13%  Similarity=0.174  Sum_probs=56.6

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      |.-.++.|++|+|||..++-.+......   +.+++++-|...-...    ...+....++...                
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~---g~~v~i~k~~~d~~~~----~~~i~~~lg~~~~----------------   58 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEER---GMKVLVFKPAIDDRYG----EGKVVSRIGLSRE----------------   58 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHc---CCeEEEEecccccccc----CCcEecCCCCccc----------------
Confidence            3446899999999998765444333222   3467877653111000    0011111111110                


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       164 ~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                         .+.+...+.+++.+..   .-.+.++||+||+|.+.    ..++..+++.+.+.-..+++++-
T Consensus        59 ---~~~~~~~~~~~~~~~~---~~~~~dvviIDEaq~l~----~~~v~~l~~~l~~~g~~vi~tgl  114 (190)
T PRK04296         59 ---AIPVSSDTDIFELIEE---EGEKIDCVLIDEAQFLD----KEQVVQLAEVLDDLGIPVICYGL  114 (190)
T ss_pred             ---ceEeCChHHHHHHHHh---hCCCCCEEEEEccccCC----HHHHHHHHHHHHHcCCeEEEEec
Confidence               0223445555555544   23467899999998642    23345555554333334444443

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.78  E-value=8.8e-05  Score=54.77  Aligned_cols=23  Identities=17%  Similarity=0.231  Sum_probs=14.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~  105 (258)
                      +++.++|.|++|+|||......+
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~   25 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLA   25 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHH
Confidence            34668999999999998764433

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.78  E-value=3.9e-05  Score=69.07  Aligned_cols=152  Identities=18%  Similarity=0.232  Sum_probs=79.1

Q ss_pred             EEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH-hcCCCCceEEEEECCcch----HHHHHHHh
Q psy4698          89 AQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA-LGDFMSVSCHACIGGTIV----RDDIRKLE  163 (258)
Q Consensus        89 i~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~~~----~~~~~~~~  163 (258)
                      +.+.||||||+++.-.+++....+.+  ..|+.|..-...+....-+-. .....-+.-....++...    ........
T Consensus         2 f~matgsgkt~~ma~lil~~y~kgyr--~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fsehn   79 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKGYR--NFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSEHN   79 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhchh--hEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCccC
Confidence            56899999999986666666555543  577877765554443221100 000000000000111100    00111234


Q ss_pred             cCCcEEEeChHHHHHHHhc---CCCCC---CCcc-EEEEccchhhhccCc-----H----HHHHHH-H--HhCCCCccEE
Q psy4698         164 AGAQVVVGTPGRVFDMISR---GALST---KQIR-MFVLDEADEMLSRGF-----K----DQIYDV-F--KHLNNDVQVI  224 (258)
Q Consensus       164 ~~~~Ilv~Tp~~l~~~l~~---~~~~~---~~l~-~lVvDE~h~~~~~~~-----~----~~~~~~-~--~~l~~~~~~i  224 (258)
                      .+..|+++|.+.|...+.+   +.+.+   .+.. +++-||+|++-...-     .    ..+... +  -.-+++.-++
T Consensus        80 d~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~l  159 (812)
T COG3421          80 DAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLLL  159 (812)
T ss_pred             CceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCceee
Confidence            5688999999999877654   33333   3333 467899999842110     1    111111 1  1124556678


Q ss_pred             EEEeeCChhHHHHHHHhcC
Q psy4698         225 LLSATMPADVLDVSMKFMR  243 (258)
Q Consensus       225 ~~SAT~~~~~~~~~~~~~~  243 (258)
                      .+|||+|++ ++...+|-.
T Consensus       160 ef~at~~k~-k~v~~ky~d  177 (812)
T COG3421         160 EFSATIPKE-KSVEDKYED  177 (812)
T ss_pred             hhhhcCCcc-ccHHHHhcc
Confidence            899999943 555555543

>KOG1015|consensus

Probab=97.72  E-value=0.00043  Score=65.60  Aligned_cols=142  Identities=13%  Similarity=0.097  Sum_probs=77.7

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhcccc-ceEEEEeccHHHHHHHHHHHHHhcCCC----CceEEEEECCcchHHH-
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKE-CQALILAPTRELAQQIQKVVIALGDFM----SVSCHACIGGTIVRDD-  158 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~-~~~lil~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~-  158 (258)
                      -.+|+..-+|-|||+..+..+...+.....+ .++||+||. ..+..|++.|.++....    .+.+..+..-...... 
T Consensus       697 sGcILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~Pl-Nt~~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R~  775 (1567)
T KOG1015|consen  697 SGCILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPL-NTALNWMNEFEKWMEGLEDDEKLEVSELATVKRPEERS  775 (1567)
T ss_pred             cchHHHHhhcccceehhhHHHHHHHHhhccCCceEEEEcch-HHHHHHHHHHHHhcccccccccceeehhhhccChHHHH
Confidence            4588888999999988655544444443333 379999995 45566777777765532    2333322222221111 


Q ss_pred             --HHHHhcCCcEEEeChHHHHHHHhcC-------------CCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccE
Q psy4698         159 --IRKLEAGAQVVVGTPGRVFDMISRG-------------ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV  223 (258)
Q Consensus       159 --~~~~~~~~~Ilv~Tp~~l~~~l~~~-------------~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~  223 (258)
                        ...-.+...|.|.-++.+..+-...             .+--+.-++||+||+|-+ .+ -...+-..+..+.-. +.
T Consensus       776 ~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiL-KN-eksa~Skam~~irtk-RR  852 (1567)
T KOG1015|consen  776 YMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHIL-KN-EKSAVSKAMNSIRTK-RR  852 (1567)
T ss_pred             HHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhh-cc-chHHHHHHHHHHHhh-ee
Confidence              1111223367776666554433221             112245679999999955 33 233444444444333 45


Q ss_pred             EEEEeeC
Q psy4698         224 ILLSATM  230 (258)
Q Consensus       224 i~~SAT~  230 (258)
                      |+++.|.
T Consensus       853 I~LTGTP  859 (1567)
T KOG1015|consen  853 IILTGTP  859 (1567)
T ss_pred             EEeecCc
Confidence            6667763

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

Probab=97.72  E-value=0.00011  Score=69.18  Aligned_cols=127  Identities=18%  Similarity=0.257  Sum_probs=94.0

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .++.+|...--.+..|+  ++.+-||-|||+++.+|+.-....+.   .+.+++-.--|+..-..++..+..++++.+.+
T Consensus        80 ~~~dVQliG~i~lh~g~--iaEM~TGEGKTL~atlp~ylnaL~gk---gVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~  154 (822)
T COG0653          80 RHFDVQLLGGIVLHLGD--IAEMRTGEGKTLVATLPAYLNALAGK---GVHVVTVNDYLARRDAEWMGPLYEFLGLSVGV  154 (822)
T ss_pred             ChhhHHHhhhhhhcCCc--eeeeecCCchHHHHHHHHHHHhcCCC---CcEEeeehHHhhhhCHHHHHHHHHHcCCceee
Confidence            56777777766666665  89999999999999999876666543   47888888889988889999998999999988


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~  202 (258)
                      ...+....+....  -.|||.++|-..+ +++++.+      .....++.+-|+||+|.++
T Consensus       155 ~~~~m~~~ek~~a--Y~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         155 ILAGMSPEEKRAA--YACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             ccCCCChHHHHHH--HhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            7777654444332  2379999998765 3344322      2234467899999999764

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.71  E-value=8.5e-05  Score=54.83  Aligned_cols=41  Identities=15%  Similarity=0.188  Sum_probs=25.5

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      +..+++.||+|+|||......+ ..+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~-~~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALA-RELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHH-hccCCCC--CCEEEECCEEcc
Confidence            4678999999999998763332 2222221  246777665443

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.70  E-value=7.8e-05  Score=65.30  Aligned_cols=59  Identities=24%  Similarity=0.296  Sum_probs=43.4

Q ss_pred             CcHHHHHHhhhh------hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHH
Q psy4698          70 PSAIQQRAIIPC------VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI  131 (258)
Q Consensus        70 ~~~~Q~~~~~~l------~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~  131 (258)
                      +++-|++++..+      .++.++++.|+.|+|||..+ -.+...+..  .+..+++++||-.-|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~-~~i~~~~~~--~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI-KAIIDYLRS--RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH-HHHHHHhcc--ccceEEEecchHHHHHhc
Confidence            678899998888      77889999999999999875 233333333  234688888887666554

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK14974 cell division protein FtsY; Provisional

Probab=97.70  E-value=0.001  Score=57.40  Aligned_cols=130  Identities=19%  Similarity=0.286  Sum_probs=76.0

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc---HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT---RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~---~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      -+++.|++|+|||++..-.+ ..+...  +.+++++...   .....|+......+    ++.+.....+.         
T Consensus       142 vi~~~G~~GvGKTTtiakLA-~~l~~~--g~~V~li~~Dt~R~~a~eqL~~~a~~l----gv~v~~~~~g~---------  205 (336)
T PRK14974        142 VIVFVGVNGTGKTTTIAKLA-YYLKKN--GFSVVIAAGDTFRAGAIEQLEEHAERL----GVKVIKHKYGA---------  205 (336)
T ss_pred             EEEEEcCCCCCHHHHHHHHH-HHHHHc--CCeEEEecCCcCcHHHHHHHHHHHHHc----CCceecccCCC---------
Confidence            48899999999998754333 233332  3356666543   33445554444443    33322111111         


Q ss_pred             hcCCcEEEeChHH-HHHHHhcCCCCCCCccEEEEccchhhhc-cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         163 EAGAQVVVGTPGR-VFDMISRGALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~-l~~~l~~~~~~~~~l~~lVvDE~h~~~~-~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                               .|.. +.+.+...  ...+.++|++|.+.++.. ......+..+.+..+++..++.++|+...+..+.++.
T Consensus       206 ---------dp~~v~~~ai~~~--~~~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~  274 (336)
T PRK14974        206 ---------DPAAVAYDAIEHA--KARGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQARE  274 (336)
T ss_pred             ---------CHHHHHHHHHHHH--HhCCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHH
Confidence                     1111 12222211  113467999999998753 3466777778777778888889999987777766666


Q ss_pred             hc
Q psy4698         241 FM  242 (258)
Q Consensus       241 ~~  242 (258)
                      |.
T Consensus       275 f~  276 (336)
T PRK14974        275 FN  276 (336)
T ss_pred             HH
Confidence            64

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.70  E-value=0.0018  Score=56.52  Aligned_cols=147  Identities=20%  Similarity=0.211  Sum_probs=81.1

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec-cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP-TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK  161 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P-~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (258)
                      +++.+.+.||||-|||++..--+.......++..-+||.+- +|.=|..+.+   .+++-+++.+               
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk---~Ya~im~vp~---------------  263 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLK---TYADIMGVPL---------------  263 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHH---HHHHHhCCce---------------
Confidence            36789999999999998754322222212222223444443 3333333222   2222223332               


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh-ccCcHHHHHHHHHhCCCCccEEEEEeeC-ChhHHHHHH
Q psy4698         162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNNDVQVILLSATM-PADVLDVSM  239 (258)
Q Consensus       162 ~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~-~~~~~~~~~~~~~~l~~~~~~i~~SAT~-~~~~~~~~~  239 (258)
                            .++-+|.-|...+.    .+.++++|.||=+-+-. +.....++..++..-.+.-..+.+|||. ..++++...
T Consensus       264 ------~vv~~~~el~~ai~----~l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei~~  333 (407)
T COG1419         264 ------EVVYSPKELAEAIE----ALRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEIIK  333 (407)
T ss_pred             ------EEecCHHHHHHHHH----HhhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHHHH
Confidence                  44446666655554    24556788888776432 2234566666666665555677889987 557888888


Q ss_pred             HhcCCC---eEEEecCCcccC
Q psy4698         240 KFMRDP---IKILVKKEELTL  257 (258)
Q Consensus       240 ~~~~~~---~~v~~~~~~~~~  257 (258)
                      .|...|   .|++=-||..++
T Consensus       334 ~f~~~~i~~~I~TKlDET~s~  354 (407)
T COG1419         334 QFSLFPIDGLIFTKLDETTSL  354 (407)
T ss_pred             HhccCCcceeEEEcccccCch
Confidence            876533   333334554443

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.69  E-value=0.001  Score=58.14  Aligned_cols=129  Identities=18%  Similarity=0.270  Sum_probs=72.5

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cH-HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TR-ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK  161 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~-~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (258)
                      +.+++.||+|+|||+....-+.. +..  .+.++.++.-  .| ..+.|+.....    ..+                  
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~-L~~--~GkkVglI~aDt~RiaAvEQLk~yae----~lg------------------  296 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQ-FHG--KKKTVGFITTDHSRIGTVQQLQDYVK----TIG------------------  296 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH-HHH--cCCcEEEEecCCcchHHHHHHHHHhh----hcC------------------
Confidence            46899999999999876544433 222  2335555543  33 23344333221    112                  


Q ss_pred             HhcCCcEE-EeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCCCCccEEEEEeeC-ChhHHHHH
Q psy4698         162 LEAGAQVV-VGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVILLSATM-PADVLDVS  238 (258)
Q Consensus       162 ~~~~~~Il-v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~~~~~i~~SAT~-~~~~~~~~  238 (258)
                          +.++ ..+|..+.+.+..-. .-.++++|+||-+=+.... .....+..++....+..-++.+|||. ++++.+.+
T Consensus       297 ----ipv~v~~d~~~L~~aL~~lk-~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i~  371 (436)
T PRK11889        297 ----FEVIAVRDEAAMTRALTYFK-EEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEII  371 (436)
T ss_pred             ----CcEEecCCHHHHHHHHHHHH-hccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHHH
Confidence                2333 346666666554311 0124778999988765432 23455555565544544466789875 56778888


Q ss_pred             HHhcC
Q psy4698         239 MKFMR  243 (258)
Q Consensus       239 ~~~~~  243 (258)
                      +.|-.
T Consensus       372 ~~F~~  376 (436)
T PRK11889        372 TNFKD  376 (436)
T ss_pred             HHhcC
Confidence            77754

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

Probab=97.65  E-value=0.00015  Score=64.58  Aligned_cols=73  Identities=27%  Similarity=0.330  Sum_probs=54.3

Q ss_pred             CCcHHHHHHhhhhhcC-----CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          69 KPSAIQQRAIIPCVRG-----NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g-----~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      .|.--|-.|+..+..|     +.-.+-|.||||||++.. -++..+.     .-+||++|.+.||.|.+..++.|.....
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~A-nVI~~~~-----rPtLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMA-NVIAKVQ-----RPTLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHH-HHHHHhC-----CCeEEEecchhHHHHHHHHHHHhCcCcc
Confidence            5666677777666544     467889999999999853 2222222     2599999999999999999999987766


Q ss_pred             ceEE
Q psy4698         144 VSCH  147 (258)
Q Consensus       144 ~~~~  147 (258)
                      +...
T Consensus        86 VEYF   89 (663)
T COG0556          86 VEYF   89 (663)
T ss_pred             eEEE
Confidence            5443

>KOG1805|consensus

Probab=97.62  E-value=0.0004  Score=65.90  Aligned_cols=136  Identities=17%  Similarity=0.180  Sum_probs=85.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCc-EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHH
Q psy4698          52 MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND-VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ  130 (258)
Q Consensus        52 ~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~-~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q  130 (258)
                      ..+.+.+.+.    -...++.-|+.|+-.++..++ .+|.|=+|+|||.+. -.++..+...+  .++|+.+-|..-+..
T Consensus       656 ~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI-~~LIkiL~~~g--kkVLLtsyThsAVDN  728 (1100)
T KOG1805|consen  656 KVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTI-SLLIKILVALG--KKVLLTSYTHSAVDN  728 (1100)
T ss_pred             cccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhH-HHHHHHHHHcC--CeEEEEehhhHHHHH
Confidence            3455555543    244788999999988776655 788899999999875 33444444433  378888888888877


Q ss_pred             HHHHHHHhcCCCCceEEEEECCcc-----------------hHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q psy4698         131 IQKVVIALGDFMSVSCHACIGGTI-----------------VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF  193 (258)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~l  193 (258)
                      +.-.++.++..    +..+-.+..                 .-...+...+...|+.||--.+..-+    +..+.++++
T Consensus       729 ILiKL~~~~i~----~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~pl----f~~R~FD~c  800 (1100)
T KOG1805|consen  729 ILIKLKGFGIY----ILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPL----FVNRQFDYC  800 (1100)
T ss_pred             HHHHHhccCcc----eeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchh----hhccccCEE
Confidence            77777665422    111111111                 11223344455788888865444332    234568999


Q ss_pred             EEccchhhh
Q psy4698         194 VLDEADEML  202 (258)
Q Consensus       194 VvDE~h~~~  202 (258)
                      |||||-.+.
T Consensus       801 IiDEASQI~  809 (1100)
T KOG1805|consen  801 IIDEASQIL  809 (1100)
T ss_pred             EEccccccc
Confidence            999999764

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.62  E-value=0.00019  Score=58.99  Aligned_cols=85  Identities=19%  Similarity=0.342  Sum_probs=63.6

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCc-chHHHHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCcc
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGT-IVRDDIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIR  191 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~  191 (258)
                      ..+.+||+|.+-.-|-++.+.++.+.. -+..+.-++... ...++...+.. .++|.||||+++..++..+.+.++++.
T Consensus       125 gsP~~lvvs~SalRa~dl~R~l~~~~~-k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l~  203 (252)
T PF14617_consen  125 GSPHVLVVSSSALRAADLIRALRSFKG-KDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNLK  203 (252)
T ss_pred             CCCEEEEEcchHHHHHHHHHHHHhhcc-CCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccCe
Confidence            357899999987778888887777631 112333334443 45566666664 589999999999999999999999999


Q ss_pred             EEEEccch
Q psy4698         192 MFVLDEAD  199 (258)
Q Consensus       192 ~lVvDE~h  199 (258)
                      +||+|--|
T Consensus       204 ~ivlD~s~  211 (252)
T PF14617_consen  204 RIVLDWSY  211 (252)
T ss_pred             EEEEcCCc
Confidence            99999876

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.53  E-value=0.00077  Score=58.85  Aligned_cols=132  Identities=19%  Similarity=0.189  Sum_probs=64.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc--HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT--RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~--~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      .|..+++.||||+|||+....-+.......+ ..++.+++-.  +.-+.   +.++.++...++.+.             
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G-~~~V~lit~D~~R~ga~---EqL~~~a~~~gv~~~-------------  198 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFG-ASKVALLTTDSYRIGGH---EQLRIFGKILGVPVH-------------  198 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcC-CCeEEEEecccccccHH---HHHHHHHHHcCCceE-------------
Confidence            3567999999999999876443333322221 1245544422  21122   222233322233322             


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH-HHHHHHHHhCCCCccEEEEEeeCCh-hHHHHH
Q psy4698         161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK-DQIYDVFKHLNNDVQVILLSATMPA-DVLDVS  238 (258)
Q Consensus       161 ~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~-~~~~~~~~~l~~~~~~i~~SAT~~~-~~~~~~  238 (258)
                              .+.+++.+...+.    .+.+.++|+||.+-+....... ..+..+.........++.+|||... .+.+..
T Consensus       199 --------~~~~~~~l~~~l~----~l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~evi  266 (374)
T PRK14722        199 --------AVKDGGDLQLALA----ELRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNEVV  266 (374)
T ss_pred             --------ecCCcccHHHHHH----HhcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHHHH
Confidence                    2223333333333    2345578999998643222222 2222222222233457888999844 456666


Q ss_pred             HHhcC
Q psy4698         239 MKFMR  243 (258)
Q Consensus       239 ~~~~~  243 (258)
                      +.|..
T Consensus       267 ~~f~~  271 (374)
T PRK14722        267 QAYRS  271 (374)
T ss_pred             HHHHH
Confidence            76643

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.51  E-value=0.0036  Score=55.91  Aligned_cols=130  Identities=18%  Similarity=0.221  Sum_probs=69.8

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHh-hhccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQV-DQNIKECQALILA--PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l-~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      ++.+++.||||+|||++....+.... ...  +.++.++.  |.+.-+.   ..++.++...++.+              
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~--g~~V~li~~D~~r~~a~---eqL~~~a~~~~vp~--------------  281 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYG--KKKVALITLDTYRIGAV---EQLKTYAKIMGIPV--------------  281 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC--CCeEEEEECCccHHHHH---HHHHHHHHHhCCce--------------
Confidence            45789999999999987654333322 222  23555555  3333222   22222222222222              


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhC-CCCccEEEEEeeCC-hhHHHH
Q psy4698         161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHL-NNDVQVILLSATMP-ADVLDV  237 (258)
Q Consensus       161 ~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l-~~~~~~i~~SAT~~-~~~~~~  237 (258)
                             ..+.+++.+...+..    +.+.++|+||.+-+.... .....+..++... .+....+.+|||.. .++.+.
T Consensus       282 -------~~~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~  350 (424)
T PRK05703        282 -------EVVYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLKDI  350 (424)
T ss_pred             -------EccCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHHHH
Confidence                   122345555555543    235789999988653221 2334555555522 23345778899875 577777


Q ss_pred             HHHhcC
Q psy4698         238 SMKFMR  243 (258)
Q Consensus       238 ~~~~~~  243 (258)
                      .+.|-.
T Consensus       351 ~~~f~~  356 (424)
T PRK05703        351 YKHFSR  356 (424)
T ss_pred             HHHhCC
Confidence            777765

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.51  E-value=0.00072  Score=53.92  Aligned_cols=128  Identities=18%  Similarity=0.246  Sum_probs=66.2

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cHHHH-HHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TRELA-QQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~~l~-~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      -+++.||||+|||.+..--+......   +.++.+++-  .|.=+ +|.....+.+    ++.+.......         
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga~eQL~~~a~~l----~vp~~~~~~~~---------   66 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGAVEQLKTYAEIL----GVPFYVARTES---------   66 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHHHHHHHHHHHHH----TEEEEESSTTS---------
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccHHHHHHHHHHHh----ccccchhhcch---------
Confidence            37899999999998865444333333   334555552  34333 3333333333    34333211111         


Q ss_pred             hcCCcEEEeChHHH-HHHHhcCCCCCCCccEEEEccchhhhc-cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         163 EAGAQVVVGTPGRV-FDMISRGALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l-~~~l~~~~~~~~~l~~lVvDE~h~~~~-~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                               .|..+ .+.+..  ...+++++|+||=+-+... .....++..++..+.+.--.+.+|||...+..+....
T Consensus        67 ---------~~~~~~~~~l~~--~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~  135 (196)
T PF00448_consen   67 ---------DPAEIAREALEK--FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALA  135 (196)
T ss_dssp             ---------CHHHHHHHHHHH--HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHH
T ss_pred             ---------hhHHHHHHHHHH--HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHH
Confidence                     11111 122221  1123466888888865432 2345677777777767667889999986654333333

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=97.47  E-value=0.00049  Score=62.52  Aligned_cols=148  Identities=14%  Similarity=0.126  Sum_probs=82.4

Q ss_pred             HHHHHHhhhhh-----cC----CcEEEEcccCCCcchHhHHHHHHHh-hhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          72 AIQQRAIIPCV-----RG----NDVIAQAQSGTGKTATFSISILQQV-DQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        72 ~~Q~~~~~~l~-----~g----~~~li~~~tGsGKT~~~l~~~l~~l-~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      |+|+-.+-.+.     .|    +.+++.-|-|-|||......++..+ ..+..+..+++.++++.-+...++.++.+...
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~   80 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEA   80 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHh
Confidence            45666655544     12    2478888999999976654444444 34445668999999999999999998887644


Q ss_pred             CCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC--CCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC
Q psy4698         142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG--ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN  219 (258)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~--~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~  219 (258)
                      ....... ..     ..... ...-.|.....+..++.+...  ...-.+..++|+||+|.+-+......+..-+.. .+
T Consensus        81 ~~~l~~~-~~-----~~~~~-~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~~~-r~  152 (477)
T PF03354_consen   81 SPELRKR-KK-----PKIIK-SNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESGMGA-RP  152 (477)
T ss_pred             Chhhccc-hh-----hhhhh-hhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhhhcc-CC
Confidence            2111000 00     00000 011234333333333333332  222335689999999987554444444444444 34


Q ss_pred             CccEEEEE
Q psy4698         220 DVQVILLS  227 (258)
Q Consensus       220 ~~~~i~~S  227 (258)
                      ++++++.|
T Consensus       153 ~pl~~~IS  160 (477)
T PF03354_consen  153 NPLIIIIS  160 (477)
T ss_pred             CceEEEEe
Confidence            55555543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.41  E-value=0.0018  Score=66.50  Aligned_cols=124  Identities=16%  Similarity=0.214  Sum_probs=74.6

Q ss_pred             CCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhh--hccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVD--QNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~--~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+++.|++++..++.+  +-++|.|..|+|||.+. -.++..+.  ....+.+++.++||-.-+....+    .    ++
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~e----~----Gi 1037 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEMRS----A----GV 1037 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHHHh----c----Cc
Confidence            6899999999998875  46999999999999874 33333332  12234578889999766654332    1    11


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHH----hcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCC-
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI----SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-  219 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l----~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~-  219 (258)
                      .                        -.|..+++...    ..+......-++|||||+-++.    ...+..+++.++. 
T Consensus      1038 ~------------------------A~TI~s~L~~~~~~~~~~~~~~~~~~llIVDEaSMv~----~~~m~~Ll~~~~~~ 1089 (1747)
T PRK13709       1038 D------------------------AQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVG----NTDMARAYALIAAG 1089 (1747)
T ss_pred             c------------------------hhhHHHHhcccccccccccCCCCCCcEEEEEcccccc----HHHHHHHHHhhhcC
Confidence            1                        01222222111    0111112234799999999652    3345555665553 


Q ss_pred             CccEEEEEee
Q psy4698         220 DVQVILLSAT  229 (258)
Q Consensus       220 ~~~~i~~SAT  229 (258)
                      .+++|++.-+
T Consensus      1090 garvVLVGD~ 1099 (1747)
T PRK13709       1090 GGRAVSSGDT 1099 (1747)
T ss_pred             CCEEEEecch
Confidence            5788887654

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.40  E-value=0.0029  Score=56.27  Aligned_cols=37  Identities=19%  Similarity=0.258  Sum_probs=25.3

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ..+++.|++|+|||... ..+.+.+.....+.+++++.
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEE
Confidence            35899999999999865 44555554443345677774

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.40  E-value=0.00082  Score=63.58  Aligned_cols=69  Identities=17%  Similarity=0.164  Sum_probs=55.0

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-ccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-NIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .+++-|.+++.+.  ..+++|.|+.|||||.+...-+...+.. +....++++++-|+..+.+...++....
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            4789999998653  4568888999999999987777776654 3344589999999999999988887653

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.39  E-value=0.011  Score=53.91  Aligned_cols=132  Identities=16%  Similarity=0.254  Sum_probs=65.0

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA--PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI  159 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (258)
                      ..|+.+.+.|++|+|||.....-+...... +.+.++.++.  +++.-+.+   .++.++...++.+..           
T Consensus       348 ~~G~vIaLVGPtGvGKTTtaakLAa~la~~-~~gkkVaLIdtDtyRigA~E---QLk~ya~iLgv~v~~-----------  412 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTIAKLAQRFAAQ-HAPRDVALVTTDTQRVGGRE---QLHSYGRQLGIAVHE-----------  412 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCceEEEecccccccHHH---HHHHhhcccCceeEe-----------
Confidence            346779999999999998763333222222 2223455554  23332222   222233222332211           


Q ss_pred             HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCCCCccEEEEEeeCC-hhHHHH
Q psy4698         160 RKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNNDVQVILLSATMP-ADVLDV  237 (258)
Q Consensus       160 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~~~~~~i~~SAT~~-~~~~~~  237 (258)
                                +.+++.+...+..    +.+.++|+||.+-...... ....+..+. .......++.++++.. .++.+.
T Consensus       413 ----------a~d~~~L~~aL~~----l~~~DLVLIDTaG~s~~D~~l~eeL~~L~-aa~~~a~lLVLpAtss~~Dl~ei  477 (559)
T PRK12727        413 ----------ADSAESLLDLLER----LRDYKLVLIDTAGMGQRDRALAAQLNWLR-AARQVTSLLVLPANAHFSDLDEV  477 (559)
T ss_pred             ----------cCcHHHHHHHHHH----hccCCEEEecCCCcchhhHHHHHHHHHHH-HhhcCCcEEEEECCCChhHHHHH
Confidence                      1133344444442    2357789999886542221 112222222 2223345777777764 466777


Q ss_pred             HHHhcC
Q psy4698         238 SMKFMR  243 (258)
Q Consensus       238 ~~~~~~  243 (258)
                      ++.|..
T Consensus       478 i~~f~~  483 (559)
T PRK12727        478 VRRFAH  483 (559)
T ss_pred             HHHHHh
Confidence            776654

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=97.39  E-value=0.0014  Score=66.58  Aligned_cols=63  Identities=21%  Similarity=0.265  Sum_probs=45.5

Q ss_pred             CCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhH--HHHHHHhhhccccceEEEEeccHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFS--ISILQQVDQNIKECQALILAPTRELAQQIQ  132 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l--~~~l~~l~~~~~~~~~lil~P~~~l~~q~~  132 (258)
                      .+++-|++++..++..  +.++|.|..|+|||.+.-  +.++..+. ...+.+++.++||-.-+....
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~-e~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLP-ESERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHh-hccCceEEEEechHHHHHHHH
Confidence            7899999999998865  679999999999998742  22222222 223457888999877665553

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.39  E-value=0.0038  Score=56.31  Aligned_cols=126  Identities=11%  Similarity=0.218  Sum_probs=64.9

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +.+++.||+|+|||... .++...+.....+.+++++.. ..+..+....++.                           
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~~~~~v~yi~~-~~~~~~~~~~~~~---------------------------  199 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKNPNAKVVYVTS-EKFTNDFVNALRN---------------------------  199 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHc---------------------------
Confidence            45899999999999865 344444444433446666643 3444433332210                           


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCC-CCccEEEEEeeCChhHH---HHHH
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLN-NDVQVILLSATMPADVL---DVSM  239 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~---~~~~  239 (258)
                      +      +.+.+...+       .+.++||+||+|.+.... ....+..++..+. ...++++.|...|..+.   .-+.
T Consensus       200 ~------~~~~~~~~~-------~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~  266 (450)
T PRK00149        200 N------TMEEFKEKY-------RSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLR  266 (450)
T ss_pred             C------cHHHHHHHH-------hcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHH
Confidence            0      112222222       246699999999874432 2234444444432 33455554444444433   2334


Q ss_pred             HhcCCCeEEEecC
Q psy4698         240 KFMRDPIKILVKK  252 (258)
Q Consensus       240 ~~~~~~~~v~~~~  252 (258)
                      ..+.....+.+..
T Consensus       267 SRl~~gl~v~i~~  279 (450)
T PRK00149        267 SRFEWGLTVDIEP  279 (450)
T ss_pred             hHhcCCeeEEecC
Confidence            4555445555543

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=97.38  E-value=0.00015  Score=56.47  Aligned_cols=125  Identities=14%  Similarity=0.194  Sum_probs=54.6

Q ss_pred             EEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCc
Q psy4698          88 IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQ  167 (258)
Q Consensus        88 li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (258)
                      ++.|+-|.|||.+.=+.+...+....  .+++|.+|+.+-+...++.+..-.+..+.+....   ............+..
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~~--~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~~~~---~~~~~~~~~~~~~~~   75 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKGK--IRILVTAPSPENVQTLFEFAEKGLKALGYKEEKK---KRIGQIIKLRFNKQR   75 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-----------------------------CCC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhcC--ceEEEecCCHHHHHHHHHHHHhhccccccccccc---cccccccccccccce
Confidence            57899999999876444433333322  5799999999988888876654433333222000   000000001112356


Q ss_pred             EEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         168 VVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       168 Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      |-+..|+.+...       ....+++|||||=.+    -...+..++    .....++||.|+..
T Consensus        76 i~f~~Pd~l~~~-------~~~~DlliVDEAAaI----p~p~L~~ll----~~~~~vv~stTi~G  125 (177)
T PF05127_consen   76 IEFVAPDELLAE-------KPQADLLIVDEAAAI----PLPLLKQLL----RRFPRVVFSTTIHG  125 (177)
T ss_dssp             --B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHH----CCSSEEEEEEEBSS
T ss_pred             EEEECCHHHHhC-------cCCCCEEEEechhcC----CHHHHHHHH----hhCCEEEEEeeccc
Confidence            777788665421       123579999999866    233334443    33446788888765

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>KOG1001|consensus

Probab=97.37  E-value=0.0012  Score=61.83  Aligned_cols=155  Identities=21%  Similarity=0.146  Sum_probs=90.5

Q ss_pred             HHHHHHhhhhhcC-----CcEEEEcccCCCcchHhHHHHHHHhhhcc------ccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          72 AIQQRAIIPCVRG-----NDVIAQAQSGTGKTATFSISILQQVDQNI------KECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        72 ~~Q~~~~~~l~~g-----~~~li~~~tGsGKT~~~l~~~l~~l~~~~------~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      ..|...+.....-     +-.|+.-..|-|||...+..++..-....      ...-.+++||. ++..||...+.+...
T Consensus       135 ~~~~~~~~~~~~~~~~~~~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~-s~~~qW~~elek~~~  213 (674)
T KOG1001|consen  135 LKQKYRWSLLKSREQQSLRGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPT-SLLTQWKTELEKVTE  213 (674)
T ss_pred             HHHHHHHHhhcccccCccccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecch-HHHHHHHHHHhccCC
Confidence            4555555443322     34788889999999887655544332222      23357788874 566777776766666


Q ss_pred             CCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCC
Q psy4698         141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND  220 (258)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~  220 (258)
                      ...+.+..++|    +..-....++++|+++|++.+-.    ..+.--..-.+|+||+|.+.+.  ..+.......+...
T Consensus       214 ~~~l~v~v~~g----r~kd~~el~~~dVVltTy~il~~----~~l~~i~w~Riildea~~ikn~--~tq~~~a~~~L~a~  283 (674)
T KOG1001|consen  214 EDKLSIYVYHG----RTKDKSELNSYDVVLTTYDILKN----SPLVKIKWLRIVLDEAHTIKNK--DTQIFKAVCQLDAK  283 (674)
T ss_pred             ccceEEEEecc----cccccchhcCCceEEeeHHHhhc----ccccceeEEEEEeccccccCCc--chHhhhhheeeccc
Confidence            66778888887    11111223458899999976553    2111122346999999988544  33344444445444


Q ss_pred             ccEEEEEeeC-ChhHHHHH
Q psy4698         221 VQVILLSATM-PADVLDVS  238 (258)
Q Consensus       221 ~~~i~~SAT~-~~~~~~~~  238 (258)
                      . .-.+|+|. -+.+.++.
T Consensus       284 ~-RWcLtgtPiqn~~~~ly  301 (674)
T KOG1001|consen  284 Y-RWCLTGTPIQNNLDELY  301 (674)
T ss_pred             e-eeeecCChhhhhHHHHH
Confidence            4 44556664 33444433

>KOG1016|consensus

Probab=97.36  E-value=0.0042  Score=58.05  Aligned_cols=182  Identities=14%  Similarity=0.097  Sum_probs=106.1

Q ss_pred             CCCCHHHHHHHHH---CCCCCCcHHHHHHhhhhh--cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          52 MELSEELLRGIYA---YGFEKPSAIQQRAIIPCV--RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        52 ~~~~~~l~~~l~~---~~~~~~~~~Q~~~~~~l~--~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      +-+.+.+.+.++-   .|+..+++--.+.+....  +|..+|+...+|-|||+..+- .+.-+..-.....+|+|+|-..
T Consensus       245 iflapqla~v~kPHQiGGiRFlYDN~iESl~rykkSsGFGCILAHSMGLGKTlQVis-F~diflRhT~AKtVL~ivPiNT  323 (1387)
T KOG1016|consen  245 IFLAPQLAHVLKPHQIGGIRFLYDNTIESLGRYKKSSGFGCILAHSMGLGKTLQVIS-FSDIFLRHTKAKTVLVIVPINT  323 (1387)
T ss_pred             eeehhhhHhhcCccccCcEEEehhhHHHHHhhccccCCcceeeeeccccCceeEEee-hhHHHhhcCccceEEEEEehHH
Confidence            3456677666643   245556666666665543  456799999999999987643 3333333333447999999766


Q ss_pred             HHHHHHHHHHHhcCC----C-----CceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcC----------
Q psy4698         127 LAQQIQKVVIALGDF----M-----SVSCHACIGGTIVRDDIRKLE----AGAQVVVGTPGRVFDMISRG----------  183 (258)
Q Consensus       127 l~~q~~~~~~~~~~~----~-----~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~~~----------  183 (258)
                      |-+ |...+..+...    .     .+.+..+.++...........    ....|+..-++.+.-++...          
T Consensus       324 lQN-WlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~KT~~~Rakvi~~Wv~~GGVlLvGYemfRLL~lk~~~~~grpkkt  402 (1387)
T KOG1016|consen  324 LQN-WLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVKTFDQRAKVIEQWVQTGGVLLVGYEMFRLLILKTLPKKGRPKKT  402 (1387)
T ss_pred             HHH-HHHHhhhhcCCCcccCCCccceeEEEEecCchhhHHHHHHHHHHHhccCCEEEehHHHHHHHHHhcccccCCcccc
Confidence            544 34444443322    2     244555555544333222211    12356666666543222110          


Q ss_pred             --C-----C-------------------CCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHH
Q psy4698         184 --A-----L-------------------STKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       184 --~-----~-------------------~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~  237 (258)
                        .     +                   .-..-+++|+||-|++  .+....+-.-++.++...++++....+-+++.+.
T Consensus       403 ~kr~~~~~i~~d~eD~~qe~~~li~~AL~~PGPDlVICDEGHrI--KN~~A~iS~aLk~IrtrRRiVLTGYPLQNNLlEY  480 (1387)
T KOG1016|consen  403 LKRISSGFIKDDSEDQRQEAYSLIRSALLEPGPDLVICDEGHRI--KNITAEISMALKAIRTRRRIVLTGYPLQNNLLEY  480 (1387)
T ss_pred             ccccCCcccCCchhhhHHHHHHHHHHHhcCCCCCeEEecCCcee--ccchHHHHHHHHHhhhceeEEEeccccccchHHH
Confidence              0     0                   0122459999999998  4445566666777778888999888888775543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.35  E-value=0.0033  Score=47.75  Aligned_cols=38  Identities=18%  Similarity=0.241  Sum_probs=24.9

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      +++.|++|+|||......+.....   .+..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~---~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT---KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHh---cCCEEEEEECCcch
Confidence            689999999999876444333322   23467777765443

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PF13173 AAA_14: AAA domain

Probab=97.32  E-value=0.0033  Score=46.37  Aligned_cols=38  Identities=13%  Similarity=0.303  Sum_probs=24.7

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      +-.+|++||+|.+  .+....+..+...- ++.++++.+..
T Consensus        61 ~~~~i~iDEiq~~--~~~~~~lk~l~d~~-~~~~ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYL--PDWEDALKFLVDNG-PNIKIILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhh--ccHHHHHHHHHHhc-cCceEEEEccc
Confidence            4558999999987  44566666666644 45656554433

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.31  E-value=0.0012  Score=63.35  Aligned_cols=52  Identities=15%  Similarity=0.291  Sum_probs=33.3

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      ...+++||||+|.|.. .-.+.+.++++..+..+.+|+.+ |-+..+...++..
T Consensus       119 ~~~KV~IIDEad~lt~-~a~NaLLK~LEEpP~~~~fIl~t-t~~~kLl~TIrSR  170 (824)
T PRK07764        119 SRYKIFIIDEAHMVTP-QGFNALLKIVEEPPEHLKFIFAT-TEPDKVIGTIRSR  170 (824)
T ss_pred             CCceEEEEechhhcCH-HHHHHHHHHHhCCCCCeEEEEEe-CChhhhhHHHHhh
Confidence            4678999999998753 34556667777766767666655 4443444434433

>PRK06893 DNA replication initiation factor; Validated

Probab=97.30  E-value=0.001  Score=54.46  Aligned_cols=45  Identities=20%  Similarity=0.470  Sum_probs=28.1

Q ss_pred             CCccEEEEccchhhhccC-cHHHHHHHHHhCCC-CccEEEEEeeCCh
Q psy4698         188 KQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNN-DVQVILLSATMPA  232 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~~-~~~~i~~SAT~~~  232 (258)
                      .+.++||+||+|.+.... ....+..++..+.. ..+++++|++.++
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p  136 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSP  136 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCCh
Confidence            356799999999875332 23345555555433 3456777777644

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.28  E-value=0.00096  Score=63.84  Aligned_cols=87  Identities=9%  Similarity=0.076  Sum_probs=73.5

Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCC------hhHHHH
Q psy4698         164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP------ADVLDV  237 (258)
Q Consensus       164 ~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~------~~~~~~  237 (258)
                      ....|++.||..|..=+-.+.+.+..+..|||||||++.....+..+.++.+.-++..-+.+|||+..      ..+++.
T Consensus         6 ~~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~~~~g~~~l~~v   85 (814)
T TIGR00596         6 LEGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEAFTMGFSPLETK   85 (814)
T ss_pred             hcCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcccccchHHHHHH
Confidence            34689999999988777777889999999999999999988899999999999888889999999975      357777


Q ss_pred             HHHhcCCCeEEEe
Q psy4698         238 SMKFMRDPIKILV  250 (258)
Q Consensus       238 ~~~~~~~~~~v~~  250 (258)
                      ++...-..+.+..
T Consensus        86 mk~L~i~~v~l~p   98 (814)
T TIGR00596        86 MRNLFLRHVYLWP   98 (814)
T ss_pred             HHHhCcCeEEEeC
Confidence            8777666666644

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

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.27  E-value=0.0037  Score=53.91  Aligned_cols=131  Identities=13%  Similarity=0.270  Sum_probs=68.4

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .++++++.|++|+|||..+. ++...+...  +..++++. ...+........  +.            ..  .      
T Consensus       182 ~~~~Lll~G~~GtGKThLa~-aIa~~l~~~--g~~V~y~t-~~~l~~~l~~~~--~~------------~~--~------  235 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSN-CIAKELLDR--GKSVIYRT-ADELIEILREIR--FN------------ND--K------  235 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHHC--CCeEEEEE-HHHHHHHHHHHH--hc------------cc--h------
Confidence            45789999999999998653 444444433  23565554 344444332210  00            00  0      


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc-HHHHHHHHHhC-CCCccEEEEEeeCChhHHH----
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF-KDQIYDVFKHL-NNDVQVILLSATMPADVLD----  236 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~-~~~~~~~~~~l-~~~~~~i~~SAT~~~~~~~----  236 (258)
                               .....++       .+.++++||+||.+......+ ...+..++... .....+|+.|.--+.++.+    
T Consensus       236 ---------~~~~~~~-------~l~~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiTSNl~~~el~~~~~e  299 (329)
T PRK06835        236 ---------ELEEVYD-------LLINCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIISTNLSLEELLKTYSE  299 (329)
T ss_pred             ---------hHHHHHH-------HhccCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhH
Confidence                     0000011       234578999999986533322 24444555443 2334566655554555533    


Q ss_pred             -HHHHhcCCCeEEEecCCcc
Q psy4698         237 -VSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       237 -~~~~~~~~~~~v~~~~~~~  255 (258)
                       +..........|.+.+++.
T Consensus       300 ri~SRL~~~~~~i~~~G~d~  319 (329)
T PRK06835        300 RISSRLLGNFTLLKFYGEDI  319 (329)
T ss_pred             HHHHHHHcCCEEEEecCcCh
Confidence             4444555666777766653

>PRK05642 DNA replication initiation factor; Validated

Probab=97.26  E-value=0.0011  Score=54.34  Aligned_cols=44  Identities=20%  Similarity=0.508  Sum_probs=27.6

Q ss_pred             CccEEEEccchhhhcc-CcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         189 QIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      +.+++|+|++|.+... .....+..++..+...-..++++++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            4568999999976433 2345566677665544445666666543

>TIGR01075 uvrD DNA helicase II

Probab=97.25  E-value=0.0016  Score=62.12  Aligned_cols=70  Identities=19%  Similarity=0.214  Sum_probs=55.9

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-ccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-NIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ..+++-|++++.+  ...+++|.|+.|||||.+..--+...+.. +....++++++-|+..|.+..+++.++.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            3689999999965  34578999999999999977666666654 3344589999999999999999887764

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.25  E-value=0.0051  Score=55.32  Aligned_cols=128  Identities=14%  Similarity=0.283  Sum_probs=66.0

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +.+++.||+|+|||..+ .++.+.+.....+.+++|+... .+..+....++                           .
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~~~~~v~yi~~~-~f~~~~~~~~~---------------------------~  181 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITSE-KFLNDLVDSMK---------------------------E  181 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEHH-HHHHHHHHHHh---------------------------c
Confidence            35999999999999765 3444455444444577777542 22222222110                           0


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCCC-CccEEEEEeeCChhHHHHH---H
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNN-DVQVILLSATMPADVLDVS---M  239 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~~-~~~~i~~SAT~~~~~~~~~---~  239 (258)
                      +      +.+.+...+.      .+.++|++||+|.+.+.. ....+..++..+.. ..++|+.|..-|.++..+.   .
T Consensus       182 ~------~~~~f~~~~~------~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~  249 (440)
T PRK14088        182 G------KLNEFREKYR------KKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLV  249 (440)
T ss_pred             c------cHHHHHHHHH------hcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHh
Confidence            0      1112222111      246799999999875442 22344445544432 3455555555555554442   2


Q ss_pred             HhcCCCeEEEecCC
Q psy4698         240 KFMRDPIKILVKKE  253 (258)
Q Consensus       240 ~~~~~~~~v~~~~~  253 (258)
                      .-+.-...+.+...
T Consensus       250 SR~~~gl~v~i~~p  263 (440)
T PRK14088        250 SRFQMGLVAKLEPP  263 (440)
T ss_pred             hHHhcCceEeeCCC
Confidence            23344455555433

>CHL00181 cbbX CbbX; Provisional

Probab=97.24  E-value=0.0063  Score=51.51  Aligned_cols=22  Identities=27%  Similarity=0.241  Sum_probs=17.6

Q ss_pred             cCCcEEEEcccCCCcchHhHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSIS  104 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~  104 (258)
                      .|.++++.||+|+|||.++-..
T Consensus        58 ~~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             CCceEEEECCCCCCHHHHHHHH
Confidence            3557999999999999887433

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.24  E-value=0.0024  Score=51.87  Aligned_cols=124  Identities=15%  Similarity=0.241  Sum_probs=68.3

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      .+++.|++|+|||-. +.++...+.....+.+++|+... +........++                           . 
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~---------------------------~-   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSAE-EFIREFADALR---------------------------D-   85 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHH---------------------------T-
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecHH-HHHHHHHHHHH---------------------------c-
Confidence            489999999999984 45666666655556677777542 33333222221                           1 


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCC-CCccEEEEEeeCChhHH---HHHHH
Q psy4698         166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLN-NDVQVILLSATMPADVL---DVSMK  240 (258)
Q Consensus       166 ~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~---~~~~~  240 (258)
                           ...+.+.+.       +...+++++|++|.+.+.. ....+..++..+. ...++|+.|...|.++.   .-+..
T Consensus        86 -----~~~~~~~~~-------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~S  153 (219)
T PF00308_consen   86 -----GEIEEFKDR-------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRS  153 (219)
T ss_dssp             -----TSHHHHHHH-------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHH
T ss_pred             -----ccchhhhhh-------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhh
Confidence                 122222222       2357799999999875432 2344555555543 34577777767676543   22334


Q ss_pred             hcCCCeEEEec
Q psy4698         241 FMRDPIKILVK  251 (258)
Q Consensus       241 ~~~~~~~v~~~  251 (258)
                      .+.-.+.+.+.
T Consensus       154 Rl~~Gl~~~l~  164 (219)
T PF00308_consen  154 RLSWGLVVELQ  164 (219)
T ss_dssp             HHHCSEEEEE-
T ss_pred             hHhhcchhhcC
Confidence            44445555543

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.23  E-value=0.0023  Score=57.56  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=16.2

Q ss_pred             cEEEEcccCCCcchHhHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~  105 (258)
                      .+++.||.|+|||.++...+
T Consensus        42 a~Lf~GP~GtGKTTlAriLA   61 (484)
T PRK14956         42 AYIFFGPRGVGKTTIARILA   61 (484)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            37999999999999874443

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=97.23  E-value=0.0019  Score=61.20  Aligned_cols=68  Identities=19%  Similarity=0.148  Sum_probs=54.3

Q ss_pred             CcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      +++-|.+++.+  ...+++|.|+.|||||.+..--+...+... ....++++++.|+..+.+....+.+..
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            68889999865  345799999999999999887777777543 344589999999999999988887653

Designed to identify rep members of the uvrD/rep subfamily.

>PRK09183 transposase/IS protein; Provisional

Probab=97.19  E-value=0.0059  Score=50.90  Aligned_cols=39  Identities=18%  Similarity=0.175  Sum_probs=25.5

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      +..|.++++.||+|+|||..+........ .  .+.+++++.
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~-~--~G~~v~~~~  137 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAV-R--AGIKVRFTT  137 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHH-H--cCCeEEEEe
Confidence            56778999999999999976543332222 2  233566553

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=97.19  E-value=0.0018  Score=57.44  Aligned_cols=147  Identities=16%  Similarity=0.260  Sum_probs=79.9

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH-HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE-LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      -.++.|+.|||||.+....++..+.....+.+++++-++.. +....+..++......++....-......  .......
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~~~~~~~~~~--~i~~~~~   80 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIEGINYEFKKSKSSM--EIKILNT   80 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChhheeecCCcc--EEEecCC
Confidence            36889999999999888777777666433468999988866 55555566655443333321111111100  0001112


Q ss_pred             CCcEEEeCh-HHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC--CCccEEEEEeeCChhHHHHHHHh
Q psy4698         165 GAQVVVGTP-GRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN--NDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       165 ~~~Ilv~Tp-~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~--~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      +..|++..- +...+ ++    ....+.++.+|||..+...    .+..++.+++  ...+.+++|.+.+..-.-+.+.|
T Consensus        81 g~~i~f~g~~d~~~~-ik----~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~~~~~~~i~~t~NP~~~~~w~~~~f  151 (396)
T TIGR01547        81 GKKFIFKGLNDKPNK-LK----SGAGIAIIWFEEASQLTFE----DIKELIPRLRETGGKKFIIFSSNPESPLHWVKKRF  151 (396)
T ss_pred             CeEEEeecccCChhH-hh----CcceeeeehhhhhhhcCHH----HHHHHHHHhhccCCccEEEEEcCcCCCccHHHHHH
Confidence            455666544 22221 11    2233689999999987322    3334444443  22224777888655333444444


Q ss_pred             cC
Q psy4698         242 MR  243 (258)
Q Consensus       242 ~~  243 (258)
                      ..
T Consensus       152 ~~  153 (396)
T TIGR01547       152 IE  153 (396)
T ss_pred             Hh
Confidence            43

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PHA02533 17 large terminase protein; Provisional

Probab=97.18  E-value=0.0045  Score=56.85  Aligned_cols=122  Identities=16%  Similarity=0.112  Sum_probs=74.5

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc--eE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV--SC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~--~~  146 (258)
                      .+.++|...+..+..++-.++..+-..|||.+....++...... .+.++++++|+...+...++.++........  ..
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~-~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P~l~~~  137 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN-KDKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC-CCCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            57899999998776566667888889999988764444333322 3458999999999999988888765432210  10


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~  202 (258)
                      ......    ...-.+.+|..|.+.|.+.       +...-.+..++++||+|.+.
T Consensus       138 ~i~~~~----~~~I~l~NGS~I~~lss~~-------~t~rG~~~~~liiDE~a~~~  182 (534)
T PHA02533        138 GIVEWN----KGSIELENGSKIGAYASSP-------DAVRGNSFAMIYIDECAFIP  182 (534)
T ss_pred             ceeecC----ccEEEeCCCCEEEEEeCCC-------CccCCCCCceEEEeccccCC
Confidence            000000    0000124566665555321       11222356689999999763

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.18  E-value=0.0023  Score=60.49  Aligned_cols=70  Identities=20%  Similarity=0.233  Sum_probs=54.3

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ..+++-|++++..  ...+++|.|+.|||||.+..--+...+... ..+.++++++.++..+....+++....
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            4689999999953  345689999999999998866665555443 234589999999999999988876643

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.16  E-value=0.0057  Score=64.17  Aligned_cols=135  Identities=16%  Similarity=0.198  Sum_probs=81.2

Q ss_pred             CCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      .+++-|.+++..++..  +-.+|.|+.|+|||.+. -.+...+...  +.+++.++||..-+....+...       .. 
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~~--G~~V~~lAPTgrAA~~L~e~~g-------~~-  497 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASEQ--GYEIQIITAGSLSAQELRQKIP-------RL-  497 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHhc--CCeEEEEeCCHHHHHHHHHHhc-------ch-
Confidence            5889999999998775  56999999999999874 3444444433  4589999999876666554321       00 


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC-CCCccEEE
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL-NNDVQVIL  225 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~~~~~~i~  225 (258)
                           ......+...+..+  .-..|...++    .....+..-++|||||+.++    -...+..+++.. +.+.++|+
T Consensus       498 -----A~Ti~~~l~~l~~~--~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl----~~~~~~~Ll~~a~~~garvVl  562 (1960)
T TIGR02760       498 -----ASTFITWVKNLFND--DQDHTVQGLL----DKSSPFSNKDIFVVDEANKL----SNNELLKLIDKAEQHNSKLIL  562 (1960)
T ss_pred             -----hhhHHHHHHhhccc--ccchhHHHhh----cccCCCCCCCEEEEECCCCC----CHHHHHHHHHHHhhcCCEEEE
Confidence                 00111111111111  1122333332    22223456789999999966    244556666655 35778887


Q ss_pred             EEee
Q psy4698         226 LSAT  229 (258)
Q Consensus       226 ~SAT  229 (258)
                      +.-+
T Consensus       563 vGD~  566 (1960)
T TIGR02760       563 LNDS  566 (1960)
T ss_pred             EcCh
Confidence            7554

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.15  E-value=0.021  Score=47.14  Aligned_cols=68  Identities=7%  Similarity=0.204  Sum_probs=39.0

Q ss_pred             CCCccEEEEccchhhhccCcHH-HHHHHHHh-CCCCccEEEEEeeCChhHHHHH-----HHh-cCCCeEEEecCCc
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKD-QIYDVFKH-LNNDVQVILLSATMPADVLDVS-----MKF-MRDPIKILVKKEE  254 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~-~~~~~~~~-l~~~~~~i~~SAT~~~~~~~~~-----~~~-~~~~~~v~~~~~~  254 (258)
                      +.++++|||||++......+.. .+..++.. ......+|+.|.--+.++.+..     ... +.+...|.++.++
T Consensus       160 l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l~~~~g~ri~sRl~~~~~~~i~f~~~s  235 (244)
T PRK07952        160 LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFNWDS  235 (244)
T ss_pred             hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHHHHHhChHHHHHHHHCCceEEEeeCCc
Confidence            3467899999999754333333 33445443 3345667777766555555432     222 3566677766554

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.14  E-value=0.0023  Score=61.12  Aligned_cols=69  Identities=17%  Similarity=0.173  Sum_probs=55.4

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-ccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-NIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .+++-|++++.+.  ..+++|.|+.|||||.+...-+...+.. +....++++++-|+..+.+..+++.++.
T Consensus         9 ~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~   78 (721)
T PRK11773          9 SLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLL   78 (721)
T ss_pred             hcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHh
Confidence            5899999999653  4578999999999999887666666653 3344589999999999999999887764

>KOG0298|consensus

Probab=97.14  E-value=0.0024  Score=62.30  Aligned_cols=143  Identities=14%  Similarity=0.072  Sum_probs=90.1

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhh-----------cc----ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQ-----------NI----KECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~-----------~~----~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      .|+.++..-..|+|||...+...+.....           .+    ..+-+|||||. ++..||+..+..-.... +.+.
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~-lKv~  450 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL-LKVL  450 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc-ceEE
Confidence            45667888899999998876555443211           11    12358999994 67789999887766543 5666


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--------------CCCC----Ccc--EEEEccchhhhccCcH
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA--------------LSTK----QIR--MFVLDEADEMLSRGFK  207 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~--------------~~~~----~l~--~lVvDE~h~~~~~~~~  207 (258)
                      .+.|-....-........+||+++|++.|..=+.+..              ..++    .+.  -|++|||+++- . ..
T Consensus       451 ~Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMve-s-ss  528 (1394)
T KOG0298|consen  451 LYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVE-S-SS  528 (1394)
T ss_pred             EEechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhc-c-hH
Confidence            6666544322222333458999999999876543321              1110    111  48999999663 3 45


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeC
Q psy4698         208 DQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       208 ~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ....+.+.+++. .-..++|+|.
T Consensus       529 S~~a~M~~rL~~-in~W~VTGTP  550 (1394)
T KOG0298|consen  529 SAAAEMVRRLHA-INRWCVTGTP  550 (1394)
T ss_pred             HHHHHHHHHhhh-hceeeecCCc
Confidence            555666666654 3478889994

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.13  E-value=0.0066  Score=47.61  Aligned_cols=49  Identities=18%  Similarity=0.216  Sum_probs=33.1

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ++|.|++|+|||...+..+...+..   +.+++|++. .+...+..+.+..++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~---g~~v~~~s~-e~~~~~~~~~~~~~g   50 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR---GEPGLYVTL-EESPEELIENAESLG   50 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC---CCcEEEEEC-CCCHHHHHHHHHHcC
Confidence            6899999999998876655555533   346888864 344556566565553

A related protein is found in archaea.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.12  E-value=0.0064  Score=49.31  Aligned_cols=21  Identities=19%  Similarity=0.243  Sum_probs=17.2

Q ss_pred             cCCcEEEEcccCCCcchHhHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSI  103 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~  103 (258)
                      .+.++++.|++|+|||..+..
T Consensus        37 ~~~~lll~G~~G~GKT~la~~   57 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQA   57 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHH
Confidence            456799999999999987643

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.12  E-value=0.0034  Score=51.53  Aligned_cols=37  Identities=8%  Similarity=0.113  Sum_probs=23.2

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +.++++.||+|+|||..... +.+.+...  +.+++|+.-
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a-~~~~~~~~--~~~v~y~~~   81 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHA-ACAELSQR--GRAVGYVPL   81 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHH-HHHHHHhC--CCeEEEEEH
Confidence            35799999999999976532 33333322  345666643

>PRK08727 hypothetical protein; Validated

Probab=97.11  E-value=0.003  Score=51.78  Aligned_cols=35  Identities=20%  Similarity=0.205  Sum_probs=22.3

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ..+++.|++|+|||-... ++...+...  +.+++|+.
T Consensus        42 ~~l~l~G~~G~GKThL~~-a~~~~~~~~--~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLAL-ALCAAAEQA--GRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHc--CCcEEEEe
Confidence            349999999999996543 333333332  23566664

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.10  E-value=0.013  Score=48.79  Aligned_cols=18  Identities=33%  Similarity=0.433  Sum_probs=15.7

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            578999999999998763

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.10  E-value=0.0028  Score=63.91  Aligned_cols=122  Identities=16%  Similarity=0.197  Sum_probs=79.0

Q ss_pred             CcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC-CCCceEEE
Q psy4698          70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD-FMSVSCHA  148 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~-~~~~~~~~  148 (258)
                      .++-|.+++.  ..+++++|.|+.|||||.+..--++..+..+..-.++++++=|+..+.+...++.+... ...-    
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~~~~----   75 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKALQQ----   75 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHHHhc----
Confidence            5788999996  46889999999999999998877777776553334799999999999998877766321 1110    


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCc--cEEEEccchh
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQI--RMFVLDEADE  200 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l--~~lVvDE~h~  200 (258)
                         ........+.+..-...-|+|...+...+-+.....-++  .+=|.||...
T Consensus        76 ---~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        76 ---EPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             ---CchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence               001111112222224578999999875443322222122  3456888774

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.09  E-value=0.0042  Score=55.36  Aligned_cols=34  Identities=21%  Similarity=0.254  Sum_probs=27.5

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhH
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l  102 (258)
                      .+.......+..+..++++++.|++|+|||..+-
T Consensus       179 i~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        179 IPETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CCHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            3455666677778889999999999999998763

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.05  E-value=0.0061  Score=53.89  Aligned_cols=36  Identities=19%  Similarity=0.344  Sum_probs=23.5

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL  121 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil  121 (258)
                      .+++|.|++|+|||.+. ..++..+.....+..++++
T Consensus        56 ~~~lI~G~~GtGKT~l~-~~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV-KKVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhcCCcEEEEE
Confidence            56999999999999875 3344444433323445555

>PLN03025 replication factor C subunit; Provisional

Probab=97.04  E-value=0.01  Score=51.04  Aligned_cols=38  Identities=24%  Similarity=0.362  Sum_probs=24.7

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ..+++|+||+|.+... ....+.+.+...+..+++++.+
T Consensus        99 ~~kviiiDE~d~lt~~-aq~aL~~~lE~~~~~t~~il~~  136 (319)
T PLN03025         99 RHKIVILDEADSMTSG-AQQALRRTMEIYSNTTRFALAC  136 (319)
T ss_pred             CeEEEEEechhhcCHH-HHHHHHHHHhcccCCceEEEEe
Confidence            4789999999987543 3445555666555556555543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.03  E-value=0.0065  Score=49.48  Aligned_cols=43  Identities=9%  Similarity=0.378  Sum_probs=26.2

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCcc-EEEEEeeCCh
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQ-VILLSATMPA  232 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~-~i~~SAT~~~  232 (258)
                      +.++||+||+|.+.. .....+..++........ +++++++.+.
T Consensus        90 ~~~~liiDdi~~l~~-~~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDD-AQQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCc-hHHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            456899999998643 334455555655443333 5677776543

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.03  E-value=0.0066  Score=55.00  Aligned_cols=45  Identities=13%  Similarity=0.309  Sum_probs=27.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADV  234 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~  234 (258)
                      .+.+++||||+|.+... ..+.+.+.+..-++...+|+.+ |-+..+
T Consensus       115 ~~~KVvIIDEah~Ls~~-A~NaLLK~LEePp~~v~fIlat-te~~Kl  159 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNS-AFNALLKTLEEPAPHVKFILAT-TEVKKI  159 (491)
T ss_pred             CCceEEEEeChHhCCHH-HHHHHHHHHhCCCCCeEEEEEe-CChHHH
Confidence            56889999999977443 3344555566555555555544 433333

>PRK06921 hypothetical protein; Provisional

Probab=97.01  E-value=0.015  Score=48.69  Aligned_cols=38  Identities=24%  Similarity=0.363  Sum_probs=25.0

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      .+.++++.|++|+|||..+ .++...+... .+..++|+.
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~-~g~~v~y~~  153 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK-KGVPVLYFP  153 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh-cCceEEEEE
Confidence            3578999999999999765 3444444433 133566665

>KOG0953|consensus

Probab=97.01  E-value=0.00093  Score=59.96  Aligned_cols=100  Identities=23%  Similarity=0.197  Sum_probs=64.2

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      -++-+|||.||||.-+    ++++....   +.+|-.|.+.||.++++.+...+    +.|..+.|.......-.  .+.
T Consensus       193 Ii~H~GPTNSGKTy~A----Lqrl~~ak---sGvycGPLrLLA~EV~~r~na~g----ipCdL~TGeE~~~~~~~--~~~  259 (700)
T KOG0953|consen  193 IIMHVGPTNSGKTYRA----LQRLKSAK---SGVYCGPLRLLAHEVYDRLNALG----IPCDLLTGEERRFVLDN--GNP  259 (700)
T ss_pred             EEEEeCCCCCchhHHH----HHHHhhhc---cceecchHHHHHHHHHHHhhhcC----CCccccccceeeecCCC--CCc
Confidence            3677899999999765    45554432   68999999999999999987775    44444444433222111  122


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       166 ~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      ++.+=||.++.-        --..++..|+||+++|-+...
T Consensus       260 a~hvScTVEM~s--------v~~~yeVAViDEIQmm~Dp~R  292 (700)
T KOG0953|consen  260 AQHVSCTVEMVS--------VNTPYEVAVIDEIQMMRDPSR  292 (700)
T ss_pred             ccceEEEEEEee--------cCCceEEEEehhHHhhcCccc
Confidence            566777775532        112356778888887765543

>KOG1131|consensus

Probab=97.01  E-value=0.0071  Score=54.18  Aligned_cols=69  Identities=13%  Similarity=0.057  Sum_probs=37.9

Q ss_pred             CCCCcHHHHHHhhh----hhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc-ccceEEEEeccHHHHHHHHHHH
Q psy4698          67 FEKPSAIQQRAIIP----CVRGNDVIAQAQSGTGKTATFSISILQQVDQNI-KECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        67 ~~~~~~~Q~~~~~~----l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~-~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      +...+|-|-+-+..    +-.+.++++.+|+|+|||.+.+-.++....... ...+.+|-+-|..-++.....+
T Consensus        14 Y~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El   87 (755)
T KOG1131|consen   14 YDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEEL   87 (755)
T ss_pred             CcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHH
Confidence            44556666544433    335567999999999999886544433222211 2234555554443333333333

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.01  E-value=0.0051  Score=58.07  Aligned_cols=39  Identities=13%  Similarity=0.329  Sum_probs=25.1

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ...+++||||+|.|... -.+.+.+.+..-+.++.+|+.+
T Consensus       118 gr~KVIIIDEah~LT~~-A~NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNH-AFNAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHH-HHHHHHHHHHhcCCCeEEEEEE
Confidence            35789999999987543 3445556666655555555543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.00  E-value=0.0034  Score=56.56  Aligned_cols=110  Identities=15%  Similarity=0.278  Sum_probs=59.6

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +.+++.|++|+|||... .++.+.+.....+.+++|+.. ..+.......+...                          
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l~~~--------------------------  193 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDILQKT--------------------------  193 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHHHHh--------------------------
Confidence            35899999999999654 455555554444557777655 44444443322110                          


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCC-CCccEEEEEeeCChhH
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLN-NDVQVILLSATMPADV  234 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~  234 (258)
                        .      +.+.....    ...+.++||+||+|.+... .....+..++..+. ...|+|+.|-..|..+
T Consensus       194 --~------~~~~~~~~----~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l  253 (450)
T PRK14087        194 --H------KEIEQFKN----EICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELL  253 (450)
T ss_pred             --h------hHHHHHHH----HhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHH
Confidence              0      11111111    1235679999999976432 22344555555443 3345666555555444

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=96.98  E-value=0.013  Score=42.88  Aligned_cols=15  Identities=33%  Similarity=0.556  Sum_probs=13.4

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      +++.||.|+|||...
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            589999999999875

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.98  E-value=0.0072  Score=52.13  Aligned_cols=39  Identities=10%  Similarity=0.325  Sum_probs=25.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ...++||+||+|.+.. .....+...+...+..+++|+.+
T Consensus       124 ~~~~vlilDe~~~l~~-~~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        124 ADYKTILLDNAEALRE-DAQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCCcEEEEeCcccCCH-HHHHHHHHHHHhccCCCeEEEEe
Confidence            4567999999997743 23445666666666666666544

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.95  E-value=0.011  Score=55.67  Aligned_cols=151  Identities=17%  Similarity=0.249  Sum_probs=86.8

Q ss_pred             HHHHHCCCCCCcHHHHHHhhhhhcCC--cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          60 RGIYAYGFEKPSAIQQRAIIPCVRGN--DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        60 ~~l~~~~~~~~~~~Q~~~~~~l~~g~--~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      ..+..........-|.+.+..+...+  -+++.|.-|.|||.+.=+++....... ...+++|.+|+.+-++..+..+.+
T Consensus       205 ~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~-~~~~iiVTAP~~~nv~~Lf~fa~~  283 (758)
T COG1444         205 RELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLA-GSVRIIVTAPTPANVQTLFEFAGK  283 (758)
T ss_pred             HHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhc-CCceEEEeCCCHHHHHHHHHHHHH
Confidence            33444444445555555666666553  599999999999988766553222222 246899999999999988887665


Q ss_pred             hcCCCCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHh
Q psy4698         138 LGDFMSVSCHACIGGTIVRDDIRKL-EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH  216 (258)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~  216 (258)
                      -....+...........   ..... .....|=+-.|....          ..-+++|||||=.+    -...+.++++.
T Consensus       284 ~l~~lg~~~~v~~d~~g---~~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaI----plplL~~l~~~  346 (758)
T COG1444         284 GLEFLGYKRKVAPDALG---EIREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAI----PLPLLHKLLRR  346 (758)
T ss_pred             hHHHhCCcccccccccc---ceeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcC----ChHHHHHHHhh
Confidence            44444433222111100   00000 111234455564322          11569999999865    23444444443


Q ss_pred             CCCCccEEEEEeeCCh
Q psy4698         217 LNNDVQVILLSATMPA  232 (258)
Q Consensus       217 l~~~~~~i~~SAT~~~  232 (258)
                          .+.++||.|+..
T Consensus       347 ----~~rv~~sTTIhG  358 (758)
T COG1444         347 ----FPRVLFSTTIHG  358 (758)
T ss_pred             ----cCceEEEeeecc
Confidence                356888999865

>PRK08116 hypothetical protein; Validated

Probab=96.95  E-value=0.016  Score=48.64  Aligned_cols=128  Identities=10%  Similarity=0.190  Sum_probs=64.4

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      .+++.|++|+|||..+. ++.+.+...  +..++++ +...+...+...+   ...          +.            
T Consensus       116 gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v~~~-~~~~ll~~i~~~~---~~~----------~~------------  166 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAA-CIANELIEK--GVPVIFV-NFPQLLNRIKSTY---KSS----------GK------------  166 (268)
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHHHc--CCeEEEE-EHHHHHHHHHHHH---hcc----------cc------------
Confidence            49999999999997653 455555443  2345554 3344443332211   000          00            


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhC-CCCccEEEEEeeCChhHHH-----HH
Q psy4698         166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHL-NNDVQVILLSATMPADVLD-----VS  238 (258)
Q Consensus       166 ~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l-~~~~~~i~~SAT~~~~~~~-----~~  238 (258)
                           .+...+.+.       +.+.++||+||++.-... .....+..++... ....++|+.|..-+.++..     +.
T Consensus       167 -----~~~~~~~~~-------l~~~dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~~~~~~ri~  234 (268)
T PRK08116        167 -----EDENEIIRS-------LVNADLLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLSLEELKNQYGKRIY  234 (268)
T ss_pred             -----ccHHHHHHH-------hcCCCEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHhHHHH
Confidence                 011112221       345679999999632111 1234445555432 3445677777666666543     33


Q ss_pred             HHhcCCCeEEEecCCc
Q psy4698         239 MKFMRDPIKILVKKEE  254 (258)
Q Consensus       239 ~~~~~~~~~v~~~~~~  254 (258)
                      .........|.+.+++
T Consensus       235 sRl~e~~~~v~~~g~d  250 (268)
T PRK08116        235 DRILEMCTPVENEGKS  250 (268)
T ss_pred             HHHHHcCEEEEeeCcC
Confidence            3333444555555543

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.95  E-value=0.026  Score=49.44  Aligned_cols=27  Identities=30%  Similarity=0.613  Sum_probs=19.6

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQN  112 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~  112 (258)
                      .|+++.|+||+|||.+.. .+++.+...
T Consensus        43 ~n~~iyG~~GTGKT~~~~-~v~~~l~~~   69 (366)
T COG1474          43 SNIIIYGPTGTGKTATVK-FVMEELEES   69 (366)
T ss_pred             ccEEEECCCCCCHhHHHH-HHHHHHHhh
Confidence            369999999999998864 444444443

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.94  E-value=0.0091  Score=53.06  Aligned_cols=133  Identities=17%  Similarity=0.165  Sum_probs=61.9

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc-HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT-RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK  161 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (258)
                      .|+.+.+.||||+|||+.....+-..+...+...-.++.+.+ +.-+.++..   .++...++.+..             
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQL~---~~a~ilGvp~~~-------------  253 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLR---IYGKLLGVSVRS-------------  253 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHHHH---HHHHHcCCceec-------------
Confidence            355699999999999987643332222222111123444443 222222222   233222333221             


Q ss_pred             HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCCCCccEEEEEeeC-ChhHHHHHH
Q psy4698         162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVILLSATM-PADVLDVSM  239 (258)
Q Consensus       162 ~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~~~~~i~~SAT~-~~~~~~~~~  239 (258)
                              +.++..+...+.    .+.+.+.+++|.+=+.... .....+..+.....+.-.++.+|||. ..++.+..+
T Consensus       254 --------v~~~~dl~~al~----~l~~~d~VLIDTaGrsqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~~~  321 (420)
T PRK14721        254 --------IKDIADLQLMLH----ELRGKHMVLIDTVGMSQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEVIS  321 (420)
T ss_pred             --------CCCHHHHHHHHH----HhcCCCEEEecCCCCCcchHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHHHH
Confidence                    122333222222    2345667888876422111 11222222222122334567889997 456777777


Q ss_pred             HhcC
Q psy4698         240 KFMR  243 (258)
Q Consensus       240 ~~~~  243 (258)
                      .|-.
T Consensus       322 ~f~~  325 (420)
T PRK14721        322 AYQG  325 (420)
T ss_pred             HhcC
Confidence            7654

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.93  E-value=0.0089  Score=55.44  Aligned_cols=133  Identities=13%  Similarity=0.180  Sum_probs=80.6

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCC-Cce-EEEEECCcchHHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVS-CHACIGGTIVRDDIRKL  162 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~~  162 (258)
                      +-.++..|--.|||.... +++..+.....+.++++++|.+..++..++.++...... .-. +....| ...   ....
T Consensus       255 k~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i~f  329 (738)
T PHA03368        255 RATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SFSF  329 (738)
T ss_pred             cceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EEEe
Confidence            457888899999999766 666656655567799999999999999998887754321 101 111111 100   0011


Q ss_pred             hcC--CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC-CCCccEEEEEeeCCh
Q psy4698         163 EAG--AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL-NNDVQVILLSATMPA  232 (258)
Q Consensus       163 ~~~--~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~~~~~~i~~SAT~~~  232 (258)
                      .+|  ..|.+.+.      -..+..+-.+++++|||||+.+-+.    .+..++-.+ ..++++|++|.|-+.
T Consensus       330 ~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~~----al~~ilp~l~~~n~k~I~ISS~Ns~  392 (738)
T PHA03368        330 PDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRPD----AVQTIMGFLNQTNCKIIFVSSTNTG  392 (738)
T ss_pred             cCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCHH----HHHHHHHHHhccCccEEEEecCCCC
Confidence            122  24444422      1223445567899999999977433    233333222 247899999988654

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.92  E-value=0.0074  Score=50.51  Aligned_cols=41  Identities=22%  Similarity=0.269  Sum_probs=28.9

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +..|..+++.|++|+|||......+...+...  +.+++|++-
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~--g~~vl~iS~   67 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLREYALDLITQH--GVRVGTISL   67 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhc--CceEEEEEc
Confidence            45667899999999999987665555444331  346888764

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.91  E-value=0.029  Score=46.97  Aligned_cols=130  Identities=16%  Similarity=0.236  Sum_probs=72.6

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--c-HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--T-RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~-~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      +..+++.|++|+|||..+...+.. +..  .+.++.++.-  . .....|+.....    ..++                
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~-l~~--~~~~v~~i~~D~~ri~~~~ql~~~~~----~~~~----------------  131 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQ-FHG--KKKTVGFITTDHSRIGTVQQLQDYVK----TIGF----------------  131 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHH-HHH--cCCeEEEEecCCCCHHHHHHHHHHhh----hcCc----------------
Confidence            357999999999999876543332 222  1234554443  2 234445443332    2222                


Q ss_pred             HHhcCCcEEE-eChHHHHHHHhcCCCCCCCccEEEEccchhhhc-cCcHHHHHHHHHhCCCCccEEEEEeeC-ChhHHHH
Q psy4698         161 KLEAGAQVVV-GTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVILLSATM-PADVLDV  237 (258)
Q Consensus       161 ~~~~~~~Ilv-~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-~~~~~~~~~~~~~l~~~~~~i~~SAT~-~~~~~~~  237 (258)
                            .+.. .+++.+.+.+..- ....+++++++|-+=+... ......+..++....++..++.+|||. ..++.+.
T Consensus       132 ------~~~~~~~~~~l~~~l~~l-~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~~  204 (270)
T PRK06731        132 ------EVIAVRDEAAMTRALTYF-KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEI  204 (270)
T ss_pred             ------eEEecCCHHHHHHHHHHH-HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHHH
Confidence                  2222 2454444444321 0123578899999876532 233455556666555555577799986 5588888


Q ss_pred             HHHhcC
Q psy4698         238 SMKFMR  243 (258)
Q Consensus       238 ~~~~~~  243 (258)
                      ++.|-.
T Consensus       205 ~~~f~~  210 (270)
T PRK06731        205 ITNFKD  210 (270)
T ss_pred             HHHhCC
Confidence            888754

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.91  E-value=0.0063  Score=57.72  Aligned_cols=129  Identities=16%  Similarity=0.148  Sum_probs=66.3

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc--HH-HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT--RE-LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~--~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      |+-+.+.||||+|||++...-+-......+ +.++.++.-.  +. ..+|+    +.++...++.+              
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G-~kkV~lit~Dt~RigA~eQL----~~~a~~~gvpv--------------  245 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREG-ADQLALLTTDSFRIGALEQL----RIYGRILGVPV--------------  245 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcC-CCeEEEecCcccchHHHHHH----HHHHHhCCCCc--------------
Confidence            345899999999999876433322222221 1245554432  21 22332    22332222222              


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCCCCccEEEEEeeCC-hhHHHHH
Q psy4698         161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVILLSATMP-ADVLDVS  238 (258)
Q Consensus       161 ~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~~~~~i~~SAT~~-~~~~~~~  238 (258)
                             ..+.+|+.+.+.+..    +.+.++|+||=+=+.... .....+..+.....+...++.+|||.- .++.+..
T Consensus       246 -------~~~~~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i~  314 (767)
T PRK14723        246 -------HAVKDAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEVV  314 (767)
T ss_pred             -------cccCCHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHHH
Confidence                   123366666555553    335578888877654322 222333333333344556778888864 4566676


Q ss_pred             HHhc
Q psy4698         239 MKFM  242 (258)
Q Consensus       239 ~~~~  242 (258)
                      +.|-
T Consensus       315 ~~f~  318 (767)
T PRK14723        315 HAYR  318 (767)
T ss_pred             HHHh
Confidence            6664

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.91  E-value=0.0058  Score=52.33  Aligned_cols=49  Identities=16%  Similarity=0.384  Sum_probs=30.0

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~  238 (258)
                      .+.+++++||||.|.. +..+.+.+.+..-+.++.+++.+. -+..+...+
T Consensus       108 ~~~kviiidead~mt~-~A~nallk~lEep~~~~~~il~~n-~~~~il~tI  156 (325)
T COG0470         108 GGYKVVIIDEADKLTE-DAANALLKTLEEPPKNTRFILITN-DPSKILPTI  156 (325)
T ss_pred             CCceEEEeCcHHHHhH-HHHHHHHHHhccCCCCeEEEEEcC-Chhhccchh
Confidence            5788999999998854 344555555555555555555544 444444433

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.91  E-value=0.0063  Score=58.45  Aligned_cols=47  Identities=15%  Similarity=0.314  Sum_probs=28.8

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      ...+++||||+|+|. ....+.+.+.+..-+..+++|+. .|-+..+..
T Consensus       118 gk~KViIIDEAh~LT-~eAqNALLKtLEEPP~~vrFILa-TTe~~kLl~  164 (944)
T PRK14949        118 GRFKVYLIDEVHMLS-RSSFNALLKTLEEPPEHVKFLLA-TTDPQKLPV  164 (944)
T ss_pred             CCcEEEEEechHhcC-HHHHHHHHHHHhccCCCeEEEEE-CCCchhchH
Confidence            357799999999873 33445555666655556666654 444444433

>PF05729 NACHT: NACHT domain

Probab=96.91  E-value=0.028  Score=42.75  Aligned_cols=56  Identities=18%  Similarity=0.310  Sum_probs=31.6

Q ss_pred             EEEEccchhhhccC-------cHHHHHHHHHh-CCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         192 MFVLDEADEMLSRG-------FKDQIYDVFKH-LNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       192 ~lVvDE~h~~~~~~-------~~~~~~~~~~~-l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      +||+|-+|++....       ....+..++.. +++++++++.|.+  ....+ ....+.....+.+
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~--~~~~~-~~~~~~~~~~~~l  147 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP--RAFPD-LRRRLKQAQILEL  147 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC--ChHHH-HHHhcCCCcEEEE
Confidence            59999999886532       22334455554 4566776666554  33333 4455555555544

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.90  E-value=0.0026  Score=49.08  Aligned_cols=50  Identities=16%  Similarity=0.398  Sum_probs=31.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      ...+++|+||+|.|. ....+.+.+.+..-+.++.+|+.|.. +..+...++
T Consensus       101 ~~~KviiI~~ad~l~-~~a~NaLLK~LEepp~~~~fiL~t~~-~~~il~TI~  150 (162)
T PF13177_consen  101 GKYKVIIIDEADKLT-EEAQNALLKTLEEPPENTYFILITNN-PSKILPTIR  150 (162)
T ss_dssp             SSSEEEEEETGGGS--HHHHHHHHHHHHSTTTTEEEEEEES--GGGS-HHHH
T ss_pred             CCceEEEeehHhhhh-HHHHHHHHHHhcCCCCCEEEEEEECC-hHHChHHHH
Confidence            468899999999874 33566677777776666766655544 444444433

...

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.88  E-value=0.018  Score=53.72  Aligned_cols=136  Identities=13%  Similarity=0.100  Sum_probs=76.1

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc--------eEEEEECCcc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV--------SCHACIGGTI  154 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~--------~~~~~~~~~~  154 (258)
                      ..+-.++.+|-|.|||.+..+.+...+..  .+.+++|.+|...-+.+.++.++......+.        .+....++..
T Consensus       186 kq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le~lg~~~~fp~~~~iv~vkgg~E  263 (752)
T PHA03333        186 GKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVHAYQHKPWFPEEFKIVTLKGTDE  263 (752)
T ss_pred             hhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHHHhccccccCCCceEEEeeCCee
Confidence            34557888999999998876555543322  2468999999999999998887776543221        1111111110


Q ss_pred             -hHHHH-HHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC-CCccEEEEEeeC
Q psy4698         155 -VRDDI-RKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN-NDVQVILLSATM  230 (258)
Q Consensus       155 -~~~~~-~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~-~~~~~i~~SAT~  230 (258)
                       ..-.. .....| ..|.+++..       .+...-.+++++|+|||..+..    ..+..++-.+. .+.+++++|.+-
T Consensus       264 ~I~f~~p~gak~G~sti~F~Ars-------~~s~RG~~~DLLIVDEAAfI~~----~~l~aIlP~l~~~~~k~IiISS~~  332 (752)
T PHA03333        264 NLEYISDPAAKEGKTTAHFLASS-------PNAARGQNPDLVIVDEAAFVNP----GALLSVLPLMAVKGTKQIHISSPV  332 (752)
T ss_pred             EEEEecCcccccCcceeEEeccc-------CCCcCCCCCCEEEEECcccCCH----HHHHHHHHHHccCCCceEEEeCCC
Confidence             00000 000001 233343322       2223334568999999997743    33334444443 467788888876


Q ss_pred             C
Q psy4698         231 P  231 (258)
Q Consensus       231 ~  231 (258)
                      .
T Consensus       333 ~  333 (752)
T PHA03333        333 D  333 (752)
T ss_pred             C
Confidence            3

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.88  E-value=0.015  Score=53.86  Aligned_cols=125  Identities=14%  Similarity=0.229  Sum_probs=67.5

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      .++|.|++|+|||... ..+.+.+.....+.+++|+.. ..+..+....+..                           +
T Consensus       316 pL~LyG~sGsGKTHLL-~AIa~~a~~~~~g~~V~Yita-eef~~el~~al~~---------------------------~  366 (617)
T PRK14086        316 PLFIYGESGLGKTHLL-HAIGHYARRLYPGTRVRYVSS-EEFTNEFINSIRD---------------------------G  366 (617)
T ss_pred             cEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEeeH-HHHHHHHHHHHHh---------------------------c
Confidence            4899999999999754 344444444333446666653 3344433322211                           0


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCCC-CccEEEEEeeCChhHH---HHHHH
Q psy4698         166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNN-DVQVILLSATMPADVL---DVSMK  240 (258)
Q Consensus       166 ~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~~-~~~~i~~SAT~~~~~~---~~~~~  240 (258)
                            ..+.+.+.       +.++++|||||+|.+.... ....+..++..+.. +.++|+.|-..|.++.   .-++.
T Consensus       367 ------~~~~f~~~-------y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~S  433 (617)
T PRK14086        367 ------KGDSFRRR-------YREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRN  433 (617)
T ss_pred             ------cHHHHHHH-------hhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHh
Confidence                  11111111       2347899999999775432 23445555555433 4567766655565543   23444


Q ss_pred             hcCCCeEEEecC
Q psy4698         241 FMRDPIKILVKK  252 (258)
Q Consensus       241 ~~~~~~~v~~~~  252 (258)
                      -+.-..++.+..
T Consensus       434 Rf~~GLvv~I~~  445 (617)
T PRK14086        434 RFEWGLITDVQP  445 (617)
T ss_pred             hhhcCceEEcCC
Confidence            555566665543

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.88  E-value=0.011  Score=53.47  Aligned_cols=88  Identities=20%  Similarity=0.226  Sum_probs=44.0

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA--PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK  161 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (258)
                      |+-+.+.||||+|||++....+-......+. .++.++.  +.+.-+.++..   .++...++.+...............
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~-~kV~LI~~Dt~RigA~EQLr---~~AeilGVpv~~~~~~~Dl~~aL~~  331 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGA-SKVALLTTDSYRIGGHEQLR---IYGKILGVPVHAVKDAADLRLALSE  331 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCC-CeEEEEeCCccchhHHHHHH---HHHHHhCCCeeccCCchhHHHHHHh
Confidence            4568999999999998864433322222221 2444443  22333333333   3333334443333333223333334


Q ss_pred             HhcCCcEEEeChHH
Q psy4698         162 LEAGAQVVVGTPGR  175 (258)
Q Consensus       162 ~~~~~~Ilv~Tp~~  175 (258)
                      +.....++|-|+++
T Consensus       332 L~d~d~VLIDTaGr  345 (484)
T PRK06995        332 LRNKHIVLIDTIGM  345 (484)
T ss_pred             ccCCCeEEeCCCCc
Confidence            44445688889884

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.86  E-value=0.0095  Score=50.36  Aligned_cols=19  Identities=26%  Similarity=0.230  Sum_probs=16.3

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      +.++++.||+|+|||.++.
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            4579999999999998763

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.85  E-value=0.01  Score=62.27  Aligned_cols=63  Identities=29%  Similarity=0.365  Sum_probs=45.1

Q ss_pred             CCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhH---HHHHHHhhhccccceEEEEeccHHHHHHHH
Q psy4698          68 EKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFS---ISILQQVDQNIKECQALILAPTRELAQQIQ  132 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l---~~~l~~l~~~~~~~~~lil~P~~~l~~q~~  132 (258)
                      ..+++.|+.++..++.+  +-++|.|..|+|||.+..   -++.+.+..  .+.+++.++||..-+....
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHHH
Confidence            37899999999998765  457889999999998752   223333322  3457889999966665543

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=96.85  E-value=0.0055  Score=53.27  Aligned_cols=17  Identities=35%  Similarity=0.442  Sum_probs=15.1

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .+.|+.||+|+|||..+
T Consensus        49 ~SmIl~GPPG~GKTTlA   65 (436)
T COG2256          49 HSMILWGPPGTGKTTLA   65 (436)
T ss_pred             ceeEEECCCCCCHHHHH
Confidence            46899999999999876

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

Probab=96.84  E-value=0.0026  Score=53.31  Aligned_cols=58  Identities=12%  Similarity=0.265  Sum_probs=38.6

Q ss_pred             CcccccccccccCcCCCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc
Q psy4698          36 GLIETNWDHVAENFDDMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI  113 (258)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~  113 (258)
                      ++.-+..+..+.+|+++++++-+.+.... +|.                   ++|.||||||||.+ +..++..+.+..
T Consensus        95 a~vlR~Ip~~i~~~e~LglP~i~~~~~~~~~GL-------------------ILVTGpTGSGKSTT-lAamId~iN~~~  153 (353)
T COG2805          95 ALVLRLIPSKIPTLEELGLPPIVRELAESPRGL-------------------ILVTGPTGSGKSTT-LAAMIDYINKHK  153 (353)
T ss_pred             EEEEeccCccCCCHHHcCCCHHHHHHHhCCCce-------------------EEEeCCCCCcHHHH-HHHHHHHHhccC
Confidence            33444455566678888887777664321 232                   89999999999987 366666665543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.83  E-value=0.033  Score=53.61  Aligned_cols=22  Identities=36%  Similarity=0.484  Sum_probs=16.5

Q ss_pred             EEEEcccCCCcchHhHHHHHHHh
Q psy4698          87 VIAQAQSGTGKTATFSISILQQV  109 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l  109 (258)
                      ++|.|+||+|||.+.-. ++..+
T Consensus       784 LYIyG~PGTGKTATVK~-VLrEL  805 (1164)
T PTZ00112        784 LYISGMPGTGKTATVYS-VIQLL  805 (1164)
T ss_pred             EEEECCCCCCHHHHHHH-HHHHH
Confidence            46999999999998744 34444

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.80  E-value=0.012  Score=54.86  Aligned_cols=42  Identities=12%  Similarity=0.336  Sum_probs=26.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                      ...+++||||+|+|... ....+.+.+...+....+|+. +|-+
T Consensus       117 gk~KV~IIDEVh~LS~~-A~NALLKtLEEPP~~v~FILa-Ttd~  158 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTH-SFNALLKTLEEPPEHVKFLFA-TTDP  158 (702)
T ss_pred             CCcEEEEEechHhcCHH-HHHHHHHHHhcCCCCcEEEEE-ECCh
Confidence            35679999999977443 445566666665555655554 4433

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.80  E-value=0.0073  Score=57.84  Aligned_cols=70  Identities=19%  Similarity=0.252  Sum_probs=55.3

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ..+++-|.+++.+.  ..+++|.|+.|||||.+...-+...+... ....++++++-|+..+.....++.++.
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~   73 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLL   73 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHh
Confidence            35899999999653  45689999999999999877777666543 234489999999999999988887764

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.78  E-value=0.004  Score=53.47  Aligned_cols=66  Identities=23%  Similarity=0.305  Sum_probs=42.8

Q ss_pred             HHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          59 LRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        59 ~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      ++.|.+.|.  +++.|.+.+.. +..+++++|+|+||||||.. +..++..+.......+++++-.+.++
T Consensus       124 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        124 LDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            344545554  56677777765 55678999999999999954 35555544322233467777666654

>PRK12377 putative replication protein; Provisional

Probab=96.78  E-value=0.048  Score=45.12  Aligned_cols=127  Identities=12%  Similarity=0.132  Sum_probs=64.8

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      .++++.|++|+|||..+ .++...+...  +..++++ +..++...+...+.                           .
T Consensus       102 ~~l~l~G~~GtGKThLa-~AIa~~l~~~--g~~v~~i-~~~~l~~~l~~~~~---------------------------~  150 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLA-AAIGNRLLAK--GRSVIVV-TVPDVMSRLHESYD---------------------------N  150 (248)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHc--CCCeEEE-EHHHHHHHHHHHHh---------------------------c
Confidence            57999999999999765 3344444433  2234444 44455554433210                           0


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHh-CCCCccEEEEEeeCChhHHH-----H
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKH-LNNDVQVILLSATMPADVLD-----V  237 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~-l~~~~~~i~~SAT~~~~~~~-----~  237 (258)
                      + .    +...+++       .+.++++||+||++...... ....+..++.. ......+|+.|.--..++.+     +
T Consensus       151 ~-~----~~~~~l~-------~l~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl~~~~l~~~~~~ri  218 (248)
T PRK12377        151 G-Q----SGEKFLQ-------ELCKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNLNHEAMSTLLGERV  218 (248)
T ss_pred             c-c----hHHHHHH-------HhcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCCCHHHHHHHhhHHH
Confidence            0 0    1111121       23567899999996432222 22333444433 33345677766544444443     2


Q ss_pred             HHHhcC-CCeEEEecCCc
Q psy4698         238 SMKFMR-DPIKILVKKEE  254 (258)
Q Consensus       238 ~~~~~~-~~~~v~~~~~~  254 (258)
                      ...... ....|.+..++
T Consensus       219 ~dRl~~~~~~~v~~~g~s  236 (248)
T PRK12377        219 MDRMTMNGGRWVNFNWES  236 (248)
T ss_pred             HHHHhhCCCeEEEeCCcC
Confidence            222333 35667776655

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.73  E-value=0.0057  Score=52.39  Aligned_cols=40  Identities=10%  Similarity=0.225  Sum_probs=27.4

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      +.++||+||+|.+........+..++...+..+++|+.+.
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n  139 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITAN  139 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcC
Confidence            4579999999987333344556666777777777766553

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.72  E-value=0.024  Score=46.33  Aligned_cols=55  Identities=13%  Similarity=0.162  Sum_probs=34.9

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      +..|..+++.|++|+|||...+..+...+.+   +.++++++.. +...+..+.+..++
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~---g~~~~yi~~e-~~~~~~~~~~~~~g   75 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQN---GYSVSYVSTQ-LTTTEFIKQMMSLG   75 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEeCC-CCHHHHHHHHHHhC
Confidence            3456789999999999998865555544332   3468888843 33345445454443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.71  E-value=0.011  Score=54.07  Aligned_cols=39  Identities=13%  Similarity=0.327  Sum_probs=26.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ...+++|+||+|.|... ..+.+.+.+...++.+.+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~-a~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGH-SFNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHH-HHHHHHHHHhccCCCeEEEEEE
Confidence            35789999999987543 3445566666666666666644

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.70  E-value=0.028  Score=48.04  Aligned_cols=38  Identities=21%  Similarity=0.390  Sum_probs=25.0

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ..++|++||+|.+... ....+...+...+..+.+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~-~~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSD-AQQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHH-HHHHHHHHHhcCCCCCeEEEEe
Confidence            4679999999987432 3345556666666666666654

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.69  E-value=0.021  Score=51.45  Aligned_cols=124  Identities=13%  Similarity=0.307  Sum_probs=63.4

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +.+++.|++|+|||.... ++...+...  +.+++++.. ..+..+....+                           ..
T Consensus       142 npl~L~G~~G~GKTHLl~-Ai~~~l~~~--~~~v~yi~~-~~f~~~~~~~l---------------------------~~  190 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQ-AAVHALRES--GGKILYVRS-ELFTEHLVSAI---------------------------RS  190 (445)
T ss_pred             ceEEEEcCCCCCHHHHHH-HHHHHHHHc--CCCEEEeeH-HHHHHHHHHHH---------------------------hc
Confidence            458999999999997643 444444432  346777753 33333222211                           00


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cHHHHHHHHHhCC-CCccEEEEEeeCChhHHHH---HH
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLN-NDVQVILLSATMPADVLDV---SM  239 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~~~---~~  239 (258)
                      +      ..+.+...       ..+.+++++||+|.+.... ....+..++..+. ...++|+.|.+.|.++..+   +.
T Consensus       191 ~------~~~~f~~~-------~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~  257 (445)
T PRK12422        191 G------EMQRFRQF-------YRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLI  257 (445)
T ss_pred             c------hHHHHHHH-------cccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHH
Confidence            0      11111111       2356799999999875432 2344444544332 3455666555556555432   22


Q ss_pred             HhcCCCeEEEecC
Q psy4698         240 KFMRDPIKILVKK  252 (258)
Q Consensus       240 ~~~~~~~~v~~~~  252 (258)
                      ..+.-...+.+.+
T Consensus       258 SR~~~Gl~~~l~~  270 (445)
T PRK12422        258 SRFEWGIAIPLHP  270 (445)
T ss_pred             hhhcCCeEEecCC
Confidence            3344445555543

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.68  E-value=0.025  Score=50.68  Aligned_cols=52  Identities=12%  Similarity=0.280  Sum_probs=33.5

Q ss_pred             cEEEEccchhhh-ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhc
Q psy4698         191 RMFVLDEADEML-SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFM  242 (258)
Q Consensus       191 ~~lVvDE~h~~~-~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~  242 (258)
                      ++||+|.+-+.. +.....++..+.....++.-++.++|+...+..+.++.|.
T Consensus       177 DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~F~  229 (437)
T PRK00771        177 DVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKAFH  229 (437)
T ss_pred             CEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHHHH
Confidence            689999985432 2234455555655555666677888887766666666654

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=96.67  E-value=0.024  Score=44.64  Aligned_cols=105  Identities=15%  Similarity=0.144  Sum_probs=57.7

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      |+=.++.||+.||||.-.+..+-..-.   .+.++++..|...--.             +.......-|.          
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~~~~---~g~~v~vfkp~iD~R~-------------~~~~V~Sr~G~----------   57 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARRYKE---AGMKVLVFKPAIDTRY-------------GVGKVSSRIGL----------   57 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHHHHH---cCCeEEEEeccccccc-------------ccceeeeccCC----------
Confidence            344689999999999965433332222   3347888887432110             11111111111          


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHh
Q psy4698         164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH  216 (258)
Q Consensus       164 ~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~  216 (258)
                      ...-++|-....+++.+.......+ ++.|.||||+.+ +......+..+...
T Consensus        58 ~~~A~~i~~~~~i~~~i~~~~~~~~-~~~v~IDEaQF~-~~~~v~~l~~lad~  108 (201)
T COG1435          58 SSEAVVIPSDTDIFDEIAALHEKPP-VDCVLIDEAQFF-DEELVYVLNELADR  108 (201)
T ss_pred             cccceecCChHHHHHHHHhcccCCC-cCEEEEehhHhC-CHHHHHHHHHHHhh
Confidence            1124666677777777765432222 789999999954 44344444444444

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.66  E-value=0.012  Score=51.61  Aligned_cols=39  Identities=10%  Similarity=0.328  Sum_probs=24.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.+++|+||+|.+... ....+.+.+...+..+.+|+.+
T Consensus       118 ~~~kviIIDEa~~l~~~-a~naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRH-SFNALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHH-HHHHHHHHHhcCCCCeEEEEEc
Confidence            45679999999987433 2334455555555556566544

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.66  E-value=0.012  Score=54.70  Aligned_cols=40  Identities=13%  Similarity=0.335  Sum_probs=25.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      .+.+++||||+|+|... ..+.+.+.++.-+.++.+|+.|-
T Consensus       123 gr~KViIIDEah~Ls~~-AaNALLKTLEEPP~~v~FILaTt  162 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNH-AFNAMLKTLEEPPEHVKFILATT  162 (700)
T ss_pred             CCceEEEEEChHhcCHH-HHHHHHHhhccCCCCceEEEEeC
Confidence            45789999999988543 33444455555455666666553

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.65  E-value=0.0063  Score=52.22  Aligned_cols=64  Identities=17%  Similarity=0.215  Sum_probs=41.4

Q ss_pred             HHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          61 GIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        61 ~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      .+.+.|.  +++.|...+.. +..+.+++|+|+||||||... -.++..+.......+++.+=...++
T Consensus       122 ~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        122 DYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEecCCccc
Confidence            3444454  56777777655 456679999999999999864 4555555332233467776666554

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.64  E-value=0.0065  Score=53.10  Aligned_cols=25  Identities=28%  Similarity=0.530  Sum_probs=18.7

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .+++|.||+|+|||.+. ..++..+.
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l~   65 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKELE   65 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHHH
Confidence            57999999999999775 44444443

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.61  E-value=0.01  Score=54.98  Aligned_cols=47  Identities=21%  Similarity=0.367  Sum_probs=29.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      ...+++||||+|.|... -.+.+.+.+...+..+.+|+.+ |-+..+..
T Consensus       117 ~~~KVvIIDEah~Lt~~-A~NALLK~LEEpp~~~~fIL~t-te~~kll~  163 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTA-GFNALLKIVEEPPEHLIFIFAT-TEPEKVLP  163 (584)
T ss_pred             CCceEEEEECCCcCCHH-HHHHHHHHHhcCCCCeEEEEEe-CChHhhHH
Confidence            56789999999987433 4455566666655666566555 54444333

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=96.60  E-value=0.018  Score=54.11  Aligned_cols=39  Identities=13%  Similarity=0.321  Sum_probs=26.1

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.+++||||+|.+.. .....+.+.+...+..+.+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~-~A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSK-SAFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCH-HHHHHHHHHHHhCCCCcEEEEEe
Confidence            4578999999997643 23445666666656666666654

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.59  E-value=0.011  Score=55.01  Aligned_cols=47  Identities=17%  Similarity=0.316  Sum_probs=29.0

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      .+.+++||||+|.+.. +..+.+.+.+..-+..+.+|+.+ |-+..+..
T Consensus       118 ~~~KVvIIdev~~Lt~-~a~naLLk~LEepp~~~~fIl~t-~~~~kl~~  164 (576)
T PRK14965        118 SRYKIFIIDEVHMLST-NAFNALLKTLEEPPPHVKFIFAT-TEPHKVPI  164 (576)
T ss_pred             CCceEEEEEChhhCCH-HHHHHHHHHHHcCCCCeEEEEEe-CChhhhhH
Confidence            5678999999997743 34455666666655556555544 54444333

>KOG0991|consensus

Probab=96.58  E-value=0.0087  Score=48.48  Aligned_cols=43  Identities=21%  Similarity=0.352  Sum_probs=27.0

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                      .+.+.+|+||||.|.+ +....+.+.+....+.+++.+...+-.
T Consensus       112 grhKIiILDEADSMT~-gAQQAlRRtMEiyS~ttRFalaCN~s~  154 (333)
T KOG0991|consen  112 GRHKIIILDEADSMTA-GAQQALRRTMEIYSNTTRFALACNQSE  154 (333)
T ss_pred             CceeEEEeeccchhhh-HHHHHHHHHHHHHcccchhhhhhcchh
Confidence            4567999999998853 344555555555555555555444433

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.56  E-value=0.02  Score=53.69  Aligned_cols=46  Identities=13%  Similarity=0.308  Sum_probs=27.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVL  235 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~  235 (258)
                      ...+++||||+|+|... -.+.+.+.+..-+..+.+|+. .|=+..+.
T Consensus       118 g~~KV~IIDEah~Ls~~-a~NALLKtLEEPp~~v~FIL~-Tt~~~kLl  163 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLA-TTDPQKLP  163 (647)
T ss_pred             CCCEEEEEechHhCCHH-HHHHHHHHHHcCCCCeEEEEe-cCCccccc
Confidence            35789999999987433 445555566665555555554 34333333

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.56  E-value=0.042  Score=46.18  Aligned_cols=35  Identities=23%  Similarity=0.292  Sum_probs=22.8

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      +-+++.|++|+|||.+..-.+.. +..  .+.+++++.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~-l~~--~g~~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANK-LKK--QGKSVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHh--cCCEEEEEe
Confidence            45788899999999876544432 222  234676666

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.56  E-value=0.034  Score=48.67  Aligned_cols=36  Identities=19%  Similarity=0.123  Sum_probs=23.1

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ++.+++.||+|+|||....-.+.. +...  +.++.++.
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~-l~~~--g~~V~lIt  241 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQ-LLKQ--NRTVGFIT  241 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHc--CCeEEEEe
Confidence            456899999999999876544433 2222  23555555

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.56  E-value=0.021  Score=47.40  Aligned_cols=48  Identities=15%  Similarity=0.275  Sum_probs=31.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV  134 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~  134 (258)
                      +++++++.|++|.|||..+.... ..+...  + .-++++++.+++.++...
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~-~~l~~~--g-~sv~f~~~~el~~~Lk~~  151 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIG-NELLKA--G-ISVLFITAPDLLSKLKAA  151 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHH-HHHHHc--C-CeEEEEEHHHHHHHHHHH
Confidence            66799999999999998764333 334432  3 344555566666665553

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.52  E-value=0.037  Score=48.24  Aligned_cols=51  Identities=20%  Similarity=0.278  Sum_probs=31.9

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      ...+++||||+|.|.. .-.+.+.+.++.-+.++.+|++| +-+..+...++.
T Consensus       140 g~~rVviIDeAd~l~~-~aanaLLk~LEEpp~~~~fiLit-~~~~~llptIrS  190 (351)
T PRK09112        140 GNWRIVIIDPADDMNR-NAANAILKTLEEPPARALFILIS-HSSGRLLPTIRS  190 (351)
T ss_pred             CCceEEEEEchhhcCH-HHHHHHHHHHhcCCCCceEEEEE-CChhhccHHHHh
Confidence            4678999999998743 34455667777655566556655 434444444444

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.51  E-value=0.011  Score=50.89  Aligned_cols=36  Identities=17%  Similarity=0.032  Sum_probs=26.8

Q ss_pred             CcHHHHHHhhhhhcCC----cEEEEcccCCCcchHhHHHH
Q psy4698          70 PSAIQQRAIIPCVRGN----DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~----~~li~~~tGsGKT~~~l~~~  105 (258)
                      ++|+|...+..+....    ..++.||.|.||+..+...+
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A   43 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLA   43 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHH
Confidence            4678888887765442    48899999999998765443

>PHA00729 NTP-binding motif containing protein

Probab=96.51  E-value=0.016  Score=46.98  Aligned_cols=78  Identities=13%  Similarity=0.185  Sum_probs=42.1

Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-cH----HHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FK----DQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-~~----~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      +...++.+.+.+++.+....-.....+++|+||+-.-.... ..    .....+...+.+.++++.+...-+.++...++
T Consensus        58 ~~~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr  137 (226)
T PHA00729         58 VQNSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLR  137 (226)
T ss_pred             CCcEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHH
Confidence            34566666666666664321112345789999942111110 01    12223333344457777777777777777777


Q ss_pred             Hhc
Q psy4698         240 KFM  242 (258)
Q Consensus       240 ~~~  242 (258)
                      ...
T Consensus       138 ~Rg  140 (226)
T PHA00729        138 EKG  140 (226)
T ss_pred             hCC
Confidence            643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.50  E-value=0.019  Score=52.08  Aligned_cols=19  Identities=37%  Similarity=0.380  Sum_probs=15.7

Q ss_pred             cEEEEcccCCCcchHhHHH
Q psy4698          86 DVIAQAQSGTGKTATFSIS  104 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~  104 (258)
                      .+++.||+|+|||..+...
T Consensus        38 ~~Lf~GPpGtGKTTlA~~l   56 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARIL   56 (472)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3799999999999887443

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.50  E-value=0.011  Score=50.30  Aligned_cols=66  Identities=23%  Similarity=0.352  Sum_probs=41.6

Q ss_pred             HHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          59 LRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        59 ~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      ++.|.+.|.  +++.|...+.. +..+++++|+|+||||||... -.++..+.......+++++-...++
T Consensus       108 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       108 LDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhh
Confidence            344444453  44555555554 456679999999999999874 4455555432223477777766665

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

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.48  E-value=0.031  Score=44.04  Aligned_cols=40  Identities=13%  Similarity=0.300  Sum_probs=25.1

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ....+++||||+|.+... ....+...+...++..-+|+.+
T Consensus        94 ~~~~kviiide~~~l~~~-~~~~Ll~~le~~~~~~~~il~~  133 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEA-AANALLKTLEEPPPNTLFILIT  133 (188)
T ss_pred             cCCeEEEEEechhhhCHH-HHHHHHHHhcCCCCCeEEEEEE
Confidence            356789999999987433 3445556666544455455443

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.48  E-value=0.015  Score=54.30  Aligned_cols=44  Identities=14%  Similarity=0.321  Sum_probs=25.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChh
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPAD  233 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~  233 (258)
                      ..++++||||+|+|... ..+.+.+.+..-+..+.+|+.+ |-+..
T Consensus       123 g~~KV~IIDEvh~Ls~~-a~NaLLKtLEEPP~~~~fIL~T-td~~k  166 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNT-AFNAMLKTLEEPPEYLKFVLAT-TDPQK  166 (618)
T ss_pred             CCceEEEEEChhhCCHH-HHHHHHHhcccCCCCeEEEEEE-CCchh
Confidence            45789999999987543 2333444444444455555543 44433

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=96.46  E-value=0.02  Score=54.52  Aligned_cols=41  Identities=15%  Similarity=0.219  Sum_probs=24.7

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhH
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADV  234 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~  234 (258)
                      ...++|+||+|++...    ....++..+ .+.++++.++|-++..
T Consensus       109 ~~~IL~IDEIh~Ln~~----qQdaLL~~l-E~g~IiLI~aTTenp~  149 (725)
T PRK13341        109 KRTILFIDEVHRFNKA----QQDALLPWV-ENGTITLIGATTENPY  149 (725)
T ss_pred             CceEEEEeChhhCCHH----HHHHHHHHh-cCceEEEEEecCCChH
Confidence            3458999999987322    222333333 3456788888865443

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=96.45  E-value=0.068  Score=48.87  Aligned_cols=20  Identities=25%  Similarity=0.316  Sum_probs=16.6

Q ss_pred             cEEEEcccCCCcchHhHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~  105 (258)
                      .++++||.|+|||.++.+.+
T Consensus        45 a~Lf~Gp~G~GKTT~ArilA   64 (507)
T PRK06645         45 GYLLTGIRGVGKTTSARIIA   64 (507)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            58999999999999874433

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

Probab=96.43  E-value=0.013  Score=50.20  Aligned_cols=69  Identities=16%  Similarity=0.220  Sum_probs=45.4

Q ss_pred             HHHHHHCCCCCCcHHHHHHhhhhhcCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          59 LRGIYAYGFEKPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        59 ~~~l~~~~~~~~~~~Q~~~~~~l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      +..|-+  +..+++-|-..+..+..++ |++++|.||||||+.. -.+...+....   |+|.+--+-+|--+.-.
T Consensus       149 l~dli~--~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlL-Nal~~~i~~~e---RvItiEDtaELql~~ph  218 (355)
T COG4962         149 LLDLII--FGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLL-NALSGFIDSDE---RVITIEDTAELQLAHPH  218 (355)
T ss_pred             HHHHHH--cCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHH-HHHHhcCCCcc---cEEEEeehhhhccCCCc
Confidence            334443  4478888888887776665 9999999999999852 22222222222   78888777776554433

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.41  E-value=0.028  Score=50.62  Aligned_cols=89  Identities=19%  Similarity=0.212  Sum_probs=53.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|.-+++.|++|+|||...+..+.....   .+.+++|+.- .+...|....+.+++-..+                   
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a~---~g~~vlYvs~-Ees~~qi~~ra~rlg~~~~-------------------  135 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLAA---AGGKVLYVSG-EESASQIKLRAERLGLPSD-------------------  135 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEEc-cccHHHHHHHHHHcCCChh-------------------
Confidence            3456899999999999876555544332   2347888875 3445566665655542111                   


Q ss_pred             hcCCcEEEe---ChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         163 EAGAQVVVG---TPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       163 ~~~~~Ilv~---Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                          ++.+.   ..+.+.+.+..     .+.++||+|+++.+..
T Consensus       136 ----~l~~~~e~~l~~i~~~i~~-----~~~~lVVIDSIq~l~~  170 (446)
T PRK11823        136 ----NLYLLAETNLEAILATIEE-----EKPDLVVIDSIQTMYS  170 (446)
T ss_pred             ----cEEEeCCCCHHHHHHHHHh-----hCCCEEEEechhhhcc
Confidence                02222   23334444432     2467999999997754

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.39  E-value=0.021  Score=53.13  Aligned_cols=20  Identities=25%  Similarity=0.275  Sum_probs=16.6

Q ss_pred             cEEEEcccCCCcchHhHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~  105 (258)
                      .+++.||.|+|||.++...+
T Consensus        40 a~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         40 AYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            48899999999999875444

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.39  E-value=0.018  Score=52.73  Aligned_cols=40  Identities=15%  Similarity=0.324  Sum_probs=27.5

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ....+++|+||+|.|.. .....+.+.+...++.+.+|+.+
T Consensus       115 ~~~~KVvIIDEad~Lt~-~A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        115 MARFKIFIIDEVHMLTK-EAFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             cCCeEEEEEECcccCCH-HHHHHHHHHHhhcCCceEEEEEE
Confidence            35678999999998743 34455566666666667666655

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.38  E-value=0.027  Score=48.31  Aligned_cols=38  Identities=29%  Similarity=0.220  Sum_probs=28.2

Q ss_pred             CCCcHHHHHHhhhhh----cCC---cEEEEcccCCCcchHhHHHH
Q psy4698          68 EKPSAIQQRAIIPCV----RGN---DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~----~g~---~~li~~~tGsGKT~~~l~~~  105 (258)
                      ..++|+|..++..+.    .|+   -+++.||.|.||+..+...+
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA   47 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALA   47 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHH
Confidence            357788888887754    343   48999999999998765443

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.38  E-value=0.045  Score=48.77  Aligned_cols=56  Identities=14%  Similarity=0.087  Sum_probs=30.7

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      -++++|++|+|||++..--+. .+..  .+.++++++-  .|.-+.++   ++.++...++.+.
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~-~l~~--~G~kV~lV~~D~~R~aA~eQ---Lk~~a~~~~vp~~  159 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAY-YYQR--KGFKPCLVCADTFRAGAFDQ---LKQNATKARIPFY  159 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHH--CCCCEEEEcCcccchhHHHH---HHHHhhccCCeEE
Confidence            478999999999977643332 2222  2346666663  44433333   3334444445443

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.37  E-value=0.055  Score=49.82  Aligned_cols=39  Identities=13%  Similarity=0.290  Sum_probs=26.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.+++||||+|.+... ..+.+.+.+...+..+.+|+.+
T Consensus       118 g~~kViIIDEa~~ls~~-a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        118 GRYKVYLIDEVHMLSKQ-SFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CCcEEEEEechhhccHH-HHHHHHHHHhcCCCCceEEEEE
Confidence            45679999999987433 4455666666655666666654

>PTZ00293 thymidine kinase; Provisional

Probab=96.37  E-value=0.034  Score=44.62  Aligned_cols=39  Identities=13%  Similarity=0.164  Sum_probs=25.8

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      |+=-++.||++||||.-.+..+.. ...  .+.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~-y~~--ag~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKR-FTY--SEKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHH-HHH--cCCceEEEEecc
Confidence            455689999999999765444333 322  234688888853

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=96.36  E-value=0.021  Score=46.38  Aligned_cols=54  Identities=17%  Similarity=0.257  Sum_probs=35.1

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .|..+++.|++|+|||...+..+.+.+.+.  +-+++|++- .+-..+..+.++.++
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs~-ee~~~~l~~~~~s~g   71 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVSF-EEPPEELIENMKSFG   71 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEES-SS-HHHHHHHHHTTT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEEe-cCCHHHHHHHHHHcC
Confidence            346799999999999988877777766662  125888873 333355555555443

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.36  E-value=0.013  Score=53.48  Aligned_cols=86  Identities=22%  Similarity=0.209  Sum_probs=56.5

Q ss_pred             HHHHHHHHHCCCCCCcH----HHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEeccHH
Q psy4698          56 EELLRGIYAYGFEKPSA----IQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPTRE  126 (258)
Q Consensus        56 ~~l~~~l~~~~~~~~~~----~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~~~  126 (258)
                      +-+...|.+.--.+++.    +|.+-=+.+...  +-++|.|..|||||.+++--+...++.-   -....++++.|.+.
T Consensus       192 EvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~v  271 (747)
T COG3973         192 EVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRV  271 (747)
T ss_pred             HHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHH
Confidence            34445665543333332    344444444433  4589999999999999876555555432   12234999999999


Q ss_pred             HHHHHHHHHHHhcCC
Q psy4698         127 LAQQIQKVVIALGDF  141 (258)
Q Consensus       127 l~~q~~~~~~~~~~~  141 (258)
                      ....+.+++..+|..
T Consensus       272 FleYis~VLPeLGe~  286 (747)
T COG3973         272 FLEYISRVLPELGEE  286 (747)
T ss_pred             HHHHHHHhchhhccC
Confidence            999999999888753

>PRK13342 recombination factor protein RarA; Reviewed

Probab=96.36  E-value=0.039  Score=49.24  Aligned_cols=18  Identities=33%  Similarity=0.409  Sum_probs=15.3

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|+|||..+.
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            368999999999998763

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=96.35  E-value=0.044  Score=43.28  Aligned_cols=140  Identities=16%  Similarity=0.209  Sum_probs=76.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH-HHHHHHHHHhcCCCCceEEEEECCcc-----hH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA-QQIQKVVIALGDFMSVSCHACIGGTI-----VR  156 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~-~q~~~~~~~~~~~~~~~~~~~~~~~~-----~~  156 (258)
                      ....+++.+++|.|||.+++--++..+..+   .+++++.=.+.-. .--...++.+.   ++....+-.+..     ..
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G---~~V~ivQFlKg~~~~GE~~~l~~l~---~v~~~~~g~~~~~~~~~~~   94 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGHG---KKVGVVQFIKGAWSTGERNLLEFGG---GVEFHVMGTGFTWETQDRE   94 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHCC---CeEEEEEEecCCCccCHHHHHhcCC---CcEEEECCCCCcccCCCcH
Confidence            456799999999999999876666655544   3566665222110 01112222221   222222111110     00


Q ss_pred             HHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc--HHHHHHHHHhCCCCccEEEEEeeCChhH
Q psy4698         157 DDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF--KDQIYDVFKHLNNDVQVILLSATMPADV  234 (258)
Q Consensus       157 ~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~--~~~~~~~~~~l~~~~~~i~~SAT~~~~~  234 (258)
                      ....           .....+..... .+.-..+++||+||+-..++.++  ...+..++...|...-+|+..-..|.++
T Consensus        95 e~~~-----------~~~~~~~~a~~-~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~L  162 (191)
T PRK05986         95 RDIA-----------AAREGWEEAKR-MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPREL  162 (191)
T ss_pred             HHHH-----------HHHHHHHHHHH-HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHH
Confidence            0000           11111222111 12235688999999998877764  4677788888777777777777778877


Q ss_pred             HHHHHH
Q psy4698         235 LDVSMK  240 (258)
Q Consensus       235 ~~~~~~  240 (258)
                      .+.+..
T Consensus       163 ie~ADl  168 (191)
T PRK05986        163 IEAADL  168 (191)
T ss_pred             HHhCch
Confidence            766543

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.33  E-value=0.039  Score=45.27  Aligned_cols=40  Identities=20%  Similarity=0.137  Sum_probs=29.2

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ..|.-++|.|++|+|||...+.-+.+.+.+.  +.+++|++.
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~   50 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSL   50 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeC
Confidence            4566799999999999987765565555542  336888884

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.32  E-value=0.037  Score=51.64  Aligned_cols=40  Identities=10%  Similarity=0.306  Sum_probs=27.2

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ....+++||||+|.+... ..+.+.+.+...+..+.+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~~-a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTA-AFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCHH-HHHHHHHHHHhCCCCeEEEEEe
Confidence            456789999999987432 3445555666666667666655

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.31  E-value=0.0073  Score=55.89  Aligned_cols=126  Identities=15%  Similarity=0.130  Sum_probs=74.8

Q ss_pred             CCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHH-HHHHHhcCCCCce
Q psy4698          69 KPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ-KVVIALGDFMSVS  145 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~-~~~~~~~~~~~~~  145 (258)
                      ..+|||.+.++.+...  +.+++..++.+|||.+.+..+...+...  ...++++.||...+.... ..+..+......-
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~--P~~~l~v~Pt~~~a~~~~~~rl~Pmi~~sp~l   93 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQD--PGPMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeC--CCCEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            5689999999887655  5799999999999997655554444443  347999999999999987 4454444322211


Q ss_pred             EEEEEC---C-cchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         146 CHACIG---G-TIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       146 ~~~~~~---~-~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      -..+..   . .......+... +..+.+....+-      ..+.-..++++++||+|.+..
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S~------~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANSP------SNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             HHHhCchhhcccCCchhheecC-CCEEEEEeCCCC------cccccCCcCEEEEechhhccc
Confidence            011111   0 11111111222 334444432111      113344678999999998743

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.31  E-value=0.027  Score=46.30  Aligned_cols=53  Identities=19%  Similarity=0.237  Sum_probs=37.0

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .|..++|.|++|+|||...+..+...+.+   +.+++|++- .+...+..+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs~-ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVAL-EEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEEe-eCCHHHHHHHHHHhC
Confidence            45679999999999998776666665533   336888873 445556666666654

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=96.30  E-value=0.059  Score=47.15  Aligned_cols=45  Identities=20%  Similarity=0.297  Sum_probs=29.8

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhC-CCCccEEEEEeeCChhH
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHL-NNDVQVILLSATMPADV  234 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~~~~~~i~~SAT~~~~~  234 (258)
                      +..+|++||.| +.+-.-.-.+.+++..+ ....-+|..|.+.|.++
T Consensus       127 ~~~lLcfDEF~-V~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  127 ESRLLCFDEFQ-VTDIADAMILKRLFEALFKRGVVLVATSNRPPEDL  172 (362)
T ss_pred             cCCEEEEeeee-ccchhHHHHHHHHHHHHHHCCCEEEecCCCChHHH
Confidence            45689999999 33444344444455443 45677888888888764

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=96.30  E-value=0.16  Score=43.93  Aligned_cols=145  Identities=16%  Similarity=0.160  Sum_probs=63.6

Q ss_pred             EEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH-HHH---HHHHHHHhcCC-CCceEEEEECCcchHHHHHHH
Q psy4698          88 IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL-AQQ---IQKVVIALGDF-MSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        88 li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l-~~q---~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      ++.++.|+|||.+....++..+.......++++. ++... ...   .......+... ..............      +
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~   73 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDRKII------L   73 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSEEE------E
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCCcEE------e
Confidence            4778999999998877777766655433355555 55444 443   23334444333 22222211111111      1


Q ss_pred             hcCCcEEEeChHHH--HHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC--ChhHHHHH
Q psy4698         163 EAGAQVVVGTPGRV--FDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM--PADVLDVS  238 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l--~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~--~~~~~~~~  238 (258)
                      .+|..|.+.+.+.-  ..-+..     ..++++++||+-.+.+..+...+...+... .....++.|.|.  ......+.
T Consensus        74 ~nG~~i~~~~~~~~~~~~~~~G-----~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~-~~~~~~~~s~p~~~~~~~~~~~  147 (384)
T PF03237_consen   74 PNGSRIQFRGADSPDSGDNIRG-----FEYDLIIIDEAAKVPDDAFSELIRRLRATW-GGSIRMYISTPPNPGGWFYEIF  147 (384)
T ss_dssp             TTS-EEEEES-----SHHHHHT-----S--SEEEEESGGGSTTHHHHHHHHHHHHCS-TT--EEEEEE---SSSHHHHHH
T ss_pred             cCceEEEEeccccccccccccc-----cccceeeeeecccCchHHHHHHHHhhhhcc-cCcceEEeecCCCCCCceeeee
Confidence            56666777764321  112221     467799999988664443333333333322 222222444432  33455555


Q ss_pred             HHhcCCC
Q psy4698         239 MKFMRDP  245 (258)
Q Consensus       239 ~~~~~~~  245 (258)
                      .....+.
T Consensus       148 ~~~~~~~  154 (384)
T PF03237_consen  148 QRNLDDD  154 (384)
T ss_dssp             HHHHCTS
T ss_pred             ehhhcCC
Confidence            5555443

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=96.30  E-value=0.03  Score=50.75  Aligned_cols=148  Identities=12%  Similarity=0.061  Sum_probs=83.1

Q ss_pred             CCcHHHHHHhhhhhc------C----CcEEEEcccCCCcchHhH-HHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVR------G----NDVIAQAQSGTGKTATFS-ISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~------g----~~~li~~~tGsGKT~~~l-~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      .+-|+|..++-.+..      |    +.++|..|-+-|||..+. +.+...+.....+.+..|++|+.+-+.+.+..++.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F~~ar~  140 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSFNPARD  140 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhhHHHHH
Confidence            578999999977651      1    247888899999996553 33444444445566899999999999999988877


Q ss_pred             hcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC--CCCCCccEEEEccchhhhccCcHHHHHHHHH
Q psy4698         138 LGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA--LSTKQIRMFVLDEADEMLSRGFKDQIYDVFK  215 (258)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~  215 (258)
                      ......          ........-.....|.+.--....+.+..+.  ..-.+..+.|+||.|...+.+  ..+..+..
T Consensus       141 mv~~~~----------~l~~~~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~--~~~~~~~~  208 (546)
T COG4626         141 MVKRDD----------DLRDLCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE--DMYSEAKG  208 (546)
T ss_pred             HHHhCc----------chhhhhccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH--HHHHHHHh
Confidence            543322          0000000000111122322223333443322  233456799999999764441  22333332


Q ss_pred             hC--CCCccEEEEEe
Q psy4698         216 HL--NNDVQVILLSA  228 (258)
Q Consensus       216 ~l--~~~~~~i~~SA  228 (258)
                      -+  +++.++++.|-
T Consensus       209 g~~ar~~~l~~~ITT  223 (546)
T COG4626         209 GLGARPEGLVVYITT  223 (546)
T ss_pred             hhccCcCceEEEEec
Confidence            22  24556666554

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.28  E-value=0.0076  Score=50.80  Aligned_cols=38  Identities=21%  Similarity=0.507  Sum_probs=25.5

Q ss_pred             CccEEEEccchhhhccC--cHHHHHHHHHhCCCCc--cEEEE
Q psy4698         189 QIRMFVLDEADEMLSRG--FKDQIYDVFKHLNNDV--QVILL  226 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~--~~~~~~~~~~~l~~~~--~~i~~  226 (258)
                      +++++||||+|+++...  ....+...++.+.+..  .+|++
T Consensus       145 ~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~v  186 (302)
T PF05621_consen  145 GVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGV  186 (302)
T ss_pred             CCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEe
Confidence            57799999999987654  3345556677776543  44443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.27  E-value=0.057  Score=47.71  Aligned_cols=64  Identities=11%  Similarity=0.258  Sum_probs=40.3

Q ss_pred             CccEEEEccchhhhcc-CcHHHHHHHHHhCCC-CccEEEEEeeCChhHHH---HHHHhcCCCeEEEecC
Q psy4698         189 QIRMFVLDEADEMLSR-GFKDQIYDVFKHLNN-DVQVILLSATMPADVLD---VSMKFMRDPIKILVKK  252 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~-~~~~i~~SAT~~~~~~~---~~~~~~~~~~~v~~~~  252 (258)
                      +++++++|+++.+... .....+..++..+.. ..|+|+.|...|.++..   -++.-+.-..++.+.+
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~  243 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEP  243 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCC
Confidence            5789999999987544 234555556666543 34888888777877553   3344444445555543

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=96.27  E-value=0.028  Score=46.79  Aligned_cols=141  Identities=18%  Similarity=0.190  Sum_probs=72.2

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH--
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR--  160 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  160 (258)
                      .|.-++|.|.+|.|||..++-.+.+.+...+  ..++|++.--. ..+...++-.........  ....+.....++.  
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~--~~vly~SlEm~-~~~l~~R~la~~s~v~~~--~i~~g~l~~~e~~~~   92 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGG--YPVLYFSLEMS-EEELAARLLARLSGVPYN--KIRSGDLSDEEFERL   92 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTS--SEEEEEESSS--HHHHHHHHHHHHHTSTHH--HHHCCGCHHHHHHHH
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcC--CeEEEEcCCCC-HHHHHHHHHHHhhcchhh--hhhccccCHHHHHHH
Confidence            4456899999999999988777776665532  46888885322 122222221111111111  0111111111111  


Q ss_pred             -----HHhcCCcEEE-e----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHhCC-----CCc
Q psy4698         161 -----KLEAGAQVVV-G----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKHLN-----NDV  221 (258)
Q Consensus       161 -----~~~~~~~Ilv-~----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~l~-----~~~  221 (258)
                           .+.. ..++| .    |++.+...+..-.....++++||||-+|.+...    +....+..+.+.++     .++
T Consensus        93 ~~~~~~l~~-~~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i  171 (259)
T PF03796_consen   93 QAAAEKLSD-LPLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNI  171 (259)
T ss_dssp             HHHHHHHHT-SEEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHhh-CcEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCC
Confidence                 2222 34554 3    455555555432112267889999999977542    34455555544432     256


Q ss_pred             cEEEEEee
Q psy4698         222 QVILLSAT  229 (258)
Q Consensus       222 ~~i~~SAT  229 (258)
                      .++.+|..
T Consensus       172 ~vi~~sQl  179 (259)
T PF03796_consen  172 PVIALSQL  179 (259)
T ss_dssp             EEEEEEEB
T ss_pred             eEEEcccc
Confidence            66666654

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.23  E-value=0.029  Score=51.59  Aligned_cols=39  Identities=13%  Similarity=0.330  Sum_probs=26.0

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.+++||||+|.|... -.+.+.+.+...+..+.+|+.+
T Consensus       118 ~~~kVvIIDEad~ls~~-a~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKS-AFNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHH-HHHHHHHHHhCCCCCEEEEEEe
Confidence            45789999999987543 3344555666655666666655

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.23  E-value=0.0083  Score=53.78  Aligned_cols=42  Identities=19%  Similarity=0.376  Sum_probs=30.4

Q ss_pred             CcHHHHHHhhhhhcCCc--EEEEcccCCCcchHhHHHHHHHhhhc
Q psy4698          70 PSAIQQRAIIPCVRGND--VIAQAQSGTGKTATFSISILQQVDQN  112 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~--~li~~~tGsGKT~~~l~~~l~~l~~~  112 (258)
                      +.+.|...+..+.+...  +++.||||||||++. ..++..+...
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~~  285 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNTP  285 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcCC
Confidence            36677777777666654  899999999999874 5555555544

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.22  E-value=0.022  Score=49.91  Aligned_cols=41  Identities=22%  Similarity=0.308  Sum_probs=26.8

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ...+++||||+|.+. ....+.+.+.++.-+..+.+|++|..
T Consensus       140 ~~~kVviIDead~m~-~~aanaLLK~LEepp~~~~~IL~t~~  180 (365)
T PRK07471        140 GGWRVVIVDTADEMN-ANAANALLKVLEEPPARSLFLLVSHA  180 (365)
T ss_pred             CCCEEEEEechHhcC-HHHHHHHHHHHhcCCCCeEEEEEECC
Confidence            467799999999873 33455666666665555555554443

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.20  E-value=0.042  Score=50.95  Aligned_cols=20  Identities=30%  Similarity=0.346  Sum_probs=16.3

Q ss_pred             cEEEEcccCCCcchHhHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~  105 (258)
                      .++++||.|+|||.++-..+
T Consensus        40 ayLf~Gp~GtGKTt~Ak~lA   59 (559)
T PRK05563         40 AYLFSGPRGTGKTSAAKIFA   59 (559)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            47899999999998875443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.20  E-value=0.018  Score=52.62  Aligned_cols=17  Identities=29%  Similarity=0.432  Sum_probs=14.8

Q ss_pred             EEEEcccCCCcchHhHH
Q psy4698          87 VIAQAQSGTGKTATFSI  103 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~  103 (258)
                      +++.||.|+|||.++..
T Consensus        39 ~Lf~GppGtGKTTlA~~   55 (504)
T PRK14963         39 YLFSGPRGVGKTTTARL   55 (504)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            59999999999998743

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.19  E-value=0.05  Score=41.74  Aligned_cols=53  Identities=19%  Similarity=0.419  Sum_probs=40.7

Q ss_pred             CCCccEEEEccchhhhccC--cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         187 TKQIRMFVLDEADEMLSRG--FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~--~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      ...++++|+||+=.....+  -...+..+++..+...-+|+.+-..|+++.+.+.
T Consensus        93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            4568999999998776555  3467778888887777788888888888777653

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.17  E-value=0.015  Score=49.05  Aligned_cols=22  Identities=27%  Similarity=0.389  Sum_probs=17.0

Q ss_pred             CCcEEEEcccCCCcchHhHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~  105 (258)
                      ++.+++.||||+|||.+....+
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa  215 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLA  215 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3468999999999998764333

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=96.16  E-value=0.14  Score=47.31  Aligned_cols=128  Identities=17%  Similarity=0.193  Sum_probs=79.5

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh-cCCCCceEEEEECCcchHHHHHHHh
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL-GDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      |-.++--|--.|||.. +.|++..+.....+.++-|++.-+..++-.++++... .++.+.......            +
T Consensus       203 kaTVFLVPRRHGKTWf-~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~------------k  269 (668)
T PHA03372        203 KATVFLVPRRHGKTWF-IIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIEN------------K  269 (668)
T ss_pred             cceEEEecccCCceeh-HHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeee------------c
Confidence            3456777999999975 5788888888778889999999988887777665432 122221111000            1


Q ss_pred             cCCcEEEeChHH-----HHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC-CCccEEEEEeeC
Q psy4698         164 AGAQVVVGTPGR-----VFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN-NDVQVILLSATM  230 (258)
Q Consensus       164 ~~~~Ilv~Tp~~-----l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~-~~~~~i~~SAT~  230 (258)
                      + --|.+.-|+.     +......+.++-.++.+++|||||-+    ....+..++-.+. +++++|..|.|-
T Consensus       270 ~-~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI----~~~a~~tilgfm~q~~~KiIfISS~N  337 (668)
T PHA03372        270 D-NVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFI----KKDAFNTILGFLAQNTTKIIFISSTN  337 (668)
T ss_pred             C-cEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhcc----CHHHHHHhhhhhcccCceEEEEeCCC
Confidence            1 2355544432     11112335566778899999999965    2334444554443 567888888774

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=96.12  E-value=0.064  Score=50.14  Aligned_cols=110  Identities=23%  Similarity=0.356  Sum_probs=68.7

Q ss_pred             CCcHHHHHHhhhhh--------cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          69 KPSAIQQRAIIPCV--------RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~--------~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .+-.+-.+.++.+.        .|.=+++.||+|-|||...                           ..+++.+   ++
T Consensus       327 GLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLg---------------------------kSIA~al---~R  376 (782)
T COG0466         327 GLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLG---------------------------KSIAKAL---GR  376 (782)
T ss_pred             CchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHH---------------------------HHHHHHh---CC
Confidence            45555555555532        3344899999999999753                           1222211   11


Q ss_pred             CCCceEEEEECCcchHHHHHHHhcCCcEEEeC-hHHHHHHHhcCC-CCCCCccEEEEccchhhhccCcHHHHHHHHHhCC
Q psy4698         141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGT-PGRVFDMISRGA-LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN  218 (258)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T-p~~l~~~l~~~~-~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~  218 (258)
                         -.+....||.....+.+   ..-+-+||. |+++.+-++... .+.    ++++||+|-|..+..+..-.+++.-|.
T Consensus       377 ---kfvR~sLGGvrDEAEIR---GHRRTYIGamPGrIiQ~mkka~~~NP----v~LLDEIDKm~ss~rGDPaSALLEVLD  446 (782)
T COG0466         377 ---KFVRISLGGVRDEAEIR---GHRRTYIGAMPGKIIQGMKKAGVKNP----VFLLDEIDKMGSSFRGDPASALLEVLD  446 (782)
T ss_pred             ---CEEEEecCccccHHHhc---cccccccccCChHHHHHHHHhCCcCC----eEEeechhhccCCCCCChHHHHHhhcC
Confidence               12334456655544443   334567775 999999887632 222    899999999987777777777777764

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.11  E-value=0.03  Score=52.84  Aligned_cols=67  Identities=27%  Similarity=0.356  Sum_probs=51.4

Q ss_pred             CCcHHHHHHhhhhhcC-----CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          69 KPSAIQQRAIIPCVRG-----NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g-----~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      .|+-.|..++..+.++     +..++.|.||||||+... .++..+     +..+||++|+..++.|++..++.+...
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a-~~~~~~-----~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA-NVIAQV-----NRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHH-HHHHHh-----CCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            6788888888776544     256799999999998753 222221     235999999999999999999998754

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

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.10  E-value=0.063  Score=47.16  Aligned_cols=89  Identities=15%  Similarity=0.194  Sum_probs=52.0

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|.-+++.|++|+|||...+..+......   +.+++|+.-. +...|....+.+++-..+                   
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~~a~~---g~~VlYvs~E-Es~~qi~~Ra~rlg~~~~-------------------  137 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAARLAKR---GGKVLYVSGE-ESPEQIKLRADRLGISTE-------------------  137 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEECC-cCHHHHHHHHHHcCCCcc-------------------
Confidence            35668999999999998765554433322   2478888754 334555555555432110                   


Q ss_pred             hcCCcEEEe---ChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         163 EAGAQVVVG---TPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       163 ~~~~~Ilv~---Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                          ++.+.   ..+.+.+.+..     .+.++||||+++.+..
T Consensus       138 ----~l~l~~e~~le~I~~~i~~-----~~~~lVVIDSIq~l~~  172 (372)
T cd01121         138 ----NLYLLAETNLEDILASIEE-----LKPDLVIIDSIQTVYS  172 (372)
T ss_pred             ----cEEEEccCcHHHHHHHHHh-----cCCcEEEEcchHHhhc
Confidence                11111   23444444433     2467999999998753

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=96.09  E-value=0.034  Score=49.78  Aligned_cols=143  Identities=17%  Similarity=0.212  Sum_probs=70.0

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      +..|.-+++.|++|+|||...+--+.+.....  +..++|++. -.-..++..++-....  ++.......+.....++.
T Consensus       191 ~~~g~liviag~pg~GKT~~al~ia~~~a~~~--g~~v~~fSl-Em~~~~l~~Rl~~~~~--~v~~~~~~~~~l~~~~~~  265 (421)
T TIGR03600       191 LVKGDLIVIGARPSMGKTTLALNIAENVALRE--GKPVLFFSL-EMSAEQLGERLLASKS--GINTGNIRTGRFNDSDFN  265 (421)
T ss_pred             CCCCceEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEEC-CCCHHHHHHHHHHHHc--CCCHHHHhcCCCCHHHHH
Confidence            34456799999999999987765554443222  335777763 2234444433322111  121111111111111111


Q ss_pred             -------HHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhc---cCcHHHHHHHHHhCC-----CC
Q psy4698         161 -------KLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLS---RGFKDQIYDVFKHLN-----ND  220 (258)
Q Consensus       161 -------~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~---~~~~~~~~~~~~~l~-----~~  220 (258)
                             .+. +..+.|.     |++.+...+++-.....++++||||=.+.+..   .+....+..+.+.++     .+
T Consensus       266 ~~~~~~~~l~-~~~l~i~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~~~~~~~~~~~~~i~~~Lk~lAke~~  344 (421)
T TIGR03600       266 RLLNAVDRLS-EKDLYIDDTGGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELD  344 (421)
T ss_pred             HHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence                   222 2356664     44445444432111122588999999997753   122333334433332     25


Q ss_pred             ccEEEEEee
Q psy4698         221 VQVILLSAT  229 (258)
Q Consensus       221 ~~~i~~SAT  229 (258)
                      +.+|++|..
T Consensus       345 i~Vi~lsQl  353 (421)
T TIGR03600       345 VPVVLLAQL  353 (421)
T ss_pred             CcEEEeccc
Confidence            667776653

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>KOG0741|consensus

Probab=96.09  E-value=0.051  Score=49.15  Aligned_cols=53  Identities=21%  Similarity=0.149  Sum_probs=30.4

Q ss_pred             cCcCCCC---CCHHHHHHHHHCCCCCCcHHHHHHhhh--hhcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDME---LSEELLRGIYAYGFEKPSAIQQRAIIP--CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~---~~~~l~~~l~~~~~~~~~~~Q~~~~~~--l~~g~~~li~~~tGsGKT~~~  101 (258)
                      -.|+++|   ++.+.-+.++...-.+.+|  -+.+..  +.+-+.+++.||+|+|||+.+
T Consensus       216 f~Fe~mGIGGLd~EFs~IFRRAFAsRvFp--p~vie~lGi~HVKGiLLyGPPGTGKTLiA  273 (744)
T KOG0741|consen  216 FNFESMGIGGLDKEFSDIFRRAFASRVFP--PEVIEQLGIKHVKGILLYGPPGTGKTLIA  273 (744)
T ss_pred             CChhhcccccchHHHHHHHHHHHHhhcCC--HHHHHHcCccceeeEEEECCCCCChhHHH
Confidence            3677775   5565555554322111111  112222  234467999999999999976

>PRK06904 replicative DNA helicase; Validated

Probab=96.08  E-value=0.084  Score=47.95  Aligned_cols=149  Identities=17%  Similarity=0.142  Sum_probs=74.3

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      +..|.-+++.|.+|.|||..++-.+.+.....  +..++|++. -....|+..++-........... ..+..-...++.
T Consensus       218 l~~G~LiiIaarPg~GKTafalnia~~~a~~~--g~~Vl~fSl-EMs~~ql~~Rlla~~s~v~~~~i-~~g~~l~~~e~~  293 (472)
T PRK06904        218 LQPSDLIIVAARPSMGKTTFAMNLCENAAMAS--EKPVLVFSL-EMPAEQIMMRMLASLSRVDQTKI-RTGQNLDQQDWA  293 (472)
T ss_pred             cCCCcEEEEEeCCCCChHHHHHHHHHHHHHhc--CCeEEEEec-cCCHHHHHHHHHHhhCCCCHHHh-ccCCCCCHHHHH
Confidence            33445689999999999987654444443332  235767654 34455555544332222221111 112111122221


Q ss_pred             -------HHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhccC----cHHHHHHHHHhCC-----C
Q psy4698         161 -------KLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG----FKDQIYDVFKHLN-----N  219 (258)
Q Consensus       161 -------~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~----~~~~~~~~~~~l~-----~  219 (258)
                             .+....++.|.     |+..+...+++-...-.++++||||-.+.+...+    ....+..+.+.++     -
T Consensus       294 ~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel  373 (472)
T PRK06904        294 KISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKEL  373 (472)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHh
Confidence                   22223446663     5555554443211111358899999999774322    2334444444442     2


Q ss_pred             CccEEEEEeeCChhH
Q psy4698         220 DVQVILLSATMPADV  234 (258)
Q Consensus       220 ~~~~i~~SAT~~~~~  234 (258)
                      ++.+|++| -+++.+
T Consensus       374 ~ipVi~ls-QLnR~~  387 (472)
T PRK06904        374 KVPVVALS-QLNRTL  387 (472)
T ss_pred             CCeEEEEE-ecCchh
Confidence            67777776 445443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.05  E-value=0.037  Score=51.34  Aligned_cols=46  Identities=13%  Similarity=0.227  Sum_probs=26.8

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVL  235 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~  235 (258)
                      .+.+++|+||+|.|... ....+.+.+...+..+-+|+++ +-+..+.
T Consensus       118 ~~~KVIIIDEad~Lt~~-A~NaLLKtLEEPp~~tvfIL~T-t~~~KLl  163 (605)
T PRK05896        118 FKYKVYIIDEAHMLSTS-AWNALLKTLEEPPKHVVFIFAT-TEFQKIP  163 (605)
T ss_pred             CCcEEEEEechHhCCHH-HHHHHHHHHHhCCCcEEEEEEC-CChHhhh
Confidence            35678999999987432 3445555555555555444444 4444443

>KOG2028|consensus

Probab=96.03  E-value=0.024  Score=48.96  Aligned_cols=55  Identities=16%  Similarity=0.268  Sum_probs=30.9

Q ss_pred             ccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH-hcCCCeEEE
Q psy4698         190 IRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK-FMRDPIKIL  249 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~-~~~~~~~v~  249 (258)
                      -..+.+||+|++-..    +-..++-.. .+--+++..||-.+.--++... ..+|+|+|.
T Consensus       223 kTilFiDEiHRFNks----QQD~fLP~V-E~G~I~lIGATTENPSFqln~aLlSRC~VfvL  278 (554)
T KOG2028|consen  223 KTILFIDEIHRFNKS----QQDTFLPHV-ENGDITLIGATTENPSFQLNAALLSRCRVFVL  278 (554)
T ss_pred             eeEEEeHHhhhhhhh----hhhccccee-ccCceEEEecccCCCccchhHHHHhccceeEe
Confidence            347999999986322    111222222 2345777888865544444444 344777764

>PRK08840 replicative DNA helicase; Provisional

Probab=96.02  E-value=0.098  Score=47.38  Aligned_cols=147  Identities=18%  Similarity=0.143  Sum_probs=72.4

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      +..|.-+++.|.+|.|||..++-.+.+.....  +..++|++.- .-..|+..++-.......  ...+..+.-...++.
T Consensus       214 ~~~g~LiviaarPg~GKTafalnia~~~a~~~--~~~v~~fSlE-Ms~~ql~~Rlla~~s~v~--~~~i~~~~l~~~e~~  288 (464)
T PRK08840        214 LQGSDLIIVAARPSMGKTTFAMNLCENAAMDQ--DKPVLIFSLE-MPAEQLMMRMLASLSRVD--QTKIRTGQLDDEDWA  288 (464)
T ss_pred             CCCCceEEEEeCCCCchHHHHHHHHHHHHHhC--CCeEEEEecc-CCHHHHHHHHHHhhCCCC--HHHHhcCCCCHHHHH
Confidence            44556689999999999987754444443322  3356666543 335555544433222111  111111111122222


Q ss_pred             H-------HhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHhCC-----C
Q psy4698         161 K-------LEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKHLN-----N  219 (258)
Q Consensus       161 ~-------~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~l~-----~  219 (258)
                      .       +.....+.|.     |+..+...+++-...-.++++||||-.|.+...    +....+..+.+.++     -
T Consensus       289 ~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel  368 (464)
T PRK08840        289 RISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAKEL  368 (464)
T ss_pred             HHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHhcCCCCCCCchHHHHHHHHHHHHHHHHHh
Confidence            2       2123456664     344444333221111125889999999977422    12233444444443     2


Q ss_pred             CccEEEEEeeCChh
Q psy4698         220 DVQVILLSATMPAD  233 (258)
Q Consensus       220 ~~~~i~~SAT~~~~  233 (258)
                      ++.+|++| -++++
T Consensus       369 ~ipVi~Ls-QLnR~  381 (464)
T PRK08840        369 NVPVVALS-QLNRS  381 (464)
T ss_pred             CCeEEEEE-ecCcc
Confidence            56777776 34443

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=96.02  E-value=0.088  Score=40.93  Aligned_cols=52  Identities=19%  Similarity=0.424  Sum_probs=40.0

Q ss_pred             CCccEEEEccchhhhccCc--HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGF--KDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~--~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      ..+++||+||+-..++.++  ...+..+++..|+..-+|+..-..|.++.+.+.
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD  149 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELAD  149 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCc
Confidence            4688999999998777663  467778888877777788877778887776654

Alternate name: corrinoid adenosyltransferase.

>KOG2004|consensus

Probab=96.01  E-value=0.02  Score=53.35  Aligned_cols=111  Identities=18%  Similarity=0.313  Sum_probs=69.9

Q ss_pred             CCcHHHHHHhhhhh--------cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          69 KPSAIQQRAIIPCV--------RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~--------~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .+.++-.+.++.+.        +|+-+++.||+|-|||.+.                       ++.|..       +++
T Consensus       415 gm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~-----------------------kSIA~A-------LnR  464 (906)
T KOG2004|consen  415 GMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIA-----------------------KSIARA-------LNR  464 (906)
T ss_pred             chHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHH-----------------------HHHHHH-------hCC
Confidence            55666677776653        4567999999999999865                       111111       111


Q ss_pred             CCCceEEEEECCcchHHHHHHHhcCCcEEEeC-hHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC
Q psy4698         141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGT-PGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN  218 (258)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~T-p~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~  218 (258)
                         -.+....||.....+   ++...+-+|+. |+++.+.++.-...-   -++.+||+|-+.....+..-.+++..+.
T Consensus       465 ---kFfRfSvGG~tDvAe---IkGHRRTYVGAMPGkiIq~LK~v~t~N---PliLiDEvDKlG~g~qGDPasALLElLD  534 (906)
T KOG2004|consen  465 ---KFFRFSVGGMTDVAE---IKGHRRTYVGAMPGKIIQCLKKVKTEN---PLILIDEVDKLGSGHQGDPASALLELLD  534 (906)
T ss_pred             ---ceEEEeccccccHHh---hcccceeeeccCChHHHHHHHhhCCCC---ceEEeehhhhhCCCCCCChHHHHHHhcC
Confidence               012333455544433   44456678875 999999998733211   1899999999876556666666776664

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=96.01  E-value=0.015  Score=54.16  Aligned_cols=38  Identities=24%  Similarity=0.358  Sum_probs=28.1

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVIL  225 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~  225 (258)
                      ++-.++|+||+..-+|......+...+..+.++..++.
T Consensus       482 ~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~~rT~ii  519 (567)
T COG1132         482 RNPPILILDEATSALDTETEALIQDALKKLLKGRTTLI  519 (567)
T ss_pred             cCCCEEEEeccccccCHHhHHHHHHHHHHHhcCCEEEE
Confidence            34469999999998888888888887776655533333

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.00  E-value=0.066  Score=47.54  Aligned_cols=40  Identities=10%  Similarity=0.207  Sum_probs=23.9

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ..+.+++||||+|.+... ....+.+.+...++...+|+.+
T Consensus       125 ~~~~kvvIIdea~~l~~~-~~~~LLk~LEep~~~t~~Il~t  164 (397)
T PRK14955        125 KGRYRVYIIDEVHMLSIA-AFNAFLKTLEEPPPHAIFIFAT  164 (397)
T ss_pred             cCCeEEEEEeChhhCCHH-HHHHHHHHHhcCCCCeEEEEEe
Confidence            456789999999987432 2334445555444444444433

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.99  E-value=0.14  Score=39.66  Aligned_cols=33  Identities=24%  Similarity=0.345  Sum_probs=21.0

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      +++.|++|+|||......+.. +...  +.+++++.
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~-~~~~--g~~v~~i~   35 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALY-LKKK--GKKVLLVA   35 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEE
Confidence            688999999999886444332 2222  33565554

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.96  E-value=0.2  Score=44.50  Aligned_cols=127  Identities=15%  Similarity=0.147  Sum_probs=65.0

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA--PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      ..+++.||+|+|||+.....+.......  +.++.++.  +.+..+..+..   .++...++.+..              
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~--G~~V~Lit~Dt~R~aA~eQLk---~yAe~lgvp~~~--------------  284 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHM--GKSVSLYTTDNYRIAAIEQLK---RYADTMGMPFYP--------------  284 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhc--CCeEEEecccchhhhHHHHHH---HHHHhcCCCeee--------------
Confidence            3488999999999988754444332222  23455554  33443333222   222222222111              


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc-cCcHHHHHHHHHhCC---CCccEEEEEeeCCh-hHHHH
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLN---NDVQVILLSATMPA-DVLDV  237 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-~~~~~~~~~~~~~l~---~~~~~i~~SAT~~~-~~~~~  237 (258)
                             +..+..+.+.+..     .+.++|+||=+-+... ......+..++....   +.-.++.+|||.-. ++.+.
T Consensus       285 -------~~~~~~l~~~l~~-----~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~  352 (432)
T PRK12724        285 -------VKDIKKFKETLAR-----DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTV  352 (432)
T ss_pred             -------hHHHHHHHHHHHh-----CCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHH
Confidence                   0112223333321     3567888887654321 223344455555432   22357788999865 67777


Q ss_pred             HHHhc
Q psy4698         238 SMKFM  242 (258)
Q Consensus       238 ~~~~~  242 (258)
                      .+.|-
T Consensus       353 ~~~f~  357 (432)
T PRK12724        353 LKAYE  357 (432)
T ss_pred             HHHhc
Confidence            77664

>PRK07004 replicative DNA helicase; Provisional

Probab=95.95  E-value=0.04  Score=49.83  Aligned_cols=141  Identities=18%  Similarity=0.176  Sum_probs=69.4

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH--
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI--  159 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  159 (258)
                      ..|.-++|.|.+|+|||..++--+.+.....  +..++|++. -.-..|+..++-....  ++.......+.-...++  
T Consensus       211 ~~g~liviaarpg~GKT~~al~ia~~~a~~~--~~~v~~fSl-EM~~~ql~~R~la~~~--~v~~~~i~~g~l~~~e~~~  285 (460)
T PRK07004        211 HGGELIIVAGRPSMGKTAFSMNIGEYVAVEY--GLPVAVFSM-EMPGTQLAMRMLGSVG--RLDQHRMRTGRLTDEDWPK  285 (460)
T ss_pred             CCCceEEEEeCCCCCccHHHHHHHHHHHHHc--CCeEEEEeC-CCCHHHHHHHHHHhhc--CCCHHHHhcCCCCHHHHHH
Confidence            3445689999999999987765554433332  234666652 2334444443321111  11111111112122222  


Q ss_pred             -----HHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHhCC-----CC
Q psy4698         160 -----RKLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKHLN-----ND  220 (258)
Q Consensus       160 -----~~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~l~-----~~  220 (258)
                           ..+. +..+.|.     |+..+....++-......+++||||=.+.+...    +....+..+.+.++     .+
T Consensus       286 ~~~a~~~l~-~~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~  364 (460)
T PRK07004        286 LTHAVQKMS-EAQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELD  364 (460)
T ss_pred             HHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhC
Confidence                 2222 2467764     444444433321111235789999999977522    23334445554443     26


Q ss_pred             ccEEEEEe
Q psy4698         221 VQVILLSA  228 (258)
Q Consensus       221 ~~~i~~SA  228 (258)
                      +.+|++|.
T Consensus       365 ipVi~lsQ  372 (460)
T PRK07004        365 VPVIALSQ  372 (460)
T ss_pred             CeEEEEec
Confidence            77777764

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

Probab=95.95  E-value=0.01  Score=49.04  Aligned_cols=47  Identities=28%  Similarity=0.475  Sum_probs=32.3

Q ss_pred             CcccccccccccCcCCCCCCHHHHHH-HHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          36 GLIETNWDHVAENFDDMELSEELLRG-IYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~l~~~-l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +++-+-....++.|+++++++.+.+. +.++|+                   ++++|+|||||+...
T Consensus        97 g~VlRrI~~~IPt~eeL~LPevlk~la~~kRGL-------------------viiVGaTGSGKSTtm  144 (375)
T COG5008          97 GLVLRRIETKIPTFEELKLPEVLKDLALAKRGL-------------------VIIVGATGSGKSTTM  144 (375)
T ss_pred             hhhhhhhhccCCcHHhcCCcHHHHHhhcccCce-------------------EEEECCCCCCchhhH
Confidence            44444555666778888887766652 223343                   799999999999874

>PRK10867 signal recognition particle protein; Provisional

Probab=95.93  E-value=0.07  Score=47.75  Aligned_cols=41  Identities=24%  Similarity=0.214  Sum_probs=25.0

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe--ccHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA--PTRELA  128 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~--P~~~l~  128 (258)
                      -++++|++|+|||++..-.+......  .+.+++++.  +.|..+
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~--~G~kV~lV~~D~~R~aa  144 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKK--KKKKVLLVAADVYRPAA  144 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHh--cCCcEEEEEccccchHH
Confidence            38899999999998765444332222  133566665  344443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=95.93  E-value=0.016  Score=54.69  Aligned_cols=67  Identities=27%  Similarity=0.323  Sum_probs=51.8

Q ss_pred             CCcHHHHHHhhhhhcC-----CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          69 KPSAIQQRAIIPCVRG-----NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g-----~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      .|+..|..++..+..+     +..++.|.+|+||++.+. .++..     .+..+|||+|+...+.+++..++.+...
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~-----~~r~vLIVt~~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIAR-----LQRPTLVLAHNKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHH-----hCCCEEEEECCHHHHHHHHHHHHHhcCC
Confidence            7899999999887533     257799999999998753 22222     1236999999999999999999888644

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.91  E-value=0.12  Score=41.96  Aligned_cols=53  Identities=21%  Similarity=0.230  Sum_probs=32.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .|..+++.|++|+|||......+...+.+   +..+++++- .+...+....++.++
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~-e~~~~~i~~~~~~~g   71 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTT-EESRESIIRQAAQFG   71 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEc-cCCHHHHHHHHHHhC
Confidence            46789999999999998765545444432   235777764 223344444444443

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>KOG1513|consensus

Probab=95.91  E-value=0.013  Score=54.96  Aligned_cols=156  Identities=18%  Similarity=0.181  Sum_probs=90.2

Q ss_pred             CCcHHHHHHhhhhhcCC----------cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQRAIIPCVRGN----------DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~----------~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .++..|.+++-+.++-+          .++|--..|-||-.+..-.+++...++.  .++|+++-+..|--+..+.++.+
T Consensus       264 ~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLkGR--KrAlW~SVSsDLKfDAERDL~Di  341 (1300)
T KOG1513|consen  264 HLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLKGR--KRALWFSVSSDLKFDAERDLRDI  341 (1300)
T ss_pred             chhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhccc--ceeEEEEeccccccchhhchhhc
Confidence            56889999987765432          3677666666665443333455555543  37999998888877777777776


Q ss_pred             cCCCCceEEEEECCc--c-hHHHHHHHhcCCcEEEeChHHHHHHHhc--C-----------CCCCCCccEEEEccchhhh
Q psy4698         139 GDFMSVSCHACIGGT--I-VRDDIRKLEAGAQVVVGTPGRVFDMISR--G-----------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       139 ~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~--~-----------~~~~~~l~~lVvDE~h~~~  202 (258)
                      +. .++.+..+..-.  . ...+....+  -.++++|+..|.---..  +           +..-+.=++||+||+|.--
T Consensus       342 gA-~~I~V~alnK~KYakIss~en~n~k--rGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkAK  418 (1300)
T KOG1513|consen  342 GA-TGIAVHALNKFKYAKISSKENTNTK--RGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKAK  418 (1300)
T ss_pred             CC-CCccceehhhcccccccccccCCcc--ceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhhc
Confidence            53 233333221110  0 011111122  36999999766421110  0           0001122589999999753


Q ss_pred             c---------cCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         203 S---------RGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       203 ~---------~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      +         ...+..+..+.+.+ ++.+++..|||=
T Consensus       419 NL~p~~~~k~TKtG~tVLdLQk~L-P~ARVVYASATG  454 (1300)
T KOG1513|consen  419 NLVPTAGAKSTKTGKTVLDLQKKL-PNARVVYASATG  454 (1300)
T ss_pred             ccccccCCCcCcccHhHHHHHHhC-CCceEEEeeccC
Confidence            2         12445666677777 457899999994

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.89  E-value=0.037  Score=49.00  Aligned_cols=52  Identities=25%  Similarity=0.351  Sum_probs=31.5

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      .+.+++||||+|.|... ..+.+.+.+..-+++. ++++.+|-+..+...++.-
T Consensus       116 ~~~kViiIDead~m~~~-aanaLLk~LEep~~~~-~fIL~a~~~~~llpTIrSR  167 (394)
T PRK07940        116 GRWRIVVIEDADRLTER-AANALLKAVEEPPPRT-VWLLCAPSPEDVLPTIRSR  167 (394)
T ss_pred             CCcEEEEEechhhcCHH-HHHHHHHHhhcCCCCC-eEEEEECChHHChHHHHhh
Confidence            46789999999998433 3344555555544444 5555555566655555443

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.88  E-value=0.13  Score=41.98  Aligned_cols=53  Identities=11%  Similarity=0.161  Sum_probs=33.9

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .|.-+++.|++|+|||......+...+.+   +.+++|+.-.. -..+..+.+..++
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~~---g~~~~y~~~e~-~~~~~~~~~~~~g   76 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALKQ---GKKVYVITTEN-TSKSYLKQMESVK   76 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHhC---CCEEEEEEcCC-CHHHHHHHHHHCC
Confidence            34568999999999998775555544432   34677777543 3345555555553

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=95.87  E-value=0.11  Score=45.15  Aligned_cols=17  Identities=29%  Similarity=0.370  Sum_probs=14.6

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .+++.||.|+|||..+.
T Consensus        38 ~~Ll~G~~G~GKt~~a~   54 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIAR   54 (355)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47999999999997763

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK04195 replication factor C large subunit; Provisional

Probab=95.87  E-value=0.029  Score=51.15  Aligned_cols=18  Identities=22%  Similarity=0.338  Sum_probs=15.7

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+.+++.||+|+|||..+
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467999999999999875

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=95.84  E-value=0.16  Score=39.47  Aligned_cols=140  Identities=16%  Similarity=0.232  Sum_probs=64.4

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH-HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE-LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      +.|....|-|||.+++--++..+-.   +.+++++.=.+. -..--...++.+.   ++.+..+-.+-........    
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~G~---G~rV~ivQFlKg~~~~GE~~~l~~l~---~~~~~~~g~~f~~~~~~~~----   75 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAAGH---GMRVLIVQFLKGGRYSGELKALKKLP---NVEIERFGKGFVWRMNEEE----   75 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHHCT---T--EEEEESS--SS--HHHHHHGGGT-----EEEE--TT----GGGHH----
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHhC---CCEEEEEEEecCCCCcCHHHHHHhCC---eEEEEEcCCcccccCCCcH----
Confidence            5667778999999987666555443   447888864444 1111122222221   2332221111100000000    


Q ss_pred             CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH--HHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK--DQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       166 ~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~--~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      .+  .......++.... .+.-..+++||+||+-..++.++.  ..+..+++.-|...-+|+..-..|.++.+.+.
T Consensus        76 ~~--~~~~~~~~~~a~~-~i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~AD  148 (172)
T PF02572_consen   76 ED--RAAAREGLEEAKE-AISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAAD  148 (172)
T ss_dssp             HH--HHHHHHHHHHHHH-HTT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-S
T ss_pred             HH--HHHHHHHHHHHHH-HHhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCC
Confidence            00  0011111222221 233456889999999988777644  66778888777777777777777877776653

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.82  E-value=0.014  Score=53.73  Aligned_cols=40  Identities=18%  Similarity=0.344  Sum_probs=26.5

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ++-+++|+||+-.-+|......+...+..+.++..+|..|
T Consensus       487 ~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiIt  526 (529)
T TIGR02868       487 ADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVIT  526 (529)
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence            4456888888887777777777777666665555444443

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK08006 replicative DNA helicase; Provisional

Probab=95.82  E-value=0.13  Score=46.79  Aligned_cols=147  Identities=18%  Similarity=0.122  Sum_probs=74.4

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      +..|.-++|.|.+|.|||..++--+.+.....  +..++|++.- .-..|+..++-.....  +....+..+.-...++.
T Consensus       221 l~~G~LiiIaarPgmGKTafalnia~~~a~~~--g~~V~~fSlE-M~~~ql~~Rlla~~~~--v~~~~i~~~~l~~~e~~  295 (471)
T PRK08006        221 LQPSDLIIVAARPSMGKTTFAMNLCENAAMLQ--DKPVLIFSLE-MPGEQIMMRMLASLSR--VDQTRIRTGQLDDEDWA  295 (471)
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhc--CCeEEEEecc-CCHHHHHHHHHHHhcC--CCHHHhhcCCCCHHHHH
Confidence            33445689999999999987765555443332  3356666532 3345555444322222  21111111221222222


Q ss_pred             H-------HhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHhCC-----C
Q psy4698         161 K-------LEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKHLN-----N  219 (258)
Q Consensus       161 ~-------~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~l~-----~  219 (258)
                      .       +.....+.|.     |+..+....++-.....++++||||=.|.+...    +....+..+.+.|+     -
T Consensus       296 ~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lAkel  375 (471)
T PRK08006        296 RISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALAKEL  375 (471)
T ss_pred             HHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence            2       2133456664     455554444321111135889999999977422    23344555554443     2


Q ss_pred             CccEEEEEeeCChh
Q psy4698         220 DVQVILLSATMPAD  233 (258)
Q Consensus       220 ~~~~i~~SAT~~~~  233 (258)
                      ++.+|++|. +++.
T Consensus       376 ~ipVi~LsQ-LnR~  388 (471)
T PRK08006        376 QVPVVALSQ-LNRS  388 (471)
T ss_pred             CCeEEEEEe-cCcc
Confidence            577777773 4444

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.81  E-value=0.022  Score=49.94  Aligned_cols=37  Identities=16%  Similarity=0.236  Sum_probs=23.2

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL  121 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil  121 (258)
                      +..++|+||||||||... ..++..+.......+++.+
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~~~~~~~~Ivti  185 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCGETYPDRKIVTY  185 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHHhcCCCceEEEE
Confidence            346899999999999874 4455555432222344444

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

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.75  E-value=0.061  Score=44.80  Aligned_cols=34  Identities=24%  Similarity=0.301  Sum_probs=23.0

Q ss_pred             CCcHHHHHHhhhhh----cCC-cEEEEcccCCCcchHhH
Q psy4698          69 KPSAIQQRAIIPCV----RGN-DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~-~~li~~~tGsGKT~~~l  102 (258)
                      .+++.+.+++..+.    .+. .+++.|++|+|||....
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            34555556665543    333 58999999999998753

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=95.74  E-value=0.025  Score=53.67  Aligned_cols=41  Identities=17%  Similarity=0.360  Sum_probs=36.9

Q ss_pred             EEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         192 MFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       192 ~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      ++|+|+.|.+.+......+..+++..|++...+..|=+-|.
T Consensus       132 ~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         132 YLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             EEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence            89999999998888888999999999999999999887664

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.72  E-value=0.097  Score=49.05  Aligned_cols=40  Identities=10%  Similarity=0.234  Sum_probs=24.3

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ..+.+++||||+|.+... -.+.+.+.+...+...-+|+.+
T Consensus       125 ~~~~KVvIIdEad~Lt~~-a~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        125 KGRYRVYIIDEVHMLSTA-AFNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             cCCCEEEEEeChhhcCHH-HHHHHHHHHhCCCCCeEEEEEe
Confidence            456789999999987432 2344445555544444445544

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.71  E-value=0.11  Score=48.54  Aligned_cols=20  Identities=30%  Similarity=0.340  Sum_probs=16.2

Q ss_pred             cEEEEcccCCCcchHhHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~  105 (258)
                      .+++.||.|+|||.++...+
T Consensus        40 a~Lf~Gp~G~GKTtlA~~lA   59 (585)
T PRK14950         40 AYLFTGPRGVGKTSTARILA   59 (585)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            36999999999998875443

>KOG0738|consensus

Probab=95.70  E-value=0.037  Score=48.12  Aligned_cols=64  Identities=20%  Similarity=0.320  Sum_probs=38.5

Q ss_pred             ccEEEEccchhhhccC-------cHHHHH-HHHHhC---C----CCccEEEEEee-CChhHHHHHHHhcCCCeEEEecCC
Q psy4698         190 IRMFVLDEADEMLSRG-------FKDQIY-DVFKHL---N----NDVQVILLSAT-MPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~-------~~~~~~-~~~~~l---~----~~~~~i~~SAT-~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      -+.|.|||+|.+....       ....++ .++-.+   .    ....++.+.|| +|=++-+-++.-+...++|-.++.
T Consensus       305 PStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~  384 (491)
T KOG0738|consen  305 PSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDA  384 (491)
T ss_pred             CceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCH
Confidence            3589999999886431       111121 122222   1    12235566777 677888888888888888766554

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=95.68  E-value=0.013  Score=47.46  Aligned_cols=17  Identities=24%  Similarity=0.360  Sum_probs=14.5

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .++++.||+|.|||..+
T Consensus        51 ~h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             -EEEEESSTTSSHHHHH
T ss_pred             ceEEEECCCccchhHHH
Confidence            36999999999999865

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.65  E-value=0.14  Score=44.27  Aligned_cols=50  Identities=16%  Similarity=0.258  Sum_probs=31.3

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      ...+++|+|++|.+ +......+.+.++..+....+|+ +++-+..+...++
T Consensus       112 ~~~kV~iiEp~~~L-d~~a~naLLk~LEep~~~~~~Il-vth~~~~ll~ti~  161 (325)
T PRK08699        112 GGLRVILIHPAESM-NLQAANSLLKVLEEPPPQVVFLL-VSHAADKVLPTIK  161 (325)
T ss_pred             CCceEEEEechhhC-CHHHHHHHHHHHHhCcCCCEEEE-EeCChHhChHHHH
Confidence            56789999999976 44566677777777665554555 4443334443333

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.61  E-value=0.085  Score=45.67  Aligned_cols=55  Identities=13%  Similarity=0.168  Sum_probs=31.2

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcC
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMR  243 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~  243 (258)
                      ....+++|||+||.|-. ...+.+.+.+..=+.+. ++++.+.-+..+...++.-++
T Consensus       106 ~g~~kV~iI~~ae~m~~-~AaNaLLKtLEEPp~~t-~fiL~t~~~~~lLpTIrSRCq  160 (334)
T PRK07993        106 LGGAKVVWLPDAALLTD-AAANALLKTLEEPPENT-WFFLACREPARLLATLRSRCR  160 (334)
T ss_pred             cCCceEEEEcchHhhCH-HHHHHHHHHhcCCCCCe-EEEEEECChhhChHHHHhccc
Confidence            35678999999998832 24455555555533334 444444445555555444443

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=95.56  E-value=0.17  Score=39.55  Aligned_cols=52  Identities=23%  Similarity=0.432  Sum_probs=40.0

Q ss_pred             CCccEEEEccchhhhccCc--HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGF--KDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~--~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      ..+++||+||+-...+.++  ...+..+++..|...-+|+..-..|+++.+.+.
T Consensus       114 ~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~AD  167 (178)
T PRK07414        114 GRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIAD  167 (178)
T ss_pred             CCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCC
Confidence            5688999999998877764  467778888877777777777778877776553

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.56  E-value=0.082  Score=45.84  Aligned_cols=52  Identities=15%  Similarity=0.184  Sum_probs=30.0

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      ....+++|||++|.|.. .-.+.+.+.+..-++++ ++++.++-+..+...++.
T Consensus       130 ~~~~kV~iI~~ae~m~~-~AaNaLLKtLEEPp~~t-~fiL~t~~~~~LLpTI~S  181 (342)
T PRK06964        130 RGGARVVVLYPAEALNV-AAANALLKTLEEPPPGT-VFLLVSARIDRLLPTILS  181 (342)
T ss_pred             cCCceEEEEechhhcCH-HHHHHHHHHhcCCCcCc-EEEEEECChhhCcHHHHh
Confidence            35678999999998832 24455555555544444 444444444444444444

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=95.54  E-value=0.095  Score=48.64  Aligned_cols=19  Identities=26%  Similarity=0.282  Sum_probs=15.8

Q ss_pred             cEEEEcccCCCcchHhHHH
Q psy4698          86 DVIAQAQSGTGKTATFSIS  104 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~  104 (258)
                      .+++.||.|.|||.++...
T Consensus        40 ayLf~Gp~G~GKTt~Ar~l   58 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARAF   58 (563)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3799999999999987543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=95.53  E-value=0.17  Score=48.59  Aligned_cols=18  Identities=33%  Similarity=0.473  Sum_probs=15.9

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .|+++.||+|+|||...-
T Consensus       204 ~n~lL~G~pG~GKT~l~~  221 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAE  221 (731)
T ss_pred             CceEEECCCCCCHHHHHH
Confidence            589999999999998763

>PRK06620 hypothetical protein; Validated

Probab=95.52  E-value=0.058  Score=43.62  Aligned_cols=58  Identities=12%  Similarity=0.335  Sum_probs=30.3

Q ss_pred             ccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee-CChhHH-HHHHHhcCCCeEEEec
Q psy4698         190 IRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT-MPADVL-DVSMKFMRDPIKILVK  251 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT-~~~~~~-~~~~~~~~~~~~v~~~  251 (258)
                      .+++++||+|.+-    ...+..++..+...-..+++|++ .|..+. .-++..+.-..++.+.
T Consensus        86 ~d~lliDdi~~~~----~~~lf~l~N~~~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~  145 (214)
T PRK06620         86 YNAFIIEDIENWQ----EPALLHIFNIINEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLN  145 (214)
T ss_pred             CCEEEEeccccch----HHHHHHHHHHHHhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeC
Confidence            4589999999642    23444555554433334455555 454421 2244555555555553

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.51  E-value=0.053  Score=46.69  Aligned_cols=38  Identities=5%  Similarity=0.161  Sum_probs=23.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL  226 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~  226 (258)
                      ...+++|+|+||.|.. ...+.+.+.+..-+++..+|+.
T Consensus       106 g~~KV~iI~~a~~m~~-~AaNaLLKtLEEPp~~~~fiL~  143 (325)
T PRK06871        106 GGNKVVYIQGAERLTE-AAANALLKTLEEPRPNTYFLLQ  143 (325)
T ss_pred             CCceEEEEechhhhCH-HHHHHHHHHhcCCCCCeEEEEE
Confidence            4678999999998842 2445555555554444444443

>PRK09165 replicative DNA helicase; Provisional

Probab=95.50  E-value=0.1  Score=47.79  Aligned_cols=148  Identities=16%  Similarity=0.161  Sum_probs=72.4

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhcc------------ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEE
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNI------------KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACI  150 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~------------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~  150 (258)
                      .|.-++|.|.+|.|||..++--+.+......            .+..++|++. -.-..|+..++..........  .+.
T Consensus       216 ~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSl-EMs~~ql~~R~la~~s~v~~~--~i~  292 (497)
T PRK09165        216 PSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSL-EMSAEQLATRILSEQSEISSS--KIR  292 (497)
T ss_pred             CCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeC-cCCHHHHHHHHHHHhcCCCHH--HHh
Confidence            3455899999999999877655544433211            2345666653 334455555443332222211  111


Q ss_pred             CCcchHHHHHHHh------cCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhccC------cHHHHHHH
Q psy4698         151 GGTIVRDDIRKLE------AGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG------FKDQIYDV  213 (258)
Q Consensus       151 ~~~~~~~~~~~~~------~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~------~~~~~~~~  213 (258)
                      .+.-...++..+.      ....+.|.     |++.+...+++-. .-.++++||||=.|.+....      ....+..+
T Consensus       293 ~~~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~-~~~~~~lvvIDyLqli~~~~~~~~~~r~~ev~~i  371 (497)
T PRK09165        293 RGKISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLK-RQHGLDLLVVDYLQLIRGSSKRSSDNRVQEISEI  371 (497)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHH-HhcCCCEEEEcchHhccCCCCCCCCchHHHHHHH
Confidence            1221222222211      12456654     4555554443311 11358899999999764221      22234444


Q ss_pred             HHhCC-----CCccEEEEEeeCChhHH
Q psy4698         214 FKHLN-----NDVQVILLSATMPADVL  235 (258)
Q Consensus       214 ~~~l~-----~~~~~i~~SAT~~~~~~  235 (258)
                      .+.|+     -++.+|++|. +++.++
T Consensus       372 s~~LK~lAkel~ipVi~lsQ-LnR~~e  397 (497)
T PRK09165        372 TQGLKALAKELNIPVIALSQ-LSRQVE  397 (497)
T ss_pred             HHHHHHHHHHhCCeEEEeec-ccchhh
Confidence            33332     2566666654 455443

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=95.49  E-value=0.14  Score=49.26  Aligned_cols=45  Identities=13%  Similarity=0.259  Sum_probs=28.5

Q ss_pred             cEEEEccchhhhccCc----HHHHHHHHHhCCCCccEEEEEeeCChhHH
Q psy4698         191 RMFVLDEADEMLSRGF----KDQIYDVFKHLNNDVQVILLSATMPADVL  235 (258)
Q Consensus       191 ~~lVvDE~h~~~~~~~----~~~~~~~~~~l~~~~~~i~~SAT~~~~~~  235 (258)
                      .+|++||+|.+...+.    ...+..+++.+-..-++.++.||-+.+++
T Consensus       280 ~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~vIgATt~~E~~  328 (758)
T PRK11034        280 SILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFS  328 (758)
T ss_pred             CEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCCeEEEecCChHHHH
Confidence            4899999999865432    23344445544344567777788776653

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.48  E-value=0.027  Score=49.20  Aligned_cols=27  Identities=19%  Similarity=0.436  Sum_probs=20.2

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .+..++|+||||||||... ..++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4567999999999999875 44555543

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.45  E-value=0.29  Score=41.91  Aligned_cols=129  Identities=22%  Similarity=0.361  Sum_probs=71.0

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc--HHHHHHHHHHHHHhcCCCCceEEEE-ECCcchHHHHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT--RELAQQIQKVVIALGDFMSVSCHAC-IGGTIVRDDIRKL  162 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~--~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~  162 (258)
                      .+++.|-.|+|||++.- -+...+.+.  +.++++.+-.  |+-+.++...+   +...++.+... .|+.         
T Consensus       141 Vil~vGVNG~GKTTTIa-KLA~~l~~~--g~~VllaA~DTFRAaAiEQL~~w---~er~gv~vI~~~~G~D---------  205 (340)
T COG0552         141 VILFVGVNGVGKTTTIA-KLAKYLKQQ--GKSVLLAAGDTFRAAAIEQLEVW---GERLGVPVISGKEGAD---------  205 (340)
T ss_pred             EEEEEecCCCchHhHHH-HHHHHHHHC--CCeEEEEecchHHHHHHHHHHHH---HHHhCCeEEccCCCCC---------
Confidence            48999999999998753 222333333  3356666542  55444444333   32234444331 1221         


Q ss_pred             hcCCcEEEeChHH-HHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCCCCc------cEEEEEeeCChhH
Q psy4698         163 EAGAQVVVGTPGR-VFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDV------QVILLSATMPADV  234 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~-l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~~~------~~i~~SAT~~~~~  234 (258)
                                |.. .++.+++.  .-.+++++++|=|-++.+. +.-.++.++.+.+.+..      -++.+=||.-.+.
T Consensus       206 ----------pAaVafDAi~~A--kar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAttGqna  273 (340)
T COG0552         206 ----------PAAVAFDAIQAA--KARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATTGQNA  273 (340)
T ss_pred             ----------cHHHHHHHHHHH--HHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEcccChhH
Confidence                      211 12333321  1245678888888877644 56677777777776544      3444488887665


Q ss_pred             HHHHHHh
Q psy4698         235 LDVSMKF  241 (258)
Q Consensus       235 ~~~~~~~  241 (258)
                      .+.++.|
T Consensus       274 l~QAk~F  280 (340)
T COG0552         274 LSQAKIF  280 (340)
T ss_pred             HHHHHHH
Confidence            5555555

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.44  E-value=0.21  Score=42.77  Aligned_cols=35  Identities=14%  Similarity=0.268  Sum_probs=22.8

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL  121 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil  121 (258)
                      ++++++.|++|+|||..+. ++...+...  +..+.++
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~~~--g~~v~~~  190 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELAKK--GVSSTLL  190 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHc--CCCEEEE
Confidence            4679999999999998653 444444433  2344444

>PRK09087 hypothetical protein; Validated

Probab=95.44  E-value=0.093  Score=42.81  Aligned_cols=59  Identities=5%  Similarity=0.072  Sum_probs=34.1

Q ss_pred             EEEEccchhhhccCcHHHHHHHHHhCCC-CccEEEEEeeCChhHHH---HHHHhcCCCeEEEecC
Q psy4698         192 MFVLDEADEMLSRGFKDQIYDVFKHLNN-DVQVILLSATMPADVLD---VSMKFMRDPIKILVKK  252 (258)
Q Consensus       192 ~lVvDE~h~~~~~~~~~~~~~~~~~l~~-~~~~i~~SAT~~~~~~~---~~~~~~~~~~~v~~~~  252 (258)
                      +|++||+|.+.  .....+..++..+.. ..++|+.|.+-|.....   -++..+....++.+..
T Consensus        90 ~l~iDDi~~~~--~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~  152 (226)
T PRK09087         90 PVLIEDIDAGG--FDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGE  152 (226)
T ss_pred             eEEEECCCCCC--CCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCC
Confidence            79999999652  234556666665544 44444444444443322   2556666666666644

>TIGR00959 ffh signal recognition particle protein

Probab=95.39  E-value=0.18  Score=45.08  Aligned_cols=35  Identities=20%  Similarity=0.237  Sum_probs=22.5

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      .++++|++|+|||++..-.+.......  +.+++++.
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~l~~~~--g~kV~lV~  135 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYYLKKKQ--GKKVLLVA  135 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhC--CCeEEEEe
Confidence            489999999999988654443322122  23566665

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=95.36  E-value=0.054  Score=42.97  Aligned_cols=54  Identities=13%  Similarity=0.253  Sum_probs=27.9

Q ss_pred             CccEEEEccchhhhccCcH-----HHHHHHHHhCCC-CccEEEEEeeCChhHHHHHHHhcC
Q psy4698         189 QIRMFVLDEADEMLSRGFK-----DQIYDVFKHLNN-DVQVILLSATMPADVLDVSMKFMR  243 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~-----~~~~~~~~~l~~-~~~~i~~SAT~~~~~~~~~~~~~~  243 (258)
                      .=+++|+||||........     ......+...++ ...++++|..+ ..+...++...+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hRh~g~diiliTQ~~-~~id~~ir~lve  138 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHRHYGWDIILITQSP-SQIDKFIRDLVE  138 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T----HHHHGGGGCCCTT-EEEEEES-G-GGB-HHHHCCEE
T ss_pred             CCcEEEEECChhhcCCCccccccchHHHHHHHHhCcCCcEEEEEeCCH-HHHhHHHHHHHh
Confidence            3459999999988655333     233344444443 45667776664 455555555444

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.36  E-value=0.21  Score=49.10  Aligned_cols=41  Identities=15%  Similarity=0.393  Sum_probs=32.8

Q ss_pred             EEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         192 MFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       192 ~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      +||+|++|.+.+......+..+++..+.+..+|+.|-+.|+
T Consensus       124 ~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~  164 (903)
T PRK04841        124 YLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPP  164 (903)
T ss_pred             EEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCC
Confidence            89999999875555566788888989888888888877543

>PRK05748 replicative DNA helicase; Provisional

Probab=95.35  E-value=0.13  Score=46.40  Aligned_cols=141  Identities=17%  Similarity=0.170  Sum_probs=69.5

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHH-HhcCCCCceEEEEECCcchHHHHH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI-ALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      ..|.-++|.|.+|.|||...+-.+.+.....  +..++|++. -....|+..++. ..+ .....  ....+.-...++.
T Consensus       201 ~~G~livIaarpg~GKT~~al~ia~~~a~~~--g~~v~~fSl-Ems~~~l~~R~l~~~~-~v~~~--~i~~~~l~~~e~~  274 (448)
T PRK05748        201 QPNDLIIVAARPSVGKTAFALNIAQNVATKT--DKNVAIFSL-EMGAESLVMRMLCAEG-NIDAQ--RLRTGQLTDDDWP  274 (448)
T ss_pred             CCCceEEEEeCCCCCchHHHHHHHHHHHHhC--CCeEEEEeC-CCCHHHHHHHHHHHhc-CCCHH--HhhcCCCCHHHHH
Confidence            3445689999999999987765554433322  235666653 333445544442 222 21111  1111111122222


Q ss_pred             -------HHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-----CcHHHHHHHHHhCC-----
Q psy4698         161 -------KLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-----GFKDQIYDVFKHLN-----  218 (258)
Q Consensus       161 -------~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-----~~~~~~~~~~~~l~-----  218 (258)
                             .+.+ ..+.|.     |++.+...+++-.....++++||||=.+.+...     +....+..+.+.++     
T Consensus       275 ~~~~a~~~l~~-~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke  353 (448)
T PRK05748        275 KLTIAMGSLSD-APIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKE  353 (448)
T ss_pred             HHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence                   2222 456663     445555443321111126889999999977422     12233444444442     


Q ss_pred             CCccEEEEEee
Q psy4698         219 NDVQVILLSAT  229 (258)
Q Consensus       219 ~~~~~i~~SAT  229 (258)
                      .++.+|++|..
T Consensus       354 ~~i~vi~lsQl  364 (448)
T PRK05748        354 LKVPVIALSQL  364 (448)
T ss_pred             hCCeEEEeccc
Confidence            25667776664

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.34  E-value=0.079  Score=49.75  Aligned_cols=21  Identities=29%  Similarity=0.333  Sum_probs=16.8

Q ss_pred             CcEEEEcccCCCcchHhHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~  105 (258)
                      ..+++.||.|+|||..+...+
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~lA   59 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARILA   59 (620)
T ss_pred             ceEEEECCCCCChHHHHHHHH
Confidence            357999999999998875444

>KOG2228|consensus

Probab=95.32  E-value=0.57  Score=40.28  Aligned_cols=44  Identities=20%  Similarity=0.439  Sum_probs=26.5

Q ss_pred             HHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         174 GRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       174 ~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      ..++..++.+....+.-=++|+||+|-.........+..++...
T Consensus       122 ~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDis  165 (408)
T KOG2228|consen  122 SKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDIS  165 (408)
T ss_pred             HHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHH
Confidence            45566666655444443478999999665555555555555444

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=95.32  E-value=0.039  Score=43.28  Aligned_cols=49  Identities=18%  Similarity=0.243  Sum_probs=27.3

Q ss_pred             hhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHH
Q psy4698          79 IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI  131 (258)
Q Consensus        79 ~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~  131 (258)
                      ..+..++++++.|++|+|||..+... ...+...  +..++|+ ....|....
T Consensus        42 ~~~~~~~~l~l~G~~G~GKThLa~ai-~~~~~~~--g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   42 EFIENGENLILYGPPGTGKTHLAVAI-ANEAIRK--GYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             -S-SC--EEEEEESTTSSHHHHHHHH-HHHHHHT--T--EEEE-EHHHHHHHH
T ss_pred             CCcccCeEEEEEhhHhHHHHHHHHHH-HHHhccC--CcceeEe-ecCceeccc
Confidence            34556789999999999999876433 3334432  3346555 444444443

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>PRK08506 replicative DNA helicase; Provisional

Probab=95.30  E-value=0.11  Score=47.22  Aligned_cols=139  Identities=19%  Similarity=0.213  Sum_probs=70.2

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH--
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR--  160 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  160 (258)
                      .|.-+++.|.+|.|||..++--+.+.+.   .+..++|++.- .-..|+..++-.........  .+..+.-...++.  
T Consensus       191 ~G~LivIaarpg~GKT~fal~ia~~~~~---~g~~V~~fSlE-Ms~~ql~~Rlla~~s~v~~~--~i~~~~l~~~e~~~~  264 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLCLNMALKALN---QDKGVAFFSLE-MPAEQLMLRMLSAKTSIPLQ--NLRTGDLDDDEWERL  264 (472)
T ss_pred             CCceEEEEcCCCCChHHHHHHHHHHHHh---cCCcEEEEeCc-CCHHHHHHHHHHHhcCCCHH--HHhcCCCCHHHHHHH
Confidence            4456899999999999887666655442   23357777543 34555554443322222211  1111111111221  


Q ss_pred             -----HHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhccC----cHHHHHHHHHhC---C--CCc
Q psy4698         161 -----KLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG----FKDQIYDVFKHL---N--NDV  221 (258)
Q Consensus       161 -----~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~----~~~~~~~~~~~l---~--~~~  221 (258)
                           .+.+ ..+.|.     |+..+...+++-.....++++||||=.+.+...+    ....+..+.+.|   -  -++
T Consensus       265 ~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~~~~~~~~r~~ev~~isr~LK~lAkel~i  343 (472)
T PRK08506        265 SDACDELSK-KKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISEISRGLKLLARELDI  343 (472)
T ss_pred             HHHHHHHHc-CCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhccCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence                 2222 345553     4555554443311112358899999999774222    223344443333   2  256


Q ss_pred             cEEEEEe
Q psy4698         222 QVILLSA  228 (258)
Q Consensus       222 ~~i~~SA  228 (258)
                      .++++|.
T Consensus       344 pVi~lsQ  350 (472)
T PRK08506        344 PIIALSQ  350 (472)
T ss_pred             cEEEEee
Confidence            6777764

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.25  E-value=0.24  Score=38.88  Aligned_cols=57  Identities=19%  Similarity=0.184  Sum_probs=35.5

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhc-------cccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQN-------IKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-------~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .|.-+++.|++|+|||...+-.+...+...       ..+.+++|+..... ..+..+++..+..
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            566799999999999988765555554311       14457888876555 5566666666543

>TIGR00665 DnaB replicative DNA helicase

Probab=95.23  E-value=0.25  Score=44.38  Aligned_cols=140  Identities=17%  Similarity=0.104  Sum_probs=68.4

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH----
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD----  158 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  158 (258)
                      .|.-++|.|++|+|||...+--+.+.....  +..++|++.- .-..++..++............ ..+.....++    
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~--g~~vl~~SlE-m~~~~i~~R~~~~~~~v~~~~~-~~g~l~~~~~~~~~  269 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFALNIAENAAIKE--GKPVAFFSLE-MSAEQLAMRMLSSESRVDSQKL-RTGKLSDEDWEKLT  269 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHHHHHHHHHHhC--CCeEEEEeCc-CCHHHHHHHHHHHhcCCCHHHh-ccCCCCHHHHHHHH
Confidence            345689999999999987765555444332  2357777632 2334444333332222221111 1111111111    


Q ss_pred             --HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHhCC-----CCcc
Q psy4698         159 --IRKLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKHLN-----NDVQ  222 (258)
Q Consensus       159 --~~~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~l~-----~~~~  222 (258)
                        ...+.+ ..+.|.     |++.+...+.+-.. -.++++||||=.+.+...    .....+..+.+.++     .++.
T Consensus       270 ~a~~~l~~-~~l~i~d~~~~~~~~i~~~i~~~~~-~~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk~lA~e~~i~  347 (434)
T TIGR00665       270 SAAGKLSE-APLYIDDTPGLTITELRAKARRLKR-EHGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLKALAKELNVP  347 (434)
T ss_pred             HHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCe
Confidence              112222 345552     44555544332111 134789999999977422    12233444444443     3566


Q ss_pred             EEEEEe
Q psy4698         223 VILLSA  228 (258)
Q Consensus       223 ~i~~SA  228 (258)
                      ++++|.
T Consensus       348 vi~lsq  353 (434)
T TIGR00665       348 VIALSQ  353 (434)
T ss_pred             EEEEec
Confidence            777664

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK04328 hypothetical protein; Provisional

Probab=95.22  E-value=0.2  Score=41.52  Aligned_cols=53  Identities=19%  Similarity=0.234  Sum_probs=34.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .|..+++.|++|+|||...+..+...+.++   .+++|++ +.+-..+..+.++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~g---e~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMG---EPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhcC---CcEEEEE-eeCCHHHHHHHHHHcC
Confidence            456799999999999987766565555443   3577776 3344445555555554

>PRK05636 replicative DNA helicase; Provisional

Probab=95.21  E-value=0.078  Score=48.53  Aligned_cols=143  Identities=19%  Similarity=0.217  Sum_probs=67.3

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      |.-+++.|.+|.|||...+-.+.......  +..++|++. -.-..|+..++-.........  ....+.....++..+.
T Consensus       265 G~Liiiaarpg~GKT~~al~~a~~~a~~~--g~~v~~fSl-EMs~~ql~~R~ls~~s~v~~~--~i~~g~l~~~e~~~~~  339 (505)
T PRK05636        265 GQMIIVAARPGVGKSTLALDFMRSASIKH--NKASVIFSL-EMSKSEIVMRLLSAEAEVRLS--DMRGGKMDEDAWEKLV  339 (505)
T ss_pred             CceEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEEe-eCCHHHHHHHHHHHhcCCCHH--HHhcCCCCHHHHHHHH
Confidence            34578999999999987654443333222  235666642 233344443332221111111  1112221222222211


Q ss_pred             ------cCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhccC----cHHHHHHHHHhCC-----CCccE
Q psy4698         164 ------AGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG----FKDQIYDVFKHLN-----NDVQV  223 (258)
Q Consensus       164 ------~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~----~~~~~~~~~~~l~-----~~~~~  223 (258)
                            ....+.|.     |...+...+++-.. -.++++||||=.|.|....    ....+..+.+.|+     -++.+
T Consensus       340 ~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~-~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipV  418 (505)
T PRK05636        340 QRLGKIAQAPIFIDDSANLTMMEIRSKARRLKQ-KHDLKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPL  418 (505)
T ss_pred             HHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeE
Confidence                  12456664     34444433332111 1358899999999875221    2233444444432     25777


Q ss_pred             EEEEeeCChh
Q psy4698         224 ILLSATMPAD  233 (258)
Q Consensus       224 i~~SAT~~~~  233 (258)
                      |++|. +++.
T Consensus       419 i~lsQ-LnR~  427 (505)
T PRK05636        419 IAISQ-LNRG  427 (505)
T ss_pred             EEEee-cCcc
Confidence            77764 4443

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

Probab=95.20  E-value=0.026  Score=44.51  Aligned_cols=40  Identities=18%  Similarity=0.276  Sum_probs=28.3

Q ss_pred             CCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHh
Q psy4698          69 KPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQV  109 (258)
Q Consensus        69 ~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l  109 (258)
                      .+++.|...+.. +..|..+++.|+||||||... -.++..+
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~i   49 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAFI   49 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhc
Confidence            356667666665 556789999999999999864 3344433

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

>PRK08760 replicative DNA helicase; Provisional

Probab=95.19  E-value=0.14  Score=46.52  Aligned_cols=140  Identities=17%  Similarity=0.156  Sum_probs=70.0

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH----
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD----  158 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----  158 (258)
                      .|.-++|.|.+|.|||...+-.+.......  +..++|++. -.-..|+..++........... ...+.....++    
T Consensus       228 ~G~LivIaarPg~GKTafal~iA~~~a~~~--g~~V~~fSl-EMs~~ql~~Rl~a~~s~i~~~~-i~~g~l~~~e~~~~~  303 (476)
T PRK08760        228 PTDLIILAARPAMGKTTFALNIAEYAAIKS--KKGVAVFSM-EMSASQLAMRLISSNGRINAQR-LRTGALEDEDWARVT  303 (476)
T ss_pred             CCceEEEEeCCCCChhHHHHHHHHHHHHhc--CCceEEEec-cCCHHHHHHHHHHhhCCCcHHH-HhcCCCCHHHHHHHH
Confidence            345589999999999987765554443332  235666653 2334455555444332222211 11122111111    


Q ss_pred             --HHHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHhCC---C--Ccc
Q psy4698         159 --IRKLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKHLN---N--DVQ  222 (258)
Q Consensus       159 --~~~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~l~---~--~~~  222 (258)
                        ...+.+ ..+.|.     |++.+...+++-. .-.++++||||=.+.+...    +....+..+.+.++   +  ++.
T Consensus       304 ~a~~~l~~-~~l~I~d~~~~t~~~I~~~~r~l~-~~~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ip  381 (476)
T PRK08760        304 GAIKMLKE-TKIFIDDTPGVSPEVLRSKCRRLK-REHDLGLIVIDYLQLMSVPGNSENRATEISEISRSLKGLAKELNVP  381 (476)
T ss_pred             HHHHHHhc-CCEEEeCCCCCCHHHHHHHHHHHH-HhcCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHHHHHHHhCCE
Confidence              112222 456554     4555554443211 1135789999999977422    22333444444432   2  566


Q ss_pred             EEEEEe
Q psy4698         223 VILLSA  228 (258)
Q Consensus       223 ~i~~SA  228 (258)
                      +|++|.
T Consensus       382 Vi~lsQ  387 (476)
T PRK08760        382 VIALSQ  387 (476)
T ss_pred             EEEeec
Confidence            777663

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=95.18  E-value=0.32  Score=38.15  Aligned_cols=53  Identities=17%  Similarity=0.367  Sum_probs=38.0

Q ss_pred             CCccEEEEccchhhhccCc--HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGF--KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~--~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      ..+++||+||+-..+..++  ..++..++..-|...-+|+..-..|..+.+.+..
T Consensus       121 ~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~ADl  175 (198)
T COG2109         121 GKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADL  175 (198)
T ss_pred             CCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHH
Confidence            3688999999998776654  3677777777666666666666678777666543

>KOG0739|consensus

Probab=95.17  E-value=0.37  Score=40.79  Aligned_cols=155  Identities=15%  Similarity=0.170  Sum_probs=84.8

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCC-----cEEEEcccCCCcchHhHHHHHHHhhhccccceEE
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN-----DVIAQAQSGTGKTATFSISILQQVDQNIKECQAL  119 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~-----~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~l  119 (258)
                      ....|.+..=-+...++|++.-+..      .-+|++..|+     -+++.||+|+||+..+-     .+..+.+  .+.
T Consensus       128 PNVkWsDVAGLE~AKeALKEAVILP------IKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAK-----AVATEAn--STF  194 (439)
T KOG0739|consen  128 PNVKWSDVAGLEGAKEALKEAVILP------IKFPQLFTGKRKPWRGILLYGPPGTGKSYLAK-----AVATEAN--STF  194 (439)
T ss_pred             CCCchhhhccchhHHHHHHhheeec------ccchhhhcCCCCcceeEEEeCCCCCcHHHHHH-----HHHhhcC--Cce
Confidence            3446666643344555565432111      0134566663     49999999999996542     2222222  466


Q ss_pred             EEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       120 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                      +-+.+..|+..|.-.-.++.                                  ..|+.+.+.+.     -++|.|||+|
T Consensus       195 FSvSSSDLvSKWmGESEkLV----------------------------------knLFemARe~k-----PSIIFiDEiD  235 (439)
T KOG0739|consen  195 FSVSSSDLVSKWMGESEKLV----------------------------------KNLFEMARENK-----PSIIFIDEID  235 (439)
T ss_pred             EEeehHHHHHHHhccHHHHH----------------------------------HHHHHHHHhcC-----CcEEEeehhh
Confidence            66667777766654333321                                  12334444332     3589999999


Q ss_pred             hhhccCcH------HHHH-HHHHhCC----CCccEEEEEeeC-ChhHHHHHHHhcCCCeEEEec
Q psy4698         200 EMLSRGFK------DQIY-DVFKHLN----NDVQVILLSATM-PADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       200 ~~~~~~~~------~~~~-~~~~~l~----~~~~~i~~SAT~-~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      .+......      ..+. .++-.++    .+--++.+.||- |=.+..-++..+.....|-.+
T Consensus       236 slcg~r~enEseasRRIKTEfLVQMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIPLP  299 (439)
T KOG0739|consen  236 SLCGSRSENESEASRRIKTEFLVQMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIPLP  299 (439)
T ss_pred             hhccCCCCCchHHHHHHHHHHHHhhhccccCCCceEEEecCCCchhHHHHHHHHhhcceeccCC
Confidence            87644322      2222 2333332    344678888884 556666666666666666443

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.14  E-value=0.027  Score=48.89  Aligned_cols=44  Identities=18%  Similarity=0.258  Sum_probs=29.7

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      .+..+++++|+|+||||||... -.++..+..   ..+++.+-.+.++
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll-~aLl~~i~~---~~rivtiEd~~El  201 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMS-KTLISAIPP---QERLITIEDTLEL  201 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHH-HHHHcccCC---CCCEEEECCCccc
Confidence            3557789999999999999864 344444433   2356666666554

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.11  E-value=0.072  Score=46.07  Aligned_cols=42  Identities=19%  Similarity=0.298  Sum_probs=27.8

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      +..+++++|+|+||||||... -.++..+...   .+++.+=-+.+
T Consensus       157 v~~~~nili~G~tgSGKTTll-~aL~~~ip~~---~ri~tiEd~~E  198 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTFT-NAALREIPAI---ERLITVEDARE  198 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHHH-HHHHhhCCCC---CeEEEecCCCc
Confidence            456789999999999999864 4455554432   25655533333

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=95.07  E-value=0.92  Score=39.03  Aligned_cols=36  Identities=19%  Similarity=0.201  Sum_probs=22.5

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ++-+++.||+|+|||+...--+.. +..  .+.+++++.
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~-l~~--~g~~V~Li~  149 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHK-YKA--QGKKVLLAA  149 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH-HHh--cCCeEEEEe
Confidence            345889999999999875433222 222  233666665

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.07  E-value=0.078  Score=51.68  Aligned_cols=18  Identities=39%  Similarity=0.591  Sum_probs=15.8

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .|.++.||.|.|||...-
T Consensus       209 ~n~lLvG~pGvGKTal~~  226 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVVE  226 (852)
T ss_pred             CceeEECCCCCCHHHHHH
Confidence            579999999999998763

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK05595 replicative DNA helicase; Provisional

Probab=95.02  E-value=0.25  Score=44.55  Aligned_cols=145  Identities=14%  Similarity=0.144  Sum_probs=69.5

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|.-++|.|.||.|||..++--+.......  +.+++|++.- ....|+..++..........  .+..+.....++..+
T Consensus       200 ~g~liviaarpg~GKT~~al~ia~~~a~~~--g~~vl~fSlE-ms~~~l~~R~~a~~~~v~~~--~~~~~~l~~~e~~~~  274 (444)
T PRK05595        200 KGDMILIAARPSMGKTTFALNIAEYAALRE--GKSVAIFSLE-MSKEQLAYKLLCSEANVDML--RLRTGNLEDKDWENI  274 (444)
T ss_pred             CCcEEEEEecCCCChHHHHHHHHHHHHHHc--CCcEEEEecC-CCHHHHHHHHHHHhcCCCHH--HHhcCCCCHHHHHHH
Confidence            345588999999999987655444333222  3357777642 23444444432222222211  111111111122111


Q ss_pred             h------cCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhccC----cHHHHHHHHHhCC-----CCcc
Q psy4698         163 E------AGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG----FKDQIYDVFKHLN-----NDVQ  222 (258)
Q Consensus       163 ~------~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~----~~~~~~~~~~~l~-----~~~~  222 (258)
                      .      ....+.|.     |++.+...+++-. .-.++++||||=.|.+....    ....+..+.+.++     -++.
T Consensus       275 ~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~-~~~~~~~vvIDylql~~~~~~~~~r~~~v~~is~~LK~lAke~~i~  353 (444)
T PRK05595        275 ARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLK-IEHGIDMILIDYLQLMSGGKGSESRQQEVSEISRSIKALAKEMECP  353 (444)
T ss_pred             HHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH-HhcCCCEEEEeHHHhccCCCCCccHHHHHHHHHHHHHHHHHHhCCe
Confidence            1      11345553     3444443333211 11358899999999875322    2233444444432     2566


Q ss_pred             EEEEEeeCChhH
Q psy4698         223 VILLSATMPADV  234 (258)
Q Consensus       223 ~i~~SAT~~~~~  234 (258)
                      ++++|. ++++.
T Consensus       354 vi~lsQ-LnR~~  364 (444)
T PRK05595        354 VIALSQ-LSRAP  364 (444)
T ss_pred             EEEeec-cCcch
Confidence            777654 45443

>PHA00012 I assembly protein

Probab=95.02  E-value=0.55  Score=40.26  Aligned_cols=62  Identities=13%  Similarity=0.203  Sum_probs=38.3

Q ss_pred             CCCccEEEEccchhhhccCc-----HHHHHHHHHhCC-CCccEEEEEeeCChhHHHHHHHhcCCCeEEE
Q psy4698         187 TKQIRMFVLDEADEMLSRGF-----KDQIYDVFKHLN-NDVQVILLSATMPADVLDVSMKFMRDPIKIL  249 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~-----~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~  249 (258)
                      .+.-+++|+||||..+....     ...+...+...+ ...-++++|... ..+...++..+..-++.+
T Consensus        79 ep~gsLlVlDEaq~~fp~R~~~sk~p~~vie~l~~hRh~G~DvilITQ~p-s~VDs~IR~ll~eH~v~c  146 (361)
T PHA00012         79 ESKNGLLVLDECGTWFNSRSWNDKERQPVIDWFLHARKLGWDIIFIIQDI-SIMDKQAREALAEHVVYC  146 (361)
T ss_pred             CCCCcEEEEECcccccCCCCcCcCCcHHHHHHHHHhccCCceEEEEcCCH-HHHhHHHHHhhhheEEEE
Confidence            35667999999998875321     133445444433 356677777764 477777776666555443

>KOG0058|consensus

Probab=95.01  E-value=0.067  Score=50.02  Aligned_cols=141  Identities=20%  Similarity=0.265  Sum_probs=74.8

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE-eccHHHHHHHHHHHHHhcCCCCceEE---------EE
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL-APTRELAQQIQKVVIALGDFMSVSCH---------AC  149 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil-~P~~~l~~q~~~~~~~~~~~~~~~~~---------~~  149 (258)
                      .+..|+.+.++||.|+|||.++  .++.+++.-..| ++++= +|-+.+-..+.+   +.....+-.-.         ..
T Consensus       490 ti~pGe~vALVGPSGsGKSTia--sLL~rfY~PtsG-~IllDG~~i~~~~~~~lr---~~Ig~V~QEPvLFs~sI~eNI~  563 (716)
T KOG0058|consen  490 TIRPGEVVALVGPSGSGKSTIA--SLLLRFYDPTSG-RILLDGVPISDINHKYLR---RKIGLVGQEPVLFSGSIRENIA  563 (716)
T ss_pred             eeCCCCEEEEECCCCCCHHHHH--HHHHHhcCCCCC-eEEECCeehhhcCHHHHH---HHeeeeeccceeecccHHHHHh
Confidence            3678999999999999999975  456666654322 22221 233333222222   21111110000         01


Q ss_pred             ECCcch--------------HHHHHHHhcCCcEEEeChHHHHH-------HHhcCCCCCCCccEEEEccchhhhccCcHH
Q psy4698         150 IGGTIV--------------RDDIRKLEAGAQVVVGTPGRVFD-------MISRGALSTKQIRMFVLDEADEMLSRGFKD  208 (258)
Q Consensus       150 ~~~~~~--------------~~~~~~~~~~~~Ilv~Tp~~l~~-------~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~  208 (258)
                      +|..+.              .+......+|++-.|+.-+..+.       .+-+  .-+++-..+|+|||-.-+|...+.
T Consensus       564 YG~~~~t~e~i~~AAk~ANah~FI~~~p~gY~T~VGEkG~qLSGGQKQRIAIAR--ALlr~P~VLILDEATSALDaeSE~  641 (716)
T KOG0058|consen  564 YGLDNATDEEIEAAAKMANAHEFITNFPDGYNTVVGEKGSQLSGGQKQRIAIAR--ALLRNPRVLILDEATSALDAESEY  641 (716)
T ss_pred             cCCCCCCHHHHHHHHHHhChHHHHHhCccccccccCCccccccchHHHHHHHHH--HHhcCCCEEEEechhhhcchhhHH
Confidence            111111              11223334455666655543221       0011  113455699999999999988888


Q ss_pred             HHHHHHHhCCCCccEEEEEee
Q psy4698         209 QIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       209 ~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      .+...+.++..+ +.+++=|.
T Consensus       642 lVq~aL~~~~~~-rTVlvIAH  661 (716)
T KOG0058|consen  642 LVQEALDRLMQG-RTVLVIAH  661 (716)
T ss_pred             HHHHHHHHhhcC-CeEEEEeh
Confidence            888888777666 45555554

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=95.01  E-value=0.29  Score=44.21  Aligned_cols=39  Identities=10%  Similarity=0.324  Sum_probs=23.8

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.+++||||+|.+... ....+.+.+..-+..+.+|+.+
T Consensus       120 ~~~kvvIIdead~lt~~-~~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKE-AFNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCHH-HHHHHHHHhhcCCCCceEEEEe
Confidence            45679999999987432 3344455555544555555543

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.00  E-value=0.18  Score=43.29  Aligned_cols=53  Identities=17%  Similarity=0.278  Sum_probs=31.1

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      ..+.+++|||+||.|.. ...+.+.+.+..-+++. ++++.++-+..+...++.-
T Consensus       106 ~~~~kV~iI~~ae~m~~-~AaNaLLKtLEEPp~~t-~fiL~t~~~~~lLpTI~SR  158 (319)
T PRK06090        106 LNGYRLFVIEPADAMNE-SASNALLKTLEEPAPNC-LFLLVTHNQKRLLPTIVSR  158 (319)
T ss_pred             cCCceEEEecchhhhCH-HHHHHHHHHhcCCCCCe-EEEEEECChhhChHHHHhc
Confidence            45678999999998832 24455555555544444 4444444455555554443

>TIGR03689 pup_AAA proteasome ATPase

Probab=94.95  E-value=0.053  Score=49.49  Aligned_cols=18  Identities=28%  Similarity=0.327  Sum_probs=15.7

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+.+++.||+|+|||..+
T Consensus       216 p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CcceEEECCCCCcHHHHH
Confidence            467999999999999864

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PHA00350 putative assembly protein

Probab=94.92  E-value=0.11  Score=45.88  Aligned_cols=24  Identities=13%  Similarity=0.159  Sum_probs=17.3

Q ss_pred             EEEEcccCCCcchHhHHH-HHHHhh
Q psy4698          87 VIAQAQSGTGKTATFSIS-ILQQVD  110 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~-~l~~l~  110 (258)
                      .++.|..|||||+.++-- ++..+.
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk   28 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALK   28 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHH
Confidence            478999999999887653 443333

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=94.88  E-value=0.23  Score=42.66  Aligned_cols=67  Identities=15%  Similarity=0.302  Sum_probs=37.0

Q ss_pred             EeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         170 VGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       170 v~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      |-....+.+.+....+ ....+++|||++|.|. ....+.+.+.+..-+ ++.+|+++. =+..+...++.
T Consensus       106 id~ir~i~~~l~~~p~-~~~~kVvII~~ae~m~-~~aaNaLLK~LEEPp-~~~fILi~~-~~~~Ll~TI~S  172 (314)
T PRK07399        106 LEQIREIKRFLSRPPL-EAPRKVVVIEDAETMN-EAAANALLKTLEEPG-NGTLILIAP-SPESLLPTIVS  172 (314)
T ss_pred             HHHHHHHHHHHccCcc-cCCceEEEEEchhhcC-HHHHHHHHHHHhCCC-CCeEEEEEC-ChHhCcHHHHh
Confidence            3333344444444332 3578899999999873 234555666666655 565555443 34444444433

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.87  E-value=0.18  Score=45.39  Aligned_cols=80  Identities=18%  Similarity=0.166  Sum_probs=57.5

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHH
Q psy4698          57 ELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI  136 (258)
Q Consensus        57 ~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~  136 (258)
                      .+++.+++ ++..+-..|.++.-..-.|+- .|.|-.|||||.....-+. .+...+..-+++|.+=|+.|+.+......
T Consensus       151 a~l~~ies-kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa-~lh~knPd~~I~~Tfftk~L~s~~r~lv~  227 (660)
T COG3972         151 ALLDTIES-KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAA-ELHSKNPDSRIAFTFFTKILASTMRTLVP  227 (660)
T ss_pred             HHHHHHHH-HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHHH-HHhcCCCCceEEEEeehHHHHHHHHHHHH
Confidence            44444443 344667778887766666765 7899999999987654443 34445556699999999999999988887


Q ss_pred             Hhc
Q psy4698         137 ALG  139 (258)
Q Consensus       137 ~~~  139 (258)
                      +|+
T Consensus       228 ~F~  230 (660)
T COG3972         228 EFF  230 (660)
T ss_pred             HHH
Confidence            765

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=94.86  E-value=0.035  Score=46.48  Aligned_cols=43  Identities=14%  Similarity=0.354  Sum_probs=29.6

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      +..+.+++++|+||||||... ..++..+...  ..+++++-...+
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E  166 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPE  166 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccc
Confidence            456788999999999999875 5555555544  236777765544

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.86  E-value=0.1  Score=50.18  Aligned_cols=52  Identities=19%  Similarity=0.219  Sum_probs=28.9

Q ss_pred             cCcCCCCCCHHHHHHHHHC---CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAY---GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~---~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|.+.+-...+.+.|.+.   .+..+..++..   -+...+.+++.||+|+|||..+
T Consensus       450 ~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~---g~~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       450 VRWSDIGGLEEVKQELREAVEWPLKHPEIFEKM---GIRPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             cchhhcccHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEECCCCCCHHHHH
Confidence            3566666666666655442   11111111111   1223356999999999999875

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0742|consensus

Probab=94.85  E-value=0.065  Score=47.05  Aligned_cols=17  Identities=29%  Similarity=0.419  Sum_probs=15.3

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +|+++.||+|+|||+.+
T Consensus       385 RNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFA  401 (630)
T ss_pred             hheeeeCCCCCCchHHH
Confidence            58999999999999865

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.81  E-value=0.19  Score=48.30  Aligned_cols=20  Identities=30%  Similarity=0.287  Sum_probs=16.7

Q ss_pred             hcCCcEEEEcccCCCcchHh
Q psy4698          82 VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..++.+++.||+|+|||..+
T Consensus       210 ~~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       210 EPPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCCceEEEECCCCCChHHHH
Confidence            34578999999999999764

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=94.80  E-value=0.037  Score=45.01  Aligned_cols=15  Identities=20%  Similarity=0.592  Sum_probs=12.9

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      ++|.|+.|||||...
T Consensus         1 ~vv~G~pGsGKSt~i   15 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLI   15 (234)
T ss_pred             CEEEcCCCCCHHHHH
Confidence            478999999999864

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>TIGR00767 rho transcription termination factor Rho

Probab=94.76  E-value=0.26  Score=43.54  Aligned_cols=31  Identities=26%  Similarity=0.320  Sum_probs=21.7

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhc
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQN  112 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~  112 (258)
                      +-.|..++|.||+|+|||... ..+...+..+
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~-~~i~~~I~~n  195 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLL-QKIAQAITRN  195 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHH-HHHHHhhccc
Confidence            446788999999999999754 3344444433

Members of this family differ in the specificity of RNA binding.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.73  E-value=0.23  Score=48.58  Aligned_cols=47  Identities=13%  Similarity=0.111  Sum_probs=27.7

Q ss_pred             ccEEEEccchhhhccCc---HHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         190 IRMFVLDEADEMLSRGF---KDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~---~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      -.+|+|||+|.+...+.   ......+++..-..-.+.++.||-.++++.
T Consensus       267 ~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~g~i~~IgaTt~~e~r~  316 (852)
T TIGR03346       267 QIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGATTLDEYRK  316 (852)
T ss_pred             CeEEEeccHHHhhcCCCCcchhHHHHHhchhhhcCceEEEEeCcHHHHHH
Confidence            34899999999874221   122333333332344577777887776644

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK10436 hypothetical protein; Provisional

Probab=94.73  E-value=0.048  Score=49.27  Aligned_cols=40  Identities=23%  Similarity=0.361  Sum_probs=26.1

Q ss_pred             cHHHHHHhhhhhc--CCcEEEEcccCCCcchHhHHHHHHHhhh
Q psy4698          71 SAIQQRAIIPCVR--GNDVIAQAQSGTGKTATFSISILQQVDQ  111 (258)
Q Consensus        71 ~~~Q~~~~~~l~~--g~~~li~~~tGsGKT~~~l~~~l~~l~~  111 (258)
                      .+.|.+.+..+..  +.-++++||||||||.+. ..++..+..
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~~  244 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLNT  244 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhCC
Confidence            4455555555433  345899999999999875 345555543

>KOG0732|consensus

Probab=94.72  E-value=0.074  Score=51.96  Aligned_cols=142  Identities=16%  Similarity=0.195  Sum_probs=77.1

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCC-CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFE-KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ....|.+.|-...+++.|+++-.. -++|-+..-+ .+..-+.++++||.|+|||+.+- ++......+.+         
T Consensus       260 ~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~-~itpPrgvL~~GppGTGkTl~ar-aLa~~~s~~~~---------  328 (1080)
T KOG0732|consen  260 SSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNF-NITPPRGVLFHGPPGTGKTLMAR-ALAAACSRGNR---------  328 (1080)
T ss_pred             cccCccccccHHHHHHHHHHHHHhHhhhhhHhhhc-ccCCCcceeecCCCCCchhHHHH-hhhhhhccccc---------
Confidence            335788888778888888775431 2222222222 23344669999999999998751 11111111111         


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC---CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchh
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG---AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE  200 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  200 (258)
                                   +..      +              ....|   .+--|+..++=+.++.... .-.....+.+||++=
T Consensus       329 -------------kis------f--------------fmrkgaD~lskwvgEaERqlrllFeeA-~k~qPSIIffdeIdG  374 (1080)
T KOG0732|consen  329 -------------KIS------F--------------FMRKGADCLSKWVGEAERQLRLLFEEA-QKTQPSIIFFDEIDG  374 (1080)
T ss_pred             -------------ccc------h--------------hhhcCchhhccccCcHHHHHHHHHHHH-hccCceEEecccccc
Confidence                         100      0              00111   1233666666555554321 122456899999992


Q ss_pred             h-------h---ccCcHHHHHHHHHhCCCCccEEEEEeeCC
Q psy4698         201 M-------L---SRGFKDQIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       201 ~-------~---~~~~~~~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                      +       .   .......+..++.-++...|++..+||--
T Consensus       375 lapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnR  415 (1080)
T KOG0732|consen  375 LAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNR  415 (1080)
T ss_pred             ccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCC
Confidence            2       1   11234555556666677889999999963

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=94.72  E-value=0.16  Score=43.98  Aligned_cols=52  Identities=12%  Similarity=0.298  Sum_probs=31.1

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK  240 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~  240 (258)
                      ..+.+++||||+|.+... ..+.+.+.+..-++.+.+|+ .++-+..+...++.
T Consensus       108 ~~~~kvviI~~a~~~~~~-a~NaLLK~LEEPp~~~~~Il-~t~~~~~ll~TIrS  159 (329)
T PRK08058        108 ESNKKVYIIEHADKMTAS-AANSLLKFLEEPSGGTTAIL-LTENKHQILPTILS  159 (329)
T ss_pred             ccCceEEEeehHhhhCHH-HHHHHHHHhcCCCCCceEEE-EeCChHhCcHHHHh
Confidence            356789999999987432 44556666666555565555 44434444444443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.69  E-value=0.2  Score=48.99  Aligned_cols=46  Identities=15%  Similarity=0.122  Sum_probs=26.8

Q ss_pred             cEEEEccchhhhccC---cHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         191 RMFVLDEADEMLSRG---FKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       191 ~~lVvDE~h~~~~~~---~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      .+|+|||+|.+...+   -......++...-.+-.+.++.||-+++++.
T Consensus       273 ~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~g~l~~IgaTt~~e~r~  321 (857)
T PRK10865        273 VILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQ  321 (857)
T ss_pred             eEEEEecHHHhccCCCCccchhHHHHhcchhhcCCCeEEEcCCCHHHHH
Confidence            389999999986442   1112233333222344667777887777643

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=94.68  E-value=0.2  Score=44.48  Aligned_cols=19  Identities=32%  Similarity=0.335  Sum_probs=16.7

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+.+++.||+|+|||+.+
T Consensus       178 ~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        178 PPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4578999999999999875

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.67  E-value=0.031  Score=49.33  Aligned_cols=49  Identities=27%  Similarity=0.289  Sum_probs=36.8

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ++++.|+||||||..+++|-+...     +..++|+=|.-++........+..+
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~~G   49 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRALG   49 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHHcC
Confidence            578999999999999887766542     2368888888888877666655543

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>TIGR00416 sms DNA repair protein RadA

Probab=94.67  E-value=0.23  Score=44.95  Aligned_cols=92  Identities=18%  Similarity=0.205  Sum_probs=53.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|.-+++.|++|+|||...+..+......   +.+++|+... +...|....+.+++-... .... ...          
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a~~---g~kvlYvs~E-Es~~qi~~ra~rlg~~~~-~l~~-~~e----------  156 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLAKN---QMKVLYVSGE-ESLQQIKMRAIRLGLPEP-NLYV-LSE----------  156 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEECc-CCHHHHHHHHHHcCCChH-HeEE-cCC----------
Confidence            34669999999999998876555443332   2368888754 345566555555431110 0000 000          


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                              .+.+.+...+..     .+.+++|||.+..+..
T Consensus       157 --------~~~~~I~~~i~~-----~~~~~vVIDSIq~l~~  184 (454)
T TIGR00416       157 --------TNWEQICANIEE-----ENPQACVIDSIQTLYS  184 (454)
T ss_pred             --------CCHHHHHHHHHh-----cCCcEEEEecchhhcc
Confidence                    134555555543     2457999999987653

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.67  E-value=0.34  Score=45.56  Aligned_cols=45  Identities=11%  Similarity=0.206  Sum_probs=27.4

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChh
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPAD  233 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~  233 (258)
                      ..+.+++||||+|.+.. .....+.+.+...+..+.+| +.+|-+..
T Consensus       119 ~~~~KVvIIdea~~Ls~-~a~naLLK~LEepp~~tifI-L~tt~~~k  163 (614)
T PRK14971        119 IGKYKIYIIDEVHMLSQ-AAFNAFLKTLEEPPSYAIFI-LATTEKHK  163 (614)
T ss_pred             cCCcEEEEEECcccCCH-HHHHHHHHHHhCCCCCeEEE-EEeCCchh
Confidence            45678999999998743 24445556666655555444 44443333

>PRK06321 replicative DNA helicase; Provisional

Probab=94.65  E-value=0.47  Score=43.13  Aligned_cols=139  Identities=17%  Similarity=0.161  Sum_probs=68.6

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEE-ECCcchHHHH---
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHAC-IGGTIVRDDI---  159 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~---  159 (258)
                      |.-++|.|.+|.|||.-.+--+.......  +..++|++. -.-..|+..++-.......  ...+ .+.....++.   
T Consensus       226 G~LiiiaarPgmGKTafal~ia~~~a~~~--g~~v~~fSL-EMs~~ql~~Rlla~~s~v~--~~~i~~~~l~~~e~~~~~  300 (472)
T PRK06321        226 SNLMILAARPAMGKTALALNIAENFCFQN--RLPVGIFSL-EMTVDQLIHRIICSRSEVE--SKKISVGDLSGRDFQRIV  300 (472)
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHhc--CCeEEEEec-cCCHHHHHHHHHHhhcCCC--HHHhhcCCCCHHHHHHHH
Confidence            44588999999999987655333322222  234666652 2334444444322222221  1111 1222222211   


Q ss_pred             ---HHHhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhccC-------cHHHHHHHHHhCC-----C
Q psy4698         160 ---RKLEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-------FKDQIYDVFKHLN-----N  219 (258)
Q Consensus       160 ---~~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~-------~~~~~~~~~~~l~-----~  219 (258)
                         ..+.. ..+.|.     |.+.+...+++-. .-.++++||||=.+.+...+       ....+..+.+.++     -
T Consensus       301 ~a~~~l~~-~~~~idd~~~~ti~~i~~~~r~~~-~~~~~~lvvIDyLql~~~~~~~~~~~~r~~ei~~Isr~LK~lAkel  378 (472)
T PRK06321        301 SVVNEMQE-HTLLIDDQPGLKITDLRARARRMK-ESYDIQFLIIDYLQLLSGSGNLRNSESRQTEISEISRMLKNLAREL  378 (472)
T ss_pred             HHHHHHHc-CCEEEeCCCCCCHHHHHHHHHHHH-HhcCCCEEEEcchHHcCCCCccCCcchHHHHHHHHHHHHHHHHHHh
Confidence               22222 456665     4555544443311 12458899999999774221       2234444554443     2


Q ss_pred             CccEEEEEee
Q psy4698         220 DVQVILLSAT  229 (258)
Q Consensus       220 ~~~~i~~SAT  229 (258)
                      ++.+|++|.-
T Consensus       379 ~vpVi~lsQL  388 (472)
T PRK06321        379 NIPILCLSQL  388 (472)
T ss_pred             CCcEEEEeec
Confidence            6767776653

>KOG1133|consensus

Probab=94.64  E-value=0.05  Score=50.49  Aligned_cols=42  Identities=24%  Similarity=0.303  Sum_probs=34.4

Q ss_pred             CCcHHHHHHhhh----hhcCCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          69 KPSAIQQRAIIP----CVRGNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        69 ~~~~~Q~~~~~~----l~~g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      +|+++|.+.+..    +-.|+--|+.+|||+|||+..+=..+..+.
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~   60 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLR   60 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHH
Confidence            789999887766    457888999999999999987766666653

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.63  E-value=0.4  Score=43.78  Aligned_cols=37  Identities=14%  Similarity=0.283  Sum_probs=21.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVIL  225 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~  225 (258)
                      ...+++|+||+|.+... ..+.+...+...+..+-+|+
T Consensus       118 ~~~KVvIIDEad~Lt~~-a~naLLk~LEepp~~~v~Il  154 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKE-AFNALLKTLEEPPPRTIFIL  154 (486)
T ss_pred             CCeeEEEEEChhhcCHH-HHHHHHHHHhcCCCCeEEEE
Confidence            46789999999977433 23344445554444443333

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=94.57  E-value=0.038  Score=44.53  Aligned_cols=25  Identities=16%  Similarity=0.440  Sum_probs=18.0

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQV  109 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l  109 (258)
                      +..++|.||.|+|||... ..++..+
T Consensus        20 ~~~~~l~G~rg~GKTsLl-~~~~~~~   44 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLL-KEFINEL   44 (234)
T ss_dssp             SSEEEEEESTTSSHHHHH-HHHHHHC
T ss_pred             CcEEEEEcCCcCCHHHHH-HHHHHHh
Confidence            367999999999999853 3444444

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK05973 replicative DNA helicase; Provisional

Probab=94.56  E-value=0.15  Score=41.78  Aligned_cols=56  Identities=20%  Similarity=0.200  Sum_probs=37.6

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      -+..|.-++|.|++|+|||...+..+.+.+.+   +.+++|++-. +-..+....+..++
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vlyfSlE-es~~~i~~R~~s~g  115 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGVFFTLE-YTEQDVRDRLRALG  115 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEEEe-CCHHHHHHHHHHcC
Confidence            34556679999999999998877666655543   3367787643 23466666665553

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=94.52  E-value=0.39  Score=45.74  Aligned_cols=46  Identities=13%  Similarity=0.265  Sum_probs=26.5

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVL  235 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~  235 (258)
                      ...+++|+||+|.|... ....+.+.+...+..+.+|+ .+|-+..+.
T Consensus       117 g~~KV~IIDEa~~LT~~-A~NALLKtLEEPP~~tifIL-aTte~~KLl  162 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKS-AFNALLKTLEEPPKHVIFIL-ATTEVHKIP  162 (725)
T ss_pred             CCCEEEEEEChhhCCHH-HHHHHHHHhhcCCCceEEEE-EcCChhhhh
Confidence            56789999999987432 34444555555444454444 334444443

>TIGR00763 lon ATP-dependent protease La

Probab=94.43  E-value=0.21  Score=48.33  Aligned_cols=19  Identities=26%  Similarity=0.296  Sum_probs=15.9

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+++.||+|+|||..+
T Consensus       346 ~~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3457999999999999865

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>KOG0734|consensus

Probab=94.41  E-value=0.25  Score=44.93  Aligned_cols=65  Identities=15%  Similarity=0.216  Sum_probs=35.1

Q ss_pred             cEEEEccchhhhccCc-------HHHHHHHHHh---CCCCccEEEEEeeC-ChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         191 RMFVLDEADEMLSRGF-------KDQIYDVFKH---LNNDVQVILLSATM-PADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       191 ~~lVvDE~h~~~~~~~-------~~~~~~~~~~---l~~~~~~i~~SAT~-~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      ..|.|||+|.+.....       ...+..++..   +..+--+|.+.||- |..+..-+-.-.+--..|.|+..++
T Consensus       398 cIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv  473 (752)
T KOG0734|consen  398 CIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDKALTRPGRFDRHVTVPLPDV  473 (752)
T ss_pred             eEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhHHhcCCCccceeEecCCCCc
Confidence            4789999997753211       1222233333   34566799999994 4444333333333334555555443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.40  E-value=0.36  Score=38.56  Aligned_cols=39  Identities=21%  Similarity=0.250  Sum_probs=27.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|.-+.+.|++|+|||...+..+......   +.+++|+.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            34568999999999998876555544432   3468888764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR02012 tigrfam_recA protein RecA

Probab=94.35  E-value=0.11  Score=44.72  Aligned_cols=44  Identities=18%  Similarity=0.180  Sum_probs=30.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ  129 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~  129 (258)
                      .|.-+.|.||+|+|||...+..+......   +.+++|+.....+..
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~---g~~v~yId~E~~~~~   97 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDP   97 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEcccchhHH
Confidence            34668999999999998876555554332   346888866554444

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PRK09354 recA recombinase A; Provisional

Probab=94.31  E-value=0.12  Score=44.79  Aligned_cols=43  Identities=19%  Similarity=0.150  Sum_probs=31.0

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ  129 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~  129 (258)
                      |+-+.|.||+|+|||...+..+......   +.+++|+.....+-.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~---G~~~~yId~E~s~~~  102 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDP  102 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEECCccchHH
Confidence            4568999999999998876665554432   347888887655554

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.31  E-value=0.052  Score=49.22  Aligned_cols=50  Identities=24%  Similarity=0.346  Sum_probs=38.3

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .++++.||||||||..+++|.+-.  ..   ..+||.=|..++........++.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~--~~---~s~iV~D~KgEl~~~t~~~r~~~G   94 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN--YP---GSMIVTDPKGELYEKTAGYRKKRG   94 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh--cc---CCEEEEECCCcHHHHHHHHHHHCC
Confidence            479999999999999998887633  21   257777788888887777666654

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>KOG0737|consensus

Probab=94.30  E-value=0.3  Score=42.27  Aligned_cols=56  Identities=18%  Similarity=0.072  Sum_probs=34.2

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCC-CcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEK-PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~-~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+|.+.+=-+.+++.|++.-.-. -+|-.-.-...+...+.+++.||.|+|||.++
T Consensus        88 ~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlA  144 (386)
T KOG0737|consen   88 GVSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLA  144 (386)
T ss_pred             eeehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHH
Confidence            357888877777777776532211 11111111222334478999999999999876

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=94.29  E-value=0.19  Score=41.61  Aligned_cols=30  Identities=23%  Similarity=0.295  Sum_probs=21.2

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQ  111 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~  111 (258)
                      +-.|..++|.|+.|+|||... --+++.+..
T Consensus        13 i~~Gqr~~I~G~~G~GKTTLl-r~I~n~l~~   42 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTLL-QSIANAITK   42 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHHH-HHHHhcccc
Confidence            457888999999999999643 334444433

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=94.28  E-value=0.1  Score=43.64  Aligned_cols=39  Identities=18%  Similarity=0.294  Sum_probs=25.7

Q ss_pred             cHHHHHHhhhhhc--CCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          71 SAIQQRAIIPCVR--GNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        71 ~~~Q~~~~~~l~~--g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .+.|.+.+..+..  +..++|.|+||||||... ..++..+.
T Consensus        65 ~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~  105 (264)
T cd01129          65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSELN  105 (264)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhC
Confidence            4556666655443  345899999999999875 34444443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=94.26  E-value=0.35  Score=42.66  Aligned_cols=29  Identities=24%  Similarity=0.366  Sum_probs=20.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQN  112 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~  112 (258)
                      .|.-.+|.||.|.|||..+ ..+.+.+..+
T Consensus       168 kGQR~lIvgppGvGKTTLa-K~Ian~I~~n  196 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLL-QNIANSITTN  196 (416)
T ss_pred             cCceEEEeCCCCCChhHHH-HHHHHHHHhh
Confidence            6677999999999999754 3355555443

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=94.26  E-value=0.43  Score=43.60  Aligned_cols=52  Identities=23%  Similarity=0.300  Sum_probs=37.7

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      |..+++.|++|+|||+..+..+...+.+   +.+++|++ ..+...|....++.++
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~~---ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACAN---KERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            3569999999999999776665555443   33688877 5666777777777765

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=94.20  E-value=0.069  Score=49.66  Aligned_cols=39  Identities=18%  Similarity=0.359  Sum_probs=26.1

Q ss_pred             cHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          71 SAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .+.|...+..+...  ..++++||||||||++. ..++..+.
T Consensus       301 ~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       301 EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            45555555554433  34889999999999875 45555553

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=94.20  E-value=0.25  Score=43.64  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=18.4

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .-.|.++++.|+||+||++.+
T Consensus        98 ap~~~~vLi~GetGtGKel~A  118 (403)
T COG1221          98 APSGLPVLIIGETGTGKELFA  118 (403)
T ss_pred             CCCCCcEEEecCCCccHHHHH
Confidence            457789999999999999876

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=94.19  E-value=0.028  Score=43.77  Aligned_cols=42  Identities=21%  Similarity=0.354  Sum_probs=27.3

Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCC---CCCCCccEEEEccchhhhc
Q psy4698         161 KLEAGAQVVVGTPGRVFDMISRGA---LSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       161 ~~~~~~~Ilv~Tp~~l~~~l~~~~---~~~~~l~~lVvDE~h~~~~  203 (258)
                      .....++|+|++...|++-..+..   +.+ +-.+|||||||.+.+
T Consensus       115 ~~~~~adivi~~y~yl~~~~~~~~~~~~~~-~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  115 ELAKNADIVICNYNYLFDPSIRKSLFGIDL-KDNIVIFDEAHNLED  159 (174)
T ss_dssp             HCGGG-SEEEEETHHHHSHHHHHHHCT--C-CCEEEEETTGGGCGG
T ss_pred             HhcccCCEEEeCHHHHhhHHHHhhhccccc-cCcEEEEecccchHH
Confidence            344458999999988876443322   223 346999999998754

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.18  E-value=0.032  Score=47.32  Aligned_cols=19  Identities=21%  Similarity=0.394  Sum_probs=16.2

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ..|+++.||||||||+.+.
T Consensus        97 KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eccEEEECCCCCcHHHHHH
Confidence            3479999999999998764

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=94.18  E-value=0.058  Score=49.08  Aligned_cols=15  Identities=27%  Similarity=0.363  Sum_probs=13.8

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      .+++||-|.|||.++
T Consensus        41 YlfsG~RGvGKTt~A   55 (515)
T COG2812          41 YLFSGPRGVGKTTIA   55 (515)
T ss_pred             hhhcCCCCcCchhHH
Confidence            699999999999976

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=94.17  E-value=0.66  Score=36.00  Aligned_cols=45  Identities=7%  Similarity=0.117  Sum_probs=29.7

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      ++|.|++|||||.-+...+..      .+.+++|+.-.........+++..
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~------~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE------LGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh------cCCCeEEEEccCcCCHHHHHHHHH
Confidence            588999999999876543322      234788887666665555554433

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PF12846 AAA_10: AAA-like domain

Probab=94.15  E-value=0.06  Score=45.33  Aligned_cols=25  Identities=20%  Similarity=0.328  Sum_probs=19.1

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHh
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQV  109 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l  109 (258)
                      ++++|.|+||+|||......+.+.+
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l~~~~~   26 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNLLEQLI   26 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHH
Confidence            5789999999999988764444433

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=94.13  E-value=0.078  Score=48.30  Aligned_cols=39  Identities=21%  Similarity=0.313  Sum_probs=26.4

Q ss_pred             cHHHHHHhhhhhcCC--cEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          71 SAIQQRAIIPCVRGN--DVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~--~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .+.|.+.+..+....  -++++||||||||... ..++..+.
T Consensus       227 ~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       227 SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            556666666655443  3789999999999875 33455554

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=94.12  E-value=0.092  Score=44.67  Aligned_cols=17  Identities=24%  Similarity=0.386  Sum_probs=14.9

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .++++.||+|+|||..+
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999765

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=94.05  E-value=0.59  Score=38.29  Aligned_cols=37  Identities=19%  Similarity=0.179  Sum_probs=25.6

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhh---------hccccceEEEEe
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVD---------QNIKECQALILA  122 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~---------~~~~~~~~lil~  122 (258)
                      -.++.|+.|+|||...+..++....         ....+.+++|++
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~   48 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLS   48 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEE
Confidence            4689999999999887665554321         112345788988

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.88  E-value=0.076  Score=49.58  Aligned_cols=50  Identities=20%  Similarity=0.119  Sum_probs=40.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .++++.||||||||..+++|-+...     +..++|+=|.-++........++.+
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~-----~~S~VV~DpKGEl~~~Ta~~R~~~G  208 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW-----EDSVVVHDIKLENYELTSGWREKQG  208 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC-----CCCEEEEeCcHHHHHHHHHHHHHCC
Confidence            4799999999999999999987663     2358888888888888877776654

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=93.86  E-value=0.088  Score=46.56  Aligned_cols=45  Identities=22%  Similarity=0.345  Sum_probs=26.6

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      .-...+++++.|.||||||.+ +..++..+...+  .++||.=|.-+.
T Consensus        11 ~~~e~~~~li~G~~GsGKT~~-i~~ll~~~~~~g--~~~iI~D~kg~~   55 (386)
T PF10412_consen   11 KDSENRHILIIGATGSGKTQA-IRHLLDQIRARG--DRAIIYDPKGEF   55 (386)
T ss_dssp             GGGGGG-EEEEE-TTSSHHHH-HHHHHHHHHHTT---EEEEEEETTHH
T ss_pred             cchhhCcEEEECCCCCCHHHH-HHHHHHHHHHcC--CEEEEEECCchH
Confidence            345668899999999999974 466666664432  234444444333

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>KOG0730|consensus

Probab=93.86  E-value=0.11  Score=48.03  Aligned_cols=62  Identities=23%  Similarity=0.252  Sum_probs=40.0

Q ss_pred             cccccccccccCcCCCCCCHHHHHHHHH---CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          37 LIETNWDHVAENFDDMELSEELLRGIYA---YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~---~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +.+.-+.....+|++.|=-+.+++.|++   ....+|-.+.+..   +..-+-+++.||+|+|||+++
T Consensus       421 ~Re~~ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~G---i~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  421 LREILVEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFG---ISPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             hhheeccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhc---CCCCceEEEECCCCcchHHHH
Confidence            3333455566789999866777777653   2333444343333   233467999999999999976

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=93.86  E-value=0.23  Score=45.44  Aligned_cols=53  Identities=21%  Similarity=0.227  Sum_probs=29.3

Q ss_pred             ccCcCCCCCCHHHHHHHHHC--CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          46 AENFDDMELSEELLRGIYAY--GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~--~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+|+++.-.+.+.+.+.+.  .+..+..++..-   ....+.+++.||+|+|||..+
T Consensus        51 ~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~la  105 (495)
T TIGR01241        51 KVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLLA  105 (495)
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHHH
Confidence            34677776555555444321  122222222211   122357999999999999875

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=93.84  E-value=0.093  Score=48.82  Aligned_cols=42  Identities=17%  Similarity=0.302  Sum_probs=31.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      .+-+++++||+-.-+|......+.+.+....++.-+|..|-.
T Consensus       486 ~~~~illLDEpts~LD~~~~~~i~~~L~~~~~~~tiIiitH~  527 (571)
T TIGR02203       486 KDAPILILDEATSALDNESERLVQAALERLMQGRTTLVIAHR  527 (571)
T ss_pred             cCCCEEEEeCccccCCHHHHHHHHHHHHHHhCCCEEEEEehh
Confidence            344699999999888888888888888777666556665544

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.80  E-value=0.12  Score=44.54  Aligned_cols=44  Identities=14%  Similarity=0.105  Sum_probs=30.9

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQ  130 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q  130 (258)
                      |+-+.|.||.|+|||...+..+......   +.+++|+.....+-.+
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~---g~~~vyId~E~~~~~~   98 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKL---GGTVAFIDAEHALDPV   98 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEECccccHHHH
Confidence            4668999999999998776555544332   3478888876555543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=93.80  E-value=0.095  Score=48.90  Aligned_cols=42  Identities=17%  Similarity=0.330  Sum_probs=31.9

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      +-+++|+||+-.-+|......+...+..+..++.+|..|--+
T Consensus       498 ~~~ililDEptsaLD~~t~~~i~~~l~~~~~~~tvI~VtHr~  539 (582)
T PRK11176        498 DSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRL  539 (582)
T ss_pred             CCCEEEEECccccCCHHHHHHHHHHHHHHhCCCEEEEEecch
Confidence            346899999998888888888888887776666666666543

>KOG2227|consensus

Probab=93.78  E-value=0.24  Score=44.19  Aligned_cols=49  Identities=27%  Similarity=0.320  Sum_probs=29.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE-eccHHHHHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL-APTRELAQQIQKV  134 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil-~P~~~l~~q~~~~  134 (258)
                      .++.|+|.+|.|||.+... ++..+.....++.++++ |-+...+..++..
T Consensus       176 gSlYVsG~PGtgkt~~l~r-vl~~~~~~~~~~~~v~inc~sl~~~~aiF~k  225 (529)
T KOG2227|consen  176 GSLYVSGQPGTGKTALLSR-VLDSLSKSSKSPVTVYINCTSLTEASAIFKK  225 (529)
T ss_pred             cceEeeCCCCcchHHHHHH-HHHhhhhhcccceeEEEeeccccchHHHHHH
Confidence            5799999999999987532 33344444444343444 3333555555544

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=93.72  E-value=0.24  Score=46.93  Aligned_cols=70  Identities=20%  Similarity=0.264  Sum_probs=53.6

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .+++-|++++...  ...++|.++.|||||.+..--+.+.+... -...+++.++=|+..+.+...++.++..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5789999999665  45578888899999998877776666654 2334688888888888888888877654

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=93.71  E-value=0.08  Score=49.31  Aligned_cols=43  Identities=16%  Similarity=0.319  Sum_probs=30.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ++-+++++||+-.-+|......+.+.++.+.++..+|..|--.
T Consensus       493 ~~~~ililDEpts~lD~~~~~~i~~~l~~~~~~~t~IiitH~~  535 (576)
T TIGR02204       493 KDAPILLLDEATSALDAESEQLVQQALETLMKGRTTLIIAHRL  535 (576)
T ss_pred             hCCCeEEEeCcccccCHHHHHHHHHHHHHHhCCCEEEEEecch
Confidence            3456999999998778777777777777765555555555543

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=93.70  E-value=0.14  Score=51.52  Aligned_cols=56  Identities=21%  Similarity=0.311  Sum_probs=46.2

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhcc--ccceEEEEeccHHHHHHHHHHHHH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNI--KECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~--~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      -.+.+++|.|..|||||.+...-++..+...+  .-.++++++-|+.-+.....++.+
T Consensus        14 ~~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~   71 (1139)
T COG1074          14 PPGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRD   71 (1139)
T ss_pred             CCCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHH
Confidence            45678999999999999998888888887743  445899999999988888776655

>CHL00095 clpC Clp protease ATP binding subunit

Probab=93.65  E-value=0.85  Score=44.56  Aligned_cols=21  Identities=33%  Similarity=0.302  Sum_probs=17.2

Q ss_pred             CcEEEEcccCCCcchHhHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISI  105 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~  105 (258)
                      ++.++.||+|.|||......+
T Consensus       201 ~n~lL~G~pGvGKTal~~~la  221 (821)
T CHL00095        201 NNPILIGEPGVGKTAIAEGLA  221 (821)
T ss_pred             CCeEEECCCCCCHHHHHHHHH
Confidence            589999999999998874333

>PRK13764 ATPase; Provisional

Probab=93.63  E-value=0.11  Score=48.32  Aligned_cols=29  Identities=14%  Similarity=0.276  Sum_probs=21.5

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhh
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQ  111 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~  111 (258)
                      ..+++++++|+||||||+.. ..++..+..
T Consensus       255 ~~~~~ILIsG~TGSGKTTll-~AL~~~i~~  283 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTFA-QALAEFYAD  283 (602)
T ss_pred             hcCCEEEEECCCCCCHHHHH-HHHHHHHhh
Confidence            34678999999999999864 455555543

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=93.61  E-value=0.34  Score=41.54  Aligned_cols=54  Identities=7%  Similarity=-0.021  Sum_probs=32.6

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhh---ccccceEEEEeccHHH-HHHHHHHHHHh
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQ---NIKECQALILAPTREL-AQQIQKVVIAL  138 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~---~~~~~~~lil~P~~~l-~~q~~~~~~~~  138 (258)
                      .-+.|.|++|+|||...+..++.....   .+.+.+++|+.-.... .++..+.++.+
T Consensus        97 ~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~  154 (313)
T TIGR02238        97 SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERF  154 (313)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHc
Confidence            457899999999997765555443322   2334589998754332 34444444444

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=93.55  E-value=0.049  Score=50.90  Aligned_cols=43  Identities=9%  Similarity=0.271  Sum_probs=31.3

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ++-+++++||+=.-+|......+...+..+.++..+|..|--+
T Consensus       502 ~~~~IliLDE~TSaLD~~te~~i~~~l~~~~~~~TvIiItHrl  544 (588)
T PRK11174        502 QPCQLLLLDEPTASLDAHSEQLVMQALNAASRRQTTLMVTHQL  544 (588)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHhCCCEEEEEecCh
Confidence            3456999999998888888888888777775555555555443

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=93.54  E-value=0.059  Score=51.46  Aligned_cols=42  Identities=14%  Similarity=0.293  Sum_probs=31.0

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ++-+++|+||+=.-+|......+...+..+.++..+|..|--
T Consensus       618 ~~p~iliLDE~Ts~LD~~te~~i~~~l~~~~~~~T~iiItHr  659 (694)
T TIGR03375       618 RDPPILLLDEPTSAMDNRSEERFKDRLKRWLAGKTLVLVTHR  659 (694)
T ss_pred             cCCCEEEEeCCCCCCCHHHHHHHHHHHHHHhCCCEEEEEecC
Confidence            456799999998888887888888888777665555555443

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.50  E-value=0.27  Score=39.76  Aligned_cols=43  Identities=14%  Similarity=0.038  Sum_probs=28.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEeccH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPTR  125 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~~  125 (258)
                      .|.-+.|.|++|+|||...+..+...+...   +.+.+++|+....
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            456799999999999987765555443332   1124688887643

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.48  E-value=0.22  Score=41.55  Aligned_cols=38  Identities=16%  Similarity=0.094  Sum_probs=27.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .|.-++|.|++|+|||...+..+.+.+.+   +.+++|++-
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~---Ge~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASR---GNPVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC---CCcEEEEEe
Confidence            45669999999999998776655554443   346888873

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>KOG0741|consensus

Probab=93.45  E-value=0.37  Score=43.86  Aligned_cols=69  Identities=22%  Similarity=0.203  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHHHHHCCCCCCcHHHHHHh----hhhhcC--------CcEEEEcccCCCcchHhHHHHHHHhhhccccceE
Q psy4698          51 DMELSEELLRGIYAYGFEKPSAIQQRAI----IPCVRG--------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQA  118 (258)
Q Consensus        51 ~~~~~~~l~~~l~~~~~~~~~~~Q~~~~----~~l~~g--------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~  118 (258)
                      .+|.+++-++.....|.-.-.+.-.+.+    ..+.+-        -++++.||.|||||..+...++.   +  ..+-+
T Consensus       493 AFG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA~~---S--~FPFv  567 (744)
T KOG0741|consen  493 AFGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTALAAKIALS---S--DFPFV  567 (744)
T ss_pred             ccCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHHHHHHHhh---c--CCCeE
Confidence            4567777777776665433222222222    111111        25999999999999754322222   1  23455


Q ss_pred             EEEecc
Q psy4698         119 LILAPT  124 (258)
Q Consensus       119 lil~P~  124 (258)
                      =+++|.
T Consensus       568 KiiSpe  573 (744)
T KOG0741|consen  568 KIISPE  573 (744)
T ss_pred             EEeChH
Confidence            666664

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=93.43  E-value=0.39  Score=44.25  Aligned_cols=42  Identities=17%  Similarity=0.342  Sum_probs=30.2

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ++-+++++||+-.-+|......+...+..+.++.-+|..|--
T Consensus       475 ~~~~ililDE~ts~lD~~~~~~i~~~l~~~~~~~t~i~itH~  516 (529)
T TIGR02857       475 RDAPLLLLDEPTAHLDAETEALVTEALRALAQGRTVLLVTHR  516 (529)
T ss_pred             cCCCEEEEeCcccccCHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence            445689999998888887788887777776555555555544

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.39  E-value=1.1  Score=39.28  Aligned_cols=17  Identities=24%  Similarity=0.319  Sum_probs=14.8

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .+++.||.|+|||..+.
T Consensus        41 ~~L~~G~~G~GKt~~a~   57 (367)
T PRK14970         41 ALLFCGPRGVGKTTCAR   57 (367)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999997764

>CHL00176 ftsH cell division protein; Validated

Probab=93.36  E-value=0.63  Score=43.94  Aligned_cols=17  Identities=35%  Similarity=0.427  Sum_probs=15.1

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.||+|+|||..+
T Consensus       217 ~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999875

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=93.34  E-value=0.16  Score=42.33  Aligned_cols=54  Identities=20%  Similarity=0.270  Sum_probs=36.6

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      -.|+.++|.|++|+|||+-.+..+...+..   +-++++++- .+...+..+.+..++
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~---ge~vlyvs~-~e~~~~l~~~~~~~g   74 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLYEGARE---GEPVLYVST-EESPEELLENARSFG   74 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHHHHHhc---CCcEEEEEe-cCCHHHHHHHHHHcC
Confidence            356789999999999998876666666555   235777763 444555555555544

>cd01131 PilT Pilus retraction ATPase PilT

Probab=93.32  E-value=0.11  Score=41.31  Aligned_cols=35  Identities=23%  Similarity=0.531  Sum_probs=22.3

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ++|+||||||||+.. ..++..+... .+.+++.+--
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~~~-~~~~i~t~e~   38 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYINKN-KTHHILTIED   38 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhhhc-CCcEEEEEcC
Confidence            789999999999875 3344444432 2235555544

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PF14516 AAA_35: AAA-like domain

Probab=93.31  E-value=0.48  Score=41.03  Aligned_cols=48  Identities=19%  Similarity=0.342  Sum_probs=35.7

Q ss_pred             HHHHHHhhhhhc-CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          72 AIQQRAIIPCVR-GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        72 ~~Q~~~~~~l~~-g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      +...+++..+.+ |..+.|.||-.+|||... ..+++.+...  +.+++++-
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKTSll-~~l~~~l~~~--~~~~v~id   66 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKTSLL-LRLLERLQQQ--GYRCVYID   66 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHHHHH-HHHHHHHHHC--CCEEEEEE
Confidence            488899989887 999999999999999874 4455555543  34566554

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=93.26  E-value=0.83  Score=37.69  Aligned_cols=29  Identities=21%  Similarity=0.371  Sum_probs=20.7

Q ss_pred             hhcCC-cEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          81 CVRGN-DVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        81 l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      +..|+ -+.++|+-|||||...- .++..+.
T Consensus        47 i~d~qg~~~vtGevGsGKTv~~R-al~~s~~   76 (269)
T COG3267          47 IADGQGILAVTGEVGSGKTVLRR-ALLASLN   76 (269)
T ss_pred             HhcCCceEEEEecCCCchhHHHH-HHHHhcC
Confidence            44555 68999999999998865 4444444

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=93.18  E-value=0.22  Score=50.34  Aligned_cols=56  Identities=20%  Similarity=0.286  Sum_probs=45.4

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      -..++++|.|+.|||||.+...-++..+..+....++++++-|+.-+.++..++..
T Consensus         8 dp~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~   63 (1141)
T TIGR02784         8 DPKTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFD   63 (1141)
T ss_pred             CCCCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHH
Confidence            34578999999999999998887777776655556899999999998888766554

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=93.12  E-value=0.28  Score=41.12  Aligned_cols=18  Identities=28%  Similarity=0.374  Sum_probs=15.4

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|.|||..+.
T Consensus        53 DHvLl~GPPGlGKTTLA~   70 (332)
T COG2255          53 DHVLLFGPPGLGKTTLAH   70 (332)
T ss_pred             CeEEeeCCCCCcHHHHHH
Confidence            469999999999998653

>KOG0344|consensus

Probab=93.08  E-value=2.3  Score=39.05  Aligned_cols=97  Identities=16%  Similarity=0.249  Sum_probs=71.0

Q ss_pred             cCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHhcC-CcE
Q psy4698          93 SGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLEAG-AQV  168 (258)
Q Consensus        93 tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~I  168 (258)
                      .+.||+..-++++.+.+..+ -.+.++|.+-+.+-|.|.+..+.   .+.++.+...++.....+.   ....+.| ..+
T Consensus       366 vF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~---~~~~i~v~vIh~e~~~~qrde~~~~FR~g~Iwv  441 (593)
T KOG0344|consen  366 VFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELE---IYDNINVDVIHGERSQKQRDETMERFRIGKIWV  441 (593)
T ss_pred             eeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhh---hccCcceeeEecccchhHHHHHHHHHhccCeeE
Confidence            46788888877777776666 45678999999999999998776   3345677777777544332   2333333 789


Q ss_pred             EEeChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         169 VVGTPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       169 lv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                      +|||     +++.++ ++++++.+||-++.-
T Consensus       442 LicT-----dll~RG-iDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  442 LICT-----DLLARG-IDFKGVNLVINYDFP  466 (593)
T ss_pred             EEeh-----hhhhcc-ccccCcceEEecCCC
Confidence            9999     677776 789999999998754

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=93.04  E-value=0.17  Score=40.33  Aligned_cols=29  Identities=14%  Similarity=0.296  Sum_probs=19.3

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      ....+++|.|.||||||.+....+...+.
T Consensus        36 ~~~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   36 KKNPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             GGS-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CCCceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            34458999999999999887655555544

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.03  E-value=0.089  Score=43.90  Aligned_cols=28  Identities=32%  Similarity=0.306  Sum_probs=22.9

Q ss_pred             HHHhhhhhcCCcEEEEcccCCCcchHhH
Q psy4698          75 QRAIIPCVRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        75 ~~~~~~l~~g~~~li~~~tGsGKT~~~l  102 (258)
                      ++++..+..|+++++.|++|+|||..+.
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            4455567788999999999999998764

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=92.96  E-value=0.069  Score=33.98  Aligned_cols=19  Identities=26%  Similarity=0.606  Sum_probs=16.0

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+.++|.|++|||||...
T Consensus        22 ~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3557999999999999864

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

Probab=92.83  E-value=0.14  Score=43.87  Aligned_cols=52  Identities=15%  Similarity=0.174  Sum_probs=33.3

Q ss_pred             CCcHHHHH-HhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          69 KPSAIQQR-AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        69 ~~~~~Q~~-~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .+.+.|.. .+-++..+++++++|+||||||... .+++..+....   |++.+=-+
T Consensus       127 t~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~l-nall~~Ip~~~---rivtIEdt  179 (312)
T COG0630         127 TISPEQAAYLWLAIEARKSIIICGGTASGKTTLL-NALLDFIPPEE---RIVTIEDT  179 (312)
T ss_pred             CCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHHH-HHHHHhCCchh---cEEEEecc
Confidence            45555544 4445677899999999999999863 55555544332   45555433

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=92.82  E-value=0.15  Score=48.18  Aligned_cols=50  Identities=20%  Similarity=0.193  Sum_probs=37.4

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .++++.||||||||..+++|-+..+.     ..++|+=|.-++........++.+
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~~-----gS~VV~DpKGE~~~~Ta~~R~~~G  189 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTFK-----GSVIALDVKGELFELTSRARKASG  189 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcCC-----CCEEEEeCCchHHHHHHHHHHhCC
Confidence            47999999999999999988866532     257777788777776665555543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=92.78  E-value=0.36  Score=39.26  Aligned_cols=42  Identities=17%  Similarity=0.036  Sum_probs=27.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEecc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPT  124 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~  124 (258)
                      .|.-+.+.|++|+|||...+..+.......   +.+.+++++.-.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e   62 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE   62 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence            456689999999999987765554433222   112468888753

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=92.74  E-value=0.48  Score=35.58  Aligned_cols=29  Identities=17%  Similarity=0.287  Sum_probs=22.8

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      +-+++++||.-.-++......+...++.+
T Consensus        88 ~p~illlDEP~~~LD~~~~~~l~~~l~~~  116 (144)
T cd03221          88 NPNLLLLDEPTNHLDLESIEALEEALKEY  116 (144)
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHc
Confidence            45699999998777777777777777776

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=92.74  E-value=0.13  Score=48.62  Aligned_cols=68  Identities=13%  Similarity=0.138  Sum_probs=40.5

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHhhh--hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH
Q psy4698          56 EELLRGIYAYGFEKPSAIQQRAIIP--CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA  128 (258)
Q Consensus        56 ~~l~~~l~~~~~~~~~~~Q~~~~~~--l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~  128 (258)
                      ..+.+.+++.+-..+  +..--+|.  -.+.+++++.|.||||||.+. .-++..+...  +.++||.=|.-+..
T Consensus       157 ~~l~k~lk~~~~~s~--i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~R--GdrAIIyD~~GeFv  226 (732)
T PRK13700        157 KDVARMLKKDGKDSD--IRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQR--GDMVVIYDRSGEFV  226 (732)
T ss_pred             HHHHHHHHhcCCCCC--eeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHHc--CCeEEEEeCCCchH
Confidence            566667776654333  33333333  345689999999999999964 5566655443  23455444444433

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.72  E-value=0.35  Score=45.60  Aligned_cols=55  Identities=16%  Similarity=0.290  Sum_probs=37.5

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH--HHHHHHHHHHHhcCC
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE--LAQQIQKVVIALGDF  141 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~--l~~q~~~~~~~~~~~  141 (258)
                      ..+++|.|+||+|||..+...+.+.+..+   ..++++=|...  +.......++..+..
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~g---~~viv~DpKgD~~l~~~~~~~~~~~G~~  232 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRRG---DVVIVIDPKGDADLKRRMRAEAKRAGRP  232 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHcC---CeEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence            35799999999999988755444444432   35666667643  777777777776644

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>PRK07773 replicative DNA helicase; Validated

Probab=92.69  E-value=0.63  Score=45.82  Aligned_cols=148  Identities=18%  Similarity=0.176  Sum_probs=73.1

Q ss_pred             HHhhhhhcC----CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEEC
Q psy4698          76 RAIIPCVRG----NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIG  151 (258)
Q Consensus        76 ~~~~~l~~g----~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~  151 (258)
                      ..++.+..|    .-++|.|.+|+|||...+--+.+.....  +..++|++ .-.-..|+..++.......+...  ...
T Consensus       205 ~~LD~l~~Gl~~G~livIagrPg~GKT~fal~ia~~~a~~~--~~~V~~fS-lEms~~ql~~R~~s~~~~i~~~~--i~~  279 (886)
T PRK07773        205 TELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRH--RLAVAIFS-LEMSKEQLVMRLLSAEAKIKLSD--MRS  279 (886)
T ss_pred             hHhccccCCCCCCcEEEEEeCCCCCcHHHHHHHHHHHHHhc--CCeEEEEe-cCCCHHHHHHHHHHHhcCCCHHH--Hhc
Confidence            444444443    4589999999999987765555544332  23466665 33344555555443322222111  111


Q ss_pred             CcchHHHHHHHh------cCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc----CcHHHHHHHHHh
Q psy4698         152 GTIVRDDIRKLE------AGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR----GFKDQIYDVFKH  216 (258)
Q Consensus       152 ~~~~~~~~~~~~------~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~----~~~~~~~~~~~~  216 (258)
                      +.-...++..+.      ....+.|.     |++.+...+.+-. .-.++++||||=.+.|...    +....+..+.+.
T Consensus       280 g~l~~~~~~~~~~a~~~l~~~~i~i~d~~~~~i~~i~~~~r~~~-~~~~~~lvvIDyLql~~~~~~~~~r~~ei~~isr~  358 (886)
T PRK07773        280 GRMSDDDWTRLARAMGEISEAPIFIDDTPNLTVMEIRAKARRLR-QEANLGLIVVDYLQLMTSGKKYENRQQEVSEISRH  358 (886)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH-HhcCCCEEEEcchhhcCCCCCCCCHHHHHHHHHHH
Confidence            111112221111      12456663     4555543332210 0135889999999977422    123344444444


Q ss_pred             CC-----CCccEEEEEee
Q psy4698         217 LN-----NDVQVILLSAT  229 (258)
Q Consensus       217 l~-----~~~~~i~~SAT  229 (258)
                      ++     -++.+|++|..
T Consensus       359 LK~lAkel~vpvi~lsQL  376 (886)
T PRK07773        359 LKLLAKELEVPVVALSQL  376 (886)
T ss_pred             HHHHHHHHCCcEEEeccc
Confidence            43     25666666643

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=92.69  E-value=0.39  Score=39.01  Aligned_cols=48  Identities=13%  Similarity=0.286  Sum_probs=33.1

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                      +-++|+.||----+|......+..++..+.......++=+|-...+..
T Consensus       160 ~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~  207 (226)
T COG1136         160 NPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAK  207 (226)
T ss_pred             CCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHH
Confidence            445899999987778888888889998886653333334555554444

>PRK10263 DNA translocase FtsK; Provisional

Probab=92.64  E-value=0.95  Score=45.62  Aligned_cols=25  Identities=20%  Similarity=0.405  Sum_probs=19.6

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      +++|.|.||||||.+.-..++..+.
T Consensus      1012 HLLIAGaTGSGKSv~LntLIlSLl~ 1036 (1355)
T PRK10263       1012 HLLVAGTTGSGKSVGVNAMILSMLY 1036 (1355)
T ss_pred             cEEEecCCCCCHHHHHHHHHHHHHH
Confidence            7899999999999986555554444

>COG4987 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=92.63  E-value=0.35  Score=43.97  Aligned_cols=63  Identities=13%  Similarity=0.259  Sum_probs=38.2

Q ss_pred             EEEeChHHHHHHHhcCCCC---------------CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeC
Q psy4698         168 VVVGTPGRVFDMISRGALS---------------TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       168 Ilv~Tp~~l~~~l~~~~~~---------------~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      .+-.-|+.+..++..++..               +++-.++++||.-.=+|..-..++...+..--.+..+++.|--+
T Consensus       456 l~~~~p~gl~t~lge~G~~LSGGE~rRLAlAR~LL~dapl~lLDEPTegLD~~TE~~vL~ll~~~~~~kTll~vTHrL  533 (573)
T COG4987         456 LLESAPDGLNTWLGEGGRRLSGGERRRLALARALLHDAPLWLLDEPTEGLDPITERQVLALLFEHAEGKTLLMVTHRL  533 (573)
T ss_pred             HHHhChhhhhchhccCCCcCCchHHHHHHHHHHHHcCCCeEEecCCcccCChhhHHHHHHHHHHHhcCCeEEEEeccc
Confidence            3444566666555554333               34567999999998778777777665543332344466655544

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=92.62  E-value=0.098  Score=48.94  Aligned_cols=42  Identities=14%  Similarity=0.374  Sum_probs=30.2

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ++-.++++||.-.-+|......+...+..+.+++.+|.+|--
T Consensus       493 ~~~~illlDEpts~LD~~t~~~i~~~l~~~~~~~tvIivtHr  534 (592)
T PRK10790        493 QTPQILILDEATANIDSGTEQAIQQALAAVREHTTLVVIAHR  534 (592)
T ss_pred             hCCCEEEEeCCcccCCHHHHHHHHHHHHHHhCCCEEEEEecc
Confidence            344699999999888887778887777776555555555544

>PHA02542 41 41 helicase; Provisional

Probab=92.60  E-value=0.6  Score=42.48  Aligned_cols=35  Identities=11%  Similarity=0.104  Sum_probs=24.5

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      .-+++.|.+|.|||..++--+.....   .+..++|+.
T Consensus       191 ~LiiIaarPgmGKTtfalniA~~~a~---~g~~Vl~fS  225 (473)
T PHA02542        191 TLNVLLAGVNVGKSLGLCSLAADYLQ---QGYNVLYIS  225 (473)
T ss_pred             cEEEEEcCCCccHHHHHHHHHHHHHh---cCCcEEEEe
Confidence            34889999999999887665555542   233576665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	258
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		1e-101
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		8e-99
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		5e-96
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		7e-88
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		1e-82
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		1e-82
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-82
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		3e-82
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-81
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-80
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		1e-79
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		1e-79
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		5e-75
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-74
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-45
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		4e-37
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		5e-37
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-36
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-36
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-36
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		5e-35
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		8e-34
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		8e-34
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		3e-33
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		2e-32
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-32
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		8e-32
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		9e-32
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-31
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		2e-31
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		4e-31
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		5e-31
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		8e-31
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-28
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		5e-27
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		3e-26
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		5e-26
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		8e-26
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		1e-24
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		9e-24
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-23
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-22
3ly5_A	262	Ddx18 Dead-Domain Length = 262		2e-21
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		7e-21
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-20
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		3e-19
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-19
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		3e-19
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		5e-18

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  365 bits (936), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 171/233 (73%), Positives = 207/233 (88%), Gaps = 1/233 (0%)
Query: 27  NGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G D
Sbjct: 20  NGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYD 79
Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           VIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SC
Sbjct: 80  VIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASC 139
Query: 147 HACIGGTIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG 205
           HACIGGT VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRG
Sbjct: 140 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG 199
Query: 206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           FKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 200 FKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 252

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  356 bits (913), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 166/226 (73%), Positives = 203/226 (89%), Gaps = 1/226 (0%)
Query: 34  VDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQS 93
           ++G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G DVIAQAQS
Sbjct: 1   MEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQS 60
Query: 94  GTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGT 153
           GTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SCHACIGGT
Sbjct: 61  GTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGT 120
Query: 154 IVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD 212
            VR +++KL+  A  ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRGFKDQIYD
Sbjct: 121 NVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYD 180
Query: 213 VFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           +F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKKEELTLE
Sbjct: 181 IFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLE 226

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  347 bits (889), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 162/219 (73%), Positives = 194/219 (88%), Gaps = 1/219 (0%)
Query: 36  GLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGT 95
           G+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAIIPC++G DVIAQAQSGT
Sbjct: 19  GVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGT 78
Query: 96  GKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIV 155
           GKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++ALGD+M  +CHACIGGT V
Sbjct: 79  GKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNV 138
Query: 156 RDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
           R++++KL+A A  +VVGTPGRVFDM++R  LS K I+MFVLDEADEMLSRGFKDQIY++F
Sbjct: 139 RNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIF 198
Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
           + LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKE
Sbjct: 199 QKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  319 bits (818), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 150/219 (68%), Positives = 186/219 (84%), Gaps = 1/219 (0%)
Query: 33  AVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQ 92
           +++G+IE+NW+ + ++FDDM LSE LLRGIYAYGFE PSAIQQRAI+PC+ G DVIAQAQ
Sbjct: 1   SMEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQ 60
Query: 93  SGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGG 152
           SGTG TATF+ISILQQ++ ++   QAL+LAPTRELAQQIQ VV+ALGD+M  SCHACIGG
Sbjct: 61  SGTGXTATFAISILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGG 120
Query: 153 TIVRDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY 211
           T VR +++ L+  A  ++VGTPGRVFDM++R  LS   I MFVLDEADEMLSRGF DQIY
Sbjct: 121 TNVRAEVQXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIY 180
Query: 212 DVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
           D+F+ LN++ QV+LLSATMP+DVL+V+  FMRDPI+ILV
Sbjct: 181 DIFQXLNSNTQVVLLSATMPSDVLEVTXXFMRDPIRILV 219

>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 =  302 bits (773), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 145/214 (67%), Positives = 179/214 (83%)
Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSIS 104
           V   FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTGKTATFSIS
Sbjct: 36  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSIS 95
Query: 105 ILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           +LQ +D  ++E QALILAPTRELA QIQK ++ALGD+M+V CHACIGGT V +DIRKL+ 
Sbjct: 96  VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY 155
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           G  VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++L    QV+
Sbjct: 156 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV 215
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           L+SAT+P ++L+++ KFM DPI+ILVK++ELTLE
Sbjct: 216 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE 249

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  302 bits (773), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 145/214 (67%), Positives = 179/214 (83%)
Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSIS 104
           V   FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTGKTATFSIS
Sbjct: 35  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSIS 94
Query: 105 ILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           +LQ +D  ++E QALILAPTRELA QIQK ++ALGD+M+V CHACIGGT V +DIRKL+ 
Sbjct: 95  VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY 154
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           G  VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++L    QV+
Sbjct: 155 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV 214
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           L+SAT+P ++L+++ KFM DPI+ILVK++ELTLE
Sbjct: 215 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE 248

>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 =  301 bits (772), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 145/214 (67%), Positives = 179/214 (83%)
Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSIS 104
           V   FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTGKTATFSIS
Sbjct: 36  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSIS 95
Query: 105 ILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           +LQ +D  ++E QALILAPTRELA QIQK ++ALGD+M+V CHACIGGT V +DIRKL+ 
Sbjct: 96  VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY 155
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           G  VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++L    QV+
Sbjct: 156 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV 215
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           L+SAT+P ++L+++ KFM DPI+ILVK++ELTLE
Sbjct: 216 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE 249

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  301 bits (770), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 145/214 (67%), Positives = 179/214 (83%)
Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSIS 104
           V   FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTGKTATFSIS
Sbjct: 14  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSIS 73
Query: 105 ILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           +LQ +D  ++E QALILAPTRELA QIQK ++ALGD+M+V CHACIGGT V +DIRKL+ 
Sbjct: 74  VLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY 133
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           G  VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++L    QV+
Sbjct: 134 GQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVV 193
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           L+SAT+P ++L+++ KFM DPI+ILVK++ELTLE
Sbjct: 194 LISATLPHEILEMTNKFMTDPIRILVKRDELTLE 227

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  298 bits (764), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 142/211 (67%), Positives = 178/211 (84%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTGKTATFS+S+LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQ 167
            +D  ++E QALILAPTRELA Q+QK ++ALGD+M+V CHACIGGT V +DIRKL+ G  
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQH 121
Query: 168 VVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS 227
           VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++L    QV+L+S
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLIS 181
Query: 228 ATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           AT+P ++L+++ KFM DPI+ILVK++ELTLE
Sbjct: 182 ATLPHEILEMTNKFMTDPIRILVKRDELTLE 212

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  295 bits (755), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 142/211 (67%), Positives = 177/211 (83%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTGKTATFS+S+LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQ 167
            +D  ++E QALILAPTRELA Q+QK ++ALGD+M+V  HACIGGT V +DIRKL+ G  
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQH 121
Query: 168 VVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS 227
           VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++L    QV+L+S
Sbjct: 122 VVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLIS 181
Query: 228 ATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           AT+P +VL+++ KFM DPI+ILVK++ELTLE
Sbjct: 182 ATLPHEVLEMTNKFMTDPIRILVKRDELTLE 212

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  292 bits (748), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 143/221 (64%), Positives = 174/221 (78%), Gaps = 1/221 (0%)
Query: 38  IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
           I+TN+D V   FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSGTGK
Sbjct: 13  IQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGK 72
Query: 98  TATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
           T TFSI+ LQ++D ++K  QAL+LAPTRELA QIQKVV+AL   M +  HACIGGT   +
Sbjct: 73  TGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVE 132
Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
           D   L   AQ+VVGTPGRVFD I R    T +I+MF+LDEADEMLS GFK+QIY +F  L
Sbjct: 133 DAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL 191
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
               QV+LLSATMP DVL+V+ KFMR+P++ILVKK+ELTLE
Sbjct: 192 PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 232

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score =  292 bits (748), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 143/221 (64%), Positives = 174/221 (78%), Gaps = 1/221 (0%)
Query: 38  IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
           I+TN+D V   FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSGTGK
Sbjct: 5   IQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGK 64
Query: 98  TATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
           T TFSI+ LQ++D ++K  QAL+LAPTRELA QIQKVV+AL   M +  HACIGGT   +
Sbjct: 65  TGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVE 124
Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
           D   L   AQ+VVGTPGRVFD I R    T +I+MF+LDEADEMLS GFK+QIY +F  L
Sbjct: 125 DAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL 183
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
               QV+LLSATMP DVL+V+ KFMR+P++ILVKK+ELTLE
Sbjct: 184 PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  277 bits (708), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 135/213 (63%), Positives = 166/213 (77%), Gaps = 1/213 (0%)
Query: 38  IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
           I+TN+  V   FDDMEL E+LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSGTGK
Sbjct: 12  IQTNYQKVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGK 71
Query: 98  TATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
           T TFSI+ LQ++D ++K  QAL+LAPTRELA QIQKVV+AL   M +  HACIGGT   +
Sbjct: 72  TGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVE 131
Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
           D   L   AQ+VVGTPGRVFD I R    T +I+MF+LDEADEMLS GFK+QIY +F  L
Sbjct: 132 DAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL 190
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
               QV+LLSATMP DVL+V+ KFMR+P++ILV
Sbjct: 191 PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  275 bits (702), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 137/221 (61%), Positives = 165/221 (74%), Gaps = 1/221 (0%)
Query: 38  IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
           I+TN+D V   FDD EL E LLRG++ YGFE+PSAIQQRAI P + G+DV+AQAQSGTGK
Sbjct: 12  IQTNYDKVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGK 71
Query: 98  TATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
           T TFSI+ LQ++D ++K  QAL LAPTRELA QIQKVV AL     +  HACIGGT   +
Sbjct: 72  TGTFSIAALQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACIGGTSFVE 131
Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
           D   L   AQ+VVGTPGRVFD I R    T +I+ F+LDEADE LS GFK+QIY +F  L
Sbjct: 132 DAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLL 190
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
               QV+LLSAT P DVL+V+ KF R+P++ILVKK+ELTLE
Sbjct: 191 PPTTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDELTLE 231

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  178 bits (451), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 95/211 (45%), Positives = 128/211 (60%), Gaps = 1/211 (0%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F+D  L  ELL GI+  GFEKPS IQ+ AI   + G D++A+A++GTGKTA F I  L+
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQ 167
           +V   + + QALI+ PTRELA Q  +VV  LG    +SC    GGT +RDDI +L     
Sbjct: 82  KVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVH 141
Query: 168 VVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS 227
           ++VGTPGRV D+ SR         +F++DEAD+MLSR FK  I  +   L    Q +L S
Sbjct: 142 ILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFS 201
Query: 228 ATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           AT P  V +  +K +  P +I +  EELTL+
Sbjct: 202 ATFPLTVKEFMVKHLHKPYEINL-MEELTLK 231

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  151 bits (381), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 82/191 (42%), Positives = 125/191 (65%), Gaps = 9/191 (4%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN---DVIAQAQSGTGKTAT 100
           + A++FD++ L+ ELL+GIYA  F+KPS IQ+RA+ P +  N   ++IAQ+QSGTGKTA 
Sbjct: 19  YSAKSFDELGLAPELLKGIYAMKFQKPSKIQERAL-PLLLHNPPRNMIAQSQSGTGKTAA 77
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
           FS+++L +V+      QA+ LAP+RELA+Q  +VV  +G F  ++    +  +  ++   
Sbjct: 78  FSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK-- 135
Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNN 219
             +  AQV+VGTPG V D++ R  +  ++I++FVLDEAD ML  +G  DQ   V + L  
Sbjct: 136 --QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPK 193
Query: 220 DVQVILLSATM 230
           D Q++L SAT 
Sbjct: 194 DTQLVLFSATF 204

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  150 bits (380), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 77/201 (38%), Positives = 120/201 (59%), Gaps = 1/201 (0%)
Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F+D  L  ELL GI+  G+EKPS IQ+ +I   + G D++A+A++GTGK+  + I +L++
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64
Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQ 167
           +D      QA+++ PTRELA Q+ ++ I +   M      A  GGT +RDDI +L+    
Sbjct: 65  LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVH 124
Query: 168 VVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS 227
           VV+ TPGR+ D+I +G      ++M VLDEAD++LS+ F   + D+   L  + Q++L S
Sbjct: 125 VVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYS 184
Query: 228 ATMPADVLDVSMKFMRDPIKI 248
           AT P  V       +  P +I
Sbjct: 185 ATFPLSVQKFMNSHLEKPYEI 205

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  149 bits (375), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 82/190 (43%), Positives = 125/190 (65%), Gaps = 9/190 (4%)
Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN---DVIAQAQSGTGKTATF 101
           +A++FD++ L+ ELL+GIYA  F+KPS IQ+RA+ P +  N   ++IAQ+QSGTGKTA F
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERAL-PLLLHNPPRNMIAQSQSGTGKTAAF 61
Query: 102 SISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
           S+++L +V+      QA+ LAP+RELA+Q  +VV  +G F  ++    +  +  ++    
Sbjct: 62  SLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK--- 118
Query: 162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNND 220
            +  AQV+VGTPG V D++ R  +  ++I++FVLDEAD ML  +G  DQ   V + L  D
Sbjct: 119 -QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKD 177
Query: 221 VQVILLSATM 230
            Q++L SAT 
Sbjct: 178 TQLVLFSATF 187

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  148 bits (374), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 82/190 (43%), Positives = 125/190 (65%), Gaps = 9/190 (4%)
Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN---DVIAQAQSGTGKTATF 101
           +A++FD++ L+ ELL+GIYA  F+KPS IQ+RA+ P +  N   ++IAQ+QSGTGKTA F
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERAL-PLLLHNPPRNMIAQSQSGTGKTAAF 61
Query: 102 SISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
           S+++L +V+      QA+ LAP+RELA+Q  +VV  +G F  ++    +  +  ++    
Sbjct: 62  SLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK--- 118
Query: 162 LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNND 220
            +  AQV+VGTPG V D++ R  +  ++I++FVLDEAD ML  +G  DQ   V + L  D
Sbjct: 119 -QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKD 177
Query: 221 VQVILLSATM 230
            Q++L SAT 
Sbjct: 178 TQLVLFSATF 187

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  147 bits (372), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 76/199 (38%), Positives = 127/199 (63%), Gaps = 5/199 (2%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN--DVIAQAQSGTGKTATFSISI 105
           NF+++ LS+ +L  I   GFEKP+ IQ + +IP    +  +++AQA++G+GKTA+F+I +
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXK-VIPLFLNDEYNIVAQARTGSGKTASFAIPL 65
Query: 106 LQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG 165
           ++ V++N    +A+IL PTRELA Q+   + +L    ++      GG  +   I+ L+  
Sbjct: 66  IELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-N 123
Query: 166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVIL 225
           A +VVGTPGR+ D I+RG L+ K ++ F+LDEADE L+ GF   +  +    N D +++L
Sbjct: 124 ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILL 183
Query: 226 LSATMPADVLDVSMKFMRD 244
            SAT P ++L+++ K+  D
Sbjct: 184 FSATXPREILNLAKKYXGD 202

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  144 bits (363), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/201 (42%), Positives = 122/201 (60%), Gaps = 5/201 (2%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVR-GNDVIAQAQSGTGKTATFSISIL 106
           +F+ + LS  +L G+ A GFE+PS +Q +AI P  R G D+I QA+SGTGKT  FS   L
Sbjct: 25  DFESLLLSRPVLEGLRAAGFERPSPVQLKAI-PLGRCGLDLIVQAKSGTGKTCVFSTIAL 83
Query: 107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAG 165
             +       Q LILAPTRE+A QI  V+ A+G  M  + CH  IGGT +  D  +L+  
Sbjct: 84  DSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK- 142
Query: 166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNNDVQVI 224
             + VG+PGR+  +I    L+   IR+F+LDEAD++L  G F++QI  ++  L    Q++
Sbjct: 143 CHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQML 202
Query: 225 LLSATMPADVLDVSMKFMRDP 245
            +SAT P  + +   K+MRDP
Sbjct: 203 AVSATYPEFLANALTKYMRDP 223

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  140 bits (353), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 81/219 (36%), Positives = 124/219 (56%), Gaps = 4/219 (1%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSI 103
           H++  F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F +
Sbjct: 5   HMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL 64
Query: 104 SILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKL 162
           + LQQ++    +   L++  TRELA QI K       +M +V      GG  ++ D   L
Sbjct: 65  ATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL 124
Query: 163 EAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNND 220
           +     +VVGTPGR+  +    +L+ K I+ F+LDE D+ML +   +  + ++F+   ++
Sbjct: 125 KKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE 184
Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKE-ELTLE 258
            QV++ SAT+  ++  V  KFM+DP++I V  E +LTL 
Sbjct: 185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLH 223

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  140 bits (353), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 81/219 (36%), Positives = 124/219 (56%), Gaps = 4/219 (1%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSI 103
           H++  F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F +
Sbjct: 5   HMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL 64
Query: 104 SILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKL 162
           + LQQ++    +   L++  TRELA QI K       +M +V      GG  ++ D   L
Sbjct: 65  ATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL 124
Query: 163 EAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNND 220
           +     +VVGTPGR+  +    +L+ K I+ F+LDE D+ML +   +  + ++F+   ++
Sbjct: 125 KKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE 184
Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKE-ELTLE 258
            QV++ SAT+  ++  V  KFM+DP++I V  E +LTL 
Sbjct: 185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLH 223

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  138 bits (347), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 81/214 (37%), Positives = 122/214 (57%), Gaps = 4/214 (1%)
Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ LQQ
Sbjct: 9   FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 68
Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGA- 166
           ++    +   L++  TRELA QI K       +M +V      GG  ++ D   L+    
Sbjct: 69  LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCP 128
Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVIL 225
            +VVGTPGR+  +    +L+ K I+ F+LDEAD+ML +   +  + ++F+   ++ QV++
Sbjct: 129 HIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQVMM 188
Query: 226 LSATMPADVLDVSMKFMRDPIKILVKKE-ELTLE 258
            SAT+  ++  V  KFM+DP++I V  E +LTL 
Sbjct: 189 FSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLH 222

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  135 bits (340), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 76/208 (36%), Positives = 117/208 (56%), Gaps = 3/208 (1%)
Query: 46  AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISI 105
           +  F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ 
Sbjct: 13  SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 72
Query: 106 LQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEA 164
           LQQ++    +   L++  TRELA QI K       +M +V      GG  ++ D   L+ 
Sbjct: 73  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 132
Query: 165 GA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQ 222
               +VVGTPGR+  +    +L+ K I+ F+LDE D+ML +   +  + ++F+   ++ Q
Sbjct: 133 NCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQ 192
Query: 223 VILLSATMPADVLDVSMKFMRDPIKILV 250
           V++ SAT+  ++  V  KFM+DP++I V
Sbjct: 193 VMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  134 bits (336), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 133/225 (59%), Gaps = 18/225 (8%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTAT 100
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+ P +      ++IAQ+QSGTGKTA 
Sbjct: 89  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAA 147
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDI 159
           F +++L QV+   K  Q L L+PT ELA Q  KV+  +G F   +     + G       
Sbjct: 148 FVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------ 201
Query: 160 RKLEAG----AQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML-SRGFKDQIYDV 213
            KLE G     Q+V+GTPG V D  S+   +  K+I++FVLDEAD M+ ++G +DQ   +
Sbjct: 202 -KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 260
Query: 214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
            + L  + Q++L SAT    V   + K + DP  I +K+EE TL+
Sbjct: 261 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 305

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  133 bits (335), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 133/225 (59%), Gaps = 18/225 (8%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTAT 100
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+ P +      ++IAQ+QSGTGKTA 
Sbjct: 22  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAA 80
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDI 159
           F +++L QV+   K  Q L L+PT ELA Q  KV+  +G F   +     + G       
Sbjct: 81  FVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------ 134
Query: 160 RKLEAG----AQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML-SRGFKDQIYDV 213
            KLE G     Q+V+GTPG V D  S+   +  K+I++FVLDEAD M+ ++G +DQ   +
Sbjct: 135 -KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 193
Query: 214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
            + L  + Q++L SAT    V   + K + DP  I +K+EE TL+
Sbjct: 194 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 238

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  133 bits (335), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 133/225 (59%), Gaps = 18/225 (8%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTAT 100
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+ P +      ++IAQ+QSGTGKTA 
Sbjct: 59  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAA 117
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDI 159
           F +++L QV+   K  Q L L+PT ELA Q  KV+  +G F   +     + G       
Sbjct: 118 FVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------ 171
Query: 160 RKLEAG----AQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML-SRGFKDQIYDV 213
            KLE G     Q+V+GTPG V D  S+   +  K+I++FVLDEAD M+ ++G +DQ   +
Sbjct: 172 -KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 230
Query: 214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
            + L  + Q++L SAT    V   + K + DP  I +K+EE TL+
Sbjct: 231 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 275

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  133 bits (334), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 133/225 (59%), Gaps = 18/225 (8%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTAT 100
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+ P +      ++IAQ+QSGTGKTA 
Sbjct: 38  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAA 96
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDI 159
           F +++L QV+   K  Q L L+PT ELA Q  KV+  +G F   +     + G       
Sbjct: 97  FVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGN------ 150
Query: 160 RKLEAGA----QVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML-SRGFKDQIYDV 213
            KLE G     Q+V+GTPG V D  S+   +  K+I++FVLDEAD M+ ++G +DQ   +
Sbjct: 151 -KLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 209
Query: 214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
            + L  + Q++L SAT    V   + K + DP  I +K+EE TL+
Sbjct: 210 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 254

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score =  132 bits (332), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 83/218 (38%), Positives = 129/218 (59%), Gaps = 12/218 (5%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTAT 100
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+ P +      ++IAQ+QSGTGKTA 
Sbjct: 22  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAA 80
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS--VSCHACIGGTIVRDD 158
           F +++L QV+   K  Q L L+PT ELA Q  KV+  +G F       +A  G  + R  
Sbjct: 81  FVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ 140
Query: 159 IRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKH 216
               +   Q+V+GTPG V D  S+   +  K+I++FVLDEAD M+ ++G +DQ   + + 
Sbjct: 141 ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 196
Query: 217 LNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE 254
           L  + Q++L SAT    V   + K + DP  I +K+EE
Sbjct: 197 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREE 234

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  131 bits (329), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 73/208 (35%), Positives = 116/208 (55%), Gaps = 5/208 (2%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F D  L  E+L  ++  G   P+ IQ  A+   + G D+I QA++GTGKT  F++ I +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 108 QV---DQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           ++    +  ++ +AL+L PTRELA Q+   + A+   + V   A  GGT        L  
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLR 119
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           GA  VV TPGR  D + +G L   ++ + VLDEADEMLS GF++++  +        Q +
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKK 252
           L SAT+P+    ++ ++M++P+ I V K
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINVIK 207

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score =  130 bits (328), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 82/217 (37%), Positives = 128/217 (58%), Gaps = 12/217 (5%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG---NDVIAQAQSGTGKTAT 100
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+ P +      ++IAQ+QSGTGKTA 
Sbjct: 89  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAA 147
Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS--VSCHACIGGTIVRDD 158
           F +++L QV+   K  Q L L+PT ELA Q  KV+  +G F       +A  G  + R  
Sbjct: 148 FVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ 207
Query: 159 IRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKH 216
               +   Q+V+GTPG V D  S+   +  K+I++FVLDEAD M+ ++G +DQ   + + 
Sbjct: 208 ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRM 263
Query: 217 LNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
           L  + Q++L SAT    V   + K + DP  I +K+E
Sbjct: 264 LPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  130 bits (326), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 72/208 (34%), Positives = 116/208 (55%), Gaps = 5/208 (2%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F D  L  E+L  ++  G   P+ I+  A+   + G D+I QA++GTGKT  F++ I +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 108 QV---DQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           ++    +  ++ +AL+L PTRELA Q+   + A+   + V   A  GGT        L  
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLR 119
Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           GA  VV TPGR  D + +G L   ++ + VLDEADEMLS GF++++  +        Q +
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179
Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKK 252
           L SAT+P+    ++ ++M++P+ I V K
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINVIK 207

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score =  117 bits (294), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 73/224 (32%), Positives = 118/224 (52%), Gaps = 17/224 (7%)
Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSI 103
           +V ENFD+++L   +   I    +++P+ IQ+ AI   +   D++A AQ+G+GKTA F I
Sbjct: 20  NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLI 79
Query: 104 SIL---------QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACI--GG 152
            I+         QQ        + LILAPTRELA QI          ++    +C+  GG
Sbjct: 80  PIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFS--LNTPLRSCVVYGG 137
Query: 153 TIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD 212
                 IR+++ G  ++V TPGR+ D I +  +S +  +  VLDEAD ML  GF+ QI  
Sbjct: 138 ADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRK 197
Query: 213 VFKHLNN----DVQVILLSATMPADVLDVSMKFMRDPIKILVKK 252
           + +  N     + Q ++ SAT P ++  ++  F+ + I + V +
Sbjct: 198 IIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGR 241

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  115 bits (287), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 66/207 (31%), Positives = 100/207 (48%), Gaps = 4/207 (1%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F        ++  I    F KP+ IQ+R I   +RG   + Q+Q+GTGKT  + + I +
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXE 64
Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS----VSCHACIGGTIVRDDIRKLE 163
           ++     E QA+I APTRELA QI    + +  F      +     IGGT  +  + KL 
Sbjct: 65  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLN 124
Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
               +V+GTPGR+ D I   AL      + V+DEAD  L  GF   +  +      D+Q 
Sbjct: 125 VQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQX 184
Query: 224 ILLSATMPADVLDVSMKFMRDPIKILV 250
           ++ SAT+P  +     K+  +P  + V
Sbjct: 185 LVFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score =  114 bits (285), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 70/215 (32%), Positives = 110/215 (51%), Gaps = 9/215 (4%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
           NF +      ++  I    F +P+AIQ +     + G D++  AQ+G+GKT ++ +  + 
Sbjct: 30  NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 89
Query: 108 QVD-QNIKE------CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
            ++ Q   E      C  L+LAPTRELAQQ+Q+V         +      GG      IR
Sbjct: 90  HINHQPFLERGDGPIC--LVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147
Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
            LE G ++ + TPGR+ D +  G  + ++    VLDEAD ML  GF+ QI  +   +  D
Sbjct: 148 DLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPD 207
Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL 255
            Q ++ SAT P +V  ++  F++D I I +   EL
Sbjct: 208 RQTLMWSATWPKEVRQLAEDFLKDYIHINIGALEL 242

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score =  113 bits (283), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 107/208 (51%), Gaps = 9/208 (4%)
Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
           NF +      ++  I    F +P+AIQ +     + G D++  AQ+G+GKT ++ +  + 
Sbjct: 44  NFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 103
Query: 108 QVD-QNIKE------CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
            ++ Q   E      C  L+LAPTRELAQQ+Q+V         +      GG      IR
Sbjct: 104 HINHQPFLERGDGPIC--LVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 161
Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
            LE G ++ + TPGR+ D +  G  + ++    VLDEAD ML  GF+ QI  +   +  D
Sbjct: 162 DLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPD 221
Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKI 248
            Q ++ SAT P +V  ++  F++D I I
Sbjct: 222 RQTLMWSATWPKEVRQLAEDFLKDYIHI 249

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  109 bits (273), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 62/205 (30%), Positives = 108/205 (52%), Gaps = 1/205 (0%)
Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISIL 106
           + F D+ +++ L       G+ KP+ IQ  AI   ++G D+I  A++G+GKT  F++ IL
Sbjct: 43  KTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPIL 102
Query: 107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
             + +  +   AL+L PTRELA QI +   ALG  + V     +GG         L    
Sbjct: 103 NALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKP 162
Query: 167 QVVVGTPGRVFDMI-SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVIL 225
            +++ TPGR+ D + +    + + ++  V+DEAD +L+  F+ ++  + K +  D +  L
Sbjct: 163 HIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFL 222
Query: 226 LSATMPADVLDVSMKFMRDPIKILV 250
            SATM   V  +    +++P+K  V
Sbjct: 223 FSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  107 bits (266), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 116/213 (54%), Gaps = 11/213 (5%)
Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISIL 106
           ++F   +L + ++  +   G++ P+ IQ+ +I     G D++A AQ+G+GKTA F + IL
Sbjct: 56  QHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPIL 115
Query: 107 QQVDQNIKEC-----QALILAPTRELAQQI--QKVVIALGDFMSVSCHACIGGTIVRDDI 159
            ++ ++  E      Q +I++PTRELA QI  +    A   ++ +      GGT  R   
Sbjct: 116 SKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGI--VYGGTSFRHQN 173
Query: 160 RKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH--L 217
             +  G  VV+ TPGR+ D + R  ++ +  R  VLDEAD ML  GF + +  +  H  +
Sbjct: 174 ECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTM 233
Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
             + Q ++ SAT P ++  ++ +F+++ + + +
Sbjct: 234 RPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAI 266

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  106 bits (264), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 113/228 (49%), Gaps = 22/228 (9%)
Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISIL 106
           E+F D+E+ E ++  I    + +P+ +Q+ AI       D++A AQ+G+GKTA F + IL
Sbjct: 15  ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPIL 74
Query: 107 QQVDQN--------IKECQ----------ALILAPTRELAQQIQKVVIALGDFMSVSCHA 148
            Q+  +        +KE            +L+LAPTRELA QI +          V    
Sbjct: 75  SQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCV 134
Query: 149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKD 208
             GG  +   IR LE G  ++V TPGR+ DM+ RG +     +  VLDEAD ML  GF+ 
Sbjct: 135 VYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEP 194
Query: 209 QIYDVFKH----LNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK 252
           QI  + +            ++ SAT P ++  ++  F+ + I + V +
Sbjct: 195 QIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGR 242

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score =  102 bits (255), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 56/189 (29%), Positives = 102/189 (53%), Gaps = 7/189 (3%)
Query: 54  LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI 113
           ++E++ + I   GF+  + +Q + I   ++G +V+ +A++G+GKTA ++I IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
              ++L++ PTREL +Q+   +  +G +M        GG   +  I ++   A +VV TP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113
Query: 174 GRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPAD 233
           GR+ D+ S+G +      + ++DEAD M   GF D I  +    +N     L SAT+P +
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173
Query: 234 VLDVSMKFM 242
           +  V   F+
Sbjct: 174 IRKVVKDFI 182

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 99.0 bits (245), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/260 (31%), Positives = 128/260 (49%), Gaps = 29/260 (11%)
Query: 4   QRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIY 63
           Q  +N E P N   E+E+E P+   P G+   G  E        N     ++E  L+ I 
Sbjct: 21  QSMNNVEKPDND--EDESEVPSL--PLGLT--GAFEDTSFASLCNL----VNENTLKAIK 70
Query: 64  AYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ----NIKECQAL 119
             GF   + IQ ++I P + G D++A A++G+GKT  F I  ++ + +           L
Sbjct: 71  EMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVL 130
Query: 120 ILAPTRELAQQIQKVVIALGDFMSVSCHA---CIGGTIVRDDIRKLEAGAQVVVGTPGRV 176
           IL+PTRELA Q   V   L + M+   H     +GG+    + +KL  G  ++V TPGR+
Sbjct: 131 ILSPTRELAMQTFGV---LKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRL 187
Query: 177 FD-MISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVL 235
            D M +      K ++  V+DEAD +L  GF++++  + K L    Q +L SAT    V 
Sbjct: 188 LDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE 247
Query: 236 DVSMKFMRDPIKILVKKEEL 255
           D++        +I +KKE L
Sbjct: 248 DLA--------RISLKKEPL 259

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 97.4 bits (241), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 106/207 (51%), Gaps = 7/207 (3%)
Query: 50  DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQV 109
           D  +   +LL+ I   G  KP+ IQ +A    ++G D+I  AQ+GTGKT ++ +     +
Sbjct: 23  DAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL 82
Query: 110 D-QNIKECQ-----ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE 163
           D Q I   Q      L+L PTRELA  ++    +   +  +      GG      I  + 
Sbjct: 83  DSQPISREQRNGPGMLVLTPTRELALHVEAEC-SKYSYKGLKSICIYGGRNRNGQIEDIS 141
Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
            G  +++ TPGR+ D+    +++ + I   V+DEAD+ML   F+ QI  +   +  D Q 
Sbjct: 142 KGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQT 201
Query: 224 ILLSATMPADVLDVSMKFMRDPIKILV 250
           ++ SAT P  V  +++ +++DP+ + V
Sbjct: 202 VMTSATWPDTVRQLALSYLKDPMIVYV 228

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 95.9 bits (237), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 111/210 (52%), Gaps = 6/210 (2%)
Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F D  LS++ L+G+    +   + IQ++ I   ++G DV+  A++G+GKT  F + +L+ 
Sbjct: 27  FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEA 86
Query: 109 VDQ----NIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           + +    +      LI++PTRELA Q  +V+  +G     S    IGG  ++ +  ++  
Sbjct: 87  LYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERIN- 145
Query: 165 GAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
              ++V TPGR+   +    +     ++M VLDEAD +L  GF D +  V ++L    Q 
Sbjct: 146 NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQT 205
Query: 224 ILLSATMPADVLDVSMKFMRDPIKILVKKE 253
           +L SAT    V D++   +++P  + V ++
Sbjct: 206 LLFSATQTKSVKDLARLSLKNPEYVWVHEK 235

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 92.0 bits (227), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/210 (32%), Positives = 110/210 (52%), Gaps = 23/210 (10%)
Query: 54  LSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQ 111
           L +E+ + I    F   + +QQ+ I P +    +DVIA+A++GTGKT  F I I Q +  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 112 NIKECQ----ALILAPTRELAQQIQKVVIALGD----FMSVSCHACIGGTIVRDDIRKL- 162
              + Q    A+I+APTR+LA QI+  V  + D        +C + +GGT  R  + K+ 
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 147
Query: 163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMF---VLDEADEMLSRGFKDQIYDVFKHLN- 218
           +    +V+ TPGR+ D++ +   S K  R     VLDEAD +L  GF+D +  +   LN 
Sbjct: 148 KLRPNIVIATPGRLIDVLEK--YSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 205
Query: 219 ------NDVQVILLSATMPADVLDVSMKFM 242
                 ++++ +L SAT+   V  ++   M
Sbjct: 206 KNSKSADNIKTLLFSATLDDKVQKLANNIM 235

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 92.0 bits (227), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 66/198 (33%), Positives = 106/198 (53%), Gaps = 23/198 (11%)
Query: 54  LSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQ 111
           L +E+ + I    F   + +QQ+ I P +    +DVIA+A++GTGKT  F I I Q +  
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 138
Query: 112 NIKECQ----ALILAPTRELAQQIQKVVIALGD----FMSVSCHACIGGTIVRDDIRKL- 162
              + Q    A+I+APTR+LA QI+  V  + D        +C + +GGT  R  + K+ 
Sbjct: 139 TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 198
Query: 163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMF---VLDEADEMLSRGFKDQIYDVFKHLN- 218
           +    +V+ TPGR+ D++ +   S K  R     VLDEAD +L  GF+D +  +   LN 
Sbjct: 199 KLRPNIVIATPGRLIDVLEK--YSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 256
Query: 219 ------NDVQVILLSATM 230
                 ++++ +L SAT+
Sbjct: 257 KNSKSADNIKTLLFSATL 274

>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 = 91.7 bits (226), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 66/198 (33%), Positives = 106/198 (53%), Gaps = 23/198 (11%)
Query: 54  LSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQ 111
           L +E+ + I    F   + +QQ+ I P +    +DVIA+A++GTGKT  F I I Q +  
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLIN 87
Query: 112 NIKECQ----ALILAPTRELAQQIQKVVIALGD----FMSVSCHACIGGTIVRDDIRKL- 162
              + Q    A+I+APTR+LA QI+  V  + D        +C + +GGT  R  + K+ 
Sbjct: 88  TKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMN 147
Query: 163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMF---VLDEADEMLSRGFKDQIYDVFKHLN- 218
           +    +V+ TPGR+ D++ +   S K  R     VLDEAD +L  GF+D +  +   LN 
Sbjct: 148 KLRPNIVIATPGRLIDVLEK--YSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNE 205
Query: 219 ------NDVQVILLSATM 230
                 ++++ +L SAT+
Sbjct: 206 KNSKSADNIKTLLFSATL 223

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 88.2 bits (217), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 58/192 (30%), Positives = 100/192 (52%), Gaps = 8/192 (4%)
Query: 51  DMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVD 110
           + +++  LL+ I   GF+ P+ IQ +AI   + G +++A A +G+GKT  FSI IL Q+ 
Sbjct: 33  EYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK 92
Query: 111 QNI-KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI-RKLEAGAQV 168
           Q   K  +ALI++PTRELA QI + +I + +      H      +       K      +
Sbjct: 93  QPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDI 152
Query: 169 VVGTPGRVFDMISRG--ALSTKQIRMFVLDEADEML---SRGFKDQIYDVF-KHLNNDVQ 222
           +V TP R+  ++ +    +    +   V+DE+D++      GF+DQ+  +F    ++ V+
Sbjct: 153 LVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVR 212
Query: 223 VILLSATMPADV 234
             + SAT   DV
Sbjct: 213 RAMFSATFAYDV 224

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	258
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-145
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-144
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-141
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-140
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-139
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-130
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-122
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-122
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-122
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-119
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-119
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-116
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-114
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	1e-112
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-110
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-84
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-77
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	2e-74
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-70
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-68
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	5e-68
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	8e-68
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	7e-63
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	5e-61
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	9e-61
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-59
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-58
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	8e-58
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	4e-57
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	9e-57
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	3e-52
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	9e-17
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	1e-11
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-09
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	4e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-09
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-08
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	5e-08
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	5e-08
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	7e-08
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	7e-08
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	8e-07
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	4e-05
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	5e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	7e-05
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	2e-04

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score =  404 bits (1040), Expect = e-145
 Identities = 143/224 (63%), Positives = 175/224 (78%), Gaps = 1/224 (0%)

Query: 35  DGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSG 94
           +  I+TN+D V   FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSG
Sbjct: 2   ESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSG 61

Query: 95  TGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTI 154
           TGKT TFSI+ LQ++D ++K  QAL+LAPTRELA QIQKVV+AL   M +  HACIGGT 
Sbjct: 62  TGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTS 121

Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
             +D   L   AQ+VVGTPGRVFD I R    T +I+MF+LDEADEMLS GFK+QIY +F
Sbjct: 122 FVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF 180

Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             L    QV+LLSATMP DVL+V+ KFMR+P++ILVKK+ELTLE
Sbjct: 181 TLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 224

>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 =  410 bits (1055), Expect = e-144
 Identities = 170/250 (68%), Positives = 210/250 (84%), Gaps = 1/250 (0%)

Query: 10  EDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEK 69
                  + ++  +   NGP GM  +G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEK
Sbjct: 3   LGSPEFMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEK 62

Query: 70  PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ 129
           PSAIQQRAI+PC++G DVIAQAQSGTGKTATF+ISILQQ++ ++K  QAL+LAPTRELAQ
Sbjct: 63  PSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQ 122

Query: 130 QIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRGALSTK 188
           QIQKVV+ALGD+M  SCHACIGGT VR +++KL+     ++VGTPGRVFDM++R  LS K
Sbjct: 123 QIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPK 182

Query: 189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKI 248
            I+MFVLDEADEMLSRGFKDQIYD+F+ LN++ QV+LLSATMP+DVL+V+ KFMRDPI+I
Sbjct: 183 YIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRI 242

Query: 249 LVKKEELTLE 258
           LVKKEELTLE
Sbjct: 243 LVKKEELTLE 252

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score =  395 bits (1016), Expect = e-141
 Identities = 161/236 (68%), Positives = 195/236 (82%), Gaps = 1/236 (0%)

Query: 19  NEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAI 78
           +     +          G+IE+NW+ + +NFDDM L E LLRGIYAYGFEKPSAIQQRAI
Sbjct: 2   HHHHHHSSGRENLYFQGGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAI 61

Query: 79  IPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL 138
           IPC++G DVIAQAQSGTGKTATF+ISILQQ++   KE QAL+LAPTRELAQQIQKV++AL
Sbjct: 62  IPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILAL 121

Query: 139 GDFMSVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDE 197
           GD+M  +CHACIGGT VR++++KL+A    +VVGTPGRVFDM++R  LS K I+MFVLDE
Sbjct: 122 GDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDE 181

Query: 198 ADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
           ADEMLSRGFKDQIY++F+ LN  +QV+LLSATMP DVL+V+ KFMRDPI+ILVKKE
Sbjct: 182 ADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  397 bits (1022), Expect = e-140
 Identities = 143/224 (63%), Positives = 175/224 (78%), Gaps = 1/224 (0%)

Query: 35  DGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSG 94
           +  I+TN+D V   FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSG
Sbjct: 9   ESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSG 68

Query: 95  TGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTI 154
           TGKT TFSI+ LQ++D ++K  QAL+LAPTRELA QIQKVV+AL   M +  HACIGGT 
Sbjct: 69  TGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTS 128

Query: 155 VRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
             +D   L   AQ+VVGTPGRVFD I R    T +I+MF+LDEADEMLS GFK+QIY +F
Sbjct: 129 FVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIF 187

Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
             L    QV+LLSATMP DVL+V+ KFMR+P++ILVKK+ELTLE
Sbjct: 188 TLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE 231

>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 =  396 bits (1021), Expect = e-139
 Identities = 147/242 (60%), Positives = 185/242 (76%)

Query: 17  AENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQR 76
           A + + +        M       +    V   FD M L E+LLRGIYAYGFEKPSAIQQR
Sbjct: 7   ATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQR 66

Query: 77  AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVI 136
           AI   ++G DVIAQ+QSGTGKTATFSIS+LQ +D  ++E QALILAPTRELA QIQK ++
Sbjct: 67  AIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLL 126

Query: 137 ALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLD 196
           ALGD+M+V CHACIGGT V +DIRKL+ G  VV GTPGRVFDMI R +L T+ I+M VLD
Sbjct: 127 ALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLD 186

Query: 197 EADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
           EADEML++GFK+QIYDV+++L    QV+L+SAT+P ++L+++ KFM DPI+ILVK++ELT
Sbjct: 187 EADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELT 246

Query: 257 LE 258
           LE
Sbjct: 247 LE 248

>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 =  374 bits (963), Expect = e-130
 Identities = 96/232 (41%), Positives = 132/232 (56%), Gaps = 2/232 (0%)

Query: 28  GP-PGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           GP          +   +     F+D  L  ELL GI+  GFEKPS IQ+ AI   + G D
Sbjct: 1   GPLGSKDTRPQTDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRD 60

Query: 87  VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC 146
           ++A+A++GTGKTA F I  L++V   + + QALI+ PTRELA Q  +VV  LG    +SC
Sbjct: 61  ILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISC 120

Query: 147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF 206
               GGT +RDDI +L     ++VGTPGRV D+ SR         +F++DEAD+MLSR F
Sbjct: 121 MVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDF 180

Query: 207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           K  I  +   L    Q +L SAT P  V +  +K +  P +I + + ELTL+
Sbjct: 181 KTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLK 231

>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 =  354 bits (910), Expect = e-122
 Identities = 83/217 (38%), Positives = 135/217 (62%), Gaps = 7/217 (3%)

Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFS 102
           +A++FD++ L+ ELL+GIYA  F+KPS IQ+RA+   +     ++IAQ+QSGTGKTA FS
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62

Query: 103 ISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL 162
           +++L +V+      QA+ LAP+RELA+Q  +VV  +G F  ++    +  +  ++     
Sbjct: 63  LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK---- 118

Query: 163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-SRGFKDQIYDVFKHLNNDV 221
           +  AQV+VGTPG V D++ R  +  ++I++FVLDEAD ML  +G  DQ   V + L  D 
Sbjct: 119 QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDT 178

Query: 222 QVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           Q++L SAT    V   + K + +   + ++  E+ ++
Sbjct: 179 QLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVD 215

>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 =  352 bits (906), Expect = e-122
 Identities = 82/220 (37%), Positives = 130/220 (59%), Gaps = 8/220 (3%)

Query: 44  HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATF 101
           +  ++F+++ L  +LL+G+YA GF +PS IQ+ A+   +     ++IAQ+QSGTGKTA F
Sbjct: 22  YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF 81

Query: 102 SISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIR 160
            +++L QV+   K  Q L L+PT ELA Q  KV+  +G F   +     + G  +    +
Sbjct: 82  VLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 141

Query: 161 KLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLN 218
                 Q+V+GTPG V D  S+   +  K+I++FVLDEAD M++ +G +DQ   + + L 
Sbjct: 142 I---SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLP 198

Query: 219 NDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
            + Q++L SAT    V   + K + DP  I +K+EE TL+
Sbjct: 199 RNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 238

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score =  345 bits (887), Expect = e-122
 Identities = 83/206 (40%), Positives = 122/206 (59%), Gaps = 3/206 (1%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
           +F+ + LS  +L G+ A GFE+PS +Q +AI     G D+I QA+SGTGKT  FS   L 
Sbjct: 25  DFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALD 84

Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGA 166
            +       Q LILAPTRE+A QI  V+ A+G  M  + CH  IGGT +  D  +L+   
Sbjct: 85  SLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KC 143

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNNDVQVIL 225
            + VG+PGR+  +I    L+   IR+F+LDEAD++L  G F++QI  ++  L    Q++ 
Sbjct: 144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLA 203

Query: 226 LSATMPADVLDVSMKFMRDPIKILVK 251
           +SAT P  + +   K+MRDP  + + 
Sbjct: 204 VSATYPEFLANALTKYMRDPTFVRLN 229

>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 =  346 bits (889), Expect = e-119
 Identities = 80/222 (36%), Positives = 124/222 (55%), Gaps = 4/222 (1%)

Query: 41  NWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTAT 100
           +  H++  F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA 
Sbjct: 2   SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 61

Query: 101 FSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDI 159
           F ++ LQQ++    +   L++  TRELA QI K       +M  V      GG  ++ D 
Sbjct: 62  FVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121

Query: 160 RKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHL 217
             L+     +VVGTPGR+  +    +L+ K I+ F+LDE D+ML +   +  + ++F+  
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMT 181

Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILVK-KEELTLE 258
            ++ QV++ SAT+  ++  V  KFM+DP++I V  + +LTL 
Sbjct: 182 PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLH 223

>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 =  348 bits (895), Expect = e-119
 Identities = 89/274 (32%), Positives = 141/274 (51%), Gaps = 23/274 (8%)

Query: 2   AEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWD------------HVAENF 49
             +   N E       E+ A Q   N         L++                +  ++F
Sbjct: 38  VVKTNANAEKTDEEEKEDRAAQSLLNKLIR---SNLVDNTNQVEVLQRDPNSPLYSVKSF 94

Query: 50  DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQ 107
           +++ L  +LL+G+YA GF +PS IQ+ A+   +     ++IAQ+QSGTGKTA F +++L 
Sbjct: 95  EELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLS 154

Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGA 166
           QV+   K  Q L L+PT ELA Q  KV+  +G F   +     + G  +    +      
Sbjct: 155 QVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SE 211

Query: 167 QVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVI 224
           Q+V+GTPG V D  S+   +  K+I++FVLDEAD M++ +G +DQ   + + L  + Q++
Sbjct: 212 QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQML 271

Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKKEELTLE 258
           L SAT    V   + K + DP  I +K+EE TL+
Sbjct: 272 LFSATFEDSVWKFAQKVVPDPNVIKLKREEETLD 305

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score =  335 bits (860), Expect = e-116
 Identities = 83/262 (31%), Positives = 134/262 (51%), Gaps = 13/262 (4%)

Query: 2   AEQRGDNWEDPKNGPAENE-----AEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSE 56
                   E+ K   A              +    + V      +  +  ++F+++ L  
Sbjct: 42  NANAEKTDEEEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKP 101

Query: 57  ELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIK 114
           +LL+G+YA GF +PS IQ+ A+   +     ++IAQ+QSGTGKTA F +++L QV+   K
Sbjct: 102 QLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK 161

Query: 115 ECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
             Q L L+PT ELA Q  KV+  +G F   +     + G  +    +      Q+V+GTP
Sbjct: 162 YPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI---SEQIVIGTP 218

Query: 174 GRVFDMISR-GALSTKQIRMFVLDEADEMLS-RGFKDQIYDVFKHLNNDVQVILLSATMP 231
           G V D  S+   +  K+I++FVLDEAD M++ +G +DQ   + + L  + Q++L SAT  
Sbjct: 219 GTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFE 278

Query: 232 ADVLDVSMKFMRDPIKILVKKE 253
             V   + K + DP  I +K+E
Sbjct: 279 DSVWKFAQKVVPDPNVIKLKRE 300

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score =  321 bits (824), Expect = e-112
 Identities = 77/202 (38%), Positives = 120/202 (59%), Gaps = 1/202 (0%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F+D  L  ELL GI+  G+EKPS IQ+ +I   + G D++A+A++GTGK+  + I +L+
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKLEAGA 166
           ++D      QA+++ PTRELA Q+ ++ I +   M      A  GGT +RDDI +L+   
Sbjct: 64  RLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
            VV+ TPGR+ D+I +G      ++M VLDEAD++LS+ F   + D+   L  + Q++L 
Sbjct: 124 HVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLY 183

Query: 227 SATMPADVLDVSMKFMRDPIKI 248
           SAT P  V       +  P +I
Sbjct: 184 SATFPLSVQKFMNSHLEKPYEI 205

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score =  315 bits (809), Expect = e-110
 Identities = 76/217 (35%), Positives = 121/217 (55%), Gaps = 4/217 (1%)

Query: 38  IETNWDHVAE-NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTG 96
           ++ ++  +    F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG G
Sbjct: 4   VKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMG 63

Query: 97  KTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM-SVSCHACIGGTIV 155
           KTA F ++ LQQ++    +   L++  TRELA QI K       +M +V      GG  +
Sbjct: 64  KTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSI 123

Query: 156 RDDIRKLEAGA-QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDV 213
           + D   L+     +VVGTPGR+  +    +L+ K I+ F+LDE D+ML +   +  + ++
Sbjct: 124 KKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEI 183

Query: 214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
           F+   ++ QV++ SAT+  ++  V  KFM+DP++I V
Sbjct: 184 FRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  250 bits (640), Expect = 2e-84
 Identities = 68/210 (32%), Positives = 107/210 (50%), Gaps = 4/210 (1%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F        ++  I    F KP+ IQ+R I   +RG  ++ Q+Q+GTGKT  + + I++
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64

Query: 108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS----VSCHACIGGTIVRDDIRKLE 163
           ++     E QA+I APTRELA QI    + +  F      +     IGGT  +  + KL 
Sbjct: 65  KIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 124

Query: 164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQV 223
               +V+GTPGR+ D I   AL      + V+DEAD ML  GF   +  +   +  D+Q+
Sbjct: 125 VQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQM 184

Query: 224 ILLSATMPADVLDVSMKFMRDPIKILVKKE 253
           ++ SAT+P  +     K+M +P  + V + 
Sbjct: 185 LVFSATIPEKLKPFLKKYMENPTFVHVLEH 214

>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 =  238 bits (609), Expect = 1e-77
 Identities = 80/210 (38%), Positives = 130/210 (61%), Gaps = 3/210 (1%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISIL 106
           NF+++ LS+ +L  I   GFEKP+ IQ + I   +    +++AQA++G+GKTA+F+I ++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
           + V++N    +A+IL PTRELA Q+   + +L    ++      GG  +   I+ L+  A
Sbjct: 67  ELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
            +VVGTPGR+ D I+RG L+ K ++ F+LDEADEML+ GF   +  +    N D +++L 
Sbjct: 125 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLF 184

Query: 227 SATMPADVLDVSMKFMRDPIKILVKKEELT 256
           SATMP ++L+++ K+M D   I  K     
Sbjct: 185 SATMPREILNLAKKYMGDYSFIKAKINANI 214

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score =  224 bits (573), Expect = 2e-74
 Identities = 73/208 (35%), Positives = 116/208 (55%), Gaps = 5/208 (2%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F D  L  E+L  ++  G   P+ IQ  A+   + G D+I QA++GTGKT  F++ I +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 108 QVDQN---IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           ++  +    ++ +AL+L PTRELA Q+   + A+   + V   A  GGT        L  
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLR 119

Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
           GA  VV TPGR  D + +G L   ++ + VLDEADEMLS GF++++  +        Q +
Sbjct: 120 GADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTL 179

Query: 225 LLSATMPADVLDVSMKFMRDPIKILVKK 252
           L SAT+P+    ++ ++M++P+ I V K
Sbjct: 180 LFSATLPSWAKRLAERYMKNPVLINVIK 207

>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 =  218 bits (558), Expect = 3e-70
 Identities = 57/198 (28%), Positives = 105/198 (53%), Gaps = 7/198 (3%)

Query: 54  LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI 113
           ++E++ + I   GF+  + +Q + I   ++G +V+ +A++G+GKTA ++I IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54

Query: 114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
              ++L++ PTREL +Q+   +  +G +M        GG   +  I ++   A +VV TP
Sbjct: 55  LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113

Query: 174 GRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPAD 233
           GR+ D+ S+G +      + ++DEAD M   GF D I  +    +N     L SAT+P +
Sbjct: 114 GRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEE 173

Query: 234 VLDVSMKFMRDPIKILVK 251
           +  V   F+ +  +I   
Sbjct: 174 IRKVVKDFITNYEEIEAC 191

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score =  211 bits (538), Expect = 1e-68
 Identities = 65/252 (25%), Positives = 115/252 (45%), Gaps = 5/252 (1%)

Query: 1   MAEQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLR 60
           M      +                 ++ P   +   + E       + F D+ +++ L  
Sbjct: 1   MHHHHHHSSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEE----TKTFKDLGVTDVLCE 56

Query: 61  GIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALI 120
                G+ KP+ IQ  AI   ++G D+I  A++G+GKT  F++ IL  + +  +   AL+
Sbjct: 57  ACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALV 116

Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
           L PTRELA QI +   ALG  + V     +GG         L     +++ TPGR+ D +
Sbjct: 117 LTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHL 176

Query: 181 SRG-ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM 239
                 + + ++  V+DEAD +L+  F+ ++  + K +  D +  L SATM   V  +  
Sbjct: 177 ENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQR 236

Query: 240 KFMRDPIKILVK 251
             +++P+K  V 
Sbjct: 237 AALKNPVKCAVS 248

>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 =  219 bits (559), Expect = 5e-68
 Identities = 67/237 (28%), Positives = 115/237 (48%), Gaps = 23/237 (9%)

Query: 45  VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP--CVRGNDVIAQAQSGTGKTATFS 102
           +    ++  L +E+ + I    F   + +QQ+ I P      +DVIA+A++GTGKT  F 
Sbjct: 19  LDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFL 78

Query: 103 ISILQQVDQNIKE----CQALILAPTRELAQQIQKVVIALGDFM----SVSCHACIGGTI 154
           I I Q +     +     +A+I+APTR+LA QI+  V  + D        +C + +GGT 
Sbjct: 79  IPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTD 138

Query: 155 VRDDIRKLE-AGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIYD 212
            R  + K+      +V+ TPGR+ D++ + +    + +   VLDEAD +L  GF+D +  
Sbjct: 139 FRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLET 198

Query: 213 VFKHLNN-------DVQVILLSATMPADVLDVSMKFMRDPIKILV----KKEELTLE 258
           +   LN        +++ +L SAT+   V  ++   M     + +    K E    E
Sbjct: 199 ISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE 255

>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 =  218 bits (557), Expect = 8e-68
 Identities = 70/279 (25%), Positives = 126/279 (45%), Gaps = 23/279 (8%)

Query: 3   EQRGDNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGI 62
             R ++    ++   ++E           + V     +    +    ++  L +E+ + I
Sbjct: 28  NSRFNSRPRTRSREDDDEVHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAI 87

Query: 63  YAYGFEKPSAIQQRAIIPC--VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKE----C 116
               F   + +QQ+ I P      +DVIA+A++GTGKT  F I I Q +     +     
Sbjct: 88  TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMV 147

Query: 117 QALILAPTRELAQQIQKVVIALGDF----MSVSCHACIGGTIVRDDIRKLE-AGAQVVVG 171
           +A+I+APTR+LA QI+  V  + D        +C + +GGT  R  + K+      +V+ 
Sbjct: 148 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIA 207

Query: 172 TPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN-------DVQV 223
           TPGR+ D++ + +    + +   VLDEAD +L  GF+D +  +   LN        +++ 
Sbjct: 208 TPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKT 267

Query: 224 ILLSATMPADVLDVSMKFMRDPIKILV----KKEELTLE 258
           +L SAT+   V  ++   M     + +    K E    E
Sbjct: 268 LLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE 306

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  195 bits (499), Expect = 7e-63
 Identities = 61/213 (28%), Positives = 109/213 (51%), Gaps = 6/213 (2%)

Query: 46  AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISI 105
              F D  LS++ L+G+    +   + IQ++ I   ++G DV+  A++G+GKT  F + +
Sbjct: 24  ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV 83

Query: 106 LQQVDQNIKE----CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK 161
           L+ + +           LI++PTRELA Q  +V+  +G     S    IGG  ++ +  +
Sbjct: 84  LEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAER 143

Query: 162 LEAGAQVVVGTPGRVFDMISRGA-LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
           +     ++V TPGR+   +          ++M VLDEAD +L  GF D +  V ++L   
Sbjct: 144 I-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKK 202

Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKE 253
            Q +L SAT    V D++   +++P  + V ++
Sbjct: 203 RQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK 235

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  191 bits (488), Expect = 5e-61
 Identities = 70/215 (32%), Positives = 108/215 (50%), Gaps = 7/215 (3%)

Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISI 105
            NF +      ++  I    F +P+AIQ +   P    G D++  AQ+G+GKT ++ +  
Sbjct: 29  LNFYEANFPANVMDVIARQNFTEPTAIQAQGW-PVALSGLDMVGVAQTGSGKTLSYLLPA 87

Query: 106 LQQV-DQNIKECQ----ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
           +  +  Q   E       L+LAPTRELAQQ+Q+V         +      GG      IR
Sbjct: 88  IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147

Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNND 220
            LE G ++ + TPGR+ D +  G  + ++    VLDEAD ML  GF+ QI  +   +  D
Sbjct: 148 DLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPD 207

Query: 221 VQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL 255
            Q ++ SAT P +V  ++  F++D I I +   EL
Sbjct: 208 RQTLMWSATWPKEVRQLAEDFLKDYIHINIGALEL 242

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score =  191 bits (487), Expect = 9e-61
 Identities = 69/217 (31%), Positives = 110/217 (50%), Gaps = 13/217 (5%)

Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISIL 106
           ENFD+++L   +   I    +++P+ IQ+ AI   +   D++A AQ+G+GKTA F I I+
Sbjct: 23  ENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII 82

Query: 107 QQVDQN---------IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
             +                + LILAPTRELA QI            +      GG     
Sbjct: 83  NHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHS 142

Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
            IR+++ G  ++V TPGR+ D I +  +S +  +  VLDEAD ML  GF+ QI  + +  
Sbjct: 143 QIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEES 202

Query: 218 N----NDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
           N     + Q ++ SAT P ++  ++  F+ + I + V
Sbjct: 203 NMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 239

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  188 bits (479), Expect = 1e-59
 Identities = 59/216 (27%), Positives = 105/216 (48%), Gaps = 12/216 (5%)

Query: 47  ENFDDME----LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFS 102
             F  ++    ++  LL+ I   GF+ P+ IQ +AI   + G +++A A +G+GKT  FS
Sbjct: 25  ATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFS 84

Query: 103 ISILQQVDQNIKE-CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI-R 160
           I IL Q+ Q   +  +ALI++PTRELA QI + +I + +      H      +       
Sbjct: 85  IPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGP 144

Query: 161 KLEAGAQVVVGTPGRVFDMISRG--ALSTKQIRMFVLDEADEML---SRGFKDQIYDVFK 215
           K      ++V TP R+  ++ +    +    +   V+DE+D++      GF+DQ+  +F 
Sbjct: 145 KSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFL 204

Query: 216 HLNND-VQVILLSATMPADVLDVSMKFMRDPIKILV 250
              +  V+  + SAT   DV       + + I + +
Sbjct: 205 ACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSI 240

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  185 bits (471), Expect = 1e-58
 Identities = 63/229 (27%), Positives = 108/229 (47%), Gaps = 11/229 (4%)

Query: 32  MAVDGLIETNWDHV---AENFDD-MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDV 87
           M  D L       +      F D  +   +LL+ I   G  KP+ IQ +A    ++G D+
Sbjct: 1   MTCDDLKSGEKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDL 60

Query: 88  IAQAQSGTGKTATFSISILQQVDQNIKECQ------ALILAPTRELAQQIQKVVIALGDF 141
           I  AQ+GTGKT ++ +     +D      +       L+L PTRELA  ++        +
Sbjct: 61  IVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-Y 119

Query: 142 MSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM 201
             +      GG      I  +  G  +++ TPGR+ D+    +++ + I   V+DEAD+M
Sbjct: 120 KGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKM 179

Query: 202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
           L   F+ QI  +   +  D Q ++ SAT P  V  +++ +++DP+ + V
Sbjct: 180 LDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  188 bits (481), Expect = 8e-58
 Identities = 62/212 (29%), Positives = 111/212 (52%), Gaps = 9/212 (4%)

Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISI 105
           ++F   +L + ++  +   G++ P+ IQ+ +I P +  G D++A AQ+G+GKTA F + I
Sbjct: 56  QHFTSADLRDIIIDNVNKSGYKIPTPIQKCSI-PVISSGRDLMACAQTGSGKTAAFLLPI 114

Query: 106 L-----QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR 160
           L        +  +   Q +I++PTRELA QI            +      GGT  R    
Sbjct: 115 LSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNE 174

Query: 161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN- 219
            +  G  VV+ TPGR+ D + R  ++ +  R  VLDEAD ML  GF + +  +  H+   
Sbjct: 175 CITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMR 234

Query: 220 -DVQVILLSATMPADVLDVSMKFMRDPIKILV 250
            + Q ++ SAT P ++  ++ +F+++ + + +
Sbjct: 235 PEHQTLMFSATFPEEIQRMAGEFLKNYVFVAI 266

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score =  182 bits (464), Expect = 4e-57
 Identities = 67/250 (26%), Positives = 116/250 (46%), Gaps = 8/250 (3%)

Query: 7   DNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDM--ELSEELLRGIYA 64
           D   +     + N  E+P  +          +         +F  +   ++E  L+ I  
Sbjct: 12  DLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKE 71

Query: 65  YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----IKECQALI 120
            GF   + IQ ++I P + G D++A A++G+GKT  F I  ++ + +           LI
Sbjct: 72  MGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLI 131

Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFD-M 179
           L+PTRELA Q   V+  L      +    +GG+    + +KL  G  ++V TPGR+ D M
Sbjct: 132 LSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHM 191

Query: 180 ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLD-VS 238
            +      K ++  V+DEAD +L  GF++++  + K L    Q +L SAT    V D   
Sbjct: 192 QNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLAR 251

Query: 239 MKFMRDPIKI 248
           +   ++P+ +
Sbjct: 252 ISLKKEPLYV 261

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  185 bits (473), Expect = 9e-57
 Identities = 71/227 (31%), Positives = 111/227 (48%), Gaps = 24/227 (10%)

Query: 47  ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISI 105
           E+F D+E+ E ++  I    + +P+ +Q+ AI P +    D++A AQ+G+GKTA F + I
Sbjct: 15  ESFSDVEMGEIIMGNIELTRYTRPTPVQKHAI-PIIKEKRDLMACAQTGSGKTAAFLLPI 73

Query: 106 LQQVDQNIK------------------ECQALILAPTRELAQQIQKVVIALGDFMSVSCH 147
           L Q+  +                       +L+LAPTRELA QI +          V   
Sbjct: 74  LSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPC 133

Query: 148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK 207
              GG  +   IR LE G  ++V TPGR+ DM+ RG +     +  VLDEAD ML  GF+
Sbjct: 134 VVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFE 193

Query: 208 DQIYDVFKHLN----NDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
            QI  + +            ++ SAT P ++  ++  F+ + I + V
Sbjct: 194 PQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAV 240

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  174 bits (442), Expect = 3e-52
 Identities = 28/200 (14%), Positives = 63/200 (31%), Gaps = 10/200 (5%)

Query: 53  ELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN 112
              E+          +  +  Q+      V+G      A +G GKT    ++ L    + 
Sbjct: 5   NEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG 64

Query: 113 IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA----GAQV 168
            K   + ++ PT  L +Q  + +  L D   V            +  +  ++       +
Sbjct: 65  KK---SALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHI 120

Query: 169 VVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA 228
           +V +   V    +R  LS K+     +D+ D +L          +   +  ++     S 
Sbjct: 121 LVFSTQFVSK--NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFST 178

Query: 229 TMPADVLDVSMKFMRDPIKI 248
                + +         + +
Sbjct: 179 IKQGKIYERPKNLKPGILVV 198

>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 = 78.3 bits (192), Expect = 9e-17
 Identities = 34/163 (20%), Positives = 66/163 (40%), Gaps = 3/163 (1%)

Query: 75  QRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV 134
           Q  I    +  + +    +G GKT    +    ++ +     + L+LAPT+ L  Q  + 
Sbjct: 14  QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG--KVLMLAPTKPLVLQHAES 71

Query: 135 VIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV 194
              L +         + G    ++  K  A A+V+V TP  + + +  G +S + + + V
Sbjct: 72  FRRLFNLPPEKI-VALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIV 130

Query: 195 LDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDV 237
            DEA   +       I   +K    +  VI L+A+  +    +
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKI 173

>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 Length = 702

 Score = 65.6 bits (160), Expect = 2e-12
 Identities = 34/191 (17%), Positives = 71/191 (37%), Gaps = 30/191 (15%)

Query: 54  LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI 113
           +S   +  +   G E+    Q  A+     G +++    +  GKT    ++++++  +  
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGG 69

Query: 114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTP 173
           K   +L + P R LA +  +          +      G     +   +      ++V T 
Sbjct: 70  K---SLYVVPLRALAGEKYESFKKWEKI-GLRIGISTGDY---ESRDEHLGDCDIIVTTS 122

Query: 174 GRVFDMISR-GALSTKQIRMFVLDE----ADE--------MLSRGFKDQIYDVFKHLNND 220
            +  D + R  A   K +   V+DE      E        ++++          + +N  
Sbjct: 123 EK-ADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTK---------MRRMNKA 172

Query: 221 VQVILLSATMP 231
           ++VI LSAT P
Sbjct: 173 LRVIGLSATAP 183

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720

 Score = 63.3 bits (154), Expect = 1e-11
 Identities = 37/204 (18%), Positives = 78/204 (38%), Gaps = 32/204 (15%)

Query: 50  DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND-VIAQAQSGTGKTATFSISILQQ 108
           D++ + E +   +   G E     Q  A+   +      +    + +GKT    I+++ +
Sbjct: 4   DELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHR 63

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDF-----MSVSCHACIGGTIVRDDIRKLE 163
           +       +A+ + P + LA++         +F     + +      G    +D+     
Sbjct: 64  ILTQGG--KAVYIVPLKALAEEK------FQEFQDWEKIGLRVAMATGDYDSKDEWLG-- 113

Query: 164 AGAQVVVGTPGRVFDMISRGALS-TKQIRMFVLDE----ADEMLSRGFKDQIYDVFKHLN 218
               +++ T  + FD + R   S  K +++ V DE          RG    +  +  H+ 
Sbjct: 114 -KYDIIIATAEK-FDSLLRHGSSWIKDVKILVADEIHLIGSR--DRG--ATLEVILAHML 167

Query: 219 NDVQVILLSATMP-----ADVLDV 237
              Q+I LSAT+      A+ L+ 
Sbjct: 168 GKAQIIGLSATIGNPEELAEWLNA 191

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 54.8 bits (132), Expect = 2e-09
 Identities = 25/180 (13%), Positives = 57/180 (31%), Gaps = 25/180 (13%)

Query: 74  QQRAIIPCVRGNDVIAQAQSGTGKT--ATFSI-SILQQVDQNIKECQALILAPTRELA-Q 129
           Q     P + G ++I    +G+GKT  A +     L +  +  +  + ++L     L  Q
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQ 97

Query: 130 QIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI------SRG 183
             +K                 G T ++    ++     +++ T   + + +         
Sbjct: 98  LFRKEFQPFLKKWYRVIGLS-GDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDA 156

Query: 184 ALSTKQIRMFVLDEA-------------DEMLSRGFKDQIYDVFKHLNNDVQVIL-LSAT 229
            +      + ++DE                 L +  K+            +  IL L+A+
Sbjct: 157 GVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS 216

>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 = 55.8 bits (133), Expect = 4e-09
 Identities = 31/213 (14%), Positives = 72/213 (33%), Gaps = 3/213 (1%)

Query: 7   DNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYG 66
           + W+  ++   + ++E    +     A     E        + +    +E + +    Y 
Sbjct: 186 ELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYE 245

Query: 67  FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALILAPT 124
            +K  + Q     P + G + +  A +G+GKT  +        Q     ++ + + LA  
Sbjct: 246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATK 305

Query: 125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA 184
             + +Q + V     +    S     G       + K+   + ++V TP  + +    G 
Sbjct: 306 VPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGT 365

Query: 185 L-STKQIRMFVLDEADEMLSRGFKDQIYDVFKH 216
           L S     + + DE          + +   +  
Sbjct: 366 LTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE 398

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 55.2 bits (132), Expect = 7e-09
 Identities = 49/321 (15%), Positives = 102/321 (31%), Gaps = 110/321 (34%)

Query: 32  MAVDGLIETNWDHVAENFDDMELSEELLRGIYAYG----------FEK-----PSAIQQ- 75
             V+ ++  N+  +       +    ++  +Y             F K          + 
Sbjct: 81  KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL 140

Query: 76  -RAIIPCVRGNDVIAQAQSGTGKT-----ATFSISILQQVDQNI-----KECQ--ALILA 122
            +A++      +V+     G+GKT        S  +  ++D  I     K C     +L 
Sbjct: 141 RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLE 200

Query: 123 PTRELAQQIQKVVIALGDFMS---VSCHA----------------CIGGTIVRDDI---R 160
             ++L  QI     +  D  S   +  H+                C+   +V  ++   +
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLLNVQNAK 257

Query: 161 KLEA---GAQVVVGTPGR---VFDMISRGALSTKQIRM------FVLDEADEMLSR---- 204
              A     ++++ T  R   V D +S  A +T  I +         DE   +L +    
Sbjct: 258 AWNAFNLSCKILLTT--RFKQVTDFLS--AATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313

Query: 205 ----------------------GFKDQI--YDVFKHLNNDVQVILLSATM----PADV-- 234
                                   +D +  +D +KH+N D    ++ +++    PA+   
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373

Query: 235 --LDVSMKFMRD---PIKILV 250
               +S+ F      P  +L 
Sbjct: 374 MFDRLSV-FPPSAHIPTILLS 393

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 52.7 bits (125), Expect = 4e-08
 Identities = 23/151 (15%), Positives = 54/151 (35%), Gaps = 3/151 (1%)

Query: 69  KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKEC--QALILAPTRE 126
           KP   Q    +P ++G + I  A +G GKT    +     + +  +    + +  A    
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72

Query: 127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL- 185
           + +Q + V     +          G T     + ++     +++ TP  + + + +G + 
Sbjct: 73  VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIP 132

Query: 186 STKQIRMFVLDEADEMLSRGFKDQIYDVFKH 216
           S     + + DE      +   + I   +  
Sbjct: 133 SLSIFTLMIFDECHNTSKQHPYNMIMFNYLD 163

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 52.4 bits (126), Expect = 5e-08
 Identities = 35/190 (18%), Positives = 73/190 (38%), Gaps = 22/190 (11%)

Query: 50  DDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND-VIAQAQSGTGKTATFSISILQQ 108
           +D++L   ++  I   G +K +  Q  A+   +   + ++  + +G+GKT    + I+  
Sbjct: 11  EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISF 70

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDF--MSVSCHACIGGTIVRDDIRKLEAGA 166
           + +N    +A+ + P R L  +     +   D+  +        G     D         
Sbjct: 71  LLKNGG--KAIYVTPLRALTNE---KYLTFKDWELIGFKVAMTSGDY---DTDDAWLKNY 122

Query: 167 QVVVGTPGRVFDMISRGALS-TKQIRMFVLDE----ADEMLSRGFKDQIYDVFKHLNNDV 221
            +++ T  +  D + R       ++  FVLDE     D    RG    + +         
Sbjct: 123 DIIITTYEK-LDSLWRHRPEWLNEVNYFVLDELHYLNDP--ERG---PVVESVTIRAKRR 176

Query: 222 QVILLSATMP 231
            ++ LSAT+ 
Sbjct: 177 NLLALSATIS 186

>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 = 52.2 bits (124), Expect = 5e-08
 Identities = 28/189 (14%), Positives = 63/189 (33%), Gaps = 8/189 (4%)

Query: 69  KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL--APTRE 126
           K  + Q     P + G + +  A +G+GKT    +             +A ++  A    
Sbjct: 7   KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66

Query: 127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL- 185
           + +Q + V     +    S     G       + K+   + ++V TP  + +    G L 
Sbjct: 67  VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 126

Query: 186 STKQIRMFVLDEA-----DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK 240
           S     + + DE      +   +      +   F   +   Q++ L+A++         +
Sbjct: 127 SLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEE 186

Query: 241 FMRDPIKIL 249
            +     + 
Sbjct: 187 TIEHICSLC 195

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 51.8 bits (123), Expect = 7e-08
 Identities = 29/185 (15%), Positives = 68/185 (36%), Gaps = 9/185 (4%)

Query: 74  QQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQ--ALILAPTRELAQQI 131
           Q    +P  +G + I  A +G GKT    +     + +     +   +  A    + +Q 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68

Query: 132 QKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQI 190
             V     + +  +  +  G T     ++ +     +++ TP  + + ++ GA+ S    
Sbjct: 69  ATVFSRYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVF 128

Query: 191 RMFVLDEADEMLSRGFKDQIYDVFKHL------NNDVQVILLSATMPADVLDVSMKFMRD 244
            + + DE          +QI   +         +   QV+ L+A++       + + M+ 
Sbjct: 129 TLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGVGDAKTAEEAMQH 188

Query: 245 PIKIL 249
             K+ 
Sbjct: 189 ICKLC 193

>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 = 51.9 bits (123), Expect = 7e-08
 Identities = 34/232 (14%), Positives = 79/232 (34%), Gaps = 8/232 (3%)

Query: 7   DNWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYG 66
           + W+  ++   + ++E    +     A     E        + +    +E + +    Y 
Sbjct: 186 ELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYE 245

Query: 67  FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL--APT 124
            +K  + Q     P + G + +  A +G+GKT    +             +A ++  A  
Sbjct: 246 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATK 305

Query: 125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA 184
             + +Q + V     +    S     G       + K+   + ++V TP  + +    G 
Sbjct: 306 VPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGT 365

Query: 185 L-STKQIRMFVLDEADEM-----LSRGFKDQIYDVFKHLNNDVQVILLSATM 230
           L S     + + DE          +      +   F   +   Q++ L+A++
Sbjct: 366 LTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASV 417

>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* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 48.9 bits (116), Expect = 8e-07
 Identities = 36/197 (18%), Positives = 60/197 (30%), Gaps = 42/197 (21%)

Query: 58  LLRGIYAYGFEKPSAIQQRAIIPCV------------RGNDVIAQAQSGTGKTATFSISI 105
             RG+       P    +  +   V                    A +G+GK+      +
Sbjct: 194 CTRGVAKAVDFVPVESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKST----KV 249

Query: 106 LQQ-VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
                 Q  K    L+L P+           +  G +MS +         +R  +R +  
Sbjct: 250 PAAYAAQGYK---VLVLNPSVAAT-------LGFGAYMSKAHG---IDPNIRTGVRTITT 296

Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM-----LSRGFKDQIYDVFKHLNN 219
           GA V   T G+    ++ G  S     + + DE         L  G    + D  +    
Sbjct: 297 GAPVTYSTYGK---FLADGGCSGGAYDIIICDECHSTDSTTILGIGT---VLDQAETA-G 349

Query: 220 DVQVILLSATMPADVLD 236
              V+L +AT P  V  
Sbjct: 350 ARLVVLATATPPGSVTV 366

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score = 43.7 bits (102), Expect = 4e-05
 Identities = 47/209 (22%), Positives = 86/209 (41%), Gaps = 25/209 (11%)

Query: 28  GPPGMAVDGLIETNWDHVAE-NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND 86
           GP  M     ++  W HV + N       E +     ++ FE     Q+ A+    +G+ 
Sbjct: 1   GPDSMVP---VKKEWAHVVDLNHKIENFDELIPNPARSWPFE-LDTFQKEAVYHLEQGDS 56

Query: 87  VIAQAQSGTGKT--ATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV 144
           V   A +  GKT  A ++I++  +        + +  +P + L+ Q  +      D +++
Sbjct: 57  VFVAAHTSAGKTVVAEYAIAMAHRNMT-----KTIYTSPIKALSNQKFRDFKETFDDVNI 111

Query: 145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML-- 202
                  G I  D   ++   A  ++ T   +  M+ RGA   + +   + DE   +   
Sbjct: 112 -------GLITGDV--QINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQ 162

Query: 203 SRGFKDQIYDVFKHLNNDVQVILLSATMP 231
            RG   +  +V   L   V+ ILLSAT+P
Sbjct: 163 DRGVVWE--EVIIMLPQHVKFILLSATVP 189

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 43.2 bits (101), Expect = 5e-05
 Identities = 37/171 (21%), Positives = 69/171 (40%), Gaps = 19/171 (11%)

Query: 63  YAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALI 120
             Y F      Q  AI    RG  V+  A +  GKT  A ++I+   +  Q     + + 
Sbjct: 81  RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ-----RVIY 134

Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
            +P + L+ Q         +   ++    +G  ++  DI  +   A  +V T   +  M+
Sbjct: 135 TSPIKALSNQK------YREL--LAEFGDVG--LMTGDI-TINPDAGCLVMTTEILRSML 183

Query: 181 SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP 231
            RG+   +++   + DE   M  +       +    L + V+ + LSAT+P
Sbjct: 184 YRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 234

>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* Length = 440

 Score = 42.5 bits (100), Expect = 7e-05
 Identities = 26/156 (16%), Positives = 53/156 (33%), Gaps = 14/156 (8%)

Query: 83  RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM 142
           +G   +     G GKT  F   IL +     +  + L+LAPTR +  ++++   A    +
Sbjct: 7   KGMTTVLDFHPGAGKTRRFLPQILAE--CARRRLRTLVLAPTRVVLSEMKE---AFHG-L 60

Query: 143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML 202
            V  H        +           +       +   +           + ++DEA  + 
Sbjct: 61  DVKFH-------TQAFSAHGSGREVIDAMCHATLTYRMLEPTRV-VNWEVIIMDEAHFLD 112

Query: 203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS 238
                 + +   +   N+   IL++AT P    +  
Sbjct: 113 PASIAARGWAAHRARANESATILMTATPPGTSDEFP 148

>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} Length = 1108

 Score = 41.4 bits (96), Expect = 2e-04
 Identities = 37/171 (21%), Positives = 69/171 (40%), Gaps = 19/171 (11%)

Query: 63  YAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALI 120
             Y F      Q  AI    RG  V+  A +  GKT  A ++I+   +  Q     + + 
Sbjct: 179 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ-----RVIY 232

Query: 121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI 180
            +P + L+ Q         +   ++    +G  ++  DI  +   A  +V T   +  M+
Sbjct: 233 TSPIKALSNQK------YREL--LAEFGDVG--LMTGDI-TINPDAGCLVMTTEILRSML 281

Query: 181 SRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP 231
            RG+   +++   + DE   M  +       +    L + V+ + LSAT+P
Sbjct: 282 YRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 332

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	258
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.98
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.97
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.96
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.96
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.96
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.96
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.95
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.95
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.95
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.95
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.95
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.94
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.94
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.94
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.94
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.94
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.94
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.93
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.93
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.93
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.92
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.91
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.91
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.9
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.9
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.89
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.89
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.88
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.88
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.86
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.85
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.85
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.85
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.84
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.84
3h1t_A	590	Type I site-specific restriction-modification syst	99.81
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.8
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.78
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.77
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.76
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.76
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.76
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.71
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.7
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.65
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.64
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.61
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.61
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.6
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.41
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.22
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.07
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.58
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.53
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.53
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.52
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.46
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.42
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.74
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.61
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.56
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.56
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.53
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.53
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.51
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.43
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.33
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.28
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.28
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.28
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.27
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.25
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.22
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.22
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.21
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.18
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.12
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.06
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.04
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.96
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.94
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.88
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.88
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.84
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.83
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.8
3bos_A	242	Putative DNA replication factor; P-loop containing	96.76
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.73
3co5_A	143	Putative two-component system transcriptional RES	96.71
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	96.62
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.62
2qgz_A	308	Helicase loader, putative primosome component; str	96.61
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.54
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	96.54
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.53
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	96.52
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.49
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.49
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.45
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.4
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	96.37
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.19
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.18
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.11
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	95.99
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.98
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.97
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.95
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.93
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.85
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.75
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.65
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.65
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	95.64
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.57
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.41
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	95.39
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.36
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	95.3
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.3
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	95.3
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.26
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.25
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	95.19
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.13
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.12
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.97
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	94.62
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	94.59
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	94.57
3pvs_A	447	Replication-associated recombination protein A; ma	94.49
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.34
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	94.13
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	93.87
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	93.81
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	93.55
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	92.96
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	92.85
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	92.75
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	92.73
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	92.64
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.63
1xp8_A	366	RECA protein, recombinase A; recombination, radior	92.56
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	92.38
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.28
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	92.14
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	92.11
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	92.02
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	92.02
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	91.95
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	91.8
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	91.66
3io5_A	333	Recombination and repair protein; storage dimer, i	91.44
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	91.42
2eyu_A	261	Twitching motility protein PILT; pilus retraction	91.41
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	91.37
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	91.32
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	91.04
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	90.71
2ewv_A	372	Twitching motility protein PILT; pilus retraction	90.58
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	90.41
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	90.21
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	90.05
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	90.0
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	89.9
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	89.78
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	89.55
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	89.43
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	89.4
1p9r_A	418	General secretion pathway protein E; bacterial typ	89.26
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	89.19
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	89.01
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	88.94
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	88.91
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	88.64
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	88.64
2cvh_A	220	DNA repair and recombination protein RADB; filamen	88.63
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	88.54
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	88.37
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	88.3
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	88.22
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	88.2
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	88.17
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	88.17
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	88.12
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	88.1
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	88.08
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	88.08
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	88.07
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	87.99
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	87.95
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.92
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	87.89
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	87.88
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	87.83
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	87.79
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	87.78
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	87.74
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	87.73
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	87.69
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	87.67
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	87.65
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	87.59
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	87.57
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	87.27
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	87.27
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	87.2
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	87.12
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	87.12
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	87.12
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	87.05
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	87.03
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	87.01
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	86.97
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	86.95
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	86.94
2z43_A	324	DNA repair and recombination protein RADA; archaea	86.93
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	86.91
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	86.9
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	86.89
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	86.87
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	86.84
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	86.84
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	86.72
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	86.69
2r44_A	331	Uncharacterized protein; putative ATPase, structur	86.56
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	86.56
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	86.52
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	86.4
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	86.3
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	86.25
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	86.21
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	86.08
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	86.02
3u06_A	412	Protein claret segregational; motor domain, stalk	85.9
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	85.9
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	85.89
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	85.88
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	85.87
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	85.85
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	85.8
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	85.72
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	85.66
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	85.55
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	85.49
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	85.48
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	85.43
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	85.41
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	85.28
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	85.28
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	85.23
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	85.22
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	85.16
1tue_A	212	Replication protein E1; helicase, replication, E1E	85.0
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	84.98
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	84.9
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	84.87
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	84.72
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	84.44
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	84.36
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	84.3
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	84.29
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	84.07
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	84.04
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	83.78
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	83.74
1yks_A	440	Genome polyprotein [contains: flavivirin protease	83.66
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	83.53
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	83.32
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	83.28
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	83.26
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	83.23
1u94_A	356	RECA protein, recombinase A; homologous recombinat	83.22
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	83.16
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	83.13
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	83.12
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	83.09
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	83.04
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	83.03
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	82.89
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	82.59
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	82.46
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	82.33
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	82.26
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	82.2
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	82.18
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	82.12
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	82.09
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	81.9
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	81.87
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	81.87
2vli_A	183	Antibiotic resistance protein; transferase, tunica	81.83
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	81.74
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	81.72
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	81.71
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	81.7
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	81.69
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	81.6
1via_A	175	Shikimate kinase; structural genomics, transferase	81.51
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	81.29
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	81.27
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	81.13
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	81.11
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	81.09
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	81.08
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	81.05
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	80.99
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	80.95
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	80.85
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	80.7
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	80.69
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	80.38
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	80.3
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	80.28
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	80.2
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	80.13
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	80.11
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	80.04

>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=100.00  E-value=1.6e-42  Score=285.24  Aligned_cols=215  Identities=32%  Similarity=0.504  Sum_probs=197.2

Q ss_pred             cccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-----ccc
Q psy4698          41 NWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-----IKE  115 (258)
Q Consensus        41 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-----~~~  115 (258)
                      +.+.....|+++++++.+.+.+.+.|+..|+++|.++++.+..|+++++.+|||||||++|++|++..+...     ..+
T Consensus        23 ~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~  102 (242)
T 3fe2_A           23 NCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDG  102 (242)
T ss_dssp             CCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCC
T ss_pred             CCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCC
Confidence            344556789999999999999999999999999999999999999999999999999999999999988643     346


Q ss_pred             ceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEE
Q psy4698         116 CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVL  195 (258)
Q Consensus       116 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVv  195 (258)
                      ++++|++|+++|+.|+.+.++.++...++.+...+|+.........+..+++|+|+||+++.+++.++...++++++||+
T Consensus       103 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lVi  182 (242)
T 3fe2_A          103 PICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVL  182 (242)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEE
T ss_pred             CEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEE
Confidence            68999999999999999999999888888999999998888888888888999999999999999988888999999999


Q ss_pred             ccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         196 DEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       196 DE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      ||||++.+.++...+..+++.+++++|++++|||+|++++++++.++++|+.|.+.++++
T Consensus       183 DEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~el  242 (242)
T 3fe2_A          183 DEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGALEL  242 (242)
T ss_dssp             TTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC---
T ss_pred             eCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCCCC
Confidence            999999999999999999999999999999999999999999999999999999988764

>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=100.00  E-value=7.7e-42  Score=277.61  Aligned_cols=219  Identities=65%  Similarity=1.000  Sum_probs=186.2

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceE
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQA  118 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~  118 (258)
                      +.++++....|+++++++.+.+.+.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++++++.+.....+.++
T Consensus         6 ~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~   85 (224)
T 1qde_A            6 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQA   85 (224)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCE
T ss_pred             ccccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceE
Confidence            34555666789999999999999999999999999999999999999999999999999999999999998777667799


Q ss_pred             EEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccc
Q psy4698         119 LILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEA  198 (258)
Q Consensus       119 lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~  198 (258)
                      +|++|+++|+.|+++.++.++...+..+..+.|+.........+.. ++|+|+||+++.+.+.++...++++++||+|||
T Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEa  164 (224)
T 1qde_A           86 LMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEA  164 (224)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETH
T ss_pred             EEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEEEcCh
Confidence            9999999999999999999988888888888888766555544444 899999999999999988888999999999999


Q ss_pred             hhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcccCC
Q psy4698         199 DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELTLE  258 (258)
Q Consensus       199 h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  258 (258)
                      |++.+.++...+..++..+++++|++++|||+++++.++++.|+++|+.|.+.+++.+++
T Consensus       165 h~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~~~~~~  224 (224)
T 1qde_A          165 DEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLE  224 (224)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC---------
T ss_pred             hHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCCccCCC
Confidence            999999999999999999999999999999999999999999999999999999888764

>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=100.00  E-value=4.9e-42  Score=281.41  Aligned_cols=219  Identities=74%  Similarity=1.180  Sum_probs=182.6

Q ss_pred             cCcccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc
Q psy4698          35 DGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK  114 (258)
Q Consensus        35 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~  114 (258)
                      ++...++++....+|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|+++++..+.....
T Consensus        18 ~~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~   97 (237)
T 3bor_A           18 GGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFK   97 (237)
T ss_dssp             ---------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSC
T ss_pred             CCcccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCC
Confidence            34455666677788999999999999999999999999999999999999999999999999999999999999877666


Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEE
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMF  193 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~l  193 (258)
                      +.+++|++|+++|+.|+++.++.++...+..+....++.........+..+ ++|+|+||+++.+++.++.+.+.++++|
T Consensus        98 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~l  177 (237)
T 3bor_A           98 ETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMF  177 (237)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEE
T ss_pred             CceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEE
Confidence            679999999999999999999999888888888888887766665566555 8999999999999999888889999999


Q ss_pred             EEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         194 VLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       194 VvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      |+||||++.+.++...+..+++.+++.+|++++|||+|++++++++.|+++|+.|.+.++
T Consensus       178 ViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~~e  237 (237)
T 3bor_A          178 VLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE  237 (237)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             EECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEecCC
Confidence            999999999999999999999999999999999999999999999999999999988653

>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=100.00  E-value=9.8e-41  Score=275.66  Aligned_cols=208  Identities=30%  Similarity=0.515  Sum_probs=192.7

Q ss_pred             ccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          44 HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        44 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ....+|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|+++++..+.....+.+++|++|
T Consensus        40 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~P  119 (249)
T 3ber_A           40 EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTP  119 (249)
T ss_dssp             HHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECS
T ss_pred             cccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeC
Confidence            44568999999999999999999999999999999999999999999999999999999999999887766778999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccchhhh
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~~~  202 (258)
                      +++|+.|+++.+++++...++.+..+.|+.........+..+++|+|+||+++.+++.+ ..+.+.++++||+||||++.
T Consensus       120 tr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~  199 (249)
T 3ber_A          120 TRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRIL  199 (249)
T ss_dssp             SHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHH
T ss_pred             CHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhh
Confidence            99999999999999988888888888888877777777778899999999999998876 55678899999999999999


Q ss_pred             ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       203 ~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +.++...+..+++.++++.|++++|||++++++++++.++++|+.|.+.
T Consensus       200 ~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          200 NMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             HTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             ccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            9999999999999999999999999999999999999999999999875

>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=100.00  E-value=2.2e-40  Score=265.60  Aligned_cols=202  Identities=38%  Similarity=0.676  Sum_probs=188.0

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .+|+++++++.+.+.+.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++|++..+.....+.+++|++|+++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   82 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHH
Confidence            46999999999999999999999999999999999999999999999999999999999998877666779999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      |+.|+.+.++++.... +..+....|+.........+..+++|+|+||+++.+.+.++...+++++++|+||||++.+.+
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  162 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhC
Confidence            9999999999988766 778888888888777777777889999999999999999888888999999999999999989


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEE
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKI  248 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v  248 (258)
                      +...+..++..+++++|++++|||+|.++.++++.|+++|+.|
T Consensus       163 ~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             THHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             cHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            9999999999999899999999999999999999999999887

>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=100.00  E-value=8.9e-41  Score=272.21  Aligned_cols=208  Identities=29%  Similarity=0.491  Sum_probs=183.2

Q ss_pred             ccccccCcCC-CCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc------cc
Q psy4698          42 WDHVAENFDD-MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN------IK  114 (258)
Q Consensus        42 ~~~~~~~~~~-~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~------~~  114 (258)
                      .++...+|++ +++++.+.+.+.+.|+..|+++|.++++.+.+|+++++.+|||+|||++|++|++..+...      ..
T Consensus        14 ~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~   93 (228)
T 3iuy_A           14 IPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRN   93 (228)
T ss_dssp             CCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------C
T ss_pred             CCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccC
Confidence            3445567888 7999999999999999999999999999999999999999999999999999999887642      25


Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEE
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV  194 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lV  194 (258)
                      +++++|++|+++|+.|+.+.++++. ..+..+....|+.........+..+++|+|+||+++.+++..+...++++++||
T Consensus        94 ~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lV  172 (228)
T 3iuy_A           94 GPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLV  172 (228)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEE
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEE
Confidence            5689999999999999999999986 456777888888877777777888899999999999999998888899999999


Q ss_pred             EccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         195 LDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       195 vDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      +||||++.+.++...+..++..+++++|++++|||+|++++++++.++++|++|.|
T Consensus       173 iDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          173 IDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             ECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             EECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            99999999999999999999999999999999999999999999999999999875

>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=100.00  E-value=2.4e-40  Score=270.20  Aligned_cols=208  Identities=40%  Similarity=0.613  Sum_probs=186.0

Q ss_pred             cccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          43 DHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        43 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      +.....|+++++++.+.+.+.+.|+..|+++|.++++.+..|+++++.+|||+|||++|+++++..+.....+.+++|++
T Consensus        20 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~   99 (230)
T 2oxc_A           20 LAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILA   99 (230)
T ss_dssp             ----CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEe
Confidence            34456799999999999999999999999999999999999999999999999999999999999987766677999999


Q ss_pred             ccHHHHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         123 PTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       123 P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      |+++|+.|+++.++.++... ++.+..+.|+.....+...+ .+++|+|+||+++.+++..+.+.+.++++||+||+|++
T Consensus       100 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~  178 (230)
T 2oxc_A          100 PTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKL  178 (230)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHH
T ss_pred             CCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHh
Confidence            99999999999999987665 78888888887766655544 46899999999999999888888899999999999999


Q ss_pred             hccC-cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         202 LSRG-FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       202 ~~~~-~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      .+.+ +...+..+++.+++.+|++++|||+++++.++++.|+++|++|.++
T Consensus       179 ~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~~  229 (230)
T 2oxc_A          179 LEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLN  229 (230)
T ss_dssp             HSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC-
T ss_pred             hcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEcC
Confidence            9886 9999999999999899999999999999999999999999998764

>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=100.00  E-value=2e-40  Score=280.77  Aligned_cols=206  Identities=38%  Similarity=0.611  Sum_probs=184.5

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ...+|+++++++.+.+.|.+.||..|+++|.++++.++.|  +++++++|||||||++|++|+++.+.....++++||++
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~  169 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEc
Confidence            4468999999999999999999999999999999999988  89999999999999999999999998877778999999


Q ss_pred             ccHHHHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccchh
Q psy4698         123 PTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADE  200 (258)
Q Consensus       123 P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~  200 (258)
                      |+++|+.|+++.++.++... ++.+....++.......   ..+++|+|+||++|++++.+ +.+.++++++||+||||+
T Consensus       170 PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~  246 (300)
T 3fmo_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (300)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHH
T ss_pred             CcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHH
Confidence            99999999999999998754 56777777665443221   45589999999999999966 567789999999999999


Q ss_pred             hhc-cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         201 MLS-RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       201 ~~~-~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      +++ .++...+..+++.+++++|++++|||+++++.++++.++.+|++|.+..|
T Consensus       247 l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~e  300 (300)
T 3fmo_B          247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE  300 (300)
T ss_dssp             HHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECCC
T ss_pred             HhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecCC
Confidence            997 68999999999999999999999999999999999999999999998764

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=8.5e-41  Score=270.78  Aligned_cols=206  Identities=33%  Similarity=0.563  Sum_probs=187.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .+|+++++++.+.+.+.+.|+..|+++|.++++.+.+|+++++.+|||+|||++|+++++..+.....+.+++|++|+++
T Consensus         4 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   83 (219)
T 1q0u_A            4 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   83 (219)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHH
Confidence            46999999999999999999999999999999999999999999999999999999999999887666779999999999


Q ss_pred             HHHHHHHHHHHhcCCC----CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh
Q psy4698         127 LAQQIQKVVIALGDFM----SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~  202 (258)
                      |+.|+++.++++....    +..+....|+.........+..+++|+|+||+++.+++.++...+++++++|+||||++.
T Consensus        84 L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~  163 (219)
T 1q0u_A           84 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLML  163 (219)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHH
T ss_pred             HHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHh
Confidence            9999999999987765    677777888876655544555678999999999999999888888999999999999999


Q ss_pred             ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       203 ~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      +.++...+..++..+++++|++++|||+|++++++++.++++|+.|.+..
T Consensus       164 ~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          164 DMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             HTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             hhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            99999999999999998999999999999999999999999999987643

>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=100.00  E-value=1.3e-39  Score=261.12  Aligned_cols=202  Identities=35%  Similarity=0.570  Sum_probs=184.8

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEecc
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPT  124 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~  124 (258)
                      +|+++++++.+.+.+.+.|+..|+++|.++++.+.+|+++++.+|||+|||++|+++++..+...   ..+++++|++|+
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~   81 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPT   81 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSS
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECC
Confidence            58999999999999999999999999999999999999999999999999999999999988642   345689999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc
Q psy4698         125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR  204 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~  204 (258)
                      ++|+.|+++.++.+...  ..+....|+.........+..+++|+|+||+++.+++.++.+.+.+++++|+||||++.+.
T Consensus        82 ~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~  159 (207)
T 2gxq_A           82 RELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSM  159 (207)
T ss_dssp             HHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhcc
Confidence            99999999999998765  5667777887777776777778999999999999999988888999999999999999999


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      ++...+..++..++++.|++++|||++++++++++.|+++|++|.+.
T Consensus       160 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          160 GFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI  206 (207)
T ss_dssp             TCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             chHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEcC
Confidence            99999999999999999999999999999999999999999999875

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=2.6e-39  Score=264.91  Aligned_cols=208  Identities=29%  Similarity=0.500  Sum_probs=185.7

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc----cccceEEE
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----IKECQALI  120 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~----~~~~~~li  120 (258)
                      ...+|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++|++..+...    ..+.+++|
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~li  102 (236)
T 2pl3_A           23 EITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLI  102 (236)
T ss_dssp             GCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEE
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEE
Confidence            44679999999999999999999999999999999999999999999999999999999999887642    34568999


Q ss_pred             EeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccch
Q psy4698         121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEAD  199 (258)
Q Consensus       121 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h  199 (258)
                      ++|+++|+.|+++.++.++...++.+..+.|+.........+ .+++|+|+||+++.+.+.+. .+.+.++++||+||||
T Consensus       103 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah  181 (236)
T 2pl3_A          103 ISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEAD  181 (236)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHH
T ss_pred             EeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChH
Confidence            999999999999999999888888888888887766655554 46899999999999988765 4678899999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      ++.+.++...+..++..+++++|++++|||++++++++.+.++.+|++|.+.++
T Consensus       182 ~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  235 (236)
T 2pl3_A          182 RILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK  235 (236)
T ss_dssp             HHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC-
T ss_pred             HHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999999999999999999999999999999999999999999999999988653

>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=100.00  E-value=4.3e-40  Score=272.26  Aligned_cols=212  Identities=33%  Similarity=0.514  Sum_probs=188.9

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc---------cc
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI---------KE  115 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~---------~~  115 (258)
                      ...+|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++|++..+....         .+
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~  100 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY  100 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCC
Confidence            346799999999999999999999999999999999999999999999999999999999999886432         34


Q ss_pred             ceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEE
Q psy4698         116 CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVL  195 (258)
Q Consensus       116 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVv  195 (258)
                      +++||++|+++|+.|+++.++.++...++.+....|+.........+..+++|+|+||+++.+++.++.+.++++++||+
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lVi  180 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVL  180 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEE
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEE
Confidence            68999999999999999999999888888888888888887777777888999999999999999988888999999999


Q ss_pred             ccchhhhccCcHHHHHHHHHhC--CC--CccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         196 DEADEMLSRGFKDQIYDVFKHL--NN--DVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       196 DE~h~~~~~~~~~~~~~~~~~l--~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      ||||++.+.++...+..++..+  +.  +.|++++|||++++++++++.++.+|+.|.+..++.+
T Consensus       181 DEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~  245 (253)
T 1wrb_A          181 DEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGST  245 (253)
T ss_dssp             ETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC-----
T ss_pred             eCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCC
Confidence            9999999999999999999854  33  6799999999999999999999999999999776554

>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=100.00  E-value=3.6e-39  Score=261.24  Aligned_cols=204  Identities=37%  Similarity=0.632  Sum_probs=184.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..|+++++++.+.+.|.+.|+..|+++|.++++.+.+|+++++.+|||+|||++|+++++..+.....+.+++|++|+++
T Consensus        14 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   93 (220)
T 1t6n_A           14 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   93 (220)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHH
Confidence            56999999999999999999999999999999999999999999999999999999999998876655669999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc-
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-  203 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-  203 (258)
                      |+.|+++.++++.... +..+..+.|+.....+...+.. .++|+|+||+++.+++.+..+.+.+++++|+||||++.+ 
T Consensus        94 L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~  173 (220)
T 1t6n_A           94 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  173 (220)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcc
Confidence            9999999999988765 7888888888776666555554 479999999999999998888899999999999999986 


Q ss_pred             cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         204 RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       204 ~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      .++...+..+++.+++++|++++|||++++++++++.|+++|+.|.+
T Consensus       174 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~v  220 (220)
T 1t6n_A          174 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  220 (220)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             cCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEeC
Confidence            46778888899999889999999999999999999999999998864

>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=100.00  E-value=3.4e-39  Score=268.40  Aligned_cols=200  Identities=31%  Similarity=0.487  Sum_probs=179.6

Q ss_pred             cCcCCCC--CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc----cccceEEE
Q psy4698          47 ENFDDME--LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN----IKECQALI  120 (258)
Q Consensus        47 ~~~~~~~--~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~----~~~~~~li  120 (258)
                      ..|++++  +++.+++.+++.|+..|+++|.++++.+..|+++++++|||||||++|++|++..+...    ..+.+++|
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~li  131 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLI  131 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEE
Confidence            4577776  99999999999999999999999999999999999999999999999999999988652    24568999


Q ss_pred             EeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccch
Q psy4698         121 LAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEAD  199 (258)
Q Consensus       121 l~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h  199 (258)
                      ++|+++|+.|+++.+++++...+..+....|+.........+..+++|+|+||+++.+++... .+.++++++||+||||
T Consensus       132 l~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah  211 (262)
T 3ly5_A          132 LSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEAD  211 (262)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHH
T ss_pred             EeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChH
Confidence            999999999999999999988888888899988888777778888999999999999988765 4678899999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCe
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPI  246 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~  246 (258)
                      ++.+.++...+..+++.+++.+|+++||||++++++++++.+++++.
T Consensus       212 ~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          212 RILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             HHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             HHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999999998544

>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=100.00  E-value=3.2e-38  Score=280.31  Aligned_cols=214  Identities=29%  Similarity=0.487  Sum_probs=196.1

Q ss_pred             ccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc-----c
Q psy4698          40 TNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI-----K  114 (258)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~-----~  114 (258)
                      .+.+....+|+++++++.+.+.+.+.|+..|+++|.++++.+++|++++++++||||||++|++|++..+....     .
T Consensus        49 ~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~  128 (434)
T 2db3_A           49 SDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELG  128 (434)
T ss_dssp             SSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTT
T ss_pred             CCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccC
Confidence            44555667899999999999999999999999999999999999999999999999999999999999887542     3


Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEE
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV  194 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lV  194 (258)
                      ++++||++|+++|+.|+++.+++++...++.+...+|+.....+...+..+++|+|+||++|.+++.++.+.+.++++||
T Consensus       129 ~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lV  208 (434)
T 2db3_A          129 RPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVV  208 (434)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEE
T ss_pred             CccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEE
Confidence            56899999999999999999999998888888889999888888888888899999999999999999888899999999


Q ss_pred             EccchhhhccCcHHHHHHHHHhC--CCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         195 LDEADEMLSRGFKDQIYDVFKHL--NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       195 vDE~h~~~~~~~~~~~~~~~~~l--~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      +||||++++.++...+..++..+  +++.|++++|||+|++++++++.++.+++.+.+...
T Consensus       209 lDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  269 (434)
T 2db3_A          209 LDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIV  269 (434)
T ss_dssp             EETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESST
T ss_pred             EccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccc
Confidence            99999999999999999999875  578899999999999999999999999999988644

>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=100.00  E-value=2.8e-38  Score=260.11  Aligned_cols=211  Identities=28%  Similarity=0.476  Sum_probs=178.2

Q ss_pred             cccccCcCCC----CCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccce
Q psy4698          43 DHVAENFDDM----ELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQ  117 (258)
Q Consensus        43 ~~~~~~~~~~----~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~  117 (258)
                      +....+|+++    ++++.+.+.+.+.|+..|+++|.++++.+.+|+++++.+|||+|||++|++|++..+... ..+.+
T Consensus        21 p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~  100 (245)
T 3dkp_A           21 PDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFR  100 (245)
T ss_dssp             CCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCC
T ss_pred             CCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCce
Confidence            3344567665    899999999999999999999999999999999999999999999999999999988653 34568


Q ss_pred             EEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH-HHHhcCCcEEEeChHHHHHHHhcC--CCCCCCccEEE
Q psy4698         118 ALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI-RKLEAGAQVVVGTPGRVFDMISRG--ALSTKQIRMFV  194 (258)
Q Consensus       118 ~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~Ilv~Tp~~l~~~l~~~--~~~~~~l~~lV  194 (258)
                      ++|++|+++|+.|+++.+++++...+..+....++....... .....+++|+|+||+++.+++.+.  .+.+.++++||
T Consensus       101 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lV  180 (245)
T 3dkp_A          101 ALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLV  180 (245)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEE
Confidence            999999999999999999999888887777666554332221 122345899999999999999876  56788999999


Q ss_pred             Eccchhhhc---cCcHHHHHHHHHhC-CCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         195 LDEADEMLS---RGFKDQIYDVFKHL-NNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       195 vDE~h~~~~---~~~~~~~~~~~~~l-~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      +||||++.+   .++...+..++..+ +++.|+++||||+|++++++++.++++|+.|.+...
T Consensus       181 iDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          181 VDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             ESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             EeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999999987   46788888887776 457899999999999999999999999999998765

>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=100.00  E-value=6.9e-37  Score=269.24  Aligned_cols=226  Identities=73%  Similarity=1.174  Sum_probs=201.5

Q ss_pred             CCcccCcccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          31 GMAVDGLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      ....+.....++......|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++++++.+.
T Consensus        24 ~~~~~~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~  103 (414)
T 3eiq_A           24 GMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIE  103 (414)
T ss_dssp             ------CCCCCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCC
T ss_pred             ccccccccCCCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHh
Confidence            33344555667777778999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             hccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         111 QNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       111 ~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      ....+.+++|++|+++|+.|+.+.++.++...+..+....++.........+. .+++|+|+||++|++++.++.+.+.+
T Consensus       104 ~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~  183 (414)
T 3eiq_A          104 LDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKY  183 (414)
T ss_dssp             TTSCSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTT
T ss_pred             hcCCceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            76667799999999999999999999999888888888888887776666655 66899999999999999998888999


Q ss_pred             ccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         190 IRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      +++||+||+|++.+.++...+..++..++++.|++++|||++.++..+.+.++.+|..+.+.....+
T Consensus       184 ~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (414)
T 3eiq_A          184 IKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELT  250 (414)
T ss_dssp             CCEEEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCC
T ss_pred             CcEEEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccC
Confidence            9999999999999999999999999999999999999999999999999999999999988766554

>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=100.00  E-value=8.9e-37  Score=268.59  Aligned_cols=212  Identities=67%  Similarity=1.056  Sum_probs=196.0

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      ...+|+++++++.+.+.+.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++|+++.+.....+.++||++|+
T Consensus        35 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt  114 (410)
T 2j0s_A           35 VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPT  114 (410)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSS
T ss_pred             CCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCc
Confidence            44679999999999999999999999999999999999999999999999999999999999988766566799999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc
Q psy4698         125 RELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR  204 (258)
Q Consensus       125 ~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~  204 (258)
                      ++|+.|+.+.++.++...++.+..+.|+.....+...+..+++|+|+||+++.+++.++.+.+.++++||+||+|++.+.
T Consensus       115 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~  194 (410)
T 2j0s_A          115 RELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK  194 (410)
T ss_dssp             HHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTST
T ss_pred             HHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhh
Confidence            99999999999999988899999999998888887788888999999999999999998888899999999999999999


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      ++...+..+++.+++..|++++|||++.++.++.+.++.+|..+.+.....+
T Consensus       195 ~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (410)
T 2j0s_A          195 GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELT  246 (410)
T ss_dssp             TTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCS
T ss_pred             hhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCcccc
Confidence            9999999999999999999999999999999999999999999887665544

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=7.5e-36  Score=263.01  Aligned_cols=212  Identities=33%  Similarity=0.486  Sum_probs=189.4

Q ss_pred             ccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc--------
Q psy4698          42 WDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI--------  113 (258)
Q Consensus        42 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~--------  113 (258)
                      .+....+|+++++++.+.+.|...|+..|+++|.++++.+..|+++++.+|||+|||++|++|++..+....        
T Consensus        10 ~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~   89 (417)
T 2i4i_A           10 CPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAM   89 (417)
T ss_dssp             CCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhcc
Confidence            345566899999999999999999999999999999999999999999999999999999999999876532        


Q ss_pred             ----------ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC
Q psy4698         114 ----------KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG  183 (258)
Q Consensus       114 ----------~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~  183 (258)
                                .+++++|++|+++|+.|+++.+++++...++.+..+.|+.........+..+++|+|+||++|.+++..+
T Consensus        90 ~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~  169 (417)
T 2i4i_A           90 KENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERG  169 (417)
T ss_dssp             HHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTT
T ss_pred             ccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcC
Confidence                      1257999999999999999999999888888888899998888777788888999999999999999988


Q ss_pred             CCCCCCccEEEEccchhhhccCcHHHHHHHHHhC--CC--CccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         184 ALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL--NN--DVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       184 ~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l--~~--~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                      .+.+.++++||+||+|++.+.++...+..++...  +.  ..|++++|||+++.+..+.+.++.++..+.+...
T Consensus       170 ~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  243 (417)
T 2i4i_A          170 KIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRV  243 (417)
T ss_dssp             SBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC--
T ss_pred             CcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCC
Confidence            8889999999999999999999999999888753  32  6799999999999999999999999998877543

>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=100.00  E-value=4.2e-35  Score=256.14  Aligned_cols=215  Identities=65%  Similarity=1.001  Sum_probs=192.5

Q ss_pred             ccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEE
Q psy4698          40 TNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQAL  119 (258)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~l  119 (258)
                      .........|+++++++.+.+.+.+.|+..|+++|.++++.+..|+++++.+|||+|||++|++|++..+.....+++++
T Consensus        14 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~l   93 (394)
T 1fuu_A           14 TNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQAL   93 (394)
T ss_dssp             ESSCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             hhcccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEE
Confidence            34445556799999999999999999999999999999999999999999999999999999999999988766677999


Q ss_pred             EEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         120 ILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       120 il~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                      |++|+++|+.|+.+.++++....+..+....|+.........+. +++|+|+||+++++.+.++.+.+.++++||+||+|
T Consensus        94 il~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah  172 (394)
T 1fuu_A           94 MLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEAD  172 (394)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHH
T ss_pred             EEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChH
Confidence            99999999999999999998888888888888877665555444 47999999999999999888888999999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      ++.+.++...+..++..+++..|++++|||+++.+.+....++.+|..+.+.....
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~  228 (394)
T 1fuu_A          173 EMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDEL  228 (394)
T ss_dssp             HHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC---
T ss_pred             HhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccc
Confidence            99999999999999999999999999999999999999999999999998876554

>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=100.00  E-value=1.5e-34  Score=253.43  Aligned_cols=207  Identities=43%  Similarity=0.705  Sum_probs=188.8

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      ..+|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|+++++..+.....+.+++|++|++
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~   99 (400)
T 1s2m_A           20 GNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR   99 (400)
T ss_dssp             -CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCH
Confidence            45799999999999999999999999999999999999999999999999999999999999887765667899999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +|+.|+.+.++.++...++.+....++............+++|+|+||+++.+++.+....+.++++||+||+|++.+.+
T Consensus       100 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~  179 (400)
T 1s2m_A          100 ELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD  179 (400)
T ss_dssp             HHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH
T ss_pred             HHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhc
Confidence            99999999999999888888888888888777766777789999999999999998888888999999999999998888


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      +...+..++..+++..|++++|||++..+.+++..++.+|..+.+..
T Consensus       180 ~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~  226 (400)
T 1s2m_A          180 FKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME  226 (400)
T ss_dssp             HHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS
T ss_pred             hHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEecc
Confidence            88888889988888999999999999999999999999998776543

>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=100.00  E-value=5e-34  Score=249.21  Aligned_cols=207  Identities=37%  Similarity=0.640  Sum_probs=185.0

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..|+++++++.+.+.|.+.|+..|+++|.++++.+..|+++++.+|||+|||++|+++++..+.....+.+++|++|+++
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            46999999999999999999999999999999999999999999999999999999999998876656679999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR  204 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~  204 (258)
                      |+.|+.+.++++.... ++.+..+.|+.........+..+ ++|+|+||+++..++.+....+.++++||+||||++.++
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~  167 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  167 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSS
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhc
Confidence            9999999999987765 78888888887766665555543 799999999999999988888999999999999999774


Q ss_pred             -CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCC
Q psy4698         205 -GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       205 -~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~  253 (258)
                       ++...+..++...++..|++++|||+++.+..+++.++.+|..+.+.++
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  217 (391)
T 1xti_A          168 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDE  217 (391)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCC
T ss_pred             cchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCc
Confidence             6777888888888889999999999999999999999999999887654

>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=100.00  E-value=2e-33  Score=245.28  Aligned_cols=206  Identities=40%  Similarity=0.656  Sum_probs=183.2

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ..+|+++++++.+.+.+.+.|+..|+++|.++++.+..+  +++++.+|||+|||++|+++++..+.....+.+++|++|
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   83 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAP   83 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECC
Confidence            468999999999999999999999999999999999998  899999999999999999999999887666779999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      +++|+.|+++.+++++...++.+....++......    ..+++|+|+||+++.+.+.+....+.++++||+||+|++.+
T Consensus        84 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~  159 (395)
T 3pey_A           84 SRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLD  159 (395)
T ss_dssp             SHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcC
Confidence            99999999999999988888877776666433221    23589999999999999998888899999999999999987


Q ss_pred             -cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         204 -RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       204 -~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                       .++...+..+...++++.|++++|||+++.+..+.+.++.++..+.+.....
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (395)
T 3pey_A          160 QQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEV  212 (395)
T ss_dssp             STTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGC
T ss_pred             ccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEcccccc
Confidence             5788888888998989999999999999999999999999998887755443

>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=100.00  E-value=2.6e-33  Score=246.11  Aligned_cols=208  Identities=38%  Similarity=0.607  Sum_probs=180.6

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ...+|+++++++.+.+.|.+.|+..|+++|.++++.+..+  +++++.+|||+|||++|++|++..+.....+++++|++
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~  102 (412)
T 3fht_A           23 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  102 (412)
T ss_dssp             CSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEEC
Confidence            3467999999999999999999999999999999999987  89999999999999999999999988777777999999


Q ss_pred             ccHHHHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccchh
Q psy4698         123 PTRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADE  200 (258)
Q Consensus       123 P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~  200 (258)
                      |+++|+.|+.+.+++++... +..+....++......   ...+++|+|+||+++.+++.+ +.+.+.++++||+||+|+
T Consensus       103 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~  179 (412)
T 3fht_A          103 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  179 (412)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHH
Confidence            99999999999999987654 5666666665543322   134579999999999999865 566788999999999999


Q ss_pred             hhc-cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCcc
Q psy4698         201 MLS-RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEEL  255 (258)
Q Consensus       201 ~~~-~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~  255 (258)
                      +.+ .++...+..+...+++++|++++|||+++.+..+.+.++.+|..+.+..+..
T Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (412)
T 3fht_A          180 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE  235 (412)
T ss_dssp             HHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGS
T ss_pred             HhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccc
Confidence            987 5788888889999999999999999999999999999999999988765543

>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=100.00  E-value=1.8e-33  Score=252.66  Aligned_cols=208  Identities=39%  Similarity=0.613  Sum_probs=177.1

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ..+|+++++++.+.+.|.++|+..|+++|.++++.++.+  +++++.+|||||||++|++|++..+.....++++||++|
T Consensus        91 ~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  170 (479)
T 3fmp_B           91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  170 (479)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECS
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeC
Confidence            357999999999999999999999999999999999987  899999999999999999999999887777779999999


Q ss_pred             cHHHHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccchhh
Q psy4698         124 TRELAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~~  201 (258)
                      +++|+.|+++.++.++... ++.+....++......   ...+++|+|+||+++++++.+ +.+.+.++++||+||+|++
T Consensus       171 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~  247 (479)
T 3fmp_B          171 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVM  247 (479)
T ss_dssp             SHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHH
T ss_pred             hHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHH
Confidence            9999999999999987653 4555555555433221   123478999999999999866 5567789999999999999


Q ss_pred             hc-cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         202 LS-RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       202 ~~-~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                      .+ .++...+..+.+.+++++|++++|||++..+..+.+.++.+|..+.+..+..+
T Consensus       248 ~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~  303 (479)
T 3fmp_B          248 IATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEET  303 (479)
T ss_dssp             HTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-----
T ss_pred             hhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccC
Confidence            87 57888888899999999999999999999999999999999999988765543

>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=100.00  E-value=1.1e-32  Score=238.38  Aligned_cols=203  Identities=39%  Similarity=0.679  Sum_probs=183.1

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .+|+++++++.+.+.|++.|+..|+++|.++++.+.++ +++++.+|||+|||++++++++..+... .+.+++|++|++
T Consensus         6 ~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~~   84 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTR   84 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCH
T ss_pred             CchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCCH
Confidence            46999999999999999999999999999999999888 6999999999999999999998877654 456899999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +|+.|+.+.++.+....++.+....++.........+. +++|+|+||+++.+.+..+...+.+++++|+||+|++.+.+
T Consensus        85 ~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~  163 (367)
T 1hv8_A           85 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG  163 (367)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhc
Confidence            99999999999998877888888888887766655555 58999999999999999888888999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +...+..++..+++..+++++|||++....+..+.++.++..+...
T Consensus       164 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  209 (367)
T 1hv8_A          164 FIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAK  209 (367)
T ss_dssp             THHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             hHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEec
Confidence            9999999999998999999999999999999999999988877653

>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=100.00  E-value=1.3e-31  Score=229.25  Aligned_cols=190  Identities=30%  Similarity=0.559  Sum_probs=172.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      +++.+.+.|+++|+..|+++|.++++.+.+|+++++.+|||+|||++|+++++..      +.+++|++|+++|+.|+++
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~------~~~~liv~P~~~L~~q~~~   74 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQVAS   74 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEECSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh------cCCEEEEeCCHHHHHHHHH
Confidence            4688999999999999999999999999999999999999999999999998763      4589999999999999999


Q ss_pred             HHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHH
Q psy4698         134 VVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDV  213 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~  213 (258)
                      .+++++...+..+....++............ ++|+|+||+++.+.+..+.+.+.++++||+||+|++.++++...+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~  153 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRVRN-ADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKII  153 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHHTT-CSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhcCC-CCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHH
Confidence            9999988888888888888777666555544 899999999999999888788889999999999999999999999999


Q ss_pred             HHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         214 FKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       214 ~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      +..++...+++++|||+++...+....++.++..+..
T Consensus       154 ~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~  190 (337)
T 2z0m_A          154 LAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEA  190 (337)
T ss_dssp             HHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEEC
T ss_pred             HhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeec
Confidence            9999999999999999999999999999998887754

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=2e-32  Score=251.23  Aligned_cols=200  Identities=32%  Similarity=0.514  Sum_probs=170.5

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHhhhhh--cCCcEEEEcccCCCcchHhHHHHHHHhhhcc----ccceEEEEeccHH
Q psy4698          53 ELSEELLRGIYAYGFEKPSAIQQRAIIPCV--RGNDVIAQAQSGTGKTATFSISILQQVDQNI----KECQALILAPTRE  126 (258)
Q Consensus        53 ~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~--~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~----~~~~~lil~P~~~  126 (258)
                      .+++.+.+.+.+.|+..|+++|.++++.++  .|+++++.+|||+|||++|++|+++.+....    .++++||++|+++
T Consensus        27 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~  106 (579)
T 3sqw_A           27 VLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRD  106 (579)
T ss_dssp             SSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHH
Confidence            399999999999999999999999999998  7789999999999999999999999887642    3458999999999


Q ss_pred             HHHHHHHHHHHhcC----CCCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccchh
Q psy4698         127 LAQQIQKVVIALGD----FMSVSCHACIGGTIVRDDIRKL-EAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEADE  200 (258)
Q Consensus       127 l~~q~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h~  200 (258)
                      |+.|+.+.++++..    .....+....++.........+ ..+++|+|+||++|.+++.+. ...++.+++||+||||+
T Consensus       107 La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  186 (579)
T 3sqw_A          107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  186 (579)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHH
Confidence            99999999998753    2345667777777766665555 346899999999999988764 34678899999999999


Q ss_pred             hhccCcHHHHHHHHHhCC-------CCccEEEEEeeCChhHHHHHHHhcCCCeEEEecC
Q psy4698         201 MLSRGFKDQIYDVFKHLN-------NDVQVILLSATMPADVLDVSMKFMRDPIKILVKK  252 (258)
Q Consensus       201 ~~~~~~~~~~~~~~~~l~-------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~  252 (258)
                      ++++++...+..++..++       ..+|++++|||+++.+.++++.++.+|..+.+..
T Consensus       187 l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~  245 (579)
T 3sqw_A          187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDT  245 (579)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEES
T ss_pred             hhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEee
Confidence            999999988888877653       2679999999999999999999999998887643

>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=99.98  E-value=3.1e-32  Score=249.08  Aligned_cols=199  Identities=32%  Similarity=0.517  Sum_probs=168.6

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHhhhhh--cCCcEEEEcccCCCcchHhHHHHHHHhhhcc----ccceEEEEeccHH
Q psy4698          53 ELSEELLRGIYAYGFEKPSAIQQRAIIPCV--RGNDVIAQAQSGTGKTATFSISILQQVDQNI----KECQALILAPTRE  126 (258)
Q Consensus        53 ~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~--~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~----~~~~~lil~P~~~  126 (258)
                      .+++.+.+.+.+.|+..|+++|.++++.++  .++++++.+|||+|||++|++|+++.+....    .+.++||++|+++
T Consensus        78 ~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~  157 (563)
T 3i5x_A           78 VLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRD  157 (563)
T ss_dssp             SSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHH
Confidence            399999999999999999999999999998  6789999999999999999999999987653    2358999999999


Q ss_pred             HHHHHHHHHHHhcC----CCCceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcC-CCCCCCccEEEEccchh
Q psy4698         127 LAQQIQKVVIALGD----FMSVSCHACIGGTIVRDDIRKL-EAGAQVVVGTPGRVFDMISRG-ALSTKQIRMFVLDEADE  200 (258)
Q Consensus       127 l~~q~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~-~~~~~~l~~lVvDE~h~  200 (258)
                      |+.|+++.++.+..    .....+....++.........+ ..+++|+|+||+++++++.+. ...++++++||+||||+
T Consensus       158 La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  237 (563)
T 3i5x_A          158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  237 (563)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHH
Confidence            99999999988643    1235566777777666555554 457899999999999988764 33578899999999999


Q ss_pred             hhccCcHHHHHHHHHhCC-------CCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         201 MLSRGFKDQIYDVFKHLN-------NDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       201 ~~~~~~~~~~~~~~~~l~-------~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +.++++...+..++..++       +.+|++++|||+++.+.++++.++.++..+.+.
T Consensus       238 l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~  295 (563)
T 3i5x_A          238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLD  295 (563)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEE
T ss_pred             HhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEe
Confidence            999999988888876653       367999999999999999999999998887764

>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=99.96  E-value=7.3e-29  Score=232.86  Aligned_cols=187  Identities=17%  Similarity=0.261  Sum_probs=160.1

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      +|+++++++.+.+.+++.|+..|+++|.++++. +..++++++++|||||||+++.+++++.+...  +.+++|++|+++
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~ra   79 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLKA   79 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSGG
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcHH
Confidence            588999999999999999999999999999998 88999999999999999999999999887743  358999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      |+.|+++.++.+.. .++.+....|+......  . ..+++|+|+||+++..++.+....++++++||+||+|.+.+.++
T Consensus        80 La~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~--~-~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r  155 (720)
T 2zj8_A           80 LAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE--W-LGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDR  155 (720)
T ss_dssp             GHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG--G-GGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTT
T ss_pred             HHHHHHHHHHHHHh-cCCEEEEecCCCCcccc--c-cCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcc
Confidence            99999999865543 46778777776543322  1 23589999999999999888766688999999999999988789


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      +..+..++.+++.+.|+|++|||+++ ..++.+++
T Consensus       156 ~~~~~~ll~~l~~~~~ii~lSATl~n-~~~~~~~l  189 (720)
T 2zj8_A          156 GATLEVILAHMLGKAQIIGLSATIGN-PEELAEWL  189 (720)
T ss_dssp             HHHHHHHHHHHBTTBEEEEEECCCSC-HHHHHHHT
T ss_pred             cHHHHHHHHHhhcCCeEEEEcCCcCC-HHHHHHHh
Confidence            99999999988778999999999986 45566544

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.96  E-value=4.9e-29  Score=219.75  Aligned_cols=178  Identities=19%  Similarity=0.210  Sum_probs=144.8

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHH
Q psy4698          57 ELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        57 ~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      .+.+.+++ .|+ .|+++|.++++.+..|+++++.+|||+|||++|+++++..+.   .+++++|++|+++|+.|+++.+
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~---~~~~~lil~Pt~~L~~q~~~~~   84 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERL   84 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc---CCCEEEEEECCHHHHHHHHHHH
Confidence            34555555 456 899999999999999999999999999999999999887662   3468999999999999999999


Q ss_pred             HHhcCCCCceEEEEECCcch---HHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc--------
Q psy4698         136 IALGDFMSVSCHACIGGTIV---RDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS--------  203 (258)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~--------  203 (258)
                      +.++. .++.+..+.|+...   ......+..+ ++|+|+||+++.+++..  +.+.++++||+||+|++..        
T Consensus        85 ~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~  161 (414)
T 3oiy_A           85 QKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTL  161 (414)
T ss_dssp             HHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHH
T ss_pred             HHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhH
Confidence            99987 78889899988876   4455566665 99999999999887765  5677899999999997653        


Q ss_pred             ---cCcHHH-HHHHHHhCC-----------CCccEEEEEee-CChhHH-HHHHHh
Q psy4698         204 ---RGFKDQ-IYDVFKHLN-----------NDVQVILLSAT-MPADVL-DVSMKF  241 (258)
Q Consensus       204 ---~~~~~~-~~~~~~~l~-----------~~~~~i~~SAT-~~~~~~-~~~~~~  241 (258)
                         .++... +..++..++           ...|++++||| .|..+. .+.+.+
T Consensus       162 l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~  216 (414)
T 3oiy_A          162 LMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDL  216 (414)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHH
T ss_pred             HhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHh
Confidence               556666 677777766           78999999999 666544 334443

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.96  E-value=1.4e-28  Score=230.88  Aligned_cols=187  Identities=18%  Similarity=0.224  Sum_probs=158.7

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .+|+++++++.+.+.+.+.|+..++++|.++++. +..++++++++|||||||+++.+++++.+...  +.+++|++|++
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~il~i~P~r   85 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--GGKAIYVTPLR   85 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--CSEEEEECSCH
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--CCeEEEEeCcH
Confidence            4699999999999999999999999999999999 78899999999999999999999999887643  35899999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +|+.|++..++.+. ..+..+....|+......  .. .+++|+|+||+++..++.+....++++++||+||+|++.+..
T Consensus        86 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~  161 (715)
T 2va8_A           86 ALTNEKYLTFKDWE-LIGFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPE  161 (715)
T ss_dssp             HHHHHHHHHHGGGG-GGTCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTT
T ss_pred             HHHHHHHHHHHHhh-cCCCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcc
Confidence            99999999986543 347777777776554332  12 258999999999999998876668899999999999988778


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      ++..+..++.+++ +.|+|+||||+++ ..++.+++
T Consensus       162 ~~~~l~~i~~~~~-~~~ii~lSATl~n-~~~~~~~l  195 (715)
T 2va8_A          162 RGPVVESVTIRAK-RRNLLALSATISN-YKQIAKWL  195 (715)
T ss_dssp             THHHHHHHHHHHH-TSEEEEEESCCTT-HHHHHHHH
T ss_pred             cchHHHHHHHhcc-cCcEEEEcCCCCC-HHHHHHHh
Confidence            8888888888876 7999999999986 46666554

>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=99.96  E-value=7.4e-29  Score=232.25  Aligned_cols=186  Identities=19%  Similarity=0.238  Sum_probs=153.3

Q ss_pred             CcCCCC--CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          48 NFDDME--LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        48 ~~~~~~--~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      +|++++  +++.+.+.+++.|+..|+++|.++++.+..++++++++|||||||+++.+++++.+..   +.+++|++|++
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~---~~~~l~i~P~r   78 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLR   78 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSH
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh---CCcEEEEeCcH
Confidence            477787  8999999999999999999999999999999999999999999999999999988764   35899999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +|+.|+++.++.+. ..+..+....|+......  . ..+++|+|+||+++..++.+....++++++||+||+|++.+++
T Consensus        79 ~La~q~~~~~~~~~-~~g~~v~~~~G~~~~~~~--~-~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~  154 (702)
T 2p6r_A           79 ALAGEKYESFKKWE-KIGLRIGISTGDYESRDE--H-LGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEK  154 (702)
T ss_dssp             HHHHHHHHHHTTTT-TTTCCEEEECSSCBCCSS--C-STTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTT
T ss_pred             HHHHHHHHHHHHHH-hcCCEEEEEeCCCCcchh--h-ccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCC
Confidence            99999999986543 347788877777654332  1 2358999999999999998876668899999999999998877


Q ss_pred             cHHHHHHHHHhC---CCCccEEEEEeeCChhHHHHHHHh
Q psy4698         206 FKDQIYDVFKHL---NNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       206 ~~~~~~~~~~~l---~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      ++..+..++.++   +++.|+|+||||+++ ..++.+++
T Consensus       155 r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l  192 (702)
T 2p6r_A          155 RGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWL  192 (702)
T ss_dssp             THHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHT
T ss_pred             cccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHh
Confidence            887777666555   578999999999986 56666544

>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=99.95  E-value=1.7e-28  Score=238.04  Aligned_cols=192  Identities=20%  Similarity=0.223  Sum_probs=162.0

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      .|..+++++.+...+...+...|+++|.++++.+..|++++++||||||||++|+++++..+..   +.+++|++|+++|
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~---g~rvlvl~PtraL  239 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKAL  239 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT---TCEEEEEESSHHH
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEcCcHHH
Confidence            5666777766666665556668999999999999999999999999999999999999988754   3589999999999


Q ss_pred             HHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH
Q psy4698         128 AQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK  207 (258)
Q Consensus       128 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~  207 (258)
                      +.|+++.++.+..    .+..+.|+..       ...+++|+|+||++|.+++.++...+.++++||+||||++.+.+++
T Consensus       240 a~Q~~~~l~~~~~----~VglltGd~~-------~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg  308 (1108)
T 3l9o_A          240 SNQKYRELLAEFG----DVGLMTGDIT-------INPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERG  308 (1108)
T ss_dssp             HHHHHHHHHHHTS----SEEEECSSCB-------CCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHH
T ss_pred             HHHHHHHHHHHhC----CccEEeCccc-------cCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchH
Confidence            9999999998765    4555666654       2345899999999999999988777889999999999999988899


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeCChh--HHHHHHHhcCCCeEEEecCC
Q psy4698         208 DQIYDVFKHLNNDVQVILLSATMPAD--VLDVSMKFMRDPIKILVKKE  253 (258)
Q Consensus       208 ~~~~~~~~~l~~~~~~i~~SAT~~~~--~~~~~~~~~~~~~~v~~~~~  253 (258)
                      ..+..++..+++.+|+|+||||+|+.  +.+.+..+..+|..+...+.
T Consensus       309 ~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~  356 (1108)
T 3l9o_A          309 VVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF  356 (1108)
T ss_dssp             HHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECC
T ss_pred             HHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC
Confidence            99999999999999999999999875  44677777777777766443

>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=99.95  E-value=1.9e-27  Score=217.86  Aligned_cols=185  Identities=18%  Similarity=0.257  Sum_probs=147.0

Q ss_pred             CCCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH
Q psy4698          50 DDMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA  128 (258)
Q Consensus        50 ~~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~  128 (258)
                      .++++++.+.+.|++ +|+..|+++|.++++.++.|+++++.+|||+|||++|++|++..      +.++||++|+++|+
T Consensus        24 ~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------~g~~lVisP~~~L~   97 (591)
T 2v1x_A           24 EDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------DGFTLVICPLISLM   97 (591)
T ss_dssp             SCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------SSEEEEECSCHHHH
T ss_pred             ccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------CCcEEEEeCHHHHH
Confidence            468899999999998 69999999999999999999999999999999999999999752      34899999999999


Q ss_pred             HHHHHHHHHhcCCCCceEEEEECCcchHHHHH---HH---hcCCcEEEeChHHHH------HHHhcCCCCCCCccEEEEc
Q psy4698         129 QQIQKVVIALGDFMSVSCHACIGGTIVRDDIR---KL---EAGAQVVVGTPGRVF------DMISRGALSTKQIRMFVLD  196 (258)
Q Consensus       129 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~---~~~~~Ilv~Tp~~l~------~~l~~~~~~~~~l~~lVvD  196 (258)
                      .|+.+.++.+    ++.+..+.++........   .+   ..+++|+|+||++|.      +.+.. ...+.++++||||
T Consensus        98 ~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~~~~~i~~iViD  172 (591)
T 2v1x_A           98 EDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AYEARRFTRIAVD  172 (591)
T ss_dssp             HHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HHHTTCEEEEEEE
T ss_pred             HHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hhhccCCcEEEEE
Confidence            9999999887    466666676665443322   22   356899999999874      22322 3346789999999


Q ss_pred             cchhhhccC--cHHHHHH--HHHhCCCCccEEEEEeeCChhHHHHHHHhcCCC
Q psy4698         197 EADEMLSRG--FKDQIYD--VFKHLNNDVQVILLSATMPADVLDVSMKFMRDP  245 (258)
Q Consensus       197 E~h~~~~~~--~~~~~~~--~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~  245 (258)
                      |||++.+++  |...+..  .+....++.+++++|||+++.+.+.+..++..+
T Consensus       173 EAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~  225 (591)
T 2v1x_A          173 EVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIE  225 (591)
T ss_dssp             TGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCC
T ss_pred             CcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCC
Confidence            999998776  5444432  344444678999999999999888887777644

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.95  E-value=9.2e-28  Score=196.23  Aligned_cols=225  Identities=18%  Similarity=0.235  Sum_probs=152.5

Q ss_pred             CCCCCCCCCCCCccCCCCCCCCCCCcccCcccccccccccCcC-CCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCc
Q psy4698           8 NWEDPKNGPAENEAEQPAYNGPPGMAVDGLIETNWDHVAENFD-DMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGND   86 (258)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~   86 (258)
                      +|.+|..+........-...+......+++...    ....|. .+..++.+.+.+...+...++++|.++++.+..|++
T Consensus         3 ~w~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~~~~~~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~   78 (235)
T 3llm_A            3 PWSPPQSNWNPWTSSNIDEGPLAFATPEQISMD----LKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSV   78 (235)
T ss_dssp             CCCCCCTTEETTTTEECCSSTTTTSCHHHHHHH----HHHHHHHHHHHCHHHHHHHHHHHTSGGGGGHHHHHHHHHHCSE
T ss_pred             CCCCCCCCCCCCcCCccCCCCcccCChhhhcHH----HHHHHHHHhhcCHHHHHHHHHHhcCChHHHHHHHHHHHhcCCE
Confidence            688887777666555433333322222211000    001111 122345555555544444689999999999999999


Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccc--cceEEEEeccHHHHHHHHHHHHHh-cCCCCceEEEEECCcchHHHHHHHh
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIK--ECQALILAPTRELAQQIQKVVIAL-GDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      +++.|+||||||+++.++++......+.  +.++++++|+++++.|..+.+... +...+..+........     ....
T Consensus        79 ~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~-----~~~~  153 (235)
T 3llm_A           79 VIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFES-----ILPR  153 (235)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEE-----ECCC
T ss_pred             EEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEEeechhh-----ccCC
Confidence            9999999999999998888887665433  458999999999999998877653 3333443332221111     0112


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh-hccCcH-HHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHh
Q psy4698         164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM-LSRGFK-DQIYDVFKHLNNDVQVILLSATMPADVLDVSMKF  241 (258)
Q Consensus       164 ~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~-~~~~~~-~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~  241 (258)
                      .+++|+|+||+++.+++..   .++++++||+||+|++ ++.++. ..+..++... ++.|++++|||++.+.  +.+.|
T Consensus       154 ~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~-~~~~~il~SAT~~~~~--~~~~~  227 (235)
T 3llm_A          154 PHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLMSATIDTSM--FCEYF  227 (235)
T ss_dssp             SSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC-TTSEEEEEECSSCCHH--HHHHT
T ss_pred             CCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC-CCCeEEEEecCCCHHH--HHHHc
Confidence            4478999999999999876   4789999999999985 555565 3445555554 5789999999999876  77777


Q ss_pred             cCCCeE
Q psy4698         242 MRDPIK  247 (258)
Q Consensus       242 ~~~~~~  247 (258)
                      .++|++
T Consensus       228 ~~~pvi  233 (235)
T 3llm_A          228 FNCPII  233 (235)
T ss_dssp             TSCCCE
T ss_pred             CCCCEE
Confidence            777764

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.95  E-value=3e-27  Score=221.03  Aligned_cols=172  Identities=17%  Similarity=0.204  Sum_probs=140.3

Q ss_pred             HHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc--cceEEEEeccHHHHHHHHHHHHH
Q psy4698          60 RGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK--ECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        60 ~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      ..+..+|+..|+++|.++++.++.|+++++++|||+|||++|++++++.+.....  +.++||++|+++|+.|+.+.+++
T Consensus         4 ~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~   83 (696)
T 2ykg_A            4 SDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSK   83 (696)
T ss_dssp             ---CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             CcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHH
Confidence            4566689999999999999999999999999999999999999999988866432  36899999999999999999999


Q ss_pred             hcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEEccchhhhccCcHHHHHH-HHH
Q psy4698         138 LGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIYD-VFK  215 (258)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~~~~~~~~~~~~~-~~~  215 (258)
                      ++...++.+..+.|+.........+..+++|+|+||+.|.+.+..+.+ .+.++++||+||||++.+...+..+.. .+.
T Consensus        84 ~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~l~  163 (696)
T 2ykg_A           84 YFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLD  163 (696)
T ss_dssp             HTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHH
T ss_pred             HhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHHHH
Confidence            988788888888888766555555666799999999999999988776 788999999999999876654433332 222


Q ss_pred             h-----CCCCccEEEEEeeCC
Q psy4698         216 H-----LNNDVQVILLSATMP  231 (258)
Q Consensus       216 ~-----l~~~~~~i~~SAT~~  231 (258)
                      .     .++.+++++||||+.
T Consensus       164 ~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          164 QKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHTTCCSCCCEEEEEESCCC
T ss_pred             HhhcccCCCCCeEEEEeCccc
Confidence            2     246789999999987

>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=99.95  E-value=4.5e-27  Score=213.98  Aligned_cols=166  Identities=16%  Similarity=0.220  Sum_probs=133.4

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc--cceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK--ECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      +...|+++|.++++.++.|+++++.+|||+|||++|++|+++.+.....  +.++||++|+++|+.|+.+.++.+....+
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~   83 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQG   83 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccC
Confidence            3448999999999999999999999999999999999999998876432  56899999999999999999999988778


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEEccchhhhccCcHHHHH-HHHHh-C---
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIY-DVFKH-L---  217 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~~~~~~~~~~~~-~~~~~-l---  217 (258)
                      +.+..+.|+............+++|+|+||++|.+++..+.+ .+.++++||+||||++.+++....+. ..+.. +   
T Consensus        84 ~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~  163 (556)
T 4a2p_A           84 YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSA  163 (556)
T ss_dssp             CCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhhhccc
Confidence            888888888876666666666789999999999999988877 78999999999999998776544443 22222 1   


Q ss_pred             CCCccEEEEEeeCC
Q psy4698         218 NNDVQVILLSATMP  231 (258)
Q Consensus       218 ~~~~~~i~~SAT~~  231 (258)
                      ++..|++++|||++
T Consensus       164 ~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          164 SQLPQILGLTASVG  177 (556)
T ss_dssp             --CCEEEEEESCCC
T ss_pred             CCCCeEEEEeCCcc
Confidence            35689999999985

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.94  E-value=6.5e-27  Score=212.66  Aligned_cols=164  Identities=18%  Similarity=0.232  Sum_probs=138.6

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc--cceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK--ECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      .|+++|.++++.++.|+++++.+|||+|||++|++|+++.+.....  +.++||++|+++|+.|+.+.+++++...++.+
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            7999999999999999999999999999999999999998876532  56899999999999999999999988888899


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEEccchhhhccCcHHHHH-HHHHhC-----CC
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIY-DVFKHL-----NN  219 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~~~~~~~~~~~~-~~~~~l-----~~  219 (258)
                      ..+.|+............+++|+|+||+++.+.+..+.+ .+.++++||+||||++.+.+....+. ..+...     .+
T Consensus        84 ~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (555)
T 3tbk_A           84 ASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGESRDP  163 (555)
T ss_dssp             EEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSSCCSC
T ss_pred             EEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhccccCC
Confidence            999998877666666666789999999999999988777 78899999999999997765433332 333321     25


Q ss_pred             CccEEEEEeeCCh
Q psy4698         220 DVQVILLSATMPA  232 (258)
Q Consensus       220 ~~~~i~~SAT~~~  232 (258)
                      .+|++++|||++.
T Consensus       164 ~~~~l~lSAT~~~  176 (555)
T 3tbk_A          164 LPQVVGLTASVGV  176 (555)
T ss_dssp             CCEEEEEESCCCC
T ss_pred             CCeEEEEecCccc
Confidence            5799999999954

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.94  E-value=2.1e-27  Score=190.85  Aligned_cols=164  Identities=13%  Similarity=0.149  Sum_probs=120.1

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc---ccceEEEEeccHHHHHH-HHHHHHHhcC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI---KECQALILAPTRELAQQ-IQKVVIALGD  140 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~---~~~~~lil~P~~~l~~q-~~~~~~~~~~  140 (258)
                      .....|+++|.++++.+..++++++.+|||+|||++++.+++..+....   .+.+++|++|+++|+.| +.+.++.+..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~  108 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLK  108 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHT
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhc
Confidence            3445899999999999999999999999999999999999988775532   35689999999999999 7777888765


Q ss_pred             CCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCC------CCCCCccEEEEccchhhhccCcHHHHHHH-
Q psy4698         141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA------LSTKQIRMFVLDEADEMLSRGFKDQIYDV-  213 (258)
Q Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~------~~~~~l~~lVvDE~h~~~~~~~~~~~~~~-  213 (258)
                      . ++.+..+.|+............+++|+|+||+.+...+....      ..+.++++||+||||++...++...+... 
T Consensus       109 ~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~  187 (216)
T 3b6e_A          109 K-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHY  187 (216)
T ss_dssp             T-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHHH
T ss_pred             c-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHHH
Confidence            4 566667776665444444444568999999999999887643      56788999999999999877666655432 


Q ss_pred             HHhC-------------CCCccEEEEEee
Q psy4698         214 FKHL-------------NNDVQVILLSAT  229 (258)
Q Consensus       214 ~~~l-------------~~~~~~i~~SAT  229 (258)
                      +...             .+.+++|++|||
T Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          188 LMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHhcccccccccccCCCCcceEEEeecC
Confidence            2211             156899999998

>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=99.94  E-value=2.7e-26  Score=217.59  Aligned_cols=167  Identities=17%  Similarity=0.228  Sum_probs=135.6

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc--cceEEEEeccHHHHHHHHHHHHHhcCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK--ECQALILAPTRELAQQIQKVVIALGDFM  142 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~  142 (258)
                      .|+..|+++|.++++.++.|+++++.+|||+|||++|++|++..+.....  +.++||++|+++|+.|+...+++++...
T Consensus       244 ~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~  323 (797)
T 4a2q_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ  323 (797)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG
T ss_pred             cCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcccC
Confidence            46789999999999999999999999999999999999999998876532  5689999999999999999999998877


Q ss_pred             CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEEccchhhhccCcHHHHH-HHHHh----
Q psy4698         143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIY-DVFKH----  216 (258)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~~~~~~~~~~~~-~~~~~----  216 (258)
                      ++.+..++|+............+++|+|+||++|.+.+..+.+ .+.++++||+||||++...+.+..+. ..+..    
T Consensus       324 ~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~~~~~  403 (797)
T 4a2q_A          324 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  403 (797)
T ss_dssp             TCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHHhhcc
Confidence            8899999998877766666777899999999999999988777 78899999999999987765444443 22222    


Q ss_pred             CCCCccEEEEEeeCC
Q psy4698         217 LNNDVQVILLSATMP  231 (258)
Q Consensus       217 l~~~~~~i~~SAT~~  231 (258)
                      ..+.+|++++|||++
T Consensus       404 ~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          404 ASQLPQILGLTASVG  418 (797)
T ss_dssp             CCCCCEEEEEESCCC
T ss_pred             CCCCCeEEEEcCCcc
Confidence            145689999999985

>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=99.94  E-value=1.7e-26  Score=209.10  Aligned_cols=192  Identities=15%  Similarity=0.207  Sum_probs=146.5

Q ss_pred             cCcCCCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          47 ENFDDMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .+|+++++++.+.+.|++ +|+..++++|.++++.+..|+++++.+|||+|||++|++|++..      ..++||++|++
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~------~g~~lvi~P~~   75 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLI   75 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCH
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh------CCCEEEECChH
Confidence            469999999999999998 89999999999999999999999999999999999999998743      24799999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HH-HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RK-LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      +|+.|+.+.++.+    ++.+..+.++.......   .. ....++|+|+||+++........+...++++|||||||++
T Consensus        76 aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i  151 (523)
T 1oyw_A           76 SLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCI  151 (523)
T ss_dssp             HHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGG
T ss_pred             HHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCcccc
Confidence            9999999999876    35566666665443321   22 2345899999999985322222233478999999999999


Q ss_pred             hccC--cHHHH---HHHHHhCCCCccEEEEEeeCChhHHH-HHHHh-cCCCeEEE
Q psy4698         202 LSRG--FKDQI---YDVFKHLNNDVQVILLSATMPADVLD-VSMKF-MRDPIKIL  249 (258)
Q Consensus       202 ~~~~--~~~~~---~~~~~~l~~~~~~i~~SAT~~~~~~~-~~~~~-~~~~~~v~  249 (258)
                      .+++  +...+   ..+...+ ++.+++++|||++....+ +.+.+ +.+|.++.
T Consensus       152 ~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~  205 (523)
T 1oyw_A          152 SQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQI  205 (523)
T ss_dssp             CTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEE
T ss_pred             CcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEe
Confidence            8765  43333   3344455 468899999999987665 44433 34665543

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.94  E-value=1.9e-26  Score=223.60  Aligned_cols=176  Identities=19%  Similarity=0.195  Sum_probs=144.9

Q ss_pred             HHHH-HCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          60 RGIY-AYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        60 ~~l~-~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      +.+. ..|+ .|+++|.++++.++.|+++++++|||||||++++++++..+.   .+.++||++|+++|+.|+++.++.+
T Consensus        69 ~~~~~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~---~~~~~Lil~PtreLa~Q~~~~l~~l  144 (1104)
T 4ddu_A           69 SFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQKL  144 (1104)
T ss_dssp             HHHHHHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh---cCCeEEEEechHHHHHHHHHHHHHh
Confidence            3443 3577 799999999999999999999999999999999888887763   3468999999999999999999998


Q ss_pred             cCCCCceEEEEECCcch---HHHHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc-----------
Q psy4698         139 GDFMSVSCHACIGGTIV---RDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS-----------  203 (258)
Q Consensus       139 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~-----------  203 (258)
                      + ..++.+..++|+...   ......+..+ ++|+|+||++|.+++..  +.++++++||+||||++..           
T Consensus       145 ~-~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~  221 (1104)
T 4ddu_A          145 A-DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMM  221 (1104)
T ss_dssp             S-CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHT
T ss_pred             h-CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHh
Confidence            7 778899999998876   5566677766 99999999999888765  5677899999999986554           


Q ss_pred             cCcHHH-HHHHHHhCC-----------CCccEEEEEee-CChhHH-HHHHHhc
Q psy4698         204 RGFKDQ-IYDVFKHLN-----------NDVQVILLSAT-MPADVL-DVSMKFM  242 (258)
Q Consensus       204 ~~~~~~-~~~~~~~l~-----------~~~~~i~~SAT-~~~~~~-~~~~~~~  242 (258)
                      .++... +..+++.++           ++.|++++||| .|..+. .+.+.++
T Consensus       222 ~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l  274 (1104)
T 4ddu_A          222 VGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLL  274 (1104)
T ss_dssp             SSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHT
T ss_pred             cCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcce
Confidence            566667 778888776           78999999999 566554 3344443

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.94  E-value=7.6e-26  Score=217.80  Aligned_cols=173  Identities=22%  Similarity=0.293  Sum_probs=144.6

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+| .|+++|.++++.+..|+++++++|||||||++|.++++..+..   +.+++|++|+++|+.|++..++.+..    
T Consensus        83 ~~f-~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~---g~rvL~l~PtkaLa~Q~~~~l~~~~~----  154 (1010)
T 2xgj_A           83 YPF-TLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG----  154 (1010)
T ss_dssp             CSS-CCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS----
T ss_pred             CCC-CCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC----
Confidence            456 5999999999999999999999999999999999999887753   35899999999999999999988764    


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                      .+..+.|+....       .+++|+|+||++|.+++.++...+.++++||+||+|++.+.+++..+..++..+++++|+|
T Consensus       155 ~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~il  227 (1010)
T 2xgj_A          155 DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYV  227 (1010)
T ss_dssp             CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCEEE
T ss_pred             CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCeEE
Confidence            455666665432       3579999999999999988878889999999999999998889999999999999999999


Q ss_pred             EEEeeCChhHH--HHHHHhcCCCeEEEecC
Q psy4698         225 LLSATMPADVL--DVSMKFMRDPIKILVKK  252 (258)
Q Consensus       225 ~~SAT~~~~~~--~~~~~~~~~~~~v~~~~  252 (258)
                      ++|||+++..+  +.+....+.+..+...+
T Consensus       228 ~LSATi~n~~e~a~~l~~~~~~~~~vi~~~  257 (1010)
T 2xgj_A          228 FLSATIPNAMEFAEWICKIHSQPCHIVYTN  257 (1010)
T ss_dssp             EEECCCTTHHHHHHHHHHHHTSCEEEEEEC
T ss_pred             EEcCCCCCHHHHHHHHHhhcCCCeEEEecC
Confidence            99999987532  33333445666665543

>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=99.93  E-value=3.3e-26  Score=221.74  Aligned_cols=179  Identities=17%  Similarity=0.198  Sum_probs=145.0

Q ss_pred             HHHH-HCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          60 RGIY-AYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        60 ~~l~-~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      +.+. ..|+. | ++|.++++.++.|+|+++.+|||||||+ |.+|++..+...  +++++|++|+++|+.|+++.++.+
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~--~~~~lil~PtreLa~Q~~~~l~~l  122 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALK--GKRCYVIFPTSLLVIQAAETIRKY  122 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTT--SCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhc--CCeEEEEeccHHHHHHHHHHHHHH
Confidence            4444 47998 9 9999999999999999999999999998 888888777653  468999999999999999999999


Q ss_pred             cCCCCc----eEEEEECCcchHH---HHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         139 GDFMSV----SCHACIGGTIVRD---DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       139 ~~~~~~----~~~~~~~~~~~~~---~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      +...++    .+..++|+.....   ....+.+ ++|+|+||++|.+++.+    ++++++||+||||++++  ++..+.
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~--~~~~~~  195 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILK--ASKNVD  195 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHT--STHHHH
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhh--ccccHH
Confidence            888887    8888888877654   3344555 89999999999987765    66899999999999987  467777


Q ss_pred             HHHHhC-----------CCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         212 DVFKHL-----------NNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       212 ~~~~~l-----------~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      .++..+           +...|++++|||++.. ..+...++.++..+.+.
T Consensus       196 ~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~  245 (1054)
T 1gku_B          196 KLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIG  245 (1054)
T ss_dssp             HHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCS
T ss_pred             HHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEcc
Confidence            777776           3568999999999887 65555555544444443

>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=99.93  E-value=2.5e-25  Score=213.68  Aligned_cols=167  Identities=17%  Similarity=0.228  Sum_probs=133.5

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccc--cceEEEEeccHHHHHHHHHHHHHhcCCC
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIK--ECQALILAPTRELAQQIQKVVIALGDFM  142 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~--~~~~lil~P~~~l~~q~~~~~~~~~~~~  142 (258)
                      .|+..|+++|.++++.++.|+++++.+|||+|||++|+++++..+.....  +.++||++|+++|+.|++..+++++...
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~  323 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ  323 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            45779999999999999999999999999999999999999988776431  5689999999999999999999998877


Q ss_pred             CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC-CCCCccEEEEccchhhhccCcHHHHH-HHHHh----
Q psy4698         143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL-STKQIRMFVLDEADEMLSRGFKDQIY-DVFKH----  216 (258)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~~~~l~~lVvDE~h~~~~~~~~~~~~-~~~~~----  216 (258)
                      ++.+..++|+.........+..+++|+|+||++|.+.+.++.+ .+.++++||+||||++...+....+. .++..    
T Consensus       324 ~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~~~~  403 (936)
T 4a2w_A          324 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  403 (936)
T ss_dssp             TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHhhcc
Confidence            8889888988866655555556689999999999999988776 78899999999999987765444433 22222    


Q ss_pred             CCCCccEEEEEeeCC
Q psy4698         217 LNNDVQVILLSATMP  231 (258)
Q Consensus       217 l~~~~~~i~~SAT~~  231 (258)
                      ..+..|++++|||+.
T Consensus       404 ~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          404 ASQLPQILGLTASVG  418 (936)
T ss_dssp             CSCCCEEEEEESCCC
T ss_pred             CCCcCeEEEecCCcc
Confidence            145689999999985

>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=99.93  E-value=1.4e-24  Score=193.45  Aligned_cols=169  Identities=22%  Similarity=0.238  Sum_probs=139.0

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .|+++|.++++.+..+ ++++.+|||+|||++++.+++..+.  ..+.++||++|+++|+.|+.+.++++.......+..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEE
Confidence            6999999999999999 9999999999999999999988776  345589999999999999999999987544557777


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      +.|+....... ....+++|+|+||+.+...+..+.+.+.++++||+||||++.+......+...+....+..+++++||
T Consensus        86 ~~g~~~~~~~~-~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTa  164 (494)
T 1wp9_A           86 LTGEKSPEERS-KAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (494)
T ss_dssp             ECSCSCHHHHH-HHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eeCCcchhhhh-hhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCeEEEEec
Confidence            77776655433 33345799999999999999888888899999999999998766666677777766677899999999


Q ss_pred             eCChh---HHHHHHHh
Q psy4698         229 TMPAD---VLDVSMKF  241 (258)
Q Consensus       229 T~~~~---~~~~~~~~  241 (258)
                      |+.++   +.+++..+
T Consensus       165 Tp~~~~~~~~~l~~~l  180 (494)
T 1wp9_A          165 SPGSTPEKIMEVINNL  180 (494)
T ss_dssp             CSCSSHHHHHHHHHHT
T ss_pred             CCCCCcHHHHHHHHhc
Confidence            99754   44444433

>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=99.93  E-value=1.8e-25  Score=223.86  Aligned_cols=172  Identities=21%  Similarity=0.319  Sum_probs=137.7

Q ss_pred             CCCCCcHHHHHHhhhhh-cCCcEEEEcccCCCcchHhHHHHHHHhhhc--------cccceEEEEeccHHHHHHHHHHHH
Q psy4698          66 GFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISILQQVDQN--------IKECQALILAPTRELAQQIQKVVI  136 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~-~g~~~li~~~tGsGKT~~~l~~~l~~l~~~--------~~~~~~lil~P~~~l~~q~~~~~~  136 (258)
                      ||..++++|.++++.+. .++|++++||||||||+++.+++++.+...        ..+.++||++|+++|+.|.++.++
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            78899999999999865 578999999999999999999999998652        235689999999999999999998


Q ss_pred             HhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCC--CCCCccEEEEccchhhhccCcHHHHHHHH
Q psy4698         137 ALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGAL--STKQIRMFVLDEADEMLSRGFKDQIYDVF  214 (258)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--~~~~l~~lVvDE~h~~~~~~~~~~~~~~~  214 (258)
                      +.....++.+..+.|+......  . ..+++|+|+|||++..++++...  .++++++||+||+|.+.+ .++..+..++
T Consensus       156 ~~~~~~gi~V~~~tGd~~~~~~--~-~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~l  231 (1724)
T 4f92_B          156 KRLATYGITVAELTGDHQLCKE--E-ISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEALV  231 (1724)
T ss_dssp             HHHTTTTCCEEECCSSCSSCCT--T-GGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHHH
T ss_pred             HHHhhCCCEEEEEECCCCCCcc--c-cCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHHH
Confidence            8878889999888887654322  1 23489999999998666654322  367899999999996644 5666665554


Q ss_pred             H-------hCCCCccEEEEEeeCChhHHHHHHHhc
Q psy4698         215 K-------HLNNDVQVILLSATMPADVLDVSMKFM  242 (258)
Q Consensus       215 ~-------~l~~~~~~i~~SAT~~~~~~~~~~~~~  242 (258)
                      .       .+++.+|+|++|||+|+ .++++++.-
T Consensus       232 ~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~wL~  265 (1724)
T 4f92_B          232 ARAIRNIEMTQEDVRLIGLSATLPN-YEDVATFLR  265 (1724)
T ss_dssp             HHHHHHHHHHTCCCEEEEEECSCTT-HHHHHHHTT
T ss_pred             HHHHHHHHhCCCCCcEEEEecccCC-HHHHHHHhC
Confidence            4       34678999999999985 566776543

>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=99.93  E-value=4.4e-25  Score=221.14  Aligned_cols=185  Identities=18%  Similarity=0.235  Sum_probs=145.4

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhc-CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVR-GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQ  132 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~-g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~  132 (258)
                      +.....+.+...+|..++|+|.++++.+.. ++|++++||||||||+++.+++++.+.... +.+++|++|+++|+.|.+
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~-~~kavyi~P~raLa~q~~  989 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSS-EGRCVYITPMEALAEQVY  989 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCT-TCCEEEECSCHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCC-CCEEEEEcChHHHHHHHH
Confidence            445667777777899999999999999865 578999999999999999999999987653 458999999999999999


Q ss_pred             HHHHH-hcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcC--CCCCCCccEEEEccchhhhccCcHHH
Q psy4698         133 KVVIA-LGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRG--ALSTKQIRMFVLDEADEMLSRGFKDQ  209 (258)
Q Consensus       133 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~--~~~~~~l~~lVvDE~h~~~~~~~~~~  209 (258)
                      +.+++ ++...+..+..+.|+......  . ..+++|+|+||+++..++++.  ...++++++||+||+|.+.+ ..+..
T Consensus       990 ~~~~~~f~~~~g~~V~~ltGd~~~~~~--~-~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d-~rg~~ 1065 (1724)
T 4f92_B          990 MDWYEKFQDRLNKKVVLLTGETSTDLK--L-LGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGG-ENGPV 1065 (1724)
T ss_dssp             HHHHHHHTTTSCCCEEECCSCHHHHHH--H-HHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGS-TTHHH
T ss_pred             HHHHHHhchhcCCEEEEEECCCCcchh--h-cCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCC-CCCcc
Confidence            98865 667788888888887654322  2 234799999999987777652  22367899999999997765 45655


Q ss_pred             HHHHHHh-------CCCCccEEEEEeeCChhHHHHHHHhcCC
Q psy4698         210 IYDVFKH-------LNNDVQVILLSATMPADVLDVSMKFMRD  244 (258)
Q Consensus       210 ~~~~~~~-------l~~~~~~i~~SAT~~~~~~~~~~~~~~~  244 (258)
                      +..++.+       +++.+|+|++|||+++ .+++.++...+
T Consensus      1066 le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~ 1106 (1724)
T 4f92_B         1066 LEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCS 1106 (1724)
T ss_dssp             HHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCC
Confidence            5544433       4678999999999985 57788776543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.92  E-value=1.6e-25  Score=215.47  Aligned_cols=164  Identities=21%  Similarity=0.256  Sum_probs=139.1

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+| .|+++|.++++.+..|+++++.+|||||||++|++++...+..   +.+++|++|+++|+.|+++.++++..  +.
T Consensus        36 ~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~---g~~vlvl~PtraLa~Q~~~~l~~~~~--~~  109 (997)
T 4a4z_A           36 WPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN---MTKTIYTSPIKALSNQKFRDFKETFD--DV  109 (997)
T ss_dssp             CSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT---TCEEEEEESCGGGHHHHHHHHHTTC----C
T ss_pred             CCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc---CCeEEEEeCCHHHHHHHHHHHHHHcC--CC
Confidence            355 6899999999999999999999999999999999988776543   35899999999999999999988653  45


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                      .+..+.|+...       ...++|+|+||++|.+++......+.++++||+||+|++.+++++..+..++..++++.|+|
T Consensus       110 ~v~~l~G~~~~-------~~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~~~v~iI  182 (997)
T 4a4z_A          110 NIGLITGDVQI-------NPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFI  182 (997)
T ss_dssp             CEEEECSSCEE-------CTTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCEEE
T ss_pred             eEEEEeCCCcc-------CCCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcccCCCEE
Confidence            66777776643       23479999999999999988877888999999999999999888988999999999999999


Q ss_pred             EEEeeCChhHHHHHHHhc
Q psy4698         225 LLSATMPADVLDVSMKFM  242 (258)
Q Consensus       225 ~~SAT~~~~~~~~~~~~~  242 (258)
                      ++|||+++.. ++..++.
T Consensus       183 lLSAT~~n~~-ef~~~l~  199 (997)
T 4a4z_A          183 LLSATVPNTY-EFANWIG  199 (997)
T ss_dssp             EEECCCTTHH-HHHHHHH
T ss_pred             EEcCCCCChH-HHHHHHh
Confidence            9999998653 5555543

>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=99.91  E-value=4.7e-25  Score=206.30  Aligned_cols=163  Identities=13%  Similarity=0.185  Sum_probs=126.7

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc---ccceEEEEeccHHHHHHH-HHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI---KECQALILAPTRELAQQI-QKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~---~~~~~lil~P~~~l~~q~-~~~~~~~~~~~~~  144 (258)
                      .|+++|.++++.++.|+++++.+|||+|||++|+++++..+....   .+.++||++|+++|+.|+ .+.+++++.. ++
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~~   85 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-WY   85 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-TS
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-Cc
Confidence            799999999999999999999999999999999999998876542   225899999999999999 9999998765 46


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHH------hcCCCCCCCccEEEEccchhhhccCcHHHHHH-HHHh-
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMI------SRGALSTKQIRMFVLDEADEMLSRGFKDQIYD-VFKH-  216 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l------~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~-~~~~-  216 (258)
                      .+..+.|+............+++|+|+||+.|.+.+      ....+.+.++++|||||||++...+.+..+.. .+.. 
T Consensus        86 ~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~l~~~  165 (699)
T 4gl2_A           86 RVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQK  165 (699)
T ss_dssp             CEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHHHHHH
T ss_pred             eEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHHHHhh
Confidence            777778877665555555677999999999999988      44557788999999999998865443333222 2211 


Q ss_pred             ---CC---------CCccEEEEEeeCCh
Q psy4698         217 ---LN---------NDVQVILLSATMPA  232 (258)
Q Consensus       217 ---l~---------~~~~~i~~SAT~~~  232 (258)
                         ..         +.++++++|||++.
T Consensus       166 ~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          166 LKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             hcccccccccccCCCCCEEEEecccccc
Confidence               11         56899999999986

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.91  E-value=1.6e-24  Score=181.67  Aligned_cols=159  Identities=21%  Similarity=0.219  Sum_probs=125.2

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .|+++|.++++.+..+++.+++++||+|||++++.++...+...  +.+++|++|+++|+.|+.+.+++++......+..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC--CCeEEEEECCHHHHHHHHHHHHHhcccccceEEE
Confidence            79999999999988888899999999999999988777665532  2389999999999999999999987766666766


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      ..++.....   ....+.+|+|+||+.+...   ....+.++++||+||||++.+    ..+..+++.+....+++++||
T Consensus       191 ~~~~~~~~~---~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~~----~~~~~il~~~~~~~~~l~lSA  260 (282)
T 1rif_A          191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCH----HHHHHHTTTCTTCCEEEEECS
T ss_pred             EeCCCcchh---hhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCCc----ccHHHHHHHhhcCCeEEEEeC
Confidence            666654322   1224589999999876533   223467889999999999853    467778888877899999999


Q ss_pred             eCChhHHHHHH
Q psy4698         229 TMPADVLDVSM  239 (258)
Q Consensus       229 T~~~~~~~~~~  239 (258)
                      |+++.......
T Consensus       261 Tp~~~~~~~~~  271 (282)
T 1rif_A          261 SLRDGKANIMQ  271 (282)
T ss_dssp             SCCTTSTTHHH
T ss_pred             CCCCcchHHHH
Confidence            99876444433

>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=99.90  E-value=2.3e-23  Score=193.27  Aligned_cols=161  Identities=18%  Similarity=0.254  Sum_probs=135.8

Q ss_pred             HCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC
Q psy4698          64 AYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS  143 (258)
Q Consensus        64 ~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~  143 (258)
                      ..|+ .|+++|..+++.+++|+  +..++||+|||++|.+|++.....   +.+++|++||++||.|..+++..++...+
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~---g~~vlVltptreLA~qd~e~~~~l~~~lg  152 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFLG  152 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            4689 99999999999999999  999999999999999999854433   34799999999999999999999999999


Q ss_pred             ceEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh-ccC----------
Q psy4698         144 VSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML-SRG----------  205 (258)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~-~~~----------  205 (258)
                      +++.+.+|+......  ....+++|+|+||+.| ++++..+      .+.++++.++|+||||+|+ +..          
T Consensus       153 l~v~~i~gg~~~~~r--~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~~  230 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEK--REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQA  230 (844)
T ss_dssp             CCEEECCTTSCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEE
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCCc
Confidence            999999998765433  3334689999999999 7776543      3567899999999999998 543          


Q ss_pred             -----cHHHHHHHHHhCC---------CCccEE-----------------EEEeeCCh
Q psy4698         206 -----FKDQIYDVFKHLN---------NDVQVI-----------------LLSATMPA  232 (258)
Q Consensus       206 -----~~~~~~~~~~~l~---------~~~~~i-----------------~~SAT~~~  232 (258)
                           ++..+..++..++         +..|++                 ++|||++.
T Consensus       231 ~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~  288 (844)
T 1tf5_A          231 AKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVA  288 (844)
T ss_dssp             ECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHH
T ss_pred             ccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccch
Confidence                 6788999999997         367777                 89999874

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.90  E-value=1.3e-23  Score=189.75  Aligned_cols=157  Identities=21%  Similarity=0.214  Sum_probs=128.2

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEE
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCH  147 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~  147 (258)
                      ..|+++|.++++.+..+++++++++||+|||++++.++...+...  +.+++|++|+++|+.|+++.+++++...+..+.
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~  189 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--SSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--CCeEEEEECcHHHHHHHHHHHHHhhcCCccceE
Confidence            379999999999999999999999999999999999888777643  248999999999999999999998776667777


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.++......   ...+++|+|+||+.+..   .....++++++||+||+|++..    ..+..+++.+++..+++++|
T Consensus       190 ~~~~~~~~~~~---~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~~~l~lS  259 (510)
T 2oca_A          190 KIGGGASKDDK---YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMFKFGLS  259 (510)
T ss_dssp             ECGGGCCTTGG---GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCCEEEEEE
T ss_pred             EEecCCccccc---cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCcEEEEEE
Confidence            77777554433   34568999999997543   3334567899999999998754    45667788888888999999


Q ss_pred             eeCChhHHH
Q psy4698         228 ATMPADVLD  236 (258)
Q Consensus       228 AT~~~~~~~  236 (258)
                      ||+++....
T Consensus       260 ATp~~~~~~  268 (510)
T 2oca_A          260 GSLRDGKAN  268 (510)
T ss_dssp             SCGGGCSSC
T ss_pred             eCCCCCccc
Confidence            999876433

>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=99.89  E-value=1.1e-22  Score=190.79  Aligned_cols=167  Identities=21%  Similarity=0.246  Sum_probs=130.4

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHhhhhhcC------CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHH
Q psy4698          56 EELLRGIYAYGFEKPSAIQQRAIIPCVRG------NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQ  129 (258)
Q Consensus        56 ~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g------~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~  129 (258)
                      ..+.+.+...+| .|+++|.++++.+..+      .+++++|+||||||++|+++++..+..+   .+++|++|+++|+.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g---~qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG---FQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT---SCEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcC---CeEEEEeCcHHHHH
Confidence            444555567888 9999999999998775      5899999999999999999999887643   58999999999999


Q ss_pred             HHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         130 QIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       130 q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      |+++.++++....++.+..++|+.....   ....+..+ ++|+|+||+.+.+     .+.++++++||+||+|++....
T Consensus       432 Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~q  506 (780)
T 1gm5_A          432 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQ  506 (780)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC----
T ss_pred             HHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHHH
Confidence            9999999998888889988888876544   23444454 8999999987643     3568899999999999863221


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHH
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLD  236 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~  236 (258)
                           ...+......+++++||||+......
T Consensus       507 -----r~~l~~~~~~~~vL~mSATp~p~tl~  532 (780)
T 1gm5_A          507 -----REALMNKGKMVDTLVMSATPIPRSMA  532 (780)
T ss_dssp             ------CCCCSSSSCCCEEEEESSCCCHHHH
T ss_pred             -----HHHHHHhCCCCCEEEEeCCCCHHHHH
Confidence                 12223334578999999998665444

>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=99.89  E-value=5.2e-22  Score=193.62  Aligned_cols=187  Identities=20%  Similarity=0.218  Sum_probs=145.1

Q ss_pred             CCCCCHHHHHHHHH-CCCCCCcHHHHHHhhhhhc----CC--cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          51 DMELSEELLRGIYA-YGFEKPSAIQQRAIIPCVR----GN--DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        51 ~~~~~~~l~~~l~~-~~~~~~~~~Q~~~~~~l~~----g~--~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .++.+....+.+.. +++ .++++|.++++.++.    |+  +++++++||+|||++++.+++..+..   +.+++|++|
T Consensus       585 ~~~~~~~~~~~~~~~f~~-~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~---g~~vlvlvP  660 (1151)
T 2eyq_A          585 AFKHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---HKQVAVLVP  660 (1151)
T ss_dssp             CCCCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---TCEEEEECS
T ss_pred             CCCCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh---CCeEEEEec
Confidence            45567777776654 566 579999999999876    66  89999999999999999888876654   348999999


Q ss_pred             cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         124 TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       124 ~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                      |++|+.|+++.+++.....++.+..+.+......   ....+..+ ++|+|+||+.+.     ..+.++++++||+||+|
T Consensus       661 t~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH  735 (1151)
T 2eyq_A          661 TTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEH  735 (1151)
T ss_dssp             SHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGG
T ss_pred             hHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechH
Confidence            9999999999999887777777777766544332   23344444 899999996542     34678899999999999


Q ss_pred             hhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         200 EMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       200 ~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      ++     +......++.++.++++++||||+++.........+.++.++..+
T Consensus       736 ~~-----g~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~  782 (1151)
T 2eyq_A          736 RF-----GVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATP  782 (1151)
T ss_dssp             GS-----CHHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCC
T ss_pred             hc-----ChHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecC
Confidence            84     344556677777889999999998777777777777776665443

>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=99.88  E-value=2.5e-22  Score=186.36  Aligned_cols=160  Identities=17%  Similarity=0.225  Sum_probs=136.6

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|+ .|+++|..+++.+++|+  +..++||+|||+++.+|++.....+   .+++|++||++||.|...++..++..+++
T Consensus       108 lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g---~~v~VvTpTreLA~Qdae~m~~l~~~lGL  181 (922)
T 1nkt_A          108 LDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAG---NGVHIVTVNDYLAKRDSEWMGRVHRFLGL  181 (922)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTT---SCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhC---CCeEEEeCCHHHHHHHHHHHHHHHhhcCC
Confidence            577 99999999999999998  9999999999999999997654432   37999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhhc--------------
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEMLS--------------  203 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~~--------------  203 (258)
                      .+.+..|+......  ....+++|+|+||+.| ++++..+      .+.++++.++|+||||+|+.              
T Consensus       182 sv~~i~gg~~~~~r--~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~~~  259 (922)
T 1nkt_A          182 QVGVILATMTPDER--RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGPAD  259 (922)
T ss_dssp             CEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEECC
T ss_pred             eEEEEeCCCCHHHH--HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCCCC
Confidence            99999988765433  3334589999999999 7888654      36678899999999999983              


Q ss_pred             --cCcHHHHHHHHHhCC---------CCccEE-----------------EEEeeCCh
Q psy4698         204 --RGFKDQIYDVFKHLN---------NDVQVI-----------------LLSATMPA  232 (258)
Q Consensus       204 --~~~~~~~~~~~~~l~---------~~~~~i-----------------~~SAT~~~  232 (258)
                        .+++..+..++..++         +..|++                 ++|||++.
T Consensus       260 ~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~  316 (922)
T 1nkt_A          260 GASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSP  316 (922)
T ss_dssp             CCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCC
T ss_pred             cchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchh
Confidence              247789999999997         677888                 89999875

>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=99.88  E-value=9.5e-23  Score=188.79  Aligned_cols=147  Identities=18%  Similarity=0.253  Sum_probs=113.2

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|+++|..+++.+++|+  +..++||+|||++|.+|++.....   +.+++|++||++||.|.+..+..++...++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~---g~~vlVltPTreLA~Q~~e~~~~l~~~lgl  144 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAENNRPLFEFLGL  144 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT---SSCCEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHHHHhcCC
Confidence            355 89999999999999999  999999999999999999865543   347999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcC------CCCCCCccEEEEccchhhh-cc------------
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRG------ALSTKQIRMFVLDEADEML-SR------------  204 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~~~~l~~lVvDE~h~~~-~~------------  204 (258)
                      .+.+++|+.....  +....+++|+|+||+.| ++++..+      .+.++++.++|+||||+|+ +.            
T Consensus       145 ~v~~i~GG~~~~~--r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~  222 (853)
T 2fsf_A          145 TVGINLPGMPAPA--KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISGPAE  222 (853)
T ss_dssp             CEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEEC--
T ss_pred             eEEEEeCCCCHHH--HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccCCCc
Confidence            9999999876542  33444689999999999 7888754      2567899999999999998 43            


Q ss_pred             ---CcHHHHHHHHHhCCC
Q psy4698         205 ---GFKDQIYDVFKHLNN  219 (258)
Q Consensus       205 ---~~~~~~~~~~~~l~~  219 (258)
                         +++..+..++..+++
T Consensus       223 ~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          223 DSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             ------------------
T ss_pred             cchhHHHHHHHHHHhchh
Confidence               356777888888764

>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=99.86  E-value=2.3e-21  Score=173.49  Aligned_cols=136  Identities=16%  Similarity=0.150  Sum_probs=110.6

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce-EE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS-CH  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~-~~  147 (258)
                      .|+++|.++++.+..+++++++++||+|||++++.++...      +.+++|++|+++|+.|+.+.++++    +.. +.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v~  162 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC----CCcceE
Confidence            6899999999999999999999999999999998888764      358999999999999999988875    456 66


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.|+...         ..+|+|+||+.+...+..-   .+++++||+||+|++.+..+..    +++.+ +..+++++|
T Consensus       163 ~~~g~~~~---------~~~Ivv~T~~~l~~~~~~~---~~~~~liIvDEaH~~~~~~~~~----~~~~~-~~~~~l~lS  225 (472)
T 2fwr_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAEKL---GNRFMLLIFDEVHHLPAESYVQ----IAQMS-IAPFRLGLT  225 (472)
T ss_dssp             EBSSSCBC---------CCSEEEEEHHHHHHTHHHH---TTTCSEEEEETGGGTTSTTTHH----HHHTC-CCSEEEEEE
T ss_pred             EECCCcCC---------cCCEEEEEcHHHHHHHHHh---cCCCCEEEEECCcCCCChHHHH----HHHhc-CCCeEEEEe
Confidence            66665532         4789999999987665421   2458999999999988766543    44444 457899999


Q ss_pred             eeCC
Q psy4698         228 ATMP  231 (258)
Q Consensus       228 AT~~  231 (258)
                      ||+.
T Consensus       226 ATp~  229 (472)
T 2fwr_A          226 ATFE  229 (472)
T ss_dssp             SCCC
T ss_pred             cCcc
Confidence            9987

>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=99.85  E-value=1.7e-20  Score=176.46  Aligned_cols=198  Identities=17%  Similarity=0.198  Sum_probs=136.6

Q ss_pred             cccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhh-cCCcEEEEcccCCCcchHhHHHHH--HHhhhccccceEEEE
Q psy4698          45 VAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCV-RGNDVIAQAQSGTGKTATFSISIL--QQVDQNIKECQALIL  121 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~-~g~~~li~~~tGsGKT~~~l~~~l--~~l~~~~~~~~~lil  121 (258)
                      ....|.++++++.+.+.+..++ ..|++.|+++++.++ .+++++++||||||||+.  +|++  ......+.+.+++++
T Consensus        70 ~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtl--lp~ll~~~~~~~~~g~~ilvl  146 (773)
T 2xau_A           70 KINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQ--IPQFVLFDEMPHLENTQVACT  146 (773)
T ss_dssp             SBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHH--HHHHHHHHHCGGGGTCEEEEE
T ss_pred             CCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHHH--HHHHHHHhccccCCCceEEec
Confidence            4567999999999999999887 688999999988765 557899999999999994  4444  222222235679999


Q ss_pred             eccHHHHHHHHHHHHH-hcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchh
Q psy4698         122 APTRELAQQIQKVVIA-LGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADE  200 (258)
Q Consensus       122 ~P~~~l~~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~  200 (258)
                      +|+++++.|++..+.. ++...+..+........      ....+.+|+|+||+.+.+.+... ..+.++++||+||+|.
T Consensus       147 ~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~  219 (773)
T 2xau_A          147 QPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHE  219 (773)
T ss_dssp             ESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGG
T ss_pred             CchHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccc
Confidence            9999999999876654 33333333332111111      11235789999999999877664 4588999999999995


Q ss_pred             -hhccCcH-HHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEecCCccc
Q psy4698         201 -MLSRGFK-DQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT  256 (258)
Q Consensus       201 -~~~~~~~-~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~  256 (258)
                       .++.... ..+..+. ...++.|+|+||||++.  ..+. .++.++.++.+.+...+
T Consensus       220 R~ld~d~~~~~l~~l~-~~~~~~~iIl~SAT~~~--~~l~-~~~~~~~vi~v~gr~~p  273 (773)
T 2xau_A          220 RTLATDILMGLLKQVV-KRRPDLKIIIMSATLDA--EKFQ-RYFNDAPLLAVPGRTYP  273 (773)
T ss_dssp             CCHHHHHHHHHHHHHH-HHCTTCEEEEEESCSCC--HHHH-HHTTSCCEEECCCCCCC
T ss_pred             cccchHHHHHHHHHHH-HhCCCceEEEEeccccH--HHHH-HHhcCCCcccccCcccc
Confidence             4443332 2333333 33467899999999964  3444 45555556666655443

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.85  E-value=1.6e-20  Score=153.37  Aligned_cols=137  Identities=16%  Similarity=0.158  Sum_probs=107.2

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce-EE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS-CH  147 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~-~~  147 (258)
                      .++++|.++++.+..++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.++++    +.. +.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v~  162 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeEE
Confidence            7899999999999999999999999999999988776553      357999999999999999988774    455 55


Q ss_pred             EEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         148 ACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.++..         ...+|+|+|++.+......   ....+++||+||+|++.+..+.    .++..++ ..+++++|
T Consensus       163 ~~~g~~~---------~~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~~~l~LS  225 (237)
T 2fz4_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAESYV----QIAQMSI-APFRLGLT  225 (237)
T ss_dssp             EESSSCB---------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTTHH----HHHHTCC-CSEEEEEE
T ss_pred             EEeCCCC---------CcCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCChHHH----HHHHhcc-CCEEEEEe
Confidence            5555543         2478999999998765543   1245889999999998655433    3445554 57899999


Q ss_pred             eeCCh
Q psy4698         228 ATMPA  232 (258)
Q Consensus       228 AT~~~  232 (258)
                      ||+++
T Consensus       226 ATp~r  230 (237)
T 2fz4_A          226 ATFER  230 (237)
T ss_dssp             ESCC-
T ss_pred             cCCCC
Confidence            99875

>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=99.85  E-value=2e-22  Score=185.29  Aligned_cols=181  Identities=15%  Similarity=0.107  Sum_probs=126.7

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHH
Q psy4698          52 MELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQI  131 (258)
Q Consensus        52 ~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~  131 (258)
                      +++++.+.+.+... ...++|+|..+++.+..|+++++.++||||||++|++|+++.+...  +.++||++|+++|+.|+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~--~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR--RLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC--CCeEEEEcChHHHHHHH
Confidence            44565555544332 3677888888899999999999999999999999999999888763  46899999999999999


Q ss_pred             HHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         132 QKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      ++.++.      ..+. +.... ..   .....+..+.++|.+.+...+... ..++++++||+||||++ +.++...+.
T Consensus       232 ~~~l~~------~~v~-~~~~~-l~---~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~  298 (618)
T 2whx_A          232 EEALRG------LPIR-YQTPA-VK---SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARG  298 (618)
T ss_dssp             HHHTTT------SCEE-ECCTT-SS---CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHH
T ss_pred             HHHhcC------Ccee-Eeccc-ce---eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHH
Confidence            987752      2222 11111 00   011233567788888887666554 45889999999999987 555666777


Q ss_pred             HHHHhCC-CCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         212 DVFKHLN-NDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       212 ~~~~~l~-~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      .++..++ ++.|+++||||++..+..+.+   .++.++.+.
T Consensus       299 ~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~  336 (618)
T 2whx_A          299 YISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIE  336 (618)
T ss_dssp             HHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEE
T ss_pred             HHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeec
Confidence            7776664 679999999999987554333   356665554

>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=99.84  E-value=1.6e-21  Score=173.71  Aligned_cols=166  Identities=16%  Similarity=0.089  Sum_probs=117.1

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcE-EEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDV-IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~-li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      |+..++++|. +++.+++++++ ++++|||||||++|++|++..+...  +.+++|++|+++|+.|+++.+.      +.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR--RLRTLILAPTRVVAAEMEEALR------GL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc--CCcEEEECCCHHHHHHHHHHhc------Cc
Confidence            5667888885 79999988876 9999999999999999998877653  4689999999999999998774      22


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHH-HhCCCCccE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF-KHLNNDVQV  223 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~-~~l~~~~~~  223 (258)
                      .+.........     ....+..|.++|++.+...+... ..++++++||+||+|++ +..+......+. ...++++|+
T Consensus        72 ~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~~~~~~~  144 (451)
T 2jlq_A           72 PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAA  144 (451)
T ss_dssp             CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHHTTSCEE
T ss_pred             eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-CcchHHHHHHHHHhhcCCCceE
Confidence            22211111100     11234679999999988877654 46789999999999976 322222222222 223467999


Q ss_pred             EEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         224 ILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       224 i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      ++||||++.....   .+..++.++.+
T Consensus       145 i~~SAT~~~~~~~---~~~~~~~~~~~  168 (451)
T 2jlq_A          145 IFMTATPPGSTDP---FPQSNSPIEDI  168 (451)
T ss_dssp             EEECSSCTTCCCS---SCCCSSCEEEE
T ss_pred             EEEccCCCccchh---hhcCCCceEec
Confidence            9999999876543   24456666654

>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=99.84  E-value=3.1e-21  Score=176.97  Aligned_cols=145  Identities=17%  Similarity=0.159  Sum_probs=115.4

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .++.+|..+++.+..++++++.||||||||.++.+++++      ++.+++|++|+++|+.|+++.+.+..   +..+..
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~------~g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg~  287 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAH---GIDPNI  287 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH------TTCCEEEEESCHHHHHHHHHHHHHHH---SCCCEE
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH------CCCeEEEEcchHHHHHHHHHHHHHHh---CCCeeE
Confidence            566778888888888999999999999999999988876      24589999999999999998776543   233344


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCcc--EEEE
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQ--VILL  226 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~--~i~~  226 (258)
                      ..++..       ...+++|+|+||++|   +....+.++++++||+||+|+ ++.++...+..+++.++...+  +++|
T Consensus       288 ~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~-l~~~~~~~l~~Il~~l~~~~~~llil~  356 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHS-TDSTTILGIGTVLDQAETAGARLVVLA  356 (666)
T ss_dssp             ECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTC-CSHHHHHHHHHHHHHTTTTTCSEEEEE
T ss_pred             EECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchh-cCccHHHHHHHHHHhhhhcCCceEEEE
Confidence            445432       345689999999997   466677888999999999975 566677778888888877666  7888


Q ss_pred             EeeCChh
Q psy4698         227 SATMPAD  233 (258)
Q Consensus       227 SAT~~~~  233 (258)
                      |||++..
T Consensus       357 SAT~~~~  363 (666)
T 3o8b_A          357 TATPPGS  363 (666)
T ss_dssp             ESSCTTC
T ss_pred             CCCCCcc
Confidence            9999974

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.81  E-value=1.6e-20  Score=172.58  Aligned_cols=150  Identities=20%  Similarity=0.239  Sum_probs=91.6

Q ss_pred             CCcHHHHHHhhhhhc----C-CcEEEEcccCCCcchHhHHHHHHHhhhcc-------ccceEEEEeccHHHHHHHH-HHH
Q psy4698          69 KPSAIQQRAIIPCVR----G-NDVIAQAQSGTGKTATFSISILQQVDQNI-------KECQALILAPTRELAQQIQ-KVV  135 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~----g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~-------~~~~~lil~P~~~l~~q~~-~~~  135 (258)
                      .|+++|.++++.+..    | ++++++++||+|||++++..+. .+...+       .+.++||++|+++|+.|+. +.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~-~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISW-KLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHH-HHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHH-HHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            699999999998875    4 6699999999999999755444 444333       5679999999999999999 766


Q ss_pred             HHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhc----CCCCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         136 IALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISR----GALSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~----~~~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      +.++.    .+....++        ....+.+|+|+||++|......    ..+....+++||+||||++.... ...+.
T Consensus       257 ~~~~~----~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~  323 (590)
T 3h1t_A          257 TPFGD----ARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWR  323 (590)
T ss_dssp             TTTCS----SEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CH
T ss_pred             Hhcch----hhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHH
Confidence            65543    22222221        2234589999999999877642    33556789999999999985432 34556


Q ss_pred             HHHHhCCCCccEEEEEeeCChh
Q psy4698         212 DVFKHLNNDVQVILLSATMPAD  233 (258)
Q Consensus       212 ~~~~~l~~~~~~i~~SAT~~~~  233 (258)
                      .++..++ ..+++++|||....
T Consensus       324 ~il~~~~-~~~~l~lTATP~~~  344 (590)
T 3h1t_A          324 EILEYFE-PAFQIGMTATPLRE  344 (590)
T ss_dssp             HHHHHST-TSEEEEEESSCSCT
T ss_pred             HHHHhCC-cceEEEeccccccc
Confidence            6777775 47799999997754

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.80  E-value=4.2e-19  Score=164.70  Aligned_cols=131  Identities=17%  Similarity=0.177  Sum_probs=112.7

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|+ .|+++|..+++.+++|+  +..+.||+|||+++.+|++.....   +.+++|++||+.||.|.+..+..+....++
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~---G~qv~VvTPTreLA~Qdae~m~~l~~~lGL  149 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT---GKGVHVVTVNDYLARRDAEWMGPVYRGLGL  149 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT---CSCCEEEESSHHHHHHHHHHHHHHHHTTTC
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh---CCCEEEEeCCHHHHHHHHHHHHHHHHhcCC
Confidence            688 99999999999999999  999999999999999999655543   247999999999999999999999999999


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCC---CccEEEEccchhhhc
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTK---QIRMFVLDEADEMLS  203 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~---~l~~lVvDE~h~~~~  203 (258)
                      .+.+..|+......  ....+++|+|+||+.| ++++..+.      +.++   ++.++|+||+|+++.
T Consensus       150 sv~~i~Gg~~~~~r--~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmLi  216 (997)
T 2ipc_A          150 SVGVIQHASTPAER--RKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILI  216 (997)
T ss_dssp             CEEECCTTCCHHHH--HHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHTT
T ss_pred             eEEEEeCCCCHHHH--HHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHHH
Confidence            99999988764333  3344689999999999 88887652      4567   899999999998863

>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=99.78  E-value=2.2e-19  Score=160.13  Aligned_cols=151  Identities=19%  Similarity=0.211  Sum_probs=101.4

Q ss_pred             HhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchH
Q psy4698          77 AIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVR  156 (258)
Q Consensus        77 ~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (258)
                      ....+..++++++++|||||||++|++|++..+...  ++++||++|+++|+.|+++.++      +..+....+...  
T Consensus        14 ~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~--~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~~~~~--   83 (459)
T 2z83_A           14 SPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ--RLRTAVLAPTRVVAAEMAEALR------GLPVRYQTSAVQ--   83 (459)
T ss_dssp             -CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT--TCCEEEEECSHHHHHHHHHHTT------TSCEEECC------
T ss_pred             HHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEECchHHHHHHHHHHhc------CceEeEEecccc--
Confidence            345567789999999999999999999999887653  4689999999999999998775      222221111100  


Q ss_pred             HHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh-----hccCcHHHHHHHHHhCCCCccEEEEEeeCC
Q psy4698         157 DDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM-----LSRGFKDQIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       157 ~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~-----~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                         .....+..+.++|.+.+...+... ..++++++||+||+|++     ...++...    +. .+++.|+++||||++
T Consensus        84 ---~~~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~----~~-~~~~~~~il~SAT~~  154 (459)
T 2z83_A           84 ---REHQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIAT----KV-ELGEAAAIFMTATPP  154 (459)
T ss_dssp             -------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHH----HH-HTTSCEEEEECSSCT
T ss_pred             ---cCCCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHH----Hh-ccCCccEEEEEcCCC
Confidence               011234567788988877666554 46889999999999973     22222111    11 236789999999999


Q ss_pred             hhHHHHHHHhcCCCeEE
Q psy4698         232 ADVLDVSMKFMRDPIKI  248 (258)
Q Consensus       232 ~~~~~~~~~~~~~~~~v  248 (258)
                      ..+..+...  ..|+.+
T Consensus       155 ~~~~~~~~~--~~pi~~  169 (459)
T 2z83_A          155 GTTDPFPDS--NAPIHD  169 (459)
T ss_dssp             TCCCSSCCC--SSCEEE
T ss_pred             cchhhhccC--CCCeEE
Confidence            876544322  455543

>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=99.77  E-value=1.4e-18  Score=167.06  Aligned_cols=153  Identities=14%  Similarity=0.066  Sum_probs=114.0

Q ss_pred             CCcHHHHHHhhhhhc--------------CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCVR--------------GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV  134 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~--------------g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~  134 (258)
                      .|+++|.+|++.++.              +++.++.++||||||+++ ++++..+.......++||++|+++|+.|+.+.
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~~  349 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDYQTMKE  349 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHHHHHHH
Confidence            599999999998765              367999999999999997 66666555433446899999999999999999


Q ss_pred             HHHhcCCCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCC--CCCCCccEEEEccchhhhccCcHHHHH
Q psy4698         135 VIALGDFMSVSCHACIGGTIVRDDIRKLE-AGAQVVVGTPGRVFDMISRGA--LSTKQIRMFVLDEADEMLSRGFKDQIY  211 (258)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~--~~~~~l~~lVvDE~h~~~~~~~~~~~~  211 (258)
                      ++.++...      ..++.........+. .+.+|+|+||++|..++....  ..++...+||+||||++...   ....
T Consensus       350 f~~f~~~~------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~---~~~~  420 (1038)
T 2w00_A          350 YQRFSPDS------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFG---EAQK  420 (1038)
T ss_dssp             HHTTSTTC------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHH---HHHH
T ss_pred             HHHhcccc------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcch---HHHH
Confidence            98876431      123333444444443 458999999999998876532  23456789999999997532   2344


Q ss_pred             HHHHhCCCCccEEEEEeeCCh
Q psy4698         212 DVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       212 ~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      .+...++ +.++++||||+..
T Consensus       421 ~I~~~~p-~a~~lgfTATP~~  440 (1038)
T 2w00_A          421 NLKKKFK-RYYQFGFTGTPIF  440 (1038)
T ss_dssp             HHHHHCS-SEEEEEEESSCCC
T ss_pred             HHHHhCC-cccEEEEeCCccc
Confidence            5566664 4789999999864

>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=99.76  E-value=6.1e-20  Score=162.92  Aligned_cols=136  Identities=21%  Similarity=0.266  Sum_probs=93.6

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI  159 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (258)
                      ++.+|+++++++|||||||++|++|+++.+...  +.+++|++||++|+.|+++.++.+.    +.  . ..+..     
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~~----v~--~-~~~~~-----   69 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGLD----VK--F-HTQAF-----   69 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTSC----EE--E-ESSCC-----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcCC----eE--E-ecccc-----
Confidence            467899999999999999999999999877654  3589999999999999999876432    21  1 11100     


Q ss_pred             HHHhcCCcEEEeChHHHHHHHhc--------CCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC-CCCccEEEEEeeC
Q psy4698         160 RKLEAGAQVVVGTPGRVFDMISR--------GALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL-NNDVQVILLSATM  230 (258)
Q Consensus       160 ~~~~~~~~Ilv~Tp~~l~~~l~~--------~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~~~~~~i~~SAT~  230 (258)
                              -.++||+.+.+++.+        ....++++++||+||+|++ +.++...+..+...+ +.++|+++||||+
T Consensus        70 --------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~  140 (440)
T 1yks_A           70 --------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATP  140 (440)
T ss_dssp             --------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSC
T ss_pred             --------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCC
Confidence                    025666554432221        2245789999999999987 333322222222222 3679999999999


Q ss_pred             ChhHHHHH
Q psy4698         231 PADVLDVS  238 (258)
Q Consensus       231 ~~~~~~~~  238 (258)
                      ++....+.
T Consensus       141 ~~~~~~~~  148 (440)
T 1yks_A          141 PGTSDEFP  148 (440)
T ss_dssp             TTCCCSSC
T ss_pred             Cchhhhhh
Confidence            88755443

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.76  E-value=3.1e-18  Score=151.56  Aligned_cols=138  Identities=14%  Similarity=0.165  Sum_probs=95.1

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|+++++++|||||||++|++++++.+...  +.+++|++|+++|+.|+++.++      +..+....+...     ...
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~--g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~-----~~~   67 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKK--RLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQ-----SER   67 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTT------TSCEEEC-------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhC--CCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCcc-----ccC
Confidence            378999999999999999999999766543  3589999999999999888664      233333332211     111


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHh-CCCCccEEEEEeeCChhHH
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH-LNNDVQVILLSATMPADVL  235 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~-l~~~~~~i~~SAT~~~~~~  235 (258)
                      ..+.-+.+.|.+.+...+.. ...++++++||+||+|++ +..+......+... .+.++|+++||||+++.+.
T Consensus        68 ~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~  139 (431)
T 2v6i_A           68 TGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTE  139 (431)
T ss_dssp             -CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCC
T ss_pred             CCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchh
Confidence            23356777888888766655 456889999999999986 33233333333322 2568999999999997644

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.76  E-value=2.8e-19  Score=165.63  Aligned_cols=154  Identities=21%  Similarity=0.234  Sum_probs=102.3

Q ss_pred             CCcHHHH-----HHhhhhh------cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          69 KPSAIQQ-----RAIIPCV------RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        69 ~~~~~Q~-----~~~~~l~------~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      .|+++|.     .+++.++      .|+++++++|||||||++|+++++..+...  +.+++|++|+++|+.|+++.++.
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~--~~~~lilaPTr~La~Q~~~~l~~  292 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK--RLRTAVLAPTRVVAAEMAEALRG  292 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTT
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC--CCcEEEEccHHHHHHHHHHHHhc
Confidence            8999999     9999888      899999999999999999999999887653  46899999999999999987764


Q ss_pred             hcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC
Q psy4698         138 LGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL  217 (258)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l  217 (258)
                      +.    +..   .... ..   .....+.-+-+.+.+.+...+... ..++++++||+||+|++ +..+...+..+...+
T Consensus       293 ~~----i~~---~~~~-l~---~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~-~~~~~~~~~~l~~~~  359 (673)
T 2wv9_A          293 LP----VRY---LTPA-VQ---REHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFT-DPASIAARGYIATRV  359 (673)
T ss_dssp             SC----CEE---CCC-------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCC-CHHHHHHHHHHHHHH
T ss_pred             CC----eee---eccc-cc---ccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCccc-CccHHHHHHHHHHhc
Confidence            42    211   0000 00   000111223344444444433332 56889999999999987 222222222333333


Q ss_pred             -CCCccEEEEEeeCChhHHHH
Q psy4698         218 -NNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       218 -~~~~~~i~~SAT~~~~~~~~  237 (258)
                       ++++|+++||||++..+..+
T Consensus       360 ~~~~~~vl~~SAT~~~~i~~~  380 (673)
T 2wv9_A          360 EAGEAAAIFMTATPPGTSDPF  380 (673)
T ss_dssp             HTTSCEEEEECSSCTTCCCSS
T ss_pred             cccCCcEEEEcCCCChhhhhh
Confidence             26789999999999875543

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.71  E-value=4.4e-17  Score=148.41  Aligned_cols=129  Identities=18%  Similarity=0.076  Sum_probs=99.9

Q ss_pred             CCcHHHHHHhhh----hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIP----CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~----l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .++++|.+++..    +..|+++++.+|||+|||++|++|++.      .+.+++|++||++|+.|+.+.++.+....++
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~------~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~   76 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE------VKPKVLFVVRTHNEFYPIYRDLTKIREKRNI   76 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH------HCSEEEEEESSGGGHHHHHHHHTTCCCSSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh------CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCc
Confidence            689999997764    557899999999999999999999987      2458999999999999999999888776677


Q ss_pred             eEEEEECCcch---------------------------------HHHH------------------HHHhcCCcEEEeCh
Q psy4698         145 SCHACIGGTIV---------------------------------RDDI------------------RKLEAGAQVVVGTP  173 (258)
Q Consensus       145 ~~~~~~~~~~~---------------------------------~~~~------------------~~~~~~~~Ilv~Tp  173 (258)
                      ++..+.|....                                 ....                  +.....++|+|+|+
T Consensus        77 ~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~adIVV~~~  156 (551)
T 3crv_A           77 TFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTY  156 (551)
T ss_dssp             CEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCSEEEEET
T ss_pred             cEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCCEEEeCc
Confidence            76665553210                                 0111                  22234589999999


Q ss_pred             HHHHHHHhcCCCCC-CCccEEEEccchhhhc
Q psy4698         174 GRVFDMISRGALST-KQIRMFVLDEADEMLS  203 (258)
Q Consensus       174 ~~l~~~l~~~~~~~-~~l~~lVvDE~h~~~~  203 (258)
                      ..|++...+..+.+ .+..++|+||||++.+
T Consensus       157 ~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          157 PYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            99988765543433 4677999999999876

>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=99.70  E-value=3.3e-17  Score=147.52  Aligned_cols=148  Identities=14%  Similarity=0.131  Sum_probs=106.3

Q ss_pred             CCcHHHHHHhhhh----hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPC----VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l----~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|+++|.++++.+    ..++++++..+||+|||++++..+. .+.......++||+|| .+|+.||.+.++++...  .
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~-~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~~--~  112 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFS-DAKKENELTPSLVICP-LSVLKNWEEELSKFAPH--L  112 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHH-HHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTT--S
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHH-HHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCCC--c
Confidence            6999999999876    4578899999999999999755444 4444444458999999 56889999999998753  4


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                      .+..+.++...     .....++|+|+|++.+.....   +....+++||+||||++-+..  ......+..++ ..+.+
T Consensus       113 ~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l~-~~~~l  181 (500)
T 1z63_A          113 RFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELK-SKYRI  181 (500)
T ss_dssp             CEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTSC-EEEEE
T ss_pred             eEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhhc-cCcEE
Confidence            44455554421     112347999999998864432   223467899999999985443  33445555664 35789


Q ss_pred             EEEeeCC
Q psy4698         225 LLSATMP  231 (258)
Q Consensus       225 ~~SAT~~  231 (258)
                      ++|||..
T Consensus       182 ~LTaTP~  188 (500)
T 1z63_A          182 ALTGTPI  188 (500)
T ss_dssp             EECSSCS
T ss_pred             EEecCCC
Confidence            9999973

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.65  E-value=3.5e-16  Score=144.69  Aligned_cols=146  Identities=16%  Similarity=0.131  Sum_probs=105.3

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI  159 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (258)
                      ..++|++++++||||||||+.    ++..+...   .+++|++|+++|+.|+++.++..    +..+....|+...... 
T Consensus       151 r~l~rk~vlv~apTGSGKT~~----al~~l~~~---~~gl~l~PtR~LA~Qi~~~l~~~----g~~v~lltG~~~~iv~-  218 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTYH----AIQKYFSA---KSGVYCGPLKLLAHEIFEKSNAA----GVPCDLVTGEERVTVQ-  218 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHHH----HHHHHHHS---SSEEEEESSHHHHHHHHHHHHHT----TCCEEEECSSCEECCS-
T ss_pred             HhcCCCEEEEEcCCCCCHHHH----HHHHHHhc---CCeEEEeCHHHHHHHHHHHHHhc----CCcEEEEECCeeEEec-
Confidence            345788999999999999983    33444333   24699999999999999999876    4566666766543100 


Q ss_pred             HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC-CCccEEEEEeeCChhHHHHH
Q psy4698         160 RKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN-NDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       160 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~~~~  238 (258)
                       ......+++++|++.+.        ....++++|+||+|++.+.+++..+..++..++ +..+++++|||.+ .++.+.
T Consensus       219 -TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~~-~i~~l~  288 (677)
T 3rc3_A          219 -PNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAID-LVMELM  288 (677)
T ss_dssp             -TTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGHH-HHHHHH
T ss_pred             -CCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchHH-HHHHHH
Confidence             00112678888886532        246789999999999998899999999888887 6789999999953 355555


Q ss_pred             HHhcCCCeEE
Q psy4698         239 MKFMRDPIKI  248 (258)
Q Consensus       239 ~~~~~~~~~v  248 (258)
                      ... .+++.|
T Consensus       289 ~~~-~~~~~v  297 (677)
T 3rc3_A          289 YTT-GEEVEV  297 (677)
T ss_dssp             HHH-TCCEEE
T ss_pred             Hhc-CCceEE
Confidence            443 344443

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.64  E-value=8.8e-16  Score=145.51  Aligned_cols=154  Identities=17%  Similarity=0.231  Sum_probs=112.7

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+++||.+++..+.    .+++.++..+||+|||++++..+...+........+||||| .+++.||.+.+.+++.  ++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~  312 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAP--DL  312 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHST--TC
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCC--Cc
Confidence            78999999998765    78899999999999999987776665555545557999999 7788999999999874  45


Q ss_pred             eEEEEECCcchHHHHHHH------------hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHH
Q psy4698         145 SCHACIGGTIVRDDIRKL------------EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD  212 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~------------~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~  212 (258)
                      .+..+.|....+......            ...++|+|+|++.+......  +....+++||+||||++-+  .......
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn--~~s~~~~  388 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKN--AESSLYE  388 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCC--SSSHHHH
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcC--chhHHHH
Confidence            666666666554433322            23478999999998754322  1123578999999999833  3345555


Q ss_pred             HHHhCCCCccEEEEEeeC
Q psy4698         213 VFKHLNNDVQVILLSATM  230 (258)
Q Consensus       213 ~~~~l~~~~~~i~~SAT~  230 (258)
                      .+..++. ...+++|||.
T Consensus       389 ~l~~l~~-~~rl~LTgTP  405 (800)
T 3mwy_W          389 SLNSFKV-ANRMLITGTP  405 (800)
T ss_dssp             HHTTSEE-EEEEEECSCC
T ss_pred             HHHHhhh-ccEEEeeCCc
Confidence            6666643 4578899996

>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=99.61  E-value=3.7e-16  Score=150.52  Aligned_cols=158  Identities=18%  Similarity=0.141  Sum_probs=104.4

Q ss_pred             CCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      .|+++|.+++..+...  .++++.++||+|||++++..+...+..+ ...+++|+||+ +|+.||...+.+..   +..+
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-~~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~v  227 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-AAERVLIIVPE-TLQHQWLVEMLRRF---NLRF  227 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-SCCCEEEECCT-TTHHHHHHHHHHHS---CCCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEeCH-HHHHHHHHHHHHHh---CCCE
Confidence            6899999999987764  4799999999999999977776655443 34589999999 99999999886654   3444


Q ss_pred             EEEECCcchHHHHH--HHhcCCcEEEeChHHHHHHHhc-CCCCCCCccEEEEccchhhhccCcH-HHHHHHHHhC-CCCc
Q psy4698         147 HACIGGTIVRDDIR--KLEAGAQVVVGTPGRVFDMISR-GALSTKQIRMFVLDEADEMLSRGFK-DQIYDVFKHL-NNDV  221 (258)
Q Consensus       147 ~~~~~~~~~~~~~~--~~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~l~~lVvDE~h~~~~~~~~-~~~~~~~~~l-~~~~  221 (258)
                      ..+.++........  ......+|+|+|++.+...... ..+...++++||+||+|++.+.+.. ......+..+ ....
T Consensus       228 ~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~~  307 (968)
T 3dmq_A          228 ALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVP  307 (968)
T ss_dssp             EECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTCS
T ss_pred             EEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcCC
Confidence            44433322211100  1112479999999877532111 1123457889999999998644322 1112233333 2445


Q ss_pred             cEEEEEeeCC
Q psy4698         222 QVILLSATMP  231 (258)
Q Consensus       222 ~~i~~SAT~~  231 (258)
                      +++++|||.-
T Consensus       308 ~~L~LTATPi  317 (968)
T 3dmq_A          308 GVLLLTATPE  317 (968)
T ss_dssp             SEEESCSSCS
T ss_pred             cEEEEEcCCc
Confidence            7999999973

>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=99.61  E-value=1e-14  Score=135.10  Aligned_cols=155  Identities=15%  Similarity=0.134  Sum_probs=106.8

Q ss_pred             CCcHHHHHHhhhhh---------cCCcEEEEcccCCCcchHhHHHHHHHhhhcc----ccceEEEEeccHHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCV---------RGNDVIAQAQSGTGKTATFSISILQQVDQNI----KECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~---------~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~----~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      .+++||.+++..+.         .++.+++..+||+|||++++..+...+....    ...++||+||+ +++.||.+.+
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            68999999998863         4567999999999999998777666554331    12369999996 8899999999


Q ss_pred             HHhcCCCCceEEEEECCcchHH--HHHHH-h-----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH
Q psy4698         136 IALGDFMSVSCHACIGGTIVRD--DIRKL-E-----AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK  207 (258)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~-----~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~  207 (258)
                      .++... .+.+..+.++.....  ..... .     ..++|+|+|++.+....  ..+....+++||+||+|++-+.  .
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~--~~l~~~~~~~vI~DEaH~ikn~--~  208 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA--EVLHKGKVGLVICDEGHRLKNS--D  208 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT--TTTTTSCCCEEEETTGGGCCTT--C
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH--HHhhcCCccEEEEECceecCCh--h
Confidence            988654 344455555443221  11111 1     13789999999887543  2234457789999999987433  2


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeC
Q psy4698         208 DQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       208 ~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ......+..++ ....+++|||.
T Consensus       209 ~~~~~al~~l~-~~~rl~LTgTP  230 (644)
T 1z3i_X          209 NQTYLALNSMN-AQRRVLISGTP  230 (644)
T ss_dssp             HHHHHHHHHHC-CSEEEEECSSC
T ss_pred             hHHHHHHHhcc-cCcEEEEecCc
Confidence            33444455554 35689999996

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.60  E-value=8.7e-16  Score=139.50  Aligned_cols=127  Identities=22%  Similarity=0.227  Sum_probs=85.1

Q ss_pred             CCCCCCcHHHHHHhh----hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          65 YGFEKPSAIQQRAII----PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~----~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .|+ .++++|.+++.    ++..|+++++.+|||+|||++|++|++..      +.+++|++||++|+.|+.+.++.+. 
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~------~~~~~~~~~t~~l~~q~~~~~~~l~-   75 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL------KKKVLIFTRTHSQLDSIYKNAKLLG-   75 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH------TCEEEEEESCHHHHHHHHHHHGGGT-
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC------CCcEEEEcCCHHHHHHHHHHHHhcC-
Confidence            466 89999999865    45688999999999999999999998753      3589999999999999998887642 


Q ss_pred             CCCceEEEEECCcc---------h-----------------------HHHH---------------HHHhcCCcEEEeCh
Q psy4698         141 FMSVSCHACIGGTI---------V-----------------------RDDI---------------RKLEAGAQVVVGTP  173 (258)
Q Consensus       141 ~~~~~~~~~~~~~~---------~-----------------------~~~~---------------~~~~~~~~Ilv~Tp  173 (258)
                         +.+..+.|...         .                       ...+               +.....++|+|+|+
T Consensus        76 ---~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~adiVV~n~  152 (540)
T 2vl7_A           76 ---LKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTY  152 (540)
T ss_dssp             ---CCEEEC---------------------------------------------------------CTTGGGCSEEEEET
T ss_pred             ---CcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCCEEEECh
Confidence               22222221110         0                       0000               01123479999999


Q ss_pred             HHHHHHHhcCCC-------CCCCccEEEEccchhhh
Q psy4698         174 GRVFDMISRGAL-------STKQIRMFVLDEADEML  202 (258)
Q Consensus       174 ~~l~~~l~~~~~-------~~~~l~~lVvDE~h~~~  202 (258)
                      ..+++-..++.+       .+.+..++|+||||++.
T Consensus       153 ~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          153 PYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             HHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             HHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            999874433221       24567899999999983

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.41  E-value=6.2e-13  Score=122.40  Aligned_cols=77  Identities=23%  Similarity=0.233  Sum_probs=62.9

Q ss_pred             CCcHHHHHHhh----hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAII----PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~----~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|++.|.+.+.    .+..|+++++.+|||+|||++|++|++..+...  +.+++|++||++++.|+.+.++.+....++
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--~~kvli~t~T~~l~~Qi~~el~~l~~~~~~   80 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--KLKVLYLVRTNSQEEQVIKELRSLSSTMKI   80 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--TCEEEEEESSHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--CCeEEEECCCHHHHHHHHHHHHHHhhccCe
Confidence            58999998885    456899999999999999999999999987653  358999999999999999998887654344


Q ss_pred             eEE
Q psy4698         145 SCH  147 (258)
Q Consensus       145 ~~~  147 (258)
                      ++.
T Consensus        81 ~~~   83 (620)
T 4a15_A           81 RAI   83 (620)
T ss_dssp             CEE
T ss_pred             EEE
Confidence            433

>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=99.22  E-value=1.4e-10  Score=106.45  Aligned_cols=131  Identities=18%  Similarity=0.189  Sum_probs=102.1

Q ss_pred             CCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .|. .|+++|....-.+.+|+  +..+.||+|||+++.+|++.....+   ..+.|++|+..||.+-+.++..+...+++
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G---~~vhVvT~ndyLA~rdae~m~~l~~~Lgl  145 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIG---KGVHLVTVNDYLARRDALWMGPVYLFLGL  145 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTS---SCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcC---CceEEEeccHHHHHhHHHHHHHHHHHhCC
Confidence            466 89999999999999998  9999999999999999998665553   36999999999999999999999999999


Q ss_pred             eEEEEECCc-------------------------------------------------chHHHHHHHhcCCcEEEeChHH
Q psy4698         145 SCHACIGGT-------------------------------------------------IVRDDIRKLEAGAQVVVGTPGR  175 (258)
Q Consensus       145 ~~~~~~~~~-------------------------------------------------~~~~~~~~~~~~~~Ilv~Tp~~  175 (258)
                      .+.+.....                                                 ......+.. -.|||.++|..-
T Consensus       146 svg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~a-Y~~DItYgTn~E  224 (822)
T 3jux_A          146 RVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEA-YLCDVTYGTNNE  224 (822)
T ss_dssp             CEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHH-HHSSEEEEEHHH
T ss_pred             EEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHH-hcCCCEEccCcc
Confidence            998877621                                                 001111111 227999999887


Q ss_pred             H-HHHHhcC------CCCCCCccEEEEccchhhh
Q psy4698         176 V-FDMISRG------ALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       176 l-~~~l~~~------~~~~~~l~~lVvDE~h~~~  202 (258)
                      + +++|+.+      ..-...+.+.||||+|.++
T Consensus       225 fgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          225 FGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             hhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            6 5566543      2234578899999999875

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=99.07  E-value=2.4e-10  Score=105.09  Aligned_cols=146  Identities=18%  Similarity=0.229  Sum_probs=89.1

Q ss_pred             cHHHHHHhhhhhcCCcEEEEcccCCCcc--hHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          71 SAIQQRAIIPCVRGNDVIAQAQSGTGKT--ATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~~li~~~tGsGKT--~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .+.|+.+++.++.++.+++.|++|+|||  ++++++.+..+.. ..+.++++++||...+.+..+.+...+...++....
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~-~~~~~vll~APTg~AA~~L~e~~~~~~~~l~l~~~~  229 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQ  229 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCSCC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh-cCCCeEEEEeCChhHHHHHHHHHHHHHhcCCCCHHH
Confidence            6899999999999999999999999999  4555666554422 234589999999999999887766543332221000


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      . ....  .....+   ..++-.+|+..  .+.........+++|||||++++ +   ...+..+++.++...|+|++.-
T Consensus       230 ~-~~~~--~~~~Ti---h~ll~~~~~~~--~~~~~~~~~l~~d~lIIDEAsml-~---~~~~~~Ll~~l~~~~~liLvGD  297 (608)
T 1w36_D          230 K-KRIP--EDASTL---HRLLGAQPGSQ--RLRHHAGNPLHLDVLVVDEASMI-D---LPMMSRLIDALPDHARVIFLGD  297 (608)
T ss_dssp             C-CSCS--CCCBTT---TSCC-------------CTTSCCSCSEEEECSGGGC-B---HHHHHHHHHTCCTTCEEEEEEC
T ss_pred             H-hccc--hhhhhh---HhhhccCCCch--HHHhccCCCCCCCEEEEechhhC-C---HHHHHHHHHhCCCCCEEEEEcc
Confidence            0 0000  000000   11121222221  11122222237889999999954 3   4567788889988899999865


Q ss_pred             e
Q psy4698         229 T  229 (258)
Q Consensus       229 T  229 (258)
                      .
T Consensus       298 ~  298 (608)
T 1w36_D          298 R  298 (608)
T ss_dssp             T
T ss_pred             h
Confidence            4

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.58  E-value=3.8e-07  Score=81.02  Aligned_cols=133  Identities=14%  Similarity=0.160  Sum_probs=79.5

Q ss_pred             CCCCCCcHHHHHHhhhhhcC----C-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          65 YGFEKPSAIQQRAIIPCVRG----N-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        65 ~~~~~~~~~Q~~~~~~l~~g----~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ..+..+++-|++++..+...    + .++|.|+.|+|||.+. ..++..+...+. .++++++||...+......+    
T Consensus        21 ~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-~~il~~a~T~~Aa~~l~~~~----   94 (459)
T 3upu_A           21 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-TGIILAAPTHAAKKILSKLS----   94 (459)
T ss_dssp             CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-CCEEEEESSHHHHHHHHHHH----
T ss_pred             CccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-ceEEEecCcHHHHHHHHhhh----
Confidence            56788999999999876432    3 8999999999999765 445555544332 36999999988777665543    


Q ss_pred             CCCCceEEEEECCcchHHHHHHHh----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHH
Q psy4698         140 DFMSVSCHACIGGTIVRDDIRKLE----AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFK  215 (258)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~  215 (258)
                         +.....++      ... ...    .....+..          .....+...++|||||++.+.    ...+..+++
T Consensus        95 ---~~~~~T~h------~~~-~~~~~~~~~~~~~~~----------~~~~~~~~~~~iiiDE~~~~~----~~~~~~l~~  150 (459)
T 3upu_A           95 ---GKEASTIH------SIL-KINPVTYEENVLFEQ----------KEVPDLAKCRVLICDEVSMYD----RKLFKILLS  150 (459)
T ss_dssp             ---SSCEEEHH------HHH-TEEEEECSSCEEEEE----------CSCCCCSSCSEEEESCGGGCC----HHHHHHHHH
T ss_pred             ---ccchhhHH------HHh-ccCcccccccchhcc----------cccccccCCCEEEEECchhCC----HHHHHHHHH
Confidence               11111100      000 000    00000000          112345578899999999652    334555666


Q ss_pred             hCCCCccEEEEE
Q psy4698         216 HLNNDVQVILLS  227 (258)
Q Consensus       216 ~l~~~~~~i~~S  227 (258)
                      .++...+++++.
T Consensus       151 ~~~~~~~~~~vG  162 (459)
T 3upu_A          151 TIPPWCTIIGIG  162 (459)
T ss_dssp             HSCTTCEEEEEE
T ss_pred             hccCCCEEEEEC
Confidence            666566666654

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.53  E-value=8e-07  Score=81.00  Aligned_cols=122  Identities=18%  Similarity=0.245  Sum_probs=81.4

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .+++.|.+++..+..++.++|.|+.|+|||.+. ..++..+...  +.++++++||...+....+..   +    ...  
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~~--g~~Vl~~ApT~~Aa~~L~e~~---~----~~a--  256 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAESL--GLEVGLCAPTGKAARRLGEVT---G----RTA--  256 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHHT--TCCEEEEESSHHHHHHHHHHH---T----SCE--
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHhc--CCeEEEecCcHHHHHHhHhhh---c----ccH--
Confidence            689999999999999999999999999999764 3444444433  357999999998887766533   1    110  


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHH----HhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDM----ISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~----l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                                            .|..+++..    +..........++|||||++++.    ...+..+++.++...++|
T Consensus       257 ----------------------~Tih~ll~~~~~~~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~~li  310 (574)
T 3e1s_A          257 ----------------------STVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGARVL  310 (574)
T ss_dssp             ----------------------EEHHHHTTEETTEESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTCEEE
T ss_pred             ----------------------HHHHHHHcCCcchhhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCCEEE
Confidence                                  111111100    11112233467899999999762    446667788887777888


Q ss_pred             EEEe
Q psy4698         225 LLSA  228 (258)
Q Consensus       225 ~~SA  228 (258)
                      ++.-
T Consensus       311 lvGD  314 (574)
T 3e1s_A          311 LVGD  314 (574)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            7643

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.53  E-value=2.3e-06  Score=78.93  Aligned_cols=69  Identities=20%  Similarity=0.234  Sum_probs=54.5

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      ..+++.|.+++..++.+..++|.||+|+|||.+..- ++..+... .+.++++++||...+.+....+...
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~-~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHH-HHHHHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHH-HHHHHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            467999999999988888899999999999987643 33333332 3458999999999999998877654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.52  E-value=2.6e-06  Score=80.54  Aligned_cols=70  Identities=20%  Similarity=0.279  Sum_probs=55.2

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ..+++.|.+|+..++.+..++|.||+|+|||.+..-.+. .+... .+.++++++||...+.+....+.+.+
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i~-~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~g  428 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVY-HLSKI-HKDRILVCAPSNVAVDHLAAKLRDLG  428 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHH-HHHHH-HCCCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHH-HHHhC-CCCeEEEEcCcHHHHHHHHHHHHhhC
Confidence            457899999999988877899999999999987644333 33321 23589999999999999998887653

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.46  E-value=3.9e-07  Score=84.34  Aligned_cols=68  Identities=25%  Similarity=0.250  Sum_probs=53.7

Q ss_pred             CCcHHHHHHhhhhhcCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          69 KPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .+++-|.+|+..++..+ -.+|.||+|+|||.+..-.+.+.+..   +.++|+++||..-++++...+...+
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~~~~  257 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLALCK  257 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHHhcC
Confidence            57899999999887655 58999999999998865544444433   3489999999999999988876543

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=98.42  E-value=5.5e-06  Score=78.27  Aligned_cols=69  Identities=20%  Similarity=0.244  Sum_probs=54.3

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      ..+++.|.+|+..++.+..++|.||+|+|||.+.. .++..+... .+.++++++||...+.+....+...
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            35789999999998888889999999999998754 333444332 3458999999999999988877654

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.74  E-value=0.00074  Score=58.26  Aligned_cols=71  Identities=14%  Similarity=0.058  Sum_probs=55.0

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .++++|...+..+...+-+++..+-+.|||.+....++..+.. ..+.+++++.|+...+...++.++.+..
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~-~~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-NKDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS-SSSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh-CCCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            6899999999877555668999999999998776655554333 2345799999999999888877776543

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.61  E-value=0.00033  Score=61.32  Aligned_cols=85  Identities=25%  Similarity=0.294  Sum_probs=54.5

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA  164 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (258)
                      +-.++.|+.|+|||....    +.+..    .+.+|++|+++++.++.+.+...+.                      ..
T Consensus       162 ~v~~I~G~aGsGKTt~I~----~~~~~----~~~lVlTpT~~aa~~l~~kl~~~~~----------------------~~  211 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL----SRVNF----EEDLILVPGRQAAEMIRRRANASGI----------------------IV  211 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH----HHCCT----TTCEEEESCHHHHHHHHHHHTTTSC----------------------CC
T ss_pred             cEEEEEcCCCCCHHHHHH----HHhcc----CCeEEEeCCHHHHHHHHHHhhhcCc----------------------cc
Confidence            347899999999998642    22221    3689999999999998886632210                      01


Q ss_pred             CCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       165 ~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      ....-|.|.++++  ++......-..+++||||+-.+
T Consensus       212 ~~~~~V~T~dsfL--~~~~~~~~~~~d~liiDE~sm~  246 (446)
T 3vkw_A          212 ATKDNVRTVDSFL--MNYGKGARCQFKRLFIDEGLML  246 (446)
T ss_dssp             CCTTTEEEHHHHH--HTTTSSCCCCCSEEEEETGGGS
T ss_pred             cccceEEEeHHhh--cCCCCCCCCcCCEEEEeCcccC
Confidence            1233467777644  2332222235789999999844

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.56  E-value=0.00022  Score=55.51  Aligned_cols=40  Identities=13%  Similarity=0.120  Sum_probs=27.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .|+-.++.|++|||||+..+-.+.. +..  .+.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r-~~~--~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRR-AKI--AKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH-HHH--TTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH-HHH--CCCEEEEEEecc
Confidence            4556899999999999886544433 332  345799998874

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=97.56  E-value=0.00039  Score=63.58  Aligned_cols=119  Identities=13%  Similarity=0.125  Sum_probs=76.2

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCC--ceE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMS--VSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~--~~~  146 (258)
                      .++++|...+..+...+..++.++-|+|||.+....++..+... .+.+++++.|+...+...+..++.+.....  +..
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~~p~~~~~  241 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELLPDFLQP  241 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTSCTTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhChHhhcc
Confidence            57999999998775567789999999999987765555444433 345899999999999998888877655432  110


Q ss_pred             -EEEECCcchHHHHHHHhcCCcEEEeC--hHHHHHHHhcCCCCCCCccEEEEccchhhh
Q psy4698         147 -HACIGGTIVRDDIRKLEAGAQVVVGT--PGRVFDMISRGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       147 -~~~~~~~~~~~~~~~~~~~~~Ilv~T--p~~l~~~l~~~~~~~~~l~~lVvDE~h~~~  202 (258)
                       .........     ...+|..|.+.+  |+.+.    .     .+.+++|+||+|.+-
T Consensus       242 ~~~~~~~~~i-----~~~nGs~i~~~s~~~~~lr----G-----~~~~~~iiDE~~~~~  286 (592)
T 3cpe_A          242 GIVEWNKGSI-----ELDNGSSIGAYASSPDAVR----G-----NSFAMIYIEDCAFIP  286 (592)
T ss_dssp             CEEEECSSEE-----EETTSCEEEEEECCHHHHH----H-----SCCSEEEEETGGGCT
T ss_pred             ccccCCccEE-----EecCCCEEEEEeCCCCCcc----C-----CCcceEEEehhccCC
Confidence             000111111     123455555443  43322    1     135689999999763

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.53  E-value=0.00023  Score=65.60  Aligned_cols=70  Identities=16%  Similarity=0.192  Sum_probs=56.2

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ..+++-|.+++..  .+..++|.|+.|||||.+..--+...+... ....+++++++|+..+.+..+.+....
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            4689999999973  356799999999999998776666666543 234589999999999999998887753

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.53  E-value=0.00023  Score=54.99  Aligned_cols=39  Identities=13%  Similarity=0.079  Sum_probs=26.8

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      |+-.++.|++|+|||+.++-.+......   +.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~~---g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKLG---KKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHT---TCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeecc
Confidence            5567899999999999865444333222   34788888874

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.51  E-value=0.00063  Score=51.99  Aligned_cols=19  Identities=26%  Similarity=0.368  Sum_probs=16.8

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+.+++.||+|+|||..+
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999865

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=97.43  E-value=0.00028  Score=56.32  Aligned_cols=91  Identities=14%  Similarity=0.151  Sum_probs=52.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|.-.++.|++|+|||+..+..+......   +.+++++.|...-.     ....+....++..                
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~---g~kVli~~~~~d~r-----~~~~i~srlG~~~----------------   66 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYA---DVKYLVFKPKIDTR-----SIRNIQSRTGTSL----------------   66 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEEECCCGG-----GCSSCCCCCCCSS----------------
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhc---CCEEEEEEeccCch-----HHHHHHHhcCCCc----------------
Confidence            35568899999999998875544443322   34788887754210     0001111111110                


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                         ..+-+.+.+.++..+.... .-...++|||||++.+
T Consensus        67 ---~~~~~~~~~~i~~~i~~~~-~~~~~dvViIDEaQ~l  101 (223)
T 2b8t_A           67 ---PSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFF  101 (223)
T ss_dssp             ---CCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGS
T ss_pred             ---cccccCCHHHHHHHHHHHh-hCCCCCEEEEecCccC
Confidence               1234556667777665432 2245789999999965

>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=97.33  E-value=0.00066  Score=62.91  Aligned_cols=69  Identities=33%  Similarity=0.384  Sum_probs=52.4

Q ss_pred             CCCCCcHHHHHHhhhhhc----CC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          66 GFEKPSAIQQRAIIPCVR----GN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~----g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      ++ .|+..|..++..+..    |. ..++.|.||||||+++.- ++...     +..+||++|+..++.|++..++.+..
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~-----~~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL-----GRPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH-----TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh-----CCCEEEEecCHHHHHHHHHHHHHHCC
Confidence            45 899999888876543    32 467889999999987632 22222     12599999999999999999999864


Q ss_pred             C
Q psy4698         141 F  141 (258)
Q Consensus       141 ~  141 (258)
                      .
T Consensus        79 ~   79 (664)
T 1c4o_A           79 E   79 (664)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.28  E-value=0.00057  Score=53.92  Aligned_cols=40  Identities=13%  Similarity=0.128  Sum_probs=27.6

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      |+-.++.|++|+|||+.++-.+......   +.+++++.|.+.
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~---g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFA---KQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHC---CCEEEEEEeccC
Confidence            4556789999999998875555444332   347999998764

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.28  E-value=0.0022  Score=53.75  Aligned_cols=36  Identities=17%  Similarity=0.224  Sum_probs=23.1

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      +..+++.||+|+|||..+- .+...+...  +..++++.
T Consensus        37 ~~~lll~G~~GtGKT~la~-~i~~~~~~~--~~~~~~i~   72 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ-AAGNEAKKR--GYRVIYSS   72 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH-HHHHHHHHT--TCCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHC--CCEEEEEE
Confidence            4679999999999998753 333333322  23466654

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=97.28  E-value=0.00056  Score=63.47  Aligned_cols=69  Identities=17%  Similarity=0.126  Sum_probs=55.7

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      .+++-|++++..  .+.+++|.|+.|||||.+..--+...+... ....++++++.|+..+.+..+.+....
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l   71 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTL   71 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHc
Confidence            478999999975  356799999999999998776666666552 244589999999999999998887764

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=97.27  E-value=0.004  Score=48.45  Aligned_cols=41  Identities=17%  Similarity=0.305  Sum_probs=26.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ..-.+||+||+|.+.. .....+..++...+....+|+.|..
T Consensus       101 ~~~~vliiDe~~~l~~-~~~~~l~~~l~~~~~~~~~i~~~~~  141 (226)
T 2chg_A          101 APFKIIFLDEADALTA-DAQAALRRTMEMYSKSCRFILSCNY  141 (226)
T ss_dssp             CSCEEEEEETGGGSCH-HHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             cCceEEEEeChhhcCH-HHHHHHHHHHHhcCCCCeEEEEeCC
Confidence            4556999999998743 2345566666666566666655443

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.25  E-value=0.00022  Score=53.16  Aligned_cols=19  Identities=21%  Similarity=0.422  Sum_probs=17.0

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+.+++.||+|+|||...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            6888999999999999864

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.22  E-value=0.001  Score=53.01  Aligned_cols=40  Identities=13%  Similarity=0.164  Sum_probs=28.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .|+-.++.|++|||||...+-.+.....   .+.+++++.|.+
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~---~g~kvli~kp~~   57 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI---AQYKCLVIKYAK   57 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT---TTCCEEEEEETT
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH---CCCeEEEEeecC
Confidence            4556789999999999887655544433   345799998865

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=97.22  E-value=0.00062  Score=67.42  Aligned_cols=68  Identities=21%  Similarity=0.312  Sum_probs=57.5

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc---ccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI---KECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~---~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .+++-|.+++..-  +++++|.|+.|||||.+.+--++..+....   ...+++++++|+..+....+++...
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            6899999999654  889999999999999998877887777643   3458999999999999998887663

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.21  E-value=0.00064  Score=57.14  Aligned_cols=26  Identities=4%  Similarity=0.004  Sum_probs=19.5

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      +.++++.||+|+|||.+. -.++..+.
T Consensus        45 ~~~lli~GpPGTGKT~~v-~~v~~~L~   70 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLV-NDVMDELI   70 (318)
T ss_dssp             CCEEEEECCCSHHHHHHH-HHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            357999999999999876 34444443

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.18  E-value=0.0012  Score=52.03  Aligned_cols=99  Identities=6%  Similarity=0.038  Sum_probs=51.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      .|.-.++.|++|+|||...+..+ .++...  +.+++++.|...-...    -..+.+..+....               
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~-~r~~~~--g~kvli~kp~~D~R~~----~~~I~Sr~G~~~~---------------   84 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRL-RRGIYA--KQKVVVFKPAIDDRYH----KEKVVSHNGNAIE---------------   84 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH-HHHHHT--TCCEEEEEEC---------------CBTTBCCE---------------
T ss_pred             CceEEEEECCCCCCHHHHHHHHH-HHHHHc--CCceEEEEeccCCcch----hhhHHHhcCCcee---------------
Confidence            45567999999999998765554 333332  3478999887542111    1112222222211               


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHH
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF  214 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~  214 (258)
                          -+.|..+..++..+      ..+.++|+||||+.+ +......+..+.
T Consensus        85 ----a~~v~~~~di~~~i------~~~~dvV~IDEaQFf-~~~~v~~l~~la  125 (219)
T 3e2i_A           85 ----AINISKASEIMTHD------LTNVDVIGIDEVQFF-DDEIVSIVEKLS  125 (219)
T ss_dssp             ----EEEESSGGGGGGSC------CTTCSEEEECCGGGS-CTHHHHHHHHHH
T ss_pred             ----eEEeCCHHHHHHHH------hcCCCEEEEechhcC-CHHHHHHHHHHH
Confidence                23344444333222      146789999999965 333444444444

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=97.12  E-value=0.0013  Score=61.67  Aligned_cols=69  Identities=20%  Similarity=0.269  Sum_probs=55.3

Q ss_pred             CCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          68 EKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        68 ~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      ..+++-|++++.+  .+.+++|.|+.|||||.+..--+...+... ....++++++.|+..+.+..+++..+
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~   79 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            4689999999976  356789999999999998776666666543 24458999999999999998887765

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=97.06  E-value=0.0043  Score=54.55  Aligned_cols=39  Identities=26%  Similarity=0.248  Sum_probs=24.6

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +.++++.||+|+|||..+- .+...+.....+.+++++..
T Consensus       130 ~~~lll~Gp~G~GKTtLa~-aia~~l~~~~~~~~v~~v~~  168 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYITS  168 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH-HHHHHHHHHCCSSCEEEEEH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEeeH
Confidence            3579999999999998653 33333433322345666543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.04  E-value=0.0025  Score=54.41  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=16.3

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+.++++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            3467999999999999875

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.96  E-value=0.0018  Score=54.74  Aligned_cols=34  Identities=18%  Similarity=0.140  Sum_probs=23.8

Q ss_pred             cHHHHHHhhhh----hcCC---cEEEEcccCCCcchHhHHH
Q psy4698          71 SAIQQRAIIPC----VRGN---DVIAQAQSGTGKTATFSIS  104 (258)
Q Consensus        71 ~~~Q~~~~~~l----~~g~---~~li~~~tGsGKT~~~l~~  104 (258)
                      .|+|.+++..+    ..|+   .+++.||.|+|||..+...
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~l   44 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYAL   44 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHH
Confidence            56666666544    3443   3899999999999876433

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.94  E-value=0.0038  Score=53.37  Aligned_cols=18  Identities=28%  Similarity=0.182  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+.+++.||+|+|||..+
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            356999999999999875

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=96.88  E-value=0.005  Score=51.28  Aligned_cols=39  Identities=21%  Similarity=0.403  Sum_probs=25.3

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+-.++|+||+|.+... ....+...+...+..+.+|+.+
T Consensus       109 ~~~~vliiDe~~~l~~~-~~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEeCCCcCCHH-HHHHHHHHHHhcCCCCeEEEEe
Confidence            45679999999987432 3445556666655666666544

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.88  E-value=0.0062  Score=44.74  Aligned_cols=38  Identities=11%  Similarity=0.172  Sum_probs=24.2

Q ss_pred             cEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         191 RMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       191 ~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      +.+++||+|.+.. .....+...+...+.+.++|+.|..
T Consensus        78 g~l~ldei~~l~~-~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           78 GTLVLSHPEHLTR-EQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             SCEEEECGGGSCH-HHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             cEEEEcChHHCCH-HHHHHHHHHHhhcCCCEEEEEECCc
Confidence            3799999998743 3445555666555556766665443

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.84  E-value=0.0033  Score=48.80  Aligned_cols=39  Identities=13%  Similarity=0.147  Sum_probs=27.5

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|+=.++.|++|||||.-.+..+-+....   +.+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~---~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIA---QYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHT---TCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEccc
Confidence            35568999999999997655554443333   2479999886

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=96.83  E-value=0.024  Score=46.05  Aligned_cols=18  Identities=28%  Similarity=0.335  Sum_probs=15.6

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|+|||..+.
T Consensus        65 ~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            469999999999998753

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.80  E-value=0.0055  Score=53.63  Aligned_cols=132  Identities=14%  Similarity=0.241  Sum_probs=72.5

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA--PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKL  162 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (258)
                      ..+++.|++|+|||+....-+. .+..  .+.+++++.  +.+.-+.++   +..++...++.+.......         
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~-~l~~--~G~kVllv~~D~~r~~a~eq---L~~~~~~~gv~~~~~~~~~---------  162 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAY-FYKK--RGYKVGLVAADVYRPAAYDQ---LLQLGNQIGVQVYGEPNNQ---------  162 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHH-HHHH--TTCCEEEEEECCSCHHHHHH---HHHHHHTTTCCEECCTTCS---------
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-HHHH--cCCeEEEEecCccchhHHHH---HHHHHHhcCCceeeccccC---------
Confidence            3588999999999987643332 2222  234676665  334333222   2223333333332211111         


Q ss_pred             hcCCcEEEeChHHHH-HHHhcCCCCCCCccEEEEccchhhh---ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHH
Q psy4698         163 EAGAQVVVGTPGRVF-DMISRGALSTKQIRMFVLDEADEML---SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~-~~l~~~~~~~~~l~~lVvDE~h~~~---~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~  238 (258)
                               .|..+. ..+..  ....+.+++|+|++-++.   +......+..+.+.+.++.-++.++|+...+..+.+
T Consensus       163 ---------dp~~i~~~al~~--a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~~~a  231 (433)
T 3kl4_A          163 ---------NPIEIAKKGVDI--FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLA  231 (433)
T ss_dssp             ---------CHHHHHHHHHHH--TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGHHHH
T ss_pred             ---------CHHHHHHHHHHH--HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHHHHH
Confidence                     122211 22222  122467899999998643   233556677777777777777888888766666666


Q ss_pred             HHhc
Q psy4698         239 MKFM  242 (258)
Q Consensus       239 ~~~~  242 (258)
                      +.|.
T Consensus       232 ~~f~  235 (433)
T 3kl4_A          232 SRFH  235 (433)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            6665

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.76  E-value=0.0024  Score=50.63  Aligned_cols=19  Identities=11%  Similarity=0.090  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+.++++.||+|+|||..+
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4578999999999999865

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.73  E-value=0.0085  Score=50.51  Aligned_cols=40  Identities=18%  Similarity=0.330  Sum_probs=26.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      ....+|++||+|.+... ....+...+...+...++|+.+.
T Consensus       132 ~~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          132 PPYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEeC
Confidence            34579999999987432 34556666666666666666543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.71  E-value=0.0018  Score=47.56  Aligned_cols=21  Identities=14%  Similarity=0.169  Sum_probs=17.6

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ...+.++++.|++|+|||..+
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHH
T ss_pred             hCCCCcEEEECCCCccHHHHH
Confidence            345678999999999999764

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.62  E-value=0.0071  Score=51.16  Aligned_cols=43  Identities=12%  Similarity=0.434  Sum_probs=30.3

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                      .+.+++|+||+|. ++......+...+...+.+..+|+.|....
T Consensus       133 ~~~~vlilDE~~~-L~~~~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          133 HRYKCVIINEANS-LTKDAQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             -CCEEEEEECTTS-SCHHHHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCCeEEEEeCccc-cCHHHHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            3567999999998 455556677777777766666666665544

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.62  E-value=0.0049  Score=56.69  Aligned_cols=114  Identities=19%  Similarity=0.251  Sum_probs=72.8

Q ss_pred             CCcHHHHHHhhhhhc--CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          69 KPSAIQQRAIIPCVR--GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~--g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      .++.-|.+++..+..  ....++.|+-|.|||.+.-+.+- .+.     .+++|.+|+..-+...++...+         
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a-~~~-----~~~~vtAP~~~a~~~l~~~~~~---------  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLIS-RIA-----GRAIVTAPAKASTDVLAQFAGE---------  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHH-HSS-----SCEEEECSSCCSCHHHHHHHGG---------
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHH-HHH-----hCcEEECCCHHHHHHHHHHhhC---------
Confidence            578899999988765  23489999999999965433333 332     1468999998766654443210         


Q ss_pred             EEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEE
Q psy4698         147 HACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL  226 (258)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~  226 (258)
                                          .|=+..|+.+.   .    ...+.+++|||||=.+    -...+..++.    ....++|
T Consensus       240 --------------------~i~~~~Pd~~~---~----~~~~~dlliVDEAAaI----p~pll~~ll~----~~~~v~~  284 (671)
T 2zpa_A          240 --------------------KFRFIAPDALL---A----SDEQADWLVVDEAAAI----PAPLLHQLVS----RFPRTLL  284 (671)
T ss_dssp             --------------------GCCBCCHHHHH---H----SCCCCSEEEEETGGGS----CHHHHHHHHT----TSSEEEE
T ss_pred             --------------------CeEEeCchhhh---h----CcccCCEEEEEchhcC----CHHHHHHHHh----hCCeEEE
Confidence                                13344675533   1    2345889999999876    2344444444    3346778


Q ss_pred             EeeCCh
Q psy4698         227 SATMPA  232 (258)
Q Consensus       227 SAT~~~  232 (258)
                      |-|+..
T Consensus       285 ~tTv~G  290 (671)
T 2zpa_A          285 TTTVQG  290 (671)
T ss_dssp             EEEBSS
T ss_pred             EecCCc
Confidence            888754

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.61  E-value=0.0072  Score=50.50  Aligned_cols=19  Identities=16%  Similarity=0.265  Sum_probs=16.6

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ++++++.||+|+|||..+.
T Consensus       152 ~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5789999999999998653

>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=96.54  E-value=0.011  Score=54.80  Aligned_cols=67  Identities=28%  Similarity=0.329  Sum_probs=50.6

Q ss_pred             CCcHHHHHHhhhhh----cCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          69 KPSAIQQRAIIPCV----RGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      .|+..|..++..+.    .|. ...+.|.||||||+++.- ++...     +..+||++|+..++.|++..++.+...
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~-----~~~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV-----NKPTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH-----CCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh-----CCCEEEEECCHHHHHHHHHHHHHHcCC
Confidence            78899988887654    343 467889999999987532 22222     125999999999999999999998643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=96.54  E-value=0.0019  Score=53.64  Aligned_cols=18  Identities=28%  Similarity=0.281  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +.++++.||+|+|||..+
T Consensus        67 ~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            347999999999999876

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.53  E-value=0.0025  Score=53.40  Aligned_cols=41  Identities=12%  Similarity=0.247  Sum_probs=27.3

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      +.+++++||+|.+........+...+...+.++++|+.+..
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~  145 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANN  145 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESS
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            67799999999875233455566666665566766664443

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=96.52  E-value=0.0039  Score=53.29  Aligned_cols=35  Identities=17%  Similarity=0.293  Sum_probs=21.8

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      .+++.||+|+|||...- .+...+.... +..++++.
T Consensus        46 ~~li~G~~G~GKTtl~~-~l~~~~~~~~-~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR-KLWELYKDKT-TARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHH-HHHHHHTTSC-CCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHhhhc-CeeEEEEe
Confidence            79999999999998753 3333333221 23455554

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.49  E-value=0.018  Score=48.86  Aligned_cols=38  Identities=21%  Similarity=0.392  Sum_probs=23.2

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccc-cceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIK-ECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~-~~~~lil~  122 (258)
                      +..+++.|++|+|||...- .+...+..... +..++++.
T Consensus        45 ~~~vli~G~~G~GKTtl~~-~l~~~~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVK-FVLSKLHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHH-HHHHHHHHHTCSSCEEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHHhcCCceEEEEE
Confidence            4679999999999998753 23333333211 33455554

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.49  E-value=0.013  Score=47.87  Aligned_cols=53  Identities=17%  Similarity=0.144  Sum_probs=29.7

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh--hhcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP--CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~--l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|+++.-.+..++.+...-. .+ -...+.+..  +..++++++.||+|+|||..+
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~-~~-~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVE-LP-LKHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTH-HH-HHCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHH-HH-hhCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            356666655666665543210 00 001111111  234577999999999999865

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=96.45  E-value=0.053  Score=42.40  Aligned_cols=39  Identities=13%  Similarity=0.351  Sum_probs=23.0

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      .-.+||+||+|.+. ......+...+...+....+|+.|.
T Consensus       126 ~~~vlviDe~~~l~-~~~~~~l~~~l~~~~~~~~~i~~t~  164 (250)
T 1njg_A          126 RFKVYLIDEVHMLS-RHSFNALLKTLEEPPEHVKFLLATT  164 (250)
T ss_dssp             SSEEEEEETGGGSC-HHHHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CceEEEEECccccc-HHHHHHHHHHHhcCCCceEEEEEeC
Confidence            34689999999863 2234445555554444555555443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.40  E-value=0.026  Score=43.60  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=15.4

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +++++.||+|+|||..+
T Consensus        55 ~~~~l~G~~GtGKT~la   71 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL   71 (202)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            67999999999999865

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.37  E-value=0.014  Score=48.46  Aligned_cols=39  Identities=18%  Similarity=0.330  Sum_probs=25.0

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      .-.+||+||+|.+... ....+...+...+..+.+|+.|.
T Consensus       107 ~~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~~  145 (323)
T 1sxj_B          107 KHKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFACN  145 (323)
T ss_dssp             CCEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECcccCCHH-HHHHHHHHHhccCCCceEEEEeC
Confidence            3679999999987432 23445556666556666666553

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.19  E-value=0.17  Score=37.84  Aligned_cols=18  Identities=33%  Similarity=0.492  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ..++++.|++|+|||..+
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            357999999999999875

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.18  E-value=0.048  Score=45.90  Aligned_cols=39  Identities=23%  Similarity=0.476  Sum_probs=26.3

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+.+++|+||+|.+.. .....+...+...+..+.+++.+
T Consensus       109 ~~~~viiiDe~~~l~~-~~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTN-AAQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCH-HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCH-HHHHHHHHHHhcCCCCeEEEEEe
Confidence            4578999999998743 24455666677666666666544

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.11  E-value=0.039  Score=43.79  Aligned_cols=52  Identities=17%  Similarity=0.162  Sum_probs=32.4

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      ..|..+++.|++|+|||...+..+...+..   +.+++|+.-... ..+....+..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~---~~~v~~~~~e~~-~~~~~~~~~~   72 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIFSQQFLWNGLKM---GEPGIYVALEEH-PVQVRQNMAQ   72 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHHHHT---TCCEEEEESSSC-HHHHHHHHHT
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEccCC-HHHHHHHHHH
Confidence            456779999999999998765444444332   236787774332 3444444443

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=95.99  E-value=0.012  Score=48.88  Aligned_cols=54  Identities=17%  Similarity=0.177  Sum_probs=29.6

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhh-hhhcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAII-PCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~-~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|+++.-...+++.+...-. .+..+...... .+..++.+++.||+|+|||..+
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~-~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQ-YPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHH-HHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHH-HHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            457777655566655543200 00000001111 1235678999999999999875

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.98  E-value=0.029  Score=42.21  Aligned_cols=19  Identities=37%  Similarity=0.477  Sum_probs=16.0

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ..++++.||+|+|||..+.
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            4579999999999998753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.97  E-value=0.019  Score=50.42  Aligned_cols=140  Identities=19%  Similarity=0.150  Sum_probs=67.9

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH-
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK-  161 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  161 (258)
                      .|.-++|.|++|+|||...+..+.......  +.+++|++..- -..++..++.......+..-  +..+.-...++.. 
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~~--g~~vl~~slE~-~~~~l~~R~~~~~~~i~~~~--l~~g~l~~~~~~~~  273 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALKE--GVGVGIYSLEM-PAAQLTLRMMCSEARIDMNR--VRLGQLTDRDFSRL  273 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHTT--CCCEEEEESSS-CHHHHHHHHHHHHTTCCTTT--CCGGGCCHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCeEEEEECCC-CHHHHHHHHHHHHcCCCHHH--HhCCCCCHHHHHHH
Confidence            445699999999999987665555444322  33688876432 22344433322111111100  0011111122211 


Q ss_pred             ------HhcCCcEEEe-----ChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-------CcHHHHHHHHHhCC-----
Q psy4698         162 ------LEAGAQVVVG-----TPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-------GFKDQIYDVFKHLN-----  218 (258)
Q Consensus       162 ------~~~~~~Ilv~-----Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-------~~~~~~~~~~~~l~-----  218 (258)
                            +.. ..+.+.     |++.+...+.+-. .-.++++||||..+.+...       +....+..+++.+.     
T Consensus       274 ~~a~~~l~~-~~l~i~d~~~~s~~~l~~~~~~l~-~~~~~~lIvID~l~~~~~~~~~~~~~~r~~~i~~i~~~Lk~lAke  351 (444)
T 2q6t_A          274 VDVASRLSE-APIYIDDTPDLTLMEVRARARRLV-SQNQVGLIIIDYLQLMSGPGSGKSGENRQQEIAAISRGLKALARE  351 (444)
T ss_dssp             HHHHHHHHT-SCEEEECCTTCBHHHHHHHHHHHH-HHSCCCEEEEECGGGCBCC-------CHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHH-HHcCCCEEEEcChhhcCCCcCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence                  222 356653     3444444333200 0125789999999987643       12233444444332     


Q ss_pred             CCccEEEEEee
Q psy4698         219 NDVQVILLSAT  229 (258)
Q Consensus       219 ~~~~~i~~SAT  229 (258)
                      .++.+|++|..
T Consensus       352 ~~v~vi~lsql  362 (444)
T 2q6t_A          352 LGIPIIALSQL  362 (444)
T ss_dssp             HTSCEEEEEEC
T ss_pred             hCCeEEEEecC
Confidence            25667777653

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=95.95  E-value=0.017  Score=47.86  Aligned_cols=16  Identities=44%  Similarity=0.576  Sum_probs=14.5

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      ++++.||+|+|||..+
T Consensus        40 ~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           40 HLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CEEEESSSSSSHHHHH
T ss_pred             eEEEECcCCcCHHHHH
Confidence            5999999999999865

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.93  E-value=0.049  Score=47.92  Aligned_cols=42  Identities=19%  Similarity=0.139  Sum_probs=28.3

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      +..|.-++|.|++|+|||...+..+.......  +.+++|+...
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~--g~~Vl~~s~E  241 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATKT--NENVAIFSLE  241 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHHS--SCCEEEEESS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHhC--CCcEEEEECC
Confidence            34456799999999999987655554444332  2368887743

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.85  E-value=0.044  Score=42.93  Aligned_cols=40  Identities=18%  Similarity=0.139  Sum_probs=25.3

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +..|..+++.|++|+|||......+......   +.+++++..
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~---~~~v~~~~~   59 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSLHFIAKGLRD---GDPCIYVTT   59 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHHHHHHH---TCCEEEEES
T ss_pred             CcCCCEEEEEcCCCCCHHHHHHHHHHHHHHC---CCeEEEEEc
Confidence            3456779999999999997654333222222   235777663

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.75  E-value=0.17  Score=44.37  Aligned_cols=56  Identities=16%  Similarity=0.144  Sum_probs=31.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe--ccHHHHHHHHHHHHHhcCCCCceE
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA--PTRELAQQIQKVVIALGDFMSVSC  146 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~--P~~~l~~q~~~~~~~~~~~~~~~~  146 (258)
                      ..+++.|++|+|||++..--+ ..+..  .+.+++++.  +.+.-+.+   .++.++...++.+
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA-~~l~~--~G~kVllv~~D~~R~aa~e---qL~~~~~~~gvpv  158 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLA-RYFQK--RGYKVGVVCSDTWRPGAYH---QLRQLLDRYHIEV  158 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH-HHHHT--TTCCEEEEECCCSSTHHHH---HHHHHHGGGTCEE
T ss_pred             eEEEEECcCCCCHHHHHHHHH-HHHHH--CCCeEEEEeCCCcchhHHH---HHHHHHHhcCCcE
Confidence            358999999999998764333 22333  234676666  44443333   2333344444444

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=95.65  E-value=0.037  Score=42.87  Aligned_cols=139  Identities=17%  Similarity=0.156  Sum_probs=71.6

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH-HHHHHHHHHHHhcCCCCceEEEEECCcchHH-HHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE-LAQQIQKVVIALGDFMSVSCHACIGGTIVRD-DIRKL  162 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~-l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~  162 (258)
                      ..+++.+++|.|||.+++--++..+..+   .+++|+.=.+. ....-...++++    ++.+..+-.+-.... .....
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G---~rV~~vQF~Kg~~~~gE~~~l~~L----~v~~~~~g~gf~~~~~~~~~~  101 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHG---KNVGVVQFIKGTWPNGERNLLEPH----GVEFQVMATGFTWETQNREAD  101 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTT---CCEEEEESSCCSSCCHHHHHHGGG----TCEEEECCTTCCCCGGGHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCC---CeEEEEEeeCCCCCccHHHHHHhC----CcEEEEcccccccCCCCcHHH
Confidence            4689999999999999877776666543   47888843221 000001122222    122222111111000 00000


Q ss_pred             hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC--cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHH
Q psy4698         163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG--FKDQIYDVFKHLNNDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       163 ~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~--~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~  238 (258)
                      ..       .....+..... .+.-..+++||+||+-..+..+  -...+..++...+...-+|+.+--.|.++.+.+
T Consensus       102 ~~-------~a~~~l~~a~~-~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~A  171 (196)
T 1g5t_A          102 TA-------ACMAVWQHGKR-MLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  171 (196)
T ss_dssp             HH-------HHHHHHHHHHH-HTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             HH-------HHHHHHHHHHH-HHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhC
Confidence            00       00111222221 1223568999999997654443  346677778776666666666666677766654

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.65  E-value=0.0047  Score=52.29  Aligned_cols=40  Identities=20%  Similarity=0.292  Sum_probs=28.2

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +..|.-+++.|++|+|||..++-.+.....   .+..++|++.
T Consensus        43 l~~G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSl   82 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSL   82 (338)
T ss_dssp             BCTTCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEES
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeC
Confidence            345567999999999999877655554444   2346888774

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.64  E-value=0.09  Score=45.43  Aligned_cols=53  Identities=19%  Similarity=0.211  Sum_probs=32.2

Q ss_pred             ccCcCCCCCCHHHHHHHHHCC---CCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          46 AENFDDMELSEELLRGIYAYG---FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~---~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+|++.+=-...++.+++.=   +..|--++..-   +...+.+++.||+|+|||+.+
T Consensus       144 ~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          144 DSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHHH
Confidence            357888875566666665421   11222222222   223467999999999999865

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=95.57  E-value=0.059  Score=44.82  Aligned_cols=50  Identities=6%  Similarity=0.080  Sum_probs=29.2

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      .+.+++|+||+|.|... ..+.+.+.+..-++.+.+|+. ++-+..+...++
T Consensus        81 ~~~kvviIdead~lt~~-a~naLLk~LEep~~~t~fIl~-t~~~~kl~~tI~  130 (305)
T 2gno_A           81 YTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLN-TRRWHYLLPTIK  130 (305)
T ss_dssp             SSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEE-ESCGGGSCHHHH
T ss_pred             CCceEEEeccHHHhCHH-HHHHHHHHHhCCCCCeEEEEE-ECChHhChHHHH
Confidence            46789999999987433 334455566654455545544 444444443333

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.41  E-value=0.053  Score=47.40  Aligned_cols=54  Identities=15%  Similarity=0.228  Sum_probs=34.7

Q ss_pred             cccCcCCCCCCHHHHHHHHHC---CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          45 VAENFDDMELSEELLRGIYAY---GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~---~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..+|++.+-....++.+.+.   -+.+|.-++..-+   ...+.+++.||+|+|||+.+
T Consensus       176 p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          176 PTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            345788888777777776542   1223333333222   23467999999999999865

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.39  E-value=0.032  Score=49.97  Aligned_cols=41  Identities=17%  Similarity=0.238  Sum_probs=26.3

Q ss_pred             CccEEEEccchhhhccC--cHHHHHHHHHhCCCCccEEEEEeeCC
Q psy4698         189 QIRMFVLDEADEMLSRG--FKDQIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~--~~~~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                      .-.+|++||+|.+....  ....+..++..  ...++|+.+++..
T Consensus       148 ~~~vliIDEid~l~~~~~~~l~~L~~~l~~--~~~~iIli~~~~~  190 (516)
T 1sxj_A          148 KHFVIIMDEVDGMSGGDRGGVGQLAQFCRK--TSTPLILICNERN  190 (516)
T ss_dssp             TSEEEEECSGGGCCTTSTTHHHHHHHHHHH--CSSCEEEEESCTT
T ss_pred             CCeEEEEECCCccchhhHHHHHHHHHHHHh--cCCCEEEEEcCCC
Confidence            45689999999886432  23455555554  3456788777653

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=95.36  E-value=0.066  Score=45.30  Aligned_cols=39  Identities=10%  Similarity=0.312  Sum_probs=23.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      .+-.++|+||+|.+... ....+...+...+..+.+|+.+
T Consensus       118 ~~~~vliiDe~~~l~~~-~~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             SSSEEEEEECGGGSCHH-HHHHHHHHHHSCCSSEEEEEEE
T ss_pred             CCeEEEEEECcchhcHH-HHHHHHHHHhcCCCceEEEEEe
Confidence            34579999999987432 3445555565554555455544

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=95.30  E-value=0.019  Score=49.41  Aligned_cols=18  Identities=28%  Similarity=0.333  Sum_probs=14.9

Q ss_pred             CcEEE--EcccCCCcchHhH
Q psy4698          85 NDVIA--QAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li--~~~tGsGKT~~~l  102 (258)
                      ..++|  .|+.|+|||....
T Consensus        51 ~~~li~i~G~~G~GKT~L~~   70 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLAK   70 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHHH
Confidence            46888  8999999998753

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=95.30  E-value=0.092  Score=43.83  Aligned_cols=49  Identities=12%  Similarity=0.062  Sum_probs=29.6

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhh-----hcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPC-----VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l-----~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|.++.-...+++.+...-.   .+   ...+.+     ...+++++.||+|+|||..+
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~---~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVI---LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTH---HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCHHHhcChHHHHHHHHHHHH---HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            457777666667766654210   01   011111     12357999999999999875

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=95.30  E-value=0.083  Score=42.29  Aligned_cols=19  Identities=21%  Similarity=0.207  Sum_probs=16.1

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+.+++.||+|+|||..+
T Consensus        38 ~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           38 VPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCCEEEEESCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3467999999999999865

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.26  E-value=0.065  Score=44.86  Aligned_cols=17  Identities=24%  Similarity=0.440  Sum_probs=15.3

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .++++.||+|+|||..+
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            57999999999999875

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=95.25  E-value=0.023  Score=46.84  Aligned_cols=41  Identities=17%  Similarity=0.120  Sum_probs=26.4

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +..|.-+++.|++|+|||......+......  .+.+++++..
T Consensus        32 l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~--~G~~v~~~~~   72 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAML   72 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHHHHHHHHHHHHT--SCCCEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHH--cCCeEEEEeC
Confidence            5567789999999999998764433332222  1225767653

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=95.19  E-value=0.079  Score=45.50  Aligned_cols=18  Identities=22%  Similarity=0.326  Sum_probs=16.0

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+++++.||+|+|||..+
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999875

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.13  E-value=0.15  Score=44.43  Aligned_cols=53  Identities=17%  Similarity=0.119  Sum_probs=31.3

Q ss_pred             ccCcCCCCCCHHHHHHHHHC---CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          46 AENFDDMELSEELLRGIYAY---GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~---~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+|.+.+=-..+++.+.+.   .+..|--++..-   +...+.+++.||+|+|||+.+
T Consensus       168 ~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          168 DVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            35788887555666555432   111222222211   223467999999999999875

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.12  E-value=0.064  Score=44.77  Aligned_cols=51  Identities=20%  Similarity=0.044  Sum_probs=32.5

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      +..|.-++|.|++|+|||...+..+.....++   .+++|++-. .-..++..++
T Consensus        65 l~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g---~~vl~~slE-~s~~~l~~R~  115 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTAFALKQAKNMSDND---DVVNLHSLE-MGKKENIKRL  115 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHHHHHHHHHHHHTTT---CEEEEEESS-SCHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcC---CeEEEEECC-CCHHHHHHHH
Confidence            34556799999999999987665555544332   468888743 2334444444

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=94.97  E-value=0.12  Score=40.80  Aligned_cols=43  Identities=16%  Similarity=-0.014  Sum_probs=27.2

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEec
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAP  123 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P  123 (258)
                      +..|.-+++.||+|+|||......+...+...   +.+..++++.-
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            34567799999999999987655444322211   11335777764

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=94.62  E-value=0.094  Score=46.64  Aligned_cols=42  Identities=21%  Similarity=0.402  Sum_probs=27.2

Q ss_pred             cEEEEccchhhhccC----------cHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         191 RMFVLDEADEMLSRG----------FKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       191 ~~lVvDE~h~~~~~~----------~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      .+|++||+|.+....          ....+...+..+.....++++.||-..
T Consensus       299 ~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~  350 (489)
T 3hu3_A          299 AIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRP  350 (489)
T ss_dssp             EEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCG
T ss_pred             cEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCc
Confidence            589999999886421          224455556655556667777777543

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.59  E-value=0.034  Score=48.92  Aligned_cols=53  Identities=13%  Similarity=0.173  Sum_probs=32.9

Q ss_pred             ccCcCCCCCCHHHHHHHHHCC---CCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          46 AENFDDMELSEELLRGIYAYG---FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~---~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+|.+.+=-..+++.|++.=   +..|-.++..-   +...+.+++.||+|+|||+.+
T Consensus       205 ~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          205 DVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHHH
Confidence            357888876677777776531   11221122111   234478999999999999865

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=94.57  E-value=0.085  Score=43.74  Aligned_cols=18  Identities=22%  Similarity=0.243  Sum_probs=15.7

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ..++++.||+|+|||..+
T Consensus        38 ~~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCCEEECCTTCCCHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            367999999999999865

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.49  E-value=0.053  Score=47.68  Aligned_cols=17  Identities=35%  Similarity=0.442  Sum_probs=15.1

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .++++.||+|+|||..+
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            46999999999999875

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=94.13  E-value=0.059  Score=47.33  Aligned_cols=39  Identities=23%  Similarity=0.112  Sum_probs=28.4

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      ..|.-++|.|++|+|||...+-.+.+....   +.+++|++-
T Consensus       195 ~~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSl  233 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSL  233 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECS
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEEC
Confidence            345669999999999998876666655544   346888874

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=93.87  E-value=0.5  Score=38.34  Aligned_cols=27  Identities=19%  Similarity=0.074  Sum_probs=21.1

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHH
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISIL  106 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l  106 (258)
                      -+..|.-++|.|++|+|||+.....+.
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHH
Confidence            356778899999999999987654443

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=93.81  E-value=0.83  Score=33.70  Aligned_cols=75  Identities=17%  Similarity=0.301  Sum_probs=52.6

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++..+......+...    +..+..++++....+..   ..... ..+|+|+|.     .+ ..++++++
T Consensus        34 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gld~~~  103 (163)
T 2hjv_A           34 NPDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----VA-ARGIDIEN  103 (163)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GG-TTTCCCSC
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hh-hcCCchhc
Confidence            3458999999999999999988775    46677788876544322   22333 478999993     22 23567888


Q ss_pred             ccEEEEccc
Q psy4698         190 IRMFVLDEA  198 (258)
Q Consensus       190 l~~lVvDE~  198 (258)
                      ++++|.-+.
T Consensus       104 ~~~Vi~~~~  112 (163)
T 2hjv_A          104 ISLVINYDL  112 (163)
T ss_dssp             CSEEEESSC
T ss_pred             CCEEEEeCC
Confidence            988887554

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=93.55  E-value=0.12  Score=45.69  Aligned_cols=17  Identities=29%  Similarity=0.421  Sum_probs=15.1

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.||+|+|||+.+
T Consensus        50 ~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            56999999999999875

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=92.96  E-value=1.4  Score=32.51  Aligned_cols=75  Identities=11%  Similarity=0.221  Sum_probs=51.9

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.++++..+......++..    +..+..++++....+..   .... ...+|+|+|.     .+ ..++++++
T Consensus        29 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~G~d~~~   98 (165)
T 1fuk_A           29 SVTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LL-ARGIDVQQ   98 (165)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GG-TTTCCCCS
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----hh-hcCCCccc
Confidence            3458999999999999999888765    45677777776544322   2223 3478999994     22 23467888


Q ss_pred             ccEEEEccc
Q psy4698         190 IRMFVLDEA  198 (258)
Q Consensus       190 l~~lVvDE~  198 (258)
                      ++++|.-+.
T Consensus        99 ~~~Vi~~~~  107 (165)
T 1fuk_A           99 VSLVINYDL  107 (165)
T ss_dssp             CSEEEESSC
T ss_pred             CCEEEEeCC
Confidence            888877543

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=92.85  E-value=0.45  Score=41.07  Aligned_cols=40  Identities=13%  Similarity=-0.068  Sum_probs=26.1

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEecc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPT  124 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~  124 (258)
                      .-+.|.|+.|+|||......++..+...   +.+.+++|+.-.
T Consensus       179 ei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E  221 (400)
T 3lda_A          179 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE  221 (400)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             cEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCC
Confidence            5689999999999987654444433321   133468887643

>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=92.75  E-value=1.1  Score=34.68  Aligned_cols=72  Identities=17%  Similarity=0.232  Sum_probs=50.8

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++.-+......+...    ++.+..++|+....+..   ....+ ..+|+|+|.     .+ ..++++++
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~-~~Gidi~~   99 (212)
T 3eaq_A           30 SPDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----VA-ARGLDIPQ   99 (212)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----TT-TCSSSCCC
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----hh-hcCCCCcc
Confidence            3458999999999999999888776    46677788876554332   23333 378999993     22 34567788


Q ss_pred             ccEEEE
Q psy4698         190 IRMFVL  195 (258)
Q Consensus       190 l~~lVv  195 (258)
                      ++++|.
T Consensus       100 v~~Vi~  105 (212)
T 3eaq_A          100 VDLVVH  105 (212)
T ss_dssp             BSEEEE
T ss_pred             CcEEEE
Confidence            888774

>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=92.73  E-value=0.99  Score=33.68  Aligned_cols=74  Identities=19%  Similarity=0.207  Sum_probs=51.7

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++..+......+...    +..+..++|+....+..   ....+ ..+|+|+|.     .+ ..++++++
T Consensus        33 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~-~~Gid~~~  102 (175)
T 2rb4_A           33 TIGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN-----VC-ARGIDVKQ  102 (175)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC-----SC-CTTTCCTT
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec-----ch-hcCCCccc
Confidence            4458999999999999998887664    46677778876544332   22333 489999994     22 34567888


Q ss_pred             ccEEEEcc
Q psy4698         190 IRMFVLDE  197 (258)
Q Consensus       190 l~~lVvDE  197 (258)
                      ++++|.=+
T Consensus       103 ~~~Vi~~d  110 (175)
T 2rb4_A          103 VTIVVNFD  110 (175)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEeC
Confidence            98888533

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=92.64  E-value=0.14  Score=46.07  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=16.7

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..+++.||+|+|||..+
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999865

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=92.63  E-value=1.1  Score=36.80  Aligned_cols=37  Identities=27%  Similarity=0.221  Sum_probs=22.2

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      .++.+.+.|+.|+|||+....-+.. +..  .+.+++++-
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~-~~~--~~~~v~l~~  133 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALY-YKG--KGRRPLLVA  133 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH-HHH--TTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH-HHH--cCCeEEEec
Confidence            3456788899999999765332222 222  233566665

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=92.56  E-value=0.23  Score=42.37  Aligned_cols=39  Identities=15%  Similarity=0.091  Sum_probs=26.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|.-++|.|++|+|||...+..+......   +.+++|+...
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~~---g~~vlyi~~E  111 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAE  111 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESS
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHHC---CCeEEEEECC
Confidence            34679999999999998765544443332   2368888754

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=92.38  E-value=0.39  Score=39.65  Aligned_cols=19  Identities=26%  Similarity=0.504  Sum_probs=16.0

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ++.+++.|++|+|||+...
T Consensus       105 g~vi~lvG~~GsGKTTl~~  123 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLA  123 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            4578999999999998754

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.28  E-value=0.12  Score=53.36  Aligned_cols=41  Identities=15%  Similarity=0.069  Sum_probs=29.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .++++++.||+|+|||..+...+.....   ++.+++|+.....
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~---~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHA 1466 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEECTTSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEEcccc
Confidence            3678999999999999887655554433   3447888886543

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=92.14  E-value=1.5  Score=36.66  Aligned_cols=53  Identities=13%  Similarity=0.265  Sum_probs=29.8

Q ss_pred             ccEEEEccchhhh-ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhc
Q psy4698         190 IRMFVLDEADEML-SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFM  242 (258)
Q Consensus       190 l~~lVvDE~h~~~-~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~  242 (258)
                      .+++++|.+-... +......+..+.+.+.++..++.+.++...++.+.++.|.
T Consensus       212 ~d~vliDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~~~~~  265 (328)
T 3e70_C          212 IDVVLIDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQFN  265 (328)
T ss_dssp             CSEEEEEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHHHHHH
T ss_pred             chhhHHhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHHHHHH
Confidence            3456667665432 2234445555555555566666777776666666666554

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=92.11  E-value=0.23  Score=47.34  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=15.6

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|+|||..+-
T Consensus       192 ~~vlL~G~pG~GKT~la~  209 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIVE  209 (854)
T ss_dssp             CCCEEEECTTSCHHHHHH
T ss_pred             CceEEEcCCCCCHHHHHH
Confidence            579999999999998653

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=92.02  E-value=0.15  Score=38.94  Aligned_cols=120  Identities=13%  Similarity=0.174  Sum_probs=72.1

Q ss_pred             cHHHHHHhhhhhcCC--cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          71 SAIQQRAIIPCVRGN--DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~--~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .+-|..++..+....  -.+|.+.-|++|+...+..++.....  .|.++.+++|+........+..       +..   
T Consensus        36 ~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~--~Gr~V~vLAp~~~s~~~l~~~~-------~l~---  103 (189)
T 2l8b_A           36 TAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE--QGREVQIIAADRRSQMNMKQDE-------RLS---  103 (189)
T ss_dssp             HHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH--TTCCEEEECSTTHHHHHHSCTT-------TCS---
T ss_pred             CccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh--cCeEEEEEcCchHHHHHHHhhc-------CcC---
Confidence            356888888876554  58889999999998865555444444  3458999999977665544321       110   


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC-CCCccEEEEE
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL-NNDVQVILLS  227 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~~~~~~i~~S  227 (258)
                                      + +++  |-    ..+......+..=+++|||||..+.    ..++..++..- ..+.|+|++-
T Consensus       104 ----------------~-~t~--t~----~~ll~~~~~~tp~s~lIVD~AekLS----~kE~~~Lld~A~~~naqvvll~  156 (189)
T 2l8b_A          104 ----------------G-ELI--TG----RRQLLEGMAFTPGSTVIVDQGEKLS----LKETLTLLDGAARHNVQVLITD  156 (189)
T ss_dssp             ----------------S-CSS--ST----TTTTTTSCCCCCCCEEEEEESSSHH----HHHHHHHHHHHHHTTCCEEEEE
T ss_pred             ----------------c-cee--eh----hhhhcCCCCCCCCCEEEEechhhcC----HHHHHHHHHHHHhcCCEEEEeC
Confidence                            0 011  11    1122233333444589999999873    44555555443 3457888775


Q ss_pred             ee
Q psy4698         228 AT  229 (258)
Q Consensus       228 AT  229 (258)
                      -+
T Consensus       157 ~~  158 (189)
T 2l8b_A          157 SG  158 (189)
T ss_dssp             SS
T ss_pred             Cc
Confidence            43

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=92.02  E-value=0.52  Score=44.18  Aligned_cols=16  Identities=31%  Similarity=0.372  Sum_probs=14.7

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      ++++.||+|+|||..+
T Consensus       523 ~~Ll~Gp~GtGKT~lA  538 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELA  538 (758)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5999999999999876

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=91.95  E-value=0.62  Score=41.26  Aligned_cols=52  Identities=12%  Similarity=0.251  Sum_probs=39.6

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      .|....+.|-+|||||++..-     +... .+..+|||+|+...+.+++..++.+..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~-----l~~~-~~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAE-----IAER-HAGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHH-----HHHH-SSSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHH-----HHHH-hCCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            456789999999999986421     1111 123599999999999999999998864

>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=91.80  E-value=1.3  Score=33.03  Aligned_cols=75  Identities=8%  Similarity=0.128  Sum_probs=52.1

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++..+......+...    +..+..++++....+..   .... ...+|+|+|.-      -..++++++
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~------~~~Gldi~~   99 (172)
T 1t5i_A           30 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIER   99 (172)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGG
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc------hhcCcchhh
Confidence            3458999999999999999988775    46677778776544322   2233 34899999941      223567778


Q ss_pred             ccEEEEccc
Q psy4698         190 IRMFVLDEA  198 (258)
Q Consensus       190 l~~lVvDE~  198 (258)
                      ++++|.-+.
T Consensus       100 ~~~Vi~~d~  108 (172)
T 1t5i_A          100 VNIAFNYDM  108 (172)
T ss_dssp             CSEEEESSC
T ss_pred             CCEEEEECC
Confidence            888876444

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=91.66  E-value=0.25  Score=46.59  Aligned_cols=17  Identities=29%  Similarity=0.421  Sum_probs=15.3

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.||+|+|||+.+
T Consensus       239 ~GILL~GPPGTGKT~LA  255 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLIA  255 (806)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            57999999999999865

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=91.44  E-value=0.22  Score=41.71  Aligned_cols=90  Identities=12%  Similarity=0.122  Sum_probs=52.0

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcC
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG  165 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (258)
                      -+.|.||.|+|||...+..+...... +.+.+++|+....++...   .+++++-..+                      
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~-g~g~~vlyId~E~s~~~~---ra~~lGvd~d----------------------   83 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQ-YPDAVCLFYDSEFGITPA---YLRSMGVDPE----------------------   83 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHH-CTTCEEEEEESSCCCCHH---HHHHTTCCGG----------------------
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEeccchhhHH---HHHHhCCCHH----------------------
Confidence            58999999999998876655554432 224579998865544322   3445542211                      


Q ss_pred             CcEEEeCh---HHH-HHHHhc-CCCCCCCccEEEEccchhhh
Q psy4698         166 AQVVVGTP---GRV-FDMISR-GALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       166 ~~Ilv~Tp---~~l-~~~l~~-~~~~~~~l~~lVvDE~h~~~  202 (258)
                       ++++..|   +.+ +.++.. ..+.-..+++||||-+..+.
T Consensus        84 -~llv~~~~~~E~~~l~i~~~l~~i~~~~~~lvVIDSI~aL~  124 (333)
T 3io5_A           84 -RVIHTPVQSLEQLRIDMVNQLDAIERGEKVVVFIDSLGNLA  124 (333)
T ss_dssp             -GEEEEECSBHHHHHHHHHHHHHTCCTTCCEEEEEECSTTCB
T ss_pred             -HeEEEcCCCHHHHHHHHHHHHHHhhccCceEEEEecccccc
Confidence             2344433   333 322211 11233467899999999775

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=91.42  E-value=0.15  Score=45.65  Aligned_cols=39  Identities=15%  Similarity=0.129  Sum_probs=25.4

Q ss_pred             HHHHCCCCCCcHHHHHHhh-hhhcCCcEEEEcccCCCcchHh
Q psy4698          61 GIYAYGFEKPSAIQQRAII-PCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        61 ~l~~~~~~~~~~~Q~~~~~-~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .|.+.|.  +.+.+...+. .+..|.++++.||||||||+..
T Consensus       238 ~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          238 DLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH
T ss_pred             hHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            3444452  3333333333 3567889999999999999864

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=91.41  E-value=0.14  Score=41.45  Aligned_cols=21  Identities=19%  Similarity=0.376  Sum_probs=17.9

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|..+++.||||||||+..
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll   42 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTI   42 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHH
Confidence            457778999999999999864

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=91.37  E-value=0.24  Score=38.62  Aligned_cols=32  Identities=19%  Similarity=0.102  Sum_probs=27.0

Q ss_pred             CcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      -+.-|..++..+..|.-+.+.||.|+|||+..
T Consensus         8 k~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            8 KTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             CCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            34557778888899999999999999999864

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=91.04  E-value=0.6  Score=43.71  Aligned_cols=19  Identities=37%  Similarity=0.461  Sum_probs=16.3

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      +.++++.|++|+|||..+-
T Consensus       207 ~~~vlL~G~~GtGKT~la~  225 (758)
T 1r6b_X          207 KNNPLLVGESGVGKTAIAE  225 (758)
T ss_dssp             SCEEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEcCCCCCHHHHHH
Confidence            4679999999999998753

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=90.71  E-value=0.23  Score=43.15  Aligned_cols=26  Identities=15%  Similarity=0.287  Sum_probs=19.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHh
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQV  109 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l  109 (258)
                      ...+++|.|+||||||... ..++..+
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~   77 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTG   77 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHH
Confidence            4578999999999999975 3334333

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=90.58  E-value=0.17  Score=43.26  Aligned_cols=21  Identities=19%  Similarity=0.376  Sum_probs=17.6

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|..+++.||||||||+..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll  153 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI  153 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH
Confidence            456778999999999999864

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=90.41  E-value=0.23  Score=39.23  Aligned_cols=52  Identities=19%  Similarity=0.282  Sum_probs=31.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      .|.-+++.|++|+|||...+-.+.+.+...+  ..++|++-. ....+....+..
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~--~~v~~~s~E-~~~~~~~~~~~~   80 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEYG--EPGVFVTLE-ERARDLRREMAS   80 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHHC--CCEEEEESS-SCHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcC--CCceeeccc-CCHHHHHHHHHH
Confidence            3466999999999999876655554444332  257777633 223444444433

>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=90.21  E-value=1.6  Score=32.95  Aligned_cols=74  Identities=15%  Similarity=0.324  Sum_probs=44.4

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++..+......++..    ++.+..++|+....+   ...... ...+|+|+|.     .+. .++++++
T Consensus        45 ~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~-~Gldi~~  114 (185)
T 2jgn_A           45 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAA-RGLDISN  114 (185)
T ss_dssp             CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEEEEEC------------CCCS
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-----hhh-cCCCccc
Confidence            4568999999999999999888775    456666776654332   222223 3478999993     222 3457778


Q ss_pred             ccEEEEcc
Q psy4698         190 IRMFVLDE  197 (258)
Q Consensus       190 l~~lVvDE  197 (258)
                      ++++|.=+
T Consensus       115 ~~~VI~~d  122 (185)
T 2jgn_A          115 VKHVINFD  122 (185)
T ss_dssp             BSEEEESS
T ss_pred             CCEEEEeC
Confidence            88877643

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=90.05  E-value=0.21  Score=49.30  Aligned_cols=41  Identities=22%  Similarity=0.233  Sum_probs=31.9

Q ss_pred             EEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHH
Q psy4698          88 IAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELA  128 (258)
Q Consensus        88 li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~  128 (258)
                      +|.|+.|||||.+.+--+...+.....+.++++++|....-
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~TF   45 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQMTF   45 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGGHH
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcccH
Confidence            78889999999998777777776654456899999976533

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=90.00  E-value=0.22  Score=42.30  Aligned_cols=20  Identities=30%  Similarity=0.509  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcccCCCcchHh
Q psy4698          82 VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+..++|.||||||||+..
T Consensus       121 ~~~g~i~I~GptGSGKTTlL  140 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTL  140 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            34557999999999999864

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=89.90  E-value=0.11  Score=51.79  Aligned_cols=40  Identities=15%  Similarity=0.306  Sum_probs=30.1

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      +-+++|+||+=.-+|......+...++...+++.+|..+-
T Consensus      1235 ~~~ILiLDEaTSaLD~~tE~~Iq~~l~~~~~~~TvI~IAH 1274 (1321)
T 4f4c_A         1235 NPKILLLDEATSALDTESEKVVQEALDRAREGRTCIVIAH 1274 (1321)
T ss_dssp             CCSEEEEESCCCSTTSHHHHHHHHHHTTTSSSSEEEEECS
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHcCCCEEEEecc
Confidence            3468999999887787777888888887767665555543

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=89.78  E-value=5.3  Score=30.25  Aligned_cols=72  Identities=19%  Similarity=0.242  Sum_probs=51.1

Q ss_pred             ceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCCcc
Q psy4698         116 CQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQIR  191 (258)
Q Consensus       116 ~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~  191 (258)
                      .++||.|+++..+......++..    ++.+..++|+....+..   .... ...+|+|+|.     .+.+ ++++++++
T Consensus        55 ~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~~~-Gldi~~v~  124 (191)
T 2p6n_A           55 PPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VASK-GLDFPAIQ  124 (191)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HHHT-TCCCCCCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----chhc-CCCcccCC
Confidence            47999999999999999988776    46677778876544322   2222 3489999993     3333 46788888


Q ss_pred             EEEEcc
Q psy4698         192 MFVLDE  197 (258)
Q Consensus       192 ~lVvDE  197 (258)
                      ++|.=+
T Consensus       125 ~VI~~d  130 (191)
T 2p6n_A          125 HVINYD  130 (191)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            887644

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=89.55  E-value=0.13  Score=39.00  Aligned_cols=19  Identities=11%  Similarity=0.200  Sum_probs=16.4

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+-+++.||+|+|||+..
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5677899999999999865

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=89.43  E-value=0.14  Score=39.39  Aligned_cols=21  Identities=19%  Similarity=0.085  Sum_probs=17.4

Q ss_pred             hcCCcEEEEcccCCCcchHhH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l  102 (258)
                      ..++.+++.|++|||||+..-
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            456789999999999998763

>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=89.40  E-value=1.9  Score=36.15  Aligned_cols=136  Identities=10%  Similarity=0.102  Sum_probs=76.4

Q ss_pred             hhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHhc-CCcEEEeChHHHHHHHhcCC
Q psy4698         109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLEA-GAQVVVGTPGRVFDMISRGA  184 (258)
Q Consensus       109 l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~Ilv~Tp~~l~~~l~~~~  184 (258)
                      +.....+.++||.++++.-+...+..++..    +..+..++++....+.   ...... ..+|+|+|.     . -..+
T Consensus       237 ~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~G  306 (395)
T 3pey_A          237 LYGLMTIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN-----V-LARG  306 (395)
T ss_dssp             HHTTTTSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG-----G-GSSS
T ss_pred             HHHhccCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC-----h-hhcC
Confidence            333334468999999999999999988775    3566677777554332   223333 478999995     2 2345


Q ss_pred             CCCCCccEEEEccchhhhccC-cHHHHHHHHHhCCC-CccEEEEEeeCCh---hHHHHHHHhcCCCeEEEecCCc
Q psy4698         185 LSTKQIRMFVLDEADEMLSRG-FKDQIYDVFKHLNN-DVQVILLSATMPA---DVLDVSMKFMRDPIKILVKKEE  254 (258)
Q Consensus       185 ~~~~~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~~-~~~~i~~SAT~~~---~~~~~~~~~~~~~~~v~~~~~~  254 (258)
                      ++++++++||.-+...+.... ....+...+-+... ...-..+.-.-+.   ...+.++.++.+..+..++.++
T Consensus       307 idip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~  381 (395)
T 3pey_A          307 IDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDD  381 (395)
T ss_dssp             CCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHHHHHHTTSCCCEECCSSC
T ss_pred             CCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHHHHHHhCCceeecCChHH
Confidence            788899999876654321110 12222233333221 1112222222222   3445556666666666655443

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=89.26  E-value=0.58  Score=40.65  Aligned_cols=19  Identities=21%  Similarity=0.468  Sum_probs=15.7

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..++|.||||||||+..
T Consensus       166 ~ggii~I~GpnGSGKTTlL  184 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTL  184 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHH
Confidence            4456899999999999864

>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=89.19  E-value=4.6  Score=35.99  Aligned_cols=87  Identities=11%  Similarity=0.150  Sum_probs=57.4

Q ss_pred             HHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHH
Q psy4698         105 ILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMI  180 (258)
Q Consensus       105 ~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l  180 (258)
                      +...+.....+.++||.|+++.-+...+..+++... .+..+..++++....+..   .... ...+|+|+|.     .+
T Consensus       329 l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~-~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~  402 (563)
T 3i5x_A          329 IKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VG  402 (563)
T ss_dssp             HHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GG
T ss_pred             HHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc-----hh
Confidence            333344334556899999999999999998877532 245677777776544322   2222 4489999995     22


Q ss_pred             hcCCCCCCCccEEEEccc
Q psy4698         181 SRGALSTKQIRMFVLDEA  198 (258)
Q Consensus       181 ~~~~~~~~~l~~lVvDE~  198 (258)
                      . .+++++++++||.-..
T Consensus       403 ~-~GiDip~v~~VI~~~~  419 (563)
T 3i5x_A          403 A-RGMDFPNVHEVLQIGV  419 (563)
T ss_dssp             T-SSCCCTTCCEEEEESC
T ss_pred             h-cCCCcccCCEEEEECC
Confidence            3 4578888888876553

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=89.01  E-value=0.19  Score=42.73  Aligned_cols=25  Identities=28%  Similarity=0.549  Sum_probs=19.7

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ++..++.|.|  ++..|.||||||.++
T Consensus        96 lv~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           96 VVSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            3445568876  888999999999875

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=88.94  E-value=2.7  Score=34.57  Aligned_cols=73  Identities=16%  Similarity=0.231  Sum_probs=50.3

Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCCc
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQI  190 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l  190 (258)
                      +.++||.|+++.-+......+...    ++.+..++|+....+..   .... ...+|+|+|-     .+. .+++++++
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----va~-~Gidi~~v   97 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----VAA-RGLDIPQV   97 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----TTT-CSTTCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----hhh-cCccccce
Confidence            458999999999999888877554    56777888876544332   2233 3478999993     222 35677888


Q ss_pred             cEEEEcc
Q psy4698         191 RMFVLDE  197 (258)
Q Consensus       191 ~~lVvDE  197 (258)
                      ++||.=+
T Consensus        98 ~~VI~~d  104 (300)
T 3i32_A           98 DLVVHYR  104 (300)
T ss_dssp             SEEEESS
T ss_pred             eEEEEcC
Confidence            8777533

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=88.91  E-value=0.21  Score=42.49  Aligned_cols=21  Identities=19%  Similarity=0.382  Sum_probs=18.4

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|..+++.||||||||+..
T Consensus       172 i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHHH
Confidence            568889999999999999853

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=88.64  E-value=0.48  Score=40.05  Aligned_cols=19  Identities=21%  Similarity=0.373  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      ...++++.||+|+|||..+
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4468999999999999876

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=88.64  E-value=0.51  Score=42.07  Aligned_cols=28  Identities=14%  Similarity=0.299  Sum_probs=20.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .+.+++|.|+||||||.+.-..+...+.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~sLl~  193 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILSMLY  193 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4568999999999999876444444443

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=88.63  E-value=0.3  Score=37.74  Aligned_cols=37  Identities=14%  Similarity=-0.014  Sum_probs=25.1

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      +..|.-+++.|++|+|||......+.    .  .+.+++++.-
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~~l~~----~--~~~~v~~i~~   53 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLALQTGL----L--SGKKVAYVDT   53 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHHHHHH----H--HCSEEEEEES
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHH----H--cCCcEEEEEC
Confidence            33556799999999999987654433    1  2336777763

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=88.54  E-value=3.5  Score=34.90  Aligned_cols=72  Identities=17%  Similarity=0.343  Sum_probs=51.5

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++..+...++.++..    +..+..++++....+..   .... ...+|+|+|.     .+.. ++++++
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~~-Gidip~  344 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAAR-GLDISN  344 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----HHHT-TSCCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhhc-CCCccc
Confidence            4568999999999999999888775    46677778776544322   2222 3478999994     3333 468888


Q ss_pred             ccEEEE
Q psy4698         190 IRMFVL  195 (258)
Q Consensus       190 l~~lVv  195 (258)
                      ++++|.
T Consensus       345 v~~Vi~  350 (417)
T 2i4i_A          345 VKHVIN  350 (417)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888775

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=88.37  E-value=0.17  Score=38.12  Aligned_cols=19  Identities=26%  Similarity=0.225  Sum_probs=16.3

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ++.+++.|++|||||...-
T Consensus         5 ~~~i~l~G~~GsGKst~a~   23 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGS   23 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            4678999999999998764

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=88.30  E-value=0.13  Score=38.97  Aligned_cols=21  Identities=24%  Similarity=0.430  Sum_probs=17.7

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|..+++.|++|||||+..
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            456778999999999999864

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=88.22  E-value=0.77  Score=37.40  Aligned_cols=18  Identities=22%  Similarity=0.418  Sum_probs=16.0

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ..++++.||+|+|||..+
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            568999999999999875

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=88.20  E-value=0.19  Score=37.80  Aligned_cols=21  Identities=19%  Similarity=0.240  Sum_probs=17.5

Q ss_pred             hcCCcEEEEcccCCCcchHhH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l  102 (258)
                      ..++.+++.|++|||||...-
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHH
Confidence            356789999999999998753

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=88.17  E-value=4  Score=35.41  Aligned_cols=36  Identities=25%  Similarity=0.207  Sum_probs=22.1

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ++.+++.|+.|+|||+.....+.. +...  +.+++++.
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~-l~~~--g~~Vllvd  133 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALY-YKGK--GRRPLLVA  133 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH-HHTT--TCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHc--CCeEEEee
Confidence            345788899999999875433322 2222  34666665

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=88.17  E-value=0.52  Score=41.95  Aligned_cols=36  Identities=17%  Similarity=0.280  Sum_probs=26.6

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..-...-..++..+..+.++++.||+|+|||..+
T Consensus        23 ~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            343444444556666778899999999999999864

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=88.12  E-value=0.96  Score=48.23  Aligned_cols=47  Identities=23%  Similarity=0.185  Sum_probs=31.9

Q ss_pred             CHHHHHHHHHCCCCCCcHHH-HH---HhhhhhcCCcEEEEcccCCCcchHhH
Q psy4698          55 SEELLRGIYAYGFEKPSAIQ-QR---AIIPCVRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        55 ~~~l~~~l~~~~~~~~~~~Q-~~---~~~~l~~g~~~li~~~tGsGKT~~~l  102 (258)
                      ...+.+.+.+.|+. +.+.+ .+   ....+...+.+++.||||+|||.++-
T Consensus       891 ~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~  941 (2695)
T 4akg_A          891 VQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWK  941 (2695)
T ss_dssp             HHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHH
Confidence            34556666677774 55554 22   23344566789999999999999873

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=88.10  E-value=0.33  Score=38.97  Aligned_cols=20  Identities=25%  Similarity=0.275  Sum_probs=16.9

Q ss_pred             hcCCcEEEEcccCCCcchHh
Q psy4698          82 VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+.++++.|++|+|||..+
T Consensus        27 ~~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHHH
T ss_pred             CCCCCEEEECCCCCcHHHHH
Confidence            34678999999999999765

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=88.08  E-value=0.18  Score=38.61  Aligned_cols=21  Identities=24%  Similarity=0.303  Sum_probs=17.1

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|.-+++.|++|||||+..
T Consensus         3 i~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHH
Confidence            345777999999999999865

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=88.08  E-value=0.96  Score=40.99  Aligned_cols=41  Identities=22%  Similarity=0.362  Sum_probs=29.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      .+-+++++||+-.-+|......+...++.+.++. .+++.+.
T Consensus       497 ~~p~illlDEpts~LD~~~~~~i~~~l~~~~~~~-tvi~itH  537 (582)
T 3b5x_A          497 RDAPVLILDEATSALDTESERAIQAALDELQKNK-TVLVIAH  537 (582)
T ss_pred             cCCCEEEEECccccCCHHHHHHHHHHHHHHcCCC-EEEEEec
Confidence            3456999999998888877888888888775544 4444443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=88.07  E-value=0.19  Score=38.74  Aligned_cols=19  Identities=26%  Similarity=0.436  Sum_probs=15.3

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+-+++.||+|+|||+..
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677999999999999865

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=87.99  E-value=0.98  Score=44.59  Aligned_cols=53  Identities=19%  Similarity=0.215  Sum_probs=41.6

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhc---------cccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQN---------IKECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~---------~~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      +.+|.|+.|||||.+...-++..+...         ....++|+++=|+.-+.+...++...
T Consensus        18 ~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            459999999999999877777777642         12348999999999988888777653

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=87.95  E-value=0.19  Score=42.23  Aligned_cols=20  Identities=35%  Similarity=0.524  Sum_probs=17.8

Q ss_pred             hhcCCcEEEEcccCCCcchH
Q psy4698          81 CVRGNDVIAQAQSGTGKTAT  100 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~  100 (258)
                      +..|..+++.||||||||+.
T Consensus       168 i~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHH
Confidence            46788999999999999984

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=87.92  E-value=0.26  Score=38.17  Aligned_cols=19  Identities=32%  Similarity=0.434  Sum_probs=16.4

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+-+++.||+|+|||...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            4667999999999999865

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=87.89  E-value=0.2  Score=38.68  Aligned_cols=21  Identities=24%  Similarity=0.295  Sum_probs=17.6

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ...|+-++++|++|||||+..
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHH
T ss_pred             cccCCEEEEECCCCCCHHHHH
Confidence            346778999999999999865

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=87.88  E-value=0.29  Score=41.04  Aligned_cols=24  Identities=29%  Similarity=0.513  Sum_probs=19.2

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      +..++.|.|  ++..|.||||||.+.
T Consensus        70 v~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           70 VKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCeEEEEEECCCCCCCceEe
Confidence            344567876  888999999999875

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=87.83  E-value=0.29  Score=41.39  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=20.7

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            5566778877  788999999999876

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=87.79  E-value=0.22  Score=41.94  Aligned_cols=19  Identities=21%  Similarity=0.254  Sum_probs=15.9

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ++.++|.||||+|||....
T Consensus        40 ~~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3468999999999998763

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=87.78  E-value=0.2  Score=37.46  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=15.5

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ++.++++|++|||||++.
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            456899999999999876

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=87.74  E-value=6.5  Score=35.31  Aligned_cols=84  Identities=11%  Similarity=0.142  Sum_probs=56.3

Q ss_pred             HhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcC
Q psy4698         108 QVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRG  183 (258)
Q Consensus       108 ~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~  183 (258)
                      .+.....+.++||.|+++.-+...+..++.... .+..+..++++....+..   .... ...+|+|+|.     .+. .
T Consensus       281 ~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~~~-~  353 (579)
T 3sqw_A          281 QIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGA-R  353 (579)
T ss_dssp             HHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGT-S
T ss_pred             HHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----hhh-c
Confidence            333334456899999999999999998877532 245677777776544322   2222 4488999995     233 3


Q ss_pred             CCCCCCccEEEEccc
Q psy4698         184 ALSTKQIRMFVLDEA  198 (258)
Q Consensus       184 ~~~~~~l~~lVvDE~  198 (258)
                      +++++++++||.-..
T Consensus       354 GiDip~v~~VI~~~~  368 (579)
T 3sqw_A          354 GMDFPNVHEVLQIGV  368 (579)
T ss_dssp             SCCCTTCCEEEEESC
T ss_pred             CCCcccCCEEEEcCC
Confidence            578888988886554

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=87.73  E-value=0.54  Score=40.23  Aligned_cols=42  Identities=19%  Similarity=0.218  Sum_probs=27.2

Q ss_pred             ccEEEEccchhhhcc---CcHHHHHHHHHhCCC-CccEEEEEeeCC
Q psy4698         190 IRMFVLDEADEMLSR---GFKDQIYDVFKHLNN-DVQVILLSATMP  231 (258)
Q Consensus       190 l~~lVvDE~h~~~~~---~~~~~~~~~~~~l~~-~~~~i~~SAT~~  231 (258)
                      -.++|+||+|.++..   .....+..+++..++ ..-+++.|.++.
T Consensus       263 ~~~i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~g~~~~~~tQ~~~  308 (392)
T 4ag6_A          263 RTVLVVDEAWMLVDPQTPQAIAFLRDTSKRIRKYNGSLIVISQNVI  308 (392)
T ss_dssp             TCEEEETTGGGGCCTTCTHHHHHHHHHHHHGGGGTCEEEEEESCGG
T ss_pred             cEEEEEecHHHHhCcCchHHHHHHHHHHHHhhhhCeEEEEEcCCHH
Confidence            468999999999852   244556667766654 344555555543

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=87.69  E-value=0.44  Score=39.60  Aligned_cols=54  Identities=15%  Similarity=0.140  Sum_probs=32.4

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhc---------ccc----ceEEEEeccHHH-HHHHHHHHHHh
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQN---------IKE----CQALILAPTREL-AQQIQKVVIAL  138 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~---------~~~----~~~lil~P~~~l-~~q~~~~~~~~  138 (258)
                      .-++|.|++|+|||...+..+.......         ..+    .+++|+.-...+ ..+....++.+
T Consensus        99 ~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           99 SVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            5689999999999987765555432221         111    578888754332 34444444444

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=87.67  E-value=0.27  Score=38.15  Aligned_cols=19  Identities=37%  Similarity=0.510  Sum_probs=15.9

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+-++|.||||+|||..+
T Consensus        33 ~g~~ilI~GpsGsGKStLA   51 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETA   51 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4566999999999999765

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=87.65  E-value=0.27  Score=41.51  Aligned_cols=23  Identities=30%  Similarity=0.440  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus        88 ~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           88 DKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hHhhCCCceEEEEecCCCCCCCeEE
Confidence            34567876  788999999999875

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=87.59  E-value=0.39  Score=48.01  Aligned_cols=40  Identities=15%  Similarity=0.312  Sum_probs=28.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ++-+++|+||+=.-+|......+...+..+.++..+|+.+
T Consensus       571 ~~~~IliLDE~tSaLD~~te~~i~~~l~~~~~~~T~iiia  610 (1321)
T 4f4c_A          571 RNPKILLLDEATSALDAESEGIVQQALDKAAKGRTTIIIA  610 (1321)
T ss_dssp             TCCSEEEEESTTTTSCTTTHHHHHHHHHHHHTTSEEEEEC
T ss_pred             cCCCEEEEecccccCCHHHHHHHHHHHHHHhCCCEEEEEc
Confidence            4456999999998888877777777777665554444443

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=87.57  E-value=0.2  Score=37.02  Aligned_cols=16  Identities=19%  Similarity=0.355  Sum_probs=14.1

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|++|||||+..
T Consensus         3 ~I~l~G~~GsGKsT~a   18 (179)
T 3lw7_A            3 VILITGMPGSGKSEFA   18 (179)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999865

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=87.27  E-value=0.34  Score=41.04  Aligned_cols=25  Identities=32%  Similarity=0.550  Sum_probs=20.8

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            5566778887  788999999999876

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=87.27  E-value=0.23  Score=38.00  Aligned_cols=20  Identities=40%  Similarity=0.469  Sum_probs=16.8

Q ss_pred             hcCCcEEEEcccCCCcchHh
Q psy4698          82 VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|.-+.+.||+|||||+..
T Consensus         5 ~~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            5 NKANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCcEEEEECcCCCCHHHHH
Confidence            35777899999999999864

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=87.20  E-value=0.3  Score=41.44  Aligned_cols=23  Identities=35%  Similarity=0.495  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.+.
T Consensus        74 ~~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           74 DDILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCcceEEEECCCCCCcceEe
Confidence            34567876  888999999999875

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=87.12  E-value=0.32  Score=40.86  Aligned_cols=25  Identities=36%  Similarity=0.702  Sum_probs=20.2

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus        72 lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           72 LVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            4555678876  788999999999875

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=87.12  E-value=0.31  Score=42.14  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=20.7

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            4556678887  788999999999886

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=87.12  E-value=0.31  Score=41.52  Aligned_cols=24  Identities=29%  Similarity=0.530  Sum_probs=19.0

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      +..++.|.|  ++..|.||||||.++
T Consensus        82 v~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           82 LQHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCeeEEEEeCCCCCCCceEe
Confidence            344567876  888999999999875

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=87.05  E-value=0.34  Score=41.02  Aligned_cols=23  Identities=35%  Similarity=0.492  Sum_probs=18.4

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus        83 ~~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           83 DAVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCceeEEeecCCCCCCCEEe
Confidence            34567876  888999999999875

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=87.03  E-value=0.3  Score=41.44  Aligned_cols=25  Identities=28%  Similarity=0.504  Sum_probs=19.8

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ++..++.|.|  ++..|.||||||.++
T Consensus        84 lv~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           84 ILQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHHhCCceeEEEeeCCCCCCCceEE
Confidence            3445668876  788999999999875

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=87.01  E-value=0.88  Score=36.93  Aligned_cols=45  Identities=13%  Similarity=0.205  Sum_probs=28.9

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHhhhhhcCC-----cEEEEcccCCCcchHhH
Q psy4698          56 EELLRGIYAYGFEKPSAIQQRAIIPCVRGN-----DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        56 ~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~-----~~li~~~tGsGKT~~~l  102 (258)
                      ..+.+.|+-.|+. |-.+-.. +...+.++     .+++.||+|+|||..+.
T Consensus        73 n~i~~~l~~qg~~-~~~~~~~-l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKILELNGYD-PQYAASV-FLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHHHHTTCC-HHHHHHH-HHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHcCCC-HHHHHHH-HHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            3677778777763 3322222 33334432     49999999999998764

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=86.97  E-value=0.35  Score=41.24  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=18.6

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.+.
T Consensus        78 ~~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           78 TDVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCceEEEeecCCCCCCceEE
Confidence            34567876  788999999999875

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=86.95  E-value=0.32  Score=42.08  Aligned_cols=23  Identities=35%  Similarity=0.511  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus       148 ~~~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          148 QTIFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHhcCCceeEEeecCCCCCCCeEe
Confidence            34567876  888999999999875

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=86.94  E-value=5.7  Score=32.57  Aligned_cols=36  Identities=19%  Similarity=0.150  Sum_probs=22.1

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      ++.+++.|++|+|||......+.. +..  .+.+++++.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~-~~~--~g~~v~l~~  133 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF-YKK--KGFKVGLVG  133 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH-HHH--TTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHH--CCCeEEEEe
Confidence            345788899999999865433322 222  233666665

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=86.93  E-value=0.53  Score=39.23  Aligned_cols=55  Identities=15%  Similarity=0.044  Sum_probs=32.6

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEeccHHH-HHHHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPTREL-AQQIQKVVIAL  138 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~~~l-~~q~~~~~~~~  138 (258)
                      |.-+++.|++|+|||...+..+.......   +.+.+++|+.-...+ ..+....++.+
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~  165 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKAL  165 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHh
Confidence            45699999999999987765554433221   113478888754322 33344444444

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=86.91  E-value=0.34  Score=41.11  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus        99 ~~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A           99 RSFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHhCCCceEEEEeCCCCCCceeee
Confidence            34567876  888999999999875

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=86.90  E-value=0.27  Score=36.56  Aligned_cols=18  Identities=17%  Similarity=0.279  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +..+++.|+.|||||+..
T Consensus         4 ~~~i~l~G~~GsGKSTl~   21 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIG   21 (173)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467899999999999865

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=86.89  E-value=0.31  Score=41.27  Aligned_cols=24  Identities=33%  Similarity=0.540  Sum_probs=19.0

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      +..++.|.|  ++..|.||||||.++
T Consensus        70 v~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           70 IDSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHcCCccceeeecCCCCCCCeEE
Confidence            344567876  788999999999875

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=86.87  E-value=0.35  Score=40.83  Aligned_cols=23  Identities=39%  Similarity=0.510  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus        77 ~~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           77 EAFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHhhcCeeEEEecccCCCceEee
Confidence            34567876  788999999999875

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=86.84  E-value=0.33  Score=41.44  Aligned_cols=23  Identities=39%  Similarity=0.557  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus        95 ~~~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           95 DSVLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHhCCCeeeEEeecCCCCCCCEeE
Confidence            34567876  788999999999875

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=86.84  E-value=0.25  Score=37.46  Aligned_cols=19  Identities=32%  Similarity=0.602  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+++.|++|||||.+.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~   27 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMA   27 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4567999999999999875

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=86.72  E-value=0.3  Score=41.54  Aligned_cols=24  Identities=38%  Similarity=0.556  Sum_probs=19.1

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      +..++.|.|  ++..|.||||||.++
T Consensus        81 v~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           81 LDEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHHhCCCceEEEEeCCCCCCCceEE
Confidence            344567876  788999999999875

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=86.56  E-value=0.21  Score=41.64  Aligned_cols=27  Identities=22%  Similarity=0.411  Sum_probs=21.2

Q ss_pred             HHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          75 QRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        75 ~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+...+..+.++++.||+|+|||..+
T Consensus        37 ~~l~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           37 NRLLIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHHHHcCCeEEEECCCCCcHHHHH
Confidence            334445667889999999999999765

>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=86.56  E-value=4.3  Score=34.21  Aligned_cols=74  Identities=16%  Similarity=0.202  Sum_probs=52.1

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++.-+...+..+...    +..+..++++....+..   ..... ..+|+|+|.     .+ ..++++++
T Consensus       265 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~~Gidip~  334 (412)
T 3fht_A          265 TIAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----VC-ARGIDVEQ  334 (412)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GG-TSSCCCTT
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC-----cc-ccCCCccC
Confidence            4458999999999999999988776    35666777776544322   22333 478999994     22 34578889


Q ss_pred             ccEEEEcc
Q psy4698         190 IRMFVLDE  197 (258)
Q Consensus       190 l~~lVvDE  197 (258)
                      +++||.-+
T Consensus       335 ~~~Vi~~~  342 (412)
T 3fht_A          335 VSVVINFD  342 (412)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEEC
Confidence            99988533

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=86.52  E-value=0.2  Score=37.58  Aligned_cols=21  Identities=24%  Similarity=0.208  Sum_probs=17.4

Q ss_pred             hcCCcEEEEcccCCCcchHhH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l  102 (258)
                      ..|.-+.+.||.|||||+.+-
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            456778999999999998653

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=86.40  E-value=0.33  Score=41.52  Aligned_cols=23  Identities=43%  Similarity=0.592  Sum_probs=18.5

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus        94 ~~~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           94 EEVLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCceEEEEeecCCCCCcceec
Confidence            34567876  888999999999875

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=86.30  E-value=0.31  Score=41.84  Aligned_cols=21  Identities=38%  Similarity=0.662  Sum_probs=17.5

Q ss_pred             hhcCCc--EEEEcccCCCcchHh
Q psy4698          81 CVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ++.|.|  ++..|.||||||.++
T Consensus        94 ~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           94 LLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             HTTTCCEEEEEESCTTSSHHHHH
T ss_pred             hhcCceeeEeeecCCCCCCCeEe
Confidence            457776  788999999999875

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=86.25  E-value=0.3  Score=38.25  Aligned_cols=21  Identities=19%  Similarity=0.167  Sum_probs=16.9

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|+-+.+.||+|+|||+..
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            457788999999999999864

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=86.21  E-value=0.37  Score=42.17  Aligned_cols=23  Identities=30%  Similarity=0.439  Sum_probs=18.6

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHh
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ..++.|.|  ++..|.||||||.++
T Consensus       130 ~~~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          130 DHNFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHhhcCCceEEEEeCCCCCCCCEEe
Confidence            33467876  888999999999876

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=86.08  E-value=0.3  Score=41.69  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=19.9

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus        71 lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           71 LVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hhHhhhcCCceEEEEECCCCCCCeEee
Confidence            4455678876  788999999999875

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=86.02  E-value=1.2  Score=39.47  Aligned_cols=35  Identities=17%  Similarity=0.208  Sum_probs=21.5

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEE
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALIL  121 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil  121 (258)
                      |.-+.+.|++|+|||+..-  .+..+... .+.++++.
T Consensus       293 GeVI~LVGpNGSGKTTLl~--~LAgll~~-~~G~V~l~  327 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIG--KLARQFEQ-QGKSVMLA  327 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHH--HHHHHHHH-TTCCEEEE
T ss_pred             CeEEEEECCCcccHHHHHH--HHHHHhhh-cCCeEEEe
Confidence            3458899999999998642  22222222 23356665

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=85.90  E-value=0.37  Score=41.76  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=20.3

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus       130 lv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          130 LIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            4556678876  788999999999875

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=85.90  E-value=0.37  Score=41.23  Aligned_cols=25  Identities=32%  Similarity=0.515  Sum_probs=19.9

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..++.|.|  ++..|.||||||.++
T Consensus       107 lv~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          107 LVQSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HHHGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCCceEEEEeCCCCCCCceEe
Confidence            4455678876  788999999999875

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=85.89  E-value=0.4  Score=41.16  Aligned_cols=24  Identities=33%  Similarity=0.495  Sum_probs=19.1

Q ss_pred             hhhhcCCc--EEEEcccCCCcchHhH
Q psy4698          79 IPCVRGND--VIAQAQSGTGKTATFS  102 (258)
Q Consensus        79 ~~l~~g~~--~li~~~tGsGKT~~~l  102 (258)
                      ..++.|.|  ++..|.||||||.++.
T Consensus       128 ~~~l~G~N~tifAYGQTGSGKTyTM~  153 (387)
T 2heh_A          128 QTIFEGGKATCFAYGQTGSGKTHTMG  153 (387)
T ss_dssp             HHHHTTCEEEEEEESCTTSSHHHHHC
T ss_pred             HHHhcCCceEEEEecCCCCCCCeEec
Confidence            34567876  8889999999998863

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=85.88  E-value=0.91  Score=40.99  Aligned_cols=40  Identities=15%  Similarity=0.396  Sum_probs=26.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhcc-ccceEEEEecc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNI-KECQALILAPT  124 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~-~~~~~lil~P~  124 (258)
                      .+++|.|.||||||.+.-..++..+.... ...+.+++=|.
T Consensus       215 pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpK  255 (574)
T 2iut_A          215 PHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPK  255 (574)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSS
T ss_pred             CeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCC
Confidence            47999999999999886555555444322 23355555454

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=85.87  E-value=0.51  Score=36.51  Aligned_cols=21  Identities=19%  Similarity=0.344  Sum_probs=16.3

Q ss_pred             EEEEcccCCCcchHhHHHHHH
Q psy4698          87 VIAQAQSGTGKTATFSISILQ  107 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~  107 (258)
                      .++.|+.|||||..+..-++.
T Consensus         8 ~l~tG~pGsGKT~~a~~~~~~   28 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMVSMMAN   28 (199)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            689999999999976544433

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=85.85  E-value=0.27  Score=39.53  Aligned_cols=17  Identities=18%  Similarity=0.059  Sum_probs=14.4

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .++|.|++|||||..+.
T Consensus         3 li~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            36899999999998763

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=85.80  E-value=0.16  Score=41.42  Aligned_cols=52  Identities=15%  Similarity=0.192  Sum_probs=27.0

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHH-HHHHhhhh--hcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAI-QQRAIIPC--VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~-Q~~~~~~l--~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|.+.+-...+++.+.+.-.   .++ ..+++..+  .-.+.+++.||+|+|||+.+
T Consensus         7 ~~~~di~g~~~~~~~l~~~i~---~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            7 VTWADIGALEDIREELTMAIL---APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             -----CCHHHHHHHHHHHHHT---HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHH---HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            568888766677776654211   111 11222221  12244999999999999864

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=85.72  E-value=0.31  Score=36.74  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.5

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +..+++.|+.|||||+..
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999865

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=85.66  E-value=0.36  Score=40.24  Aligned_cols=18  Identities=28%  Similarity=0.187  Sum_probs=14.9

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      +-++|.||||+|||..+.
T Consensus         4 ~~i~i~GptgsGKt~la~   21 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSV   21 (322)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHH
Confidence            347899999999998763

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=85.49  E-value=0.33  Score=37.26  Aligned_cols=19  Identities=32%  Similarity=0.415  Sum_probs=16.6

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..+++.|+.|||||+..
T Consensus        28 ~g~~i~l~G~~GsGKSTl~   46 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIA   46 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5677999999999999865

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=85.48  E-value=0.38  Score=40.06  Aligned_cols=17  Identities=24%  Similarity=0.290  Sum_probs=14.5

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      -++|.||||||||..+.
T Consensus        12 ~i~i~GptgsGKt~la~   28 (316)
T 3foz_A           12 AIFLMGPTASGKTALAI   28 (316)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCccCHHHHHH
Confidence            47899999999998763

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=85.43  E-value=0.3  Score=36.12  Aligned_cols=16  Identities=13%  Similarity=-0.004  Sum_probs=14.1

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|+.|||||+..
T Consensus         3 ~i~l~G~~GsGKsT~~   18 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVA   18 (173)
T ss_dssp             EEEEECSSSSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999875

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=85.41  E-value=0.3  Score=36.42  Aligned_cols=16  Identities=19%  Similarity=0.283  Sum_probs=14.1

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|++|||||+.+
T Consensus         4 ~I~i~G~~GsGKST~a   19 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWA   19 (181)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEecCCCCCHHHHH
Confidence            4789999999999865

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=85.28  E-value=0.29  Score=36.51  Aligned_cols=19  Identities=26%  Similarity=0.286  Sum_probs=16.0

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..+++.|+.|||||+..
T Consensus         7 ~g~~i~l~G~~GsGKSTl~   25 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVA   25 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3567899999999999865

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.28  E-value=0.32  Score=42.48  Aligned_cols=54  Identities=22%  Similarity=0.244  Sum_probs=31.9

Q ss_pred             cccCcCCCCCCHHHHHHHHHC---CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          45 VAENFDDMELSEELLRGIYAY---GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        45 ~~~~~~~~~~~~~l~~~l~~~---~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ...+|.+.+=-...++.+++.   -+.+|--++..-   +...+.+++.||+|+|||+.+
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHHH
Confidence            345788887555666555432   111222222221   223467999999999999875

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=85.23  E-value=0.28  Score=38.58  Aligned_cols=21  Identities=29%  Similarity=0.295  Sum_probs=14.0

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..|.-+.+.||+|+|||+..
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             EECCCEEEEECSCC----CHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            456778999999999999865

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=85.22  E-value=0.24  Score=37.28  Aligned_cols=19  Identities=32%  Similarity=0.412  Sum_probs=16.0

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..+++.|+.|||||+..
T Consensus         3 ~g~~I~l~G~~GsGKST~~   21 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQA   21 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456899999999999875

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=85.16  E-value=0.64  Score=39.13  Aligned_cols=42  Identities=12%  Similarity=-0.046  Sum_probs=27.7

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEeccH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILAPTR  125 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~P~~  125 (258)
                      |.-++|.|++|+|||...+..+.......   +.+.+++|+.-..
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            34689999999999987755554433221   1345788887544

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=85.00  E-value=0.99  Score=35.19  Aligned_cols=45  Identities=13%  Similarity=0.075  Sum_probs=27.9

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHhhhhhcC----CcEEEEcccCCCcchHh
Q psy4698          55 SEELLRGIYAYGFEKPSAIQQRAIIPCVRG----NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        55 ~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g----~~~li~~~tGsGKT~~~  101 (258)
                      -..+.+.|+=.|+ .+-.+ ...+.....+    +.+++.||.|+|||..+
T Consensus        27 w~~I~~~l~yq~~-~~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           27 WRPIVQFLRYQQI-EFITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             SHHHHHHHHHTTC-CHHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHHHHHHcCc-CHHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            3456666654443 34444 3444444444    35999999999999865

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=84.98  E-value=0.46  Score=36.71  Aligned_cols=19  Identities=16%  Similarity=0.279  Sum_probs=16.6

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+-+++.||+|+|||...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHH
Confidence            6777999999999999864

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=84.90  E-value=0.34  Score=39.55  Aligned_cols=19  Identities=21%  Similarity=0.293  Sum_probs=16.4

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .++.+++.||+|+|||..+
T Consensus        53 ~~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CCSEEEEESSSSSCHHHHH
T ss_pred             CCCeEEEECcCCCCHHHHH
Confidence            3578999999999999875

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=84.87  E-value=0.53  Score=36.41  Aligned_cols=31  Identities=16%  Similarity=0.198  Sum_probs=22.8

Q ss_pred             CcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .++.++... .+..|..+++.|+.|||||+..
T Consensus        12 ~~~~~r~~~-~~~~~~~i~~~G~~GsGKsT~~   42 (211)
T 1m7g_A           12 LTRSERTEL-RNQRGLTIWLTGLSASGKSTLA   42 (211)
T ss_dssp             CCHHHHHHH-HTSSCEEEEEECSTTSSHHHHH
T ss_pred             cCHHHhhcc-cCCCCCEEEEECCCCCCHHHHH
Confidence            345555553 3556778999999999999865

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=84.72  E-value=0.36  Score=37.25  Aligned_cols=22  Identities=27%  Similarity=0.466  Sum_probs=17.1

Q ss_pred             hhhcCCcEEEEcccCCCcchHh
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..|.-+.+.||.|+|||+..
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl   37 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVV   37 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHHH
Confidence            5678888999999999999864

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=84.44  E-value=2.1  Score=46.38  Aligned_cols=47  Identities=13%  Similarity=0.109  Sum_probs=31.7

Q ss_pred             CHHHHHHHHHCCCCCCcHHH-HHHh---hhhhcCCcEEEEcccCCCcchHhH
Q psy4698          55 SEELLRGIYAYGFEKPSAIQ-QRAI---IPCVRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        55 ~~~l~~~l~~~~~~~~~~~Q-~~~~---~~l~~g~~~li~~~tGsGKT~~~l  102 (258)
                      ...+.+.+.+.|+. +.+.+ .+++   +.+...+.+++.||||+|||.++-
T Consensus       874 ~~ai~~~~~~~~L~-~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          874 RKKIQEIAKQRHLV-TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHTTCC-CCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHcCCc-cCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            35566667778884 45544 3333   334455669999999999999873

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=84.36  E-value=0.56  Score=38.74  Aligned_cols=20  Identities=30%  Similarity=0.390  Sum_probs=16.9

Q ss_pred             hcCCcEEEEcccCCCcchHh
Q psy4698          82 VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+.++++.|++|+|||..+
T Consensus        23 ~~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             STTSCEEEESCTTSCHHHHH
T ss_pred             CCCCcEEEECCCCchHHHHH
Confidence            34568999999999999865

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=84.30  E-value=0.79  Score=38.72  Aligned_cols=39  Identities=15%  Similarity=0.147  Sum_probs=27.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|.-+++.|++|+|||...+..+......   +.+++|+.-.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~---g~~vlyi~~E   98 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA---GGIAAFIDAE   98 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            45679999999999998765555444332   3468888743

>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=84.29  E-value=14  Score=33.48  Aligned_cols=82  Identities=18%  Similarity=0.231  Sum_probs=54.4

Q ss_pred             HHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHH
Q psy4698         104 SILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDM  179 (258)
Q Consensus       104 ~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~  179 (258)
                      .++..+.....+.++||.|+++.-+.+.+..++..    ++.+..++++....+..   .... ...+|+|+|.     .
T Consensus       256 ~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~-----a  326 (591)
T 2v1x_A          256 DIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV-----A  326 (591)
T ss_dssp             HHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT-----T
T ss_pred             HHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec-----h
Confidence            34444443334568999999999999999988775    46777788876544322   2222 3478999994     1


Q ss_pred             HhcCCCCCCCccEEEE
Q psy4698         180 ISRGALSTKQIRMFVL  195 (258)
Q Consensus       180 l~~~~~~~~~l~~lVv  195 (258)
                      + ..+++.+++++||.
T Consensus       327 ~-~~GID~p~V~~VI~  341 (591)
T 2v1x_A          327 F-GMGIDKPDVRFVIH  341 (591)
T ss_dssp             S-CTTCCCSCEEEEEE
T ss_pred             h-hcCCCcccccEEEE
Confidence            1 23466777777774

>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=84.07  E-value=7.5  Score=32.64  Aligned_cols=74  Identities=12%  Similarity=0.226  Sum_probs=51.5

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++.-+...++.++..+    ..+..++++....+.   .....+ ..+|+|+|.     . -..++++++
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L~~~~----~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~-----~-~~~Gidip~  326 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKITDLG----YSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD-----L-LTRGIDIQA  326 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHHT----CCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS-----C-SSSSCCCTT
T ss_pred             CCCcEEEEEecHHHHHHHHHHHHhcC----CCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----c-cccCCCccC
Confidence            44589999999999999999887763    566677777654332   223333 478999994     2 234578888


Q ss_pred             ccEEEEcc
Q psy4698         190 IRMFVLDE  197 (258)
Q Consensus       190 l~~lVvDE  197 (258)
                      ++++|.-+
T Consensus       327 ~~~Vi~~~  334 (400)
T 1s2m_A          327 VNVVINFD  334 (400)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEeC
Confidence            88887543

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=84.04  E-value=0.41  Score=37.57  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=16.7

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ...|+-+++.||.|+|||+..
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHH
Confidence            456778999999999999864

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=83.78  E-value=0.39  Score=38.36  Aligned_cols=18  Identities=33%  Similarity=0.383  Sum_probs=15.4

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+.+++.||+|+|||..+
T Consensus        45 ~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A           45 PKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            356999999999999865

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=83.74  E-value=0.93  Score=46.22  Aligned_cols=89  Identities=13%  Similarity=0.201  Sum_probs=53.0

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      |+.+.+.||.|||||+.++-.+.+ ...  .+..++|+.+-.++....   +++++-+++                    
T Consensus      1431 g~~iei~g~~~sGkttl~~~~~a~-~~~--~g~~~~~i~~e~~~~~~~---~~~~Gv~~~-------------------- 1484 (1706)
T 3cmw_A         1431 GRIVEIYGPESSGKTTLTLQVIAA-AQR--EGKTCAFIDAEHALDPIY---ARKLGVDID-------------------- 1484 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHH-HHH--TTCCEEEECTTSCCCHHH---HHHTTCCGG--------------------
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH-HHh--cCCeEEEEecCCCCCHHH---HHHcCCCHH--------------------
Confidence            367999999999999987544433 332  244799998876665554   445543222                    


Q ss_pred             cCCcEEEeChH---HHHHHHhcCCCCCCCccEEEEccchhhh
Q psy4698         164 AGAQVVVGTPG---RVFDMISRGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       164 ~~~~Ilv~Tp~---~l~~~l~~~~~~~~~l~~lVvDE~h~~~  202 (258)
                         ++++.-|+   +.++.+.. .+.-..+++||||.+-.+.
T Consensus      1485 ---~l~~~~p~~~e~~l~~~~~-~~~s~~~~~vvvDsv~al~ 1522 (1706)
T 3cmw_A         1485 ---NLLCSQPDTGEQALEICDA-LARSGAVDVIVVDSVAALT 1522 (1706)
T ss_dssp             ---GCEEECCSSHHHHHHHHHH-HHHHTCCSEEEESCSTTCC
T ss_pred             ---HeEEeCCCcHHHHHHHHHH-HHHcCCCCEEEEccHHhCC
Confidence               25555553   33332211 0111246799999988654

>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=83.66  E-value=3  Score=36.27  Aligned_cols=68  Identities=7%  Similarity=0.040  Sum_probs=45.3

Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh-cCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE-AGAQVVVGTPGRVFDMISRGALSTKQIRMF  193 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~l  193 (258)
                      +.+++|.||++.-+...+..++..    +..+..+++.... ....... ...+|+|+|.     .+. .+++++ +++|
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~~R~-~~~~~F~~g~~~vLVaT~-----v~e-~GiDip-v~~V  244 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFE-REYPTIKQKKPDFILATD-----IAE-MGANLC-VERV  244 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC---------CCCSEEEESS-----STT-CCTTCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecchhHH-HHHhhhcCCCceEEEECC-----hhh-eeeccC-ceEE
Confidence            358999999999999999988776    4667777774322 2223333 3489999994     233 346777 8887


Q ss_pred             E
Q psy4698         194 V  194 (258)
Q Consensus       194 V  194 (258)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            7

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=83.53  E-value=0.44  Score=36.35  Aligned_cols=19  Identities=26%  Similarity=0.431  Sum_probs=16.3

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..+++.|+.|||||+..
T Consensus         3 ~~~~I~l~G~~GsGKsT~~   21 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQC   21 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3567899999999999875

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=83.32  E-value=0.37  Score=36.41  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=15.4

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +..+++.|+.|||||+..
T Consensus         5 ~~~I~l~G~~GsGKST~~   22 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLS   22 (193)
T ss_dssp             CEEEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999875

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=83.28  E-value=5  Score=35.62  Aligned_cols=35  Identities=17%  Similarity=0.225  Sum_probs=22.3

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .++++|++|+|||+...-.+. .+...  +.+++++..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~-~l~~~--G~kVllVd~  137 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAY-YYQRK--GWKTCLICA  137 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH-HHHHT--TCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHhC--CCeEEEEec
Confidence            588999999999987643332 22222  345666664

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=83.26  E-value=8.9  Score=33.69  Aligned_cols=25  Identities=24%  Similarity=0.490  Sum_probs=19.9

Q ss_pred             hhhhhcCCcEEEEcccCCCcchHhH
Q psy4698          78 IIPCVRGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        78 ~~~l~~g~~~li~~~tGsGKT~~~l  102 (258)
                      +..+..|+..++.|+.|.|||....
T Consensus       145 L~pi~kGq~~~i~G~sGvGKTtL~~  169 (473)
T 1sky_E          145 LAPYIKGGKIGLFGGAGVGKTVLIQ  169 (473)
T ss_dssp             HSCEETTCEEEEECCSSSCHHHHHH
T ss_pred             HhhhccCCEEEEECCCCCCccHHHH
Confidence            3345678889999999999998654

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=83.23  E-value=0.5  Score=39.76  Aligned_cols=19  Identities=47%  Similarity=0.613  Sum_probs=16.2

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ++.+++.||+|+|||..+.
T Consensus        70 ~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            3579999999999998763

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=83.22  E-value=1  Score=38.23  Aligned_cols=39  Identities=15%  Similarity=0.072  Sum_probs=27.5

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      .|.-+++.|++|+|||..++..+......   +.+++|+...
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~---g~~vlyid~E  100 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAE  100 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeCC
Confidence            45679999999999998876555444332   2368888753

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=83.16  E-value=0.54  Score=39.33  Aligned_cols=17  Identities=18%  Similarity=0.227  Sum_probs=14.8

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .++|.||||||||....
T Consensus         7 ~i~i~GptGsGKTtla~   23 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAM   23 (323)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999998763

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=83.13  E-value=0.47  Score=36.32  Aligned_cols=17  Identities=29%  Similarity=0.577  Sum_probs=14.6

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +-++++||.|+|||...
T Consensus         2 RpIVi~GPSG~GK~Tl~   18 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45899999999999864

>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=83.12  E-value=7.9  Score=32.32  Aligned_cols=76  Identities=8%  Similarity=0.148  Sum_probs=52.9

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.++++..+...++.++..    +..+..++++....+.   .....+ ..+|+|+|.     . -..++++++
T Consensus       249 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~-~~~Gidi~~  318 (391)
T 1xti_A          249 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----L-FGRGMDIER  318 (391)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC-----C-CSSCBCCTT
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC-----h-hhcCCCccc
Confidence            4458999999999999999888775    4566777777554332   222233 478999994     2 234578888


Q ss_pred             ccEEEEccch
Q psy4698         190 IRMFVLDEAD  199 (258)
Q Consensus       190 l~~lVvDE~h  199 (258)
                      ++++|.-+..
T Consensus       319 ~~~Vi~~~~p  328 (391)
T 1xti_A          319 VNIAFNYDMP  328 (391)
T ss_dssp             EEEEEESSCC
T ss_pred             CCEEEEeCCC
Confidence            9998875543

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=83.09  E-value=0.41  Score=36.72  Aligned_cols=31  Identities=16%  Similarity=0.257  Sum_probs=21.5

Q ss_pred             CcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          70 PSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        70 ~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+...+ ....|..+++.|+.|||||+..
T Consensus        12 ~~~~~~~~~-~~~~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           12 VEKVDRQRL-LDQKGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             CCHHHHHHH-HTSCCEEEEEECSTTSSHHHHH
T ss_pred             cCHHHHHHh-cCCCCeEEEEECCCCCCHHHHH
Confidence            344444433 2345677999999999999865

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=83.04  E-value=0.3  Score=37.65  Aligned_cols=24  Identities=13%  Similarity=0.017  Sum_probs=18.9

Q ss_pred             hhhhhcCCcEEEEcccCCCcchHh
Q psy4698          78 IIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ++.+..+.-+.+.|++|||||+..
T Consensus        15 ~~~~~~~~~i~i~G~~GsGKSTl~   38 (207)
T 2qt1_A           15 VPRGSKTFIIGISGVTNSGKTTLA   38 (207)
T ss_dssp             CCCSCCCEEEEEEESTTSSHHHHH
T ss_pred             cccCCCCeEEEEECCCCCCHHHHH
Confidence            344556677899999999999865

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=83.03  E-value=0.45  Score=35.98  Aligned_cols=19  Identities=21%  Similarity=0.366  Sum_probs=16.3

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+++.|+.|||||+..
T Consensus         8 ~~~~I~l~G~~GsGKsT~~   26 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQC   26 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4567999999999999875

>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=82.89  E-value=9.2  Score=32.23  Aligned_cols=74  Identities=12%  Similarity=0.214  Sum_probs=51.5

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      ...++||.|+++..+....+.+...    +..+..++++....+..   .... ...+|+|+|.     . -..++++++
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~-~~~Gidi~~  344 (410)
T 2j0s_A          275 TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----V-WARGLDVPQ  344 (410)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----G-GSSSCCCTT
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC-----h-hhCcCCccc
Confidence            3448999999999999999888775    45667777776543322   2222 3478999995     2 234578889


Q ss_pred             ccEEEEcc
Q psy4698         190 IRMFVLDE  197 (258)
Q Consensus       190 l~~lVvDE  197 (258)
                      ++++|.-+
T Consensus       345 v~~Vi~~~  352 (410)
T 2j0s_A          345 VSLIINYD  352 (410)
T ss_dssp             EEEEEESS
T ss_pred             CCEEEEEC
Confidence            98888643

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=82.59  E-value=0.5  Score=36.74  Aligned_cols=19  Identities=16%  Similarity=0.251  Sum_probs=16.0

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+++.|++|||||+..
T Consensus         3 ~~~~I~l~G~~GsGKsT~a   21 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQA   21 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3456899999999999875

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=82.46  E-value=0.47  Score=36.30  Aligned_cols=17  Identities=24%  Similarity=0.446  Sum_probs=15.0

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      ..+++.|+.|||||+.+
T Consensus        19 ~~I~l~G~~GsGKSTla   35 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVG   35 (202)
T ss_dssp             SCEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            46899999999999875

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=82.33  E-value=0.51  Score=36.42  Aligned_cols=19  Identities=21%  Similarity=0.228  Sum_probs=15.8

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|.-+.|.||+|||||+..
T Consensus        21 ~g~~v~I~G~sGsGKSTl~   39 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLS   39 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4567899999999999754

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=82.26  E-value=0.6  Score=39.35  Aligned_cols=17  Identities=18%  Similarity=0.200  Sum_probs=14.7

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      -++|.||||||||..+.
T Consensus         9 lI~I~GptgSGKTtla~   25 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSI   25 (340)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             eEEEECCCcCcHHHHHH
Confidence            58999999999998763

>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=82.20  E-value=8  Score=33.04  Aligned_cols=77  Identities=17%  Similarity=0.265  Sum_probs=50.6

Q ss_pred             cccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEEC--------CcchH---HHHHHHh-cCCcEEEeChHHHHHHH
Q psy4698         113 IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIG--------GTIVR---DDIRKLE-AGAQVVVGTPGRVFDMI  180 (258)
Q Consensus       113 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~~---~~~~~~~-~~~~Ilv~Tp~~l~~~l  180 (258)
                      ..+.++||.++++..+....+.++..    ++.+..++|        +....   ....... +.++|+|+|.     .+
T Consensus       359 ~~~~k~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~-----~~  429 (494)
T 1wp9_A          359 KQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS-----VG  429 (494)
T ss_dssp             CTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG-----GG
T ss_pred             CCCCeEEEEEccHHHHHHHHHHHHHc----CCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECC-----cc
Confidence            34568999999999999999888776    456666666        33222   1222233 3478999993     22


Q ss_pred             hcCCCCCCCccEEEEccch
Q psy4698         181 SRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       181 ~~~~~~~~~l~~lVvDE~h  199 (258)
                       ..++++..+++||+-+..
T Consensus       430 -~~Gldl~~~~~Vi~~d~~  447 (494)
T 1wp9_A          430 -EEGLDVPEVDLVVFYEPV  447 (494)
T ss_dssp             -GGGGGSTTCCEEEESSCC
T ss_pred             -ccCCCchhCCEEEEeCCC
Confidence             234678888888866544

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=82.18  E-value=0.5  Score=34.94  Aligned_cols=18  Identities=17%  Similarity=0.307  Sum_probs=15.6

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.|+.|||||++.-
T Consensus         8 ~~i~l~G~~GsGKSTva~   25 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQ   25 (168)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            578999999999998763

>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=82.12  E-value=6.5  Score=36.14  Aligned_cols=77  Identities=14%  Similarity=0.291  Sum_probs=54.6

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH---HHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR---KLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++..+......++..    ++.+..++++....+...   ... +..+|+|||-     . -..++++++
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~-----~-l~~GlDip~  513 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEI----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----L-LREGLDIPE  513 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC-----C-CSTTCCCTT
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc-----h-hhCCcccCC
Confidence            3458999999999999999988776    456666676654433222   233 3488999984     2 244578889


Q ss_pred             ccEEEEccchh
Q psy4698         190 IRMFVLDEADE  200 (258)
Q Consensus       190 l~~lVvDE~h~  200 (258)
                      ++++|+-+++.
T Consensus       514 v~lVi~~d~d~  524 (661)
T 2d7d_A          514 VSLVAILDADK  524 (661)
T ss_dssp             EEEEEETTTTC
T ss_pred             CCEEEEeCccc
Confidence            99999988764

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=82.09  E-value=1.1  Score=37.18  Aligned_cols=16  Identities=25%  Similarity=0.320  Sum_probs=13.7

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -++|.|+.|||||+..
T Consensus         6 v~~i~G~~GaGKTTll   21 (318)
T 1nij_A            6 VTLLTGFLGAGKTTLL   21 (318)
T ss_dssp             EEEEEESSSSSCHHHH
T ss_pred             EEEEEecCCCCHHHHH
Confidence            3789999999999864

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=81.90  E-value=0.51  Score=36.74  Aligned_cols=19  Identities=16%  Similarity=0.223  Sum_probs=15.9

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      ...+++.|++|||||+..-
T Consensus         5 ~~~I~l~G~~GsGKsT~~~   23 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCE   23 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3568999999999998763

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=81.87  E-value=0.38  Score=36.38  Aligned_cols=17  Identities=29%  Similarity=0.403  Sum_probs=14.4

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .-+++.|++|+|||+..
T Consensus         3 ~ii~l~G~~GaGKSTl~   19 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTC   19 (189)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            34789999999999865

>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=81.87  E-value=12  Score=32.20  Aligned_cols=70  Identities=13%  Similarity=0.214  Sum_probs=50.6

Q ss_pred             eEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCCccE
Q psy4698         117 QALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQIRM  192 (258)
Q Consensus       117 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~  192 (258)
                      ++||.|+++.-+....+.+...    ++.+..++|+....+..   ....+ ..+|+|+|.     .+ ..+++++++++
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----v~-~rGlDi~~v~~  371 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS-----VA-SRGLDIKNIKH  371 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG-----GG-TSSCCCTTCCE
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch-----hh-hCCCCcccCCE
Confidence            4999999999999999888765    46677788876544332   22333 479999995     23 34578889998


Q ss_pred             EEEc
Q psy4698         193 FVLD  196 (258)
Q Consensus       193 lVvD  196 (258)
                      +|.=
T Consensus       372 VI~~  375 (434)
T 2db3_A          372 VINY  375 (434)
T ss_dssp             EEES
T ss_pred             EEEE
Confidence            8853

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=81.83  E-value=0.55  Score=35.11  Aligned_cols=18  Identities=28%  Similarity=0.237  Sum_probs=11.5

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +..+++.|+.|||||+.+
T Consensus         5 ~~~I~l~G~~GsGKST~a   22 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTA   22 (183)
T ss_dssp             CCEEEEECCC----CHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999875

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=81.74  E-value=0.54  Score=38.53  Aligned_cols=17  Identities=29%  Similarity=0.423  Sum_probs=14.9

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .-++++|+.|||||+.+
T Consensus        34 ~livl~G~sGsGKSTla   50 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLR   50 (287)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45899999999999875

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=81.72  E-value=0.51  Score=36.93  Aligned_cols=18  Identities=17%  Similarity=0.169  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +..+++.|++|||||+..
T Consensus         7 ~~~I~l~G~~GsGKsT~a   24 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVS   24 (227)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456899999999999875

>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=81.71  E-value=10  Score=33.74  Aligned_cols=73  Identities=16%  Similarity=0.150  Sum_probs=50.4

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH---HHHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD---IRKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+++.-++.++..++..    ++.+..++++....+.   ..... ...+|+|+|.     . -..++++++
T Consensus       235 ~~~~~IVf~~sr~~~e~l~~~L~~~----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~-----a-~~~GiD~p~  304 (523)
T 1oyw_A          235 RGKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----A-FGMGINKPN  304 (523)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----T-SCTTTCCTT
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec-----h-hhCCCCccC
Confidence            4458999999999999999988775    4667778887654332   22222 3478999995     1 233466777


Q ss_pred             ccEEEEc
Q psy4698         190 IRMFVLD  196 (258)
Q Consensus       190 l~~lVvD  196 (258)
                      +++||.-
T Consensus       305 v~~VI~~  311 (523)
T 1oyw_A          305 VRFVVHF  311 (523)
T ss_dssp             CCEEEES
T ss_pred             ccEEEEE
Confidence            8777753

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=81.70  E-value=0.5  Score=35.39  Aligned_cols=19  Identities=42%  Similarity=0.497  Sum_probs=16.0

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|..+++.|+.|||||+..
T Consensus         4 ~g~~i~l~G~~GsGKST~~   22 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVS   22 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4566899999999999865

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=81.69  E-value=0.52  Score=35.51  Aligned_cols=18  Identities=22%  Similarity=0.206  Sum_probs=15.2

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +..+++.|++|||||+.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a   20 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQC   20 (196)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            345899999999999875

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=81.60  E-value=0.71  Score=38.44  Aligned_cols=52  Identities=13%  Similarity=0.069  Sum_probs=29.2

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHH-HHhh-hhhcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQ-RAII-PCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~-~~~~-~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ..|++++=...+++.|.+.-.   .+.+. +.+. .....+.+++.||+|+|||..+
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHH---HHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHH---HHHhCHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            467777666666666643210   00000 0000 1122367999999999999875

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=81.51  E-value=0.59  Score=34.80  Aligned_cols=16  Identities=19%  Similarity=0.358  Sum_probs=14.4

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|+.|||||...
T Consensus         6 ~i~i~G~~GsGKsTla   21 (175)
T 1via_A            6 NIVFIGFMGSGKSTLA   21 (175)
T ss_dssp             CEEEECCTTSCHHHHH
T ss_pred             EEEEEcCCCCCHHHHH
Confidence            5899999999999876

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=81.29  E-value=0.61  Score=39.60  Aligned_cols=18  Identities=22%  Similarity=0.425  Sum_probs=15.9

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ..++++.||+|+|||..+
T Consensus        72 ~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            457999999999999875

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=81.27  E-value=0.53  Score=35.69  Aligned_cols=19  Identities=16%  Similarity=0.275  Sum_probs=16.1

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+++.|++|||||+..
T Consensus        11 ~~~~I~l~G~~GsGKsT~a   29 (199)
T 2bwj_A           11 KCKIIFIIGGPGSGKGTQC   29 (199)
T ss_dssp             HSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4566899999999999875

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=81.13  E-value=0.68  Score=37.19  Aligned_cols=19  Identities=26%  Similarity=0.349  Sum_probs=17.2

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+.+++.|++|+|||+..
T Consensus        47 ~g~~i~l~G~~GsGKSTl~   65 (250)
T 3nwj_A           47 NGRSMYLVGMMGSGKTTVG   65 (250)
T ss_dssp             TTCCEEEECSTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3889999999999999875

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=81.11  E-value=0.52  Score=38.65  Aligned_cols=17  Identities=18%  Similarity=0.030  Sum_probs=14.9

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.||+|+|||..+
T Consensus        37 ~~lLl~GppGtGKT~la   53 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC   53 (293)
T ss_dssp             SEEEEEECTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            56899999999999865

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=81.09  E-value=0.65  Score=34.83  Aligned_cols=17  Identities=18%  Similarity=0.268  Sum_probs=14.8

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      ..+++.|+.|||||.+.
T Consensus         3 ~~I~l~G~~GsGKsT~a   19 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIG   19 (184)
T ss_dssp             CSEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35899999999999876

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=81.08  E-value=0.55  Score=36.26  Aligned_cols=16  Identities=19%  Similarity=0.412  Sum_probs=14.0

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|+.|||||+..
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQA   17 (216)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999876

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=81.05  E-value=1.5  Score=36.25  Aligned_cols=36  Identities=31%  Similarity=0.402  Sum_probs=22.2

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA  122 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~  122 (258)
                      |..+.+.||+|+|||+..-  .+..+.... +.++.+..
T Consensus       102 g~vi~lvG~nGsGKTTll~--~Lagll~~~-~g~V~l~g  137 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIA--KLGRYYQNL-GKKVMFCA  137 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHH--HHHHHHHTT-TCCEEEEC
T ss_pred             CeEEEEECCCCCcHHHHHH--HHHHHHHhc-CCEEEEEe
Confidence            5568899999999998642  222333322 33566654

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=80.99  E-value=0.63  Score=34.41  Aligned_cols=17  Identities=18%  Similarity=0.225  Sum_probs=14.7

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.|+.|||||.+.
T Consensus         3 ~~I~l~G~~GsGKsT~a   19 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVG   19 (173)
T ss_dssp             CCEEEESCTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            35899999999999875

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=80.95  E-value=0.54  Score=35.33  Aligned_cols=16  Identities=25%  Similarity=0.345  Sum_probs=14.0

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|+.|||||+..
T Consensus         3 ~I~i~G~~GsGKsT~~   18 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEEECTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999875

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=80.85  E-value=0.55  Score=35.95  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.5

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +.-+++.|+.|||||+..
T Consensus         4 ~~~I~i~G~~GsGKsT~~   21 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQA   21 (213)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHH
Confidence            456899999999999875

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=80.70  E-value=1.2  Score=37.77  Aligned_cols=40  Identities=23%  Similarity=0.194  Sum_probs=26.5

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .|.-++|.||+|+|||...+..+... ..  .+.+++|+....
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~-~~--~gg~VlyId~E~   99 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEA-QK--MGGVAAFIDAEH   99 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHH-HH--TTCCEEEEESSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH-Hh--cCCeEEEEeccc
Confidence            45679999999999998664444332 22  234688887543

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=80.69  E-value=0.59  Score=35.86  Aligned_cols=19  Identities=16%  Similarity=0.356  Sum_probs=16.4

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+..+++.|+.|||||+..
T Consensus         9 ~~~~I~l~G~~GsGKST~~   27 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQS   27 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHH
Confidence            4567999999999999875

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=80.38  E-value=0.59  Score=35.23  Aligned_cols=20  Identities=30%  Similarity=0.383  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHhH
Q psy4698          83 RGNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l  102 (258)
                      .|..+++.|+.|||||+..-
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~   31 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIAT   31 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHH
Confidence            45668999999999998753

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=80.30  E-value=0.55  Score=36.15  Aligned_cols=19  Identities=16%  Similarity=0.090  Sum_probs=15.6

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|.-+.+.|++|||||+..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~   23 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLA   23 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHH
Confidence            4556889999999999864

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=80.28  E-value=0.68  Score=35.34  Aligned_cols=17  Identities=24%  Similarity=0.311  Sum_probs=14.9

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      ..+++.|+.|||||+..
T Consensus        21 ~~I~l~G~~GsGKST~a   37 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQA   37 (201)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45899999999999875

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=80.20  E-value=1.3  Score=36.56  Aligned_cols=19  Identities=21%  Similarity=0.405  Sum_probs=15.6

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|.-+.+.|++|+|||+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll  117 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSL  117 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            3456889999999999864

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=80.13  E-value=0.57  Score=39.02  Aligned_cols=18  Identities=28%  Similarity=0.420  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      ..++++.||+|+|||..+
T Consensus        45 ~~~vLl~G~~GtGKT~la   62 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAV   62 (350)
T ss_dssp             GCCEEEECCGGGCTTHHH
T ss_pred             CceEEEECCCCccHHHHH
Confidence            456999999999999865

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=80.11  E-value=0.6  Score=37.04  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=27.4

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCC--CccEEEE
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNN--DVQVILL  226 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~--~~~~i~~  226 (258)
                      +-+++++||.-.-+|......+..+++.+..  ...+|+.
T Consensus       163 ~p~llllDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~v  202 (235)
T 3tif_A          163 NPPIILADQPTWALDSKTGEKIMQLLKKLNEEDGKTVVVV  202 (235)
T ss_dssp             CCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHCCEEEEE
T ss_pred             CCCEEEEeCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence            3469999999988887777888888877753  3434443

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=80.04  E-value=0.63  Score=35.97  Aligned_cols=16  Identities=19%  Similarity=0.324  Sum_probs=14.0

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.|+.|||||+..
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQG   17 (216)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999876

---

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	258
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-61
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-58
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-55
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	3e-54
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-46
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	8e-46
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	9e-44
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	4e-41
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-35
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-24
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	2e-24
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	4e-24
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	5e-21
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	1e-17
d1gm5a3	264	c.37.1.19 (A:286-549) RecG helicase domain {Thermo	8e-06
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	2e-05
d2eyqa3	233	c.37.1.19 (A:546-778) Transcription-repair couplin	4e-04

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  190 bits (484), Expect = 2e-61
 Identities = 159/218 (72%), Positives = 194/218 (88%), Gaps = 1/218 (0%)

Query: 36  GLIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGT 95
           G+IE+NW+ + ++FDDM LSE LLRGIYAYGFEKPSAIQQRAI+PC++G DVIAQAQSGT
Sbjct: 1   GVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGT 60

Query: 96  GKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIV 155
           GKTATF+ISILQQ++ ++K  QAL+LAPTRELAQQIQKVV+ALGD+M  SCHACIGGT V
Sbjct: 61  GKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNV 120

Query: 156 RDDIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVF 214
           R +++KL+     ++VGTPGRVFDM++R  LS K I+MFVLDEADEMLSRGFKDQIYD+F
Sbjct: 121 RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIF 180

Query: 215 KHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK 252
           + LN++ QV+LLSATMP+DVL+V+ KFMRDPI+ILVKK
Sbjct: 181 QKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  181 bits (461), Expect = 4e-58
 Identities = 136/213 (63%), Positives = 166/213 (77%), Gaps = 1/213 (0%)

Query: 38  IETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGK 97
           I+TN+D V   FDDMEL E LLRG++ YGFE+PSAIQQRAI+P + G+DV+AQAQSGTGK
Sbjct: 1   IQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGK 60

Query: 98  TATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRD 157
           T TFSI+ LQ++D ++K  QAL+LAPTRELA QIQKVV+AL   M +  HACIGGT   +
Sbjct: 61  TGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVE 120

Query: 158 DIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL 217
           D   L   AQ+VVGTPGRVFD I R    T +I+MF+LDEADEMLS GFK+QIY +F  L
Sbjct: 121 DAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLL 179

Query: 218 NNDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
               QV+LLSATMP DVL+V+ KFMR+P++ILV
Sbjct: 180 PPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 212

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  175 bits (444), Expect = 2e-55
 Identities = 79/205 (38%), Positives = 128/205 (62%), Gaps = 3/205 (1%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG-NDVIAQAQSGTGKTATFSISIL 106
           NF+++ LS+ +L  I   GFEKP+ IQ + I   +    +++AQA++G+GKTA+F+I ++
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 107 QQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
           + V++N      +IL PTRELA Q+   + +L    ++      GG  +   I+ L+  A
Sbjct: 65  ELVNENNGIEA-IILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 122

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
            +VVGTPGR+ D I+RG L+ K ++ F+LDEADEML+ GF   +  +    N D +++L 
Sbjct: 123 NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLF 182

Query: 227 SATMPADVLDVSMKFMRDPIKILVK 251
           SATMP ++L+++ K+M D   I  K
Sbjct: 183 SATMPREILNLAKKYMGDYSFIKAK 207

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  172 bits (437), Expect = 3e-54
 Identities = 142/216 (65%), Positives = 177/216 (81%), Gaps = 1/216 (0%)

Query: 38  IETNWD-HVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTG 96
            ET+ +  V   FD M L E+LLRGIYAYGFEKPSAIQQRAI   ++G DVIAQ+QSGTG
Sbjct: 7   FETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTG 66

Query: 97  KTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVR 156
           KTATFSIS+LQ +D  ++E QALILAPTRELA QIQK ++ALGD+M+V CHACIGGT V 
Sbjct: 67  KTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVG 126

Query: 157 DDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH 216
           +DIRKL+ G  VV GTPGRVFDMI R +L T+ I+M VLDEADEML++GFK+QIYDV+++
Sbjct: 127 EDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRY 186

Query: 217 LNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKK 252
           L    QV+L+SAT+P ++L+++ KFM DPI+ILVK+
Sbjct: 187 LPPATQVVLISATLPHEILEMTNKFMTDPIRILVKR 222

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  150 bits (380), Expect = 7e-46
 Identities = 75/205 (36%), Positives = 114/205 (55%), Gaps = 3/205 (1%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F D  L  ELLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ LQQ
Sbjct: 3   FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 62

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGG-TIVRDDIRKLEA-GA 166
           ++    +   L++  TRELA QI K       +M     A   G   ++ D   L+    
Sbjct: 63  LEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCP 122

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVIL 225
            +VVGTPGR+  +    +L+ K I+ F+LDE D+ML +   +  + ++F+   ++ QV++
Sbjct: 123 HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMM 182

Query: 226 LSATMPADVLDVSMKFMRDPIKILV 250
            SAT+  ++  V  KFM+DP++I V
Sbjct: 183 FSATLSKEIRPVCRKFMQDPMEIFV 207

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score =  151 bits (382), Expect = 8e-46
 Identities = 70/225 (31%), Positives = 114/225 (50%), Gaps = 13/225 (5%)

Query: 39  ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKT 98
           + +  +V ENFD+++L   +   I    +++P+ IQ+ AI   +   D++A AQ+G+GKT
Sbjct: 13  DYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKT 72

Query: 99  ATFSISILQQVDQN---------IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHAC 149
           A F I I+  +                + LILAPTRELA QI            +     
Sbjct: 73  AAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVV 132

Query: 150 IGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQ 209
            GG      IR+++ G  ++V TPGR+ D I +  +S +  +  VLDEAD ML  GF+ Q
Sbjct: 133 YGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQ 192

Query: 210 IYDVFKHLN----NDVQVILLSATMPADVLDVSMKFMRDPIKILV 250
           I  + +  N     + Q ++ SAT P ++  ++  F+ + I + V
Sbjct: 193 IRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV 237

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  145 bits (365), Expect = 9e-44
 Identities = 76/202 (37%), Positives = 117/202 (57%), Gaps = 1/202 (0%)

Query: 48  NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQ 107
            F+D  L  ELL GI+  G+EKPS IQ+ +I   + G D++A+A++GTGK+  + I +L+
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 108 QVDQNIKECQALILAPTRELAQQI-QKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA 166
           ++D      QA+++ PTRELA Q+ Q  +            A  GGT +RDDI +L+   
Sbjct: 64  RLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTV 123

Query: 167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILL 226
            VV+ TPGR+ D+I +G      ++M VLDEAD++LS+ F   + D+   L  + Q++L 
Sbjct: 124 HVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLY 183

Query: 227 SATMPADVLDVSMKFMRDPIKI 248
           SAT P  V       +  P +I
Sbjct: 184 SATFPLSVQKFMNSHLEKPYEI 205

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  138 bits (348), Expect = 4e-41
 Identities = 90/204 (44%), Positives = 123/204 (60%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F+D  L  ELL GI+  GFEKPS IQ+ AI   + G D++A+A++GTGKTA F I  L++
Sbjct: 3   FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 62

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQV 168
           V   + + QALI+ PTRELA Q  +VV  LG    +SC    GGT +RDDI +L     +
Sbjct: 63  VKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHI 122

Query: 169 VVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA 228
           +VGTPGRV D+ SR         +F++DEAD+MLSR FK  I  +   L    Q +L SA
Sbjct: 123 LVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSA 182

Query: 229 TMPADVLDVSMKFMRDPIKILVKK 252
           T P  V +  +K +  P +I + +
Sbjct: 183 TFPLTVKEFMVKHLHKPYEINLME 206

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score =  123 bits (308), Expect = 3e-35
 Identities = 60/206 (29%), Positives = 100/206 (48%), Gaps = 4/206 (1%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F        ++  I    F KP+ IQ+R I   +RG  ++ Q+Q+GTGKT  + + I+++
Sbjct: 3   FTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEK 62

Query: 109 VDQNIKECQALILA----PTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEA 164
           +     E QA+I A       ++  +  K+         +     IGGT  +  + KL  
Sbjct: 63  IKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNV 122

Query: 165 GAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI 224
              +V+GTPGR+ D I   AL      + V+DEAD ML  GF   +  +   +  D+Q++
Sbjct: 123 QPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQML 182

Query: 225 LLSATMPADVLDVSMKFMRDPIKILV 250
           + SAT+P  +     K+M +P  + V
Sbjct: 183 VFSATIPEKLKPFLKKYMENPTFVHV 208

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 95.7 bits (237), Expect = 2e-24
 Identities = 31/225 (13%), Positives = 67/225 (29%), Gaps = 28/225 (12%)

Query: 49  FDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQ 108
           F +  L +E     +     +P AIQ+      +R     A A +G GKT+      L  
Sbjct: 24  FPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFL 82

Query: 109 VDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS------CHACIGGTIVRDDIRKL 162
             +     +  ++ PT  L  Q  + +    +   V        +        +++  + 
Sbjct: 83  ALKG---KRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQN 139

Query: 163 EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-----------GFKDQIY 211
               ++V+ T   +                  +D+ D +L             GF   + 
Sbjct: 140 LRNFKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLK 195

Query: 212 DVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEELT 256
                      +++ +AT          +  R  +   +    +T
Sbjct: 196 TKSWVGEARGCLMVSTATAKKGKKA---ELFRQLLNFDIGSSRIT 237

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 28/207 (13%), Positives = 68/207 (32%), Gaps = 17/207 (8%)

Query: 49  FDDMELSE---ELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISI 105
            + + L     ++L+  +  G+++    Q+  I   + G D +    +G GK+  + I  
Sbjct: 4   AEVLNLESGAKQVLQETF--GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPA 61

Query: 106 LQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG 165
           L            ++++P   L +     + A G   +           +          
Sbjct: 62  LLLNG------LTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQ 115

Query: 166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQ----IYDVFKHLNNDV 221
            +++   P R+        L+     +  +DEA  +   G   +         +     +
Sbjct: 116 IRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL 175

Query: 222 QVILLSATMPADVLDVSMKF--MRDPI 246
             + L+AT         ++   + DP+
Sbjct: 176 PFMALTATADDTTRQDIVRLLGLNDPL 202

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 94.3 bits (233), Expect = 4e-24
 Identities = 31/189 (16%), Positives = 68/189 (35%), Gaps = 12/189 (6%)

Query: 48  NFDDM--ELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISI 105
             +++   +S   +  +   G E+    Q  A+     G +++    +  GKT    +++
Sbjct: 2   KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAM 61

Query: 106 LQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG 165
           +++  +  K      + P R LA +  +              +        + +      
Sbjct: 62  VREAIKGGKSLY---VVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGD---- 114

Query: 166 AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQ---IYDVFKHLNNDVQ 222
             ++V T  +   +I   A   K +   V+DE   + S         +    + +N  ++
Sbjct: 115 CDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALR 174

Query: 223 VILLSATMP 231
           VI LSAT P
Sbjct: 175 VIGLSATAP 183

>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 = 87.7 bits (216), Expect = 5e-21
 Identities = 28/164 (17%), Positives = 55/164 (33%), Gaps = 14/164 (8%)

Query: 83  RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM 142
           +    I     G GKT  +  +I+++  +  +  + LILAPTR +A ++++ +       
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEAL------- 58

Query: 143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML 202
                  +        IR    G ++V       F M     +      + ++DEA    
Sbjct: 59  -----RGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTD 113

Query: 203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPI 246
                 + Y   +    +   I ++AT P               
Sbjct: 114 PASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIMD 157

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 76.4 bits (186), Expect = 1e-17
 Identities = 34/180 (18%), Positives = 68/180 (37%), Gaps = 3/180 (1%)

Query: 75  QRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKV 134
           Q  I    +  + +    +G GKT    +    ++ +   +    +LAPT+ L  Q  + 
Sbjct: 14  QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVL--MLAPTKPLVLQHAES 71

Query: 135 VIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFV 194
              L +       A  G     +  +     A+V+V TP  + + +  G +S + + + V
Sbjct: 72  FRRLFNLPPEKIVALTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGRISLEDVSLIV 130

Query: 195 LDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVKKEE 254
            DEA   +       I   +K    +  VI L+A+  +    +        I+ +  + E
Sbjct: 131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE 190

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]} Length = 264

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 = 43.6 bits (102), Expect = 8e-06
 Identities = 24/164 (14%), Positives = 56/164 (34%), Gaps = 11/164 (6%)

Query: 67  FEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE 126
            +K +  + R  +   +  + + Q   G+GKT    ++IL   +   +    +  +    
Sbjct: 87  AQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAI 146

Query: 127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAG-AQVVVGTPGRVFDMISRGAL 185
              +      +  +            +        L  G   VV+GT   + + +     
Sbjct: 147 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVH---- 202

Query: 186 STKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT 229
             K + + ++DE       G K +  +   +    V  +++SAT
Sbjct: 203 -FKNLGLVIIDEQHRF---GVKQR--EALMNKGKMVDTLVMSAT 240

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

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 = 41.2 bits (95), Expect = 2e-05
 Identities = 25/149 (16%), Positives = 52/149 (34%), Gaps = 14/149 (9%)

Query: 83  RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFM 142
           +G   +     G GKT  F   IL +  +       ++      L++  +        F 
Sbjct: 6   KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTL-VLAPTRVVLSEMKEAFHGLDVKFH 64

Query: 143 SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML 202
           + +  A   G  V D +       +++  T    +++I             ++DEA  + 
Sbjct: 65  TQAFSAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVI-------------IMDEAHFLD 111

Query: 203 SRGFKDQIYDVFKHLNNDVQVILLSATMP 231
                 + +   +   N+   IL++AT P
Sbjct: 112 PASIAARGWAAHRARANESATILMTATPP 140

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 233

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]

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 28/151 (18%), Positives = 50/151 (33%), Gaps = 13/151 (8%)

Query: 81  CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGD 140
                D +     G GKT     +    VD +    Q  +L PT  LAQQ          
Sbjct: 73  QPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH---KQVAVLVPTTLLAQQHYDNFRDRFA 129

Query: 141 FMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGA--LSTKQIRMFVLDEA 198
              V           ++  + L    +V  G    +          +  K + + ++DE 
Sbjct: 130 NWPVRIEMISRFRSAKEQTQILA---EVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEE 186

Query: 199 DEMLSRGFKDQIYDVFKHLNNDVQVILLSAT 229
                 G + +  +  K +  +V ++ L+AT
Sbjct: 187 HR---FGVRHK--ERIKAMRANVDILTLTAT 212

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	258
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.96
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.96
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.95
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.84
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.84
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.82
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.81
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.81
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.81
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.7
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.44
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.39
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.2
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	99.17
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.61
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.17
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.92
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.76
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.64
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.53
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.39
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.28
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.15
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.09
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.02
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.92
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.91
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.87
d1okkd2	207	GTPase domain of the signal recognition particle r	96.81
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.77
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.6
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.53
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.38
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	96.29
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.22
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.05
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	95.9
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	95.73
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	95.68
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	95.39
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	95.38
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.37
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	95.28
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.24
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	94.89
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	94.74
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.69
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	94.42
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	94.11
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.09
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.07
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	94.07
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	94.05
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	93.7
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	93.66
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.42
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.36
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.31
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	93.28
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.25
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.13
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.0
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	92.92
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	92.81
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	92.69
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	92.55
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	92.53
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.09
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	92.08
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	91.86
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	91.78
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.72
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	91.7
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	91.51
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	91.38
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	91.3
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	91.09
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	91.0
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	90.64
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	90.21
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	90.15
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	90.07
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	90.03
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	89.34
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	89.32
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	89.14
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	89.02
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	88.6
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	88.35
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	88.34
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	88.25
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	88.14
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	88.1
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	88.07
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	88.05
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	87.79
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	87.71
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	87.65
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	87.46
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	87.43
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	87.34
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	87.1
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	86.97
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	86.94
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	86.87
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	86.81
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	86.81
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	86.65
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	86.4
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	86.39
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	86.33
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	85.87
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	85.74
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	85.45
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	85.44
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	85.43
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	85.42
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	85.14
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	85.13
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	85.05
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	85.04
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	84.53
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	84.43
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.27
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	84.07
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	83.61
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	83.54
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	83.5
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	82.84
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	82.53
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	82.23
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	82.01
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	81.75
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	81.68
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	81.43
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	81.16
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	80.91
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	80.8
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	80.64
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	80.2
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	80.11
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	80.05

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6.6e-47  Score=304.36  Aligned_cols=206  Identities=67%  Similarity=1.056  Sum_probs=197.7

Q ss_pred             ccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          46 AENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        46 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      ..+|+++++++.++++|++.||..|+++|..++|.++.|+|+++.++||||||++|++|+++.+.....+++++|++|++
T Consensus        16 ~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~Ptr   95 (222)
T d2j0sa1          16 TPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTR   95 (222)
T ss_dssp             CCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSH
T ss_pred             CCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchH
Confidence            35799999999999999999999999999999999999999999999999999999999999998888888999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +|+.|.++.++.++...++.+..+.|+.........+..+++|+|+||+++.+++.++.+.+++++++|+||||.+++.+
T Consensus        96 eLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  175 (222)
T d2j0sa1          96 ELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG  175 (222)
T ss_dssp             HHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcC
Confidence            99999999999999999999999999998888888888899999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +...+..+++.+++++|++++|||+|++++++++.|+++|+.|.|.
T Consensus       176 f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         176 FKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             THHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             cHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999999999999999999998764

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.1e-46  Score=298.77  Aligned_cols=215  Identities=72%  Similarity=1.158  Sum_probs=196.7

Q ss_pred             cccccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccc
Q psy4698          37 LIETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKEC  116 (258)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~  116 (258)
                      ++++++++...+|+++++++.+.++|.+.||..|+++|..++|.++.|+|+++.++||||||++|++|+++.+.....++
T Consensus         2 ~~~~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~   81 (218)
T d2g9na1           2 VIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKAT   81 (218)
T ss_dssp             CCCCCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSC
T ss_pred             CCCCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCc
Confidence            46677888888999999999999999999999999999999999999999999999999999999999999998888889


Q ss_pred             eEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH-HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEE
Q psy4698         117 QALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI-RKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVL  195 (258)
Q Consensus       117 ~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVv  195 (258)
                      +++|++|+++|+.|.++.++.+....+..+....++....... .....+++|+|+||+++.+++.++...+++++++|+
T Consensus        82 ~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVl  161 (218)
T d2g9na1          82 QALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVL  161 (218)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEE
T ss_pred             cEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEe
Confidence            9999999999999999999999999888887777765544332 233356899999999999999999999999999999


Q ss_pred             ccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         196 DEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       196 DE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      ||||++++.++...+..+++.++++.|++++|||+|++++++++.|+++|+.|.|.
T Consensus       162 DEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         162 DEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             ESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             eecchhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            99999999999999999999999999999999999999999999999999999875

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5.5e-45  Score=290.61  Aligned_cols=202  Identities=38%  Similarity=0.676  Sum_probs=189.9

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .+|+++++++.++++|.+.||..|+++|.+++|.+++|+|+++.+|||||||++|++|+++.+....++++++|++|+++
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~e   82 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecch
Confidence            57999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhcCCC-CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         127 LAQQIQKVVIALGDFM-SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      |+.|.++.+..+.... +..+....|+.........+..+++|+|+||+++.+++..+.+.+++++++|+||||.|++.+
T Consensus        83 l~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  162 (206)
T d1veca_          83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             hhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccc
Confidence            9999999999887644 456667777777777777888889999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEE
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKI  248 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v  248 (258)
                      |...+..+++.+++++|++++|||+|++++++++.|+++|+.|
T Consensus       163 f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             THHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            9999999999999999999999999999999999999999876

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.3e-45  Score=292.93  Aligned_cols=211  Identities=64%  Similarity=0.996  Sum_probs=190.0

Q ss_pred             cccccccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceE
Q psy4698          39 ETNWDHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQA  118 (258)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~  118 (258)
                      .++++....+|+++++++.+.++|++.|+..|+++|.+++|.++.|+|+++.+|||||||++|++|+++.+....+++++
T Consensus         2 ~~~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~   81 (212)
T d1qdea_           2 QTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQA   81 (212)
T ss_dssp             CBSCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCE
T ss_pred             CCCCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcce
Confidence            45677788899999999999999999999999999999999999999999999999999999999999999988888999


Q ss_pred             EEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccc
Q psy4698         119 LILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEA  198 (258)
Q Consensus       119 lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~  198 (258)
                      +|++|+++++.|....+..+............++.....+...++ +++|+|+||+++..++..+.+.+++++++|+|||
T Consensus        82 lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEa  160 (212)
T d1qdea_          82 LMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEA  160 (212)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETH
T ss_pred             EEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCceecCcceEEeehhh
Confidence            999999999999999999999888888888777776666655544 5899999999999999999999999999999999


Q ss_pred             hhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         199 DEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       199 h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      |.+++.++...+..+++.+++++|++++|||++++++++++.|+++|+.|.|
T Consensus       161 d~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~v  212 (212)
T d1qdea_         161 DEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV  212 (212)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             hhhcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            9999999999999999999999999999999999999999999999998865

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.5e-44  Score=288.29  Aligned_cols=203  Identities=37%  Similarity=0.640  Sum_probs=186.8

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      .|+++++++.+.++|.+.||..|+++|.+++|.+++|+|+++.++||||||++|++|+++.+.....+++++|++|+++|
T Consensus         2 ~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL   81 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   81 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchh
Confidence            69999999999999999999999999999999999999999999999999999999999999888888899999999999


Q ss_pred             HHHHHHHHHHhcCCCC-ceEEEEECCcchHHHHHHH-hcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-
Q psy4698         128 AQQIQKVVIALGDFMS-VSCHACIGGTIVRDDIRKL-EAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-  204 (258)
Q Consensus       128 ~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-  204 (258)
                      +.|..+.++.++...+ ..+....|+.....+...+ ..+++|+|+||+++.++++++.+.+++++++|+||||.+++. 
T Consensus        82 ~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~  161 (207)
T d1t6na_          82 AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQL  161 (207)
T ss_dssp             HHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSH
T ss_pred             hHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcC
Confidence            9999999999988764 4566677777666555554 567899999999999999999999999999999999999975 


Q ss_pred             CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         205 GFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       205 ~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      ++...+..+++.+++++|++++|||++++++++++.|+++|+.|.|
T Consensus       162 ~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         162 DMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             HHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             CcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            7889999999999999999999999999999999999999998875

>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=100.00  E-value=1.8e-43  Score=282.10  Aligned_cols=205  Identities=44%  Similarity=0.710  Sum_probs=196.8

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ++|+++++++.+++.|++.||..|+++|.+++|.+++|+|+++.++||||||++|++|+++.+.....+.++++++|+.+
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~   80 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE   80 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccchh
Confidence            47999999999999999999999999999999999999999999999999999999999999988888889999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      ++.+....+..++...++.+....|+.........+..+++|+|+||++|.+++..+.+.+.+++++|+||||.|++.+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f  160 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDF  160 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHH
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhh
Confidence            99999999999999999999999999988888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         207 KDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       207 ~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      ...+..+++.+++++|++++|||+|+++.++++.|+++|+.|.+.
T Consensus       161 ~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         161 KTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             HHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             HHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            999999999999999999999999999999999999999999764

>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=100.00  E-value=2.7e-43  Score=281.36  Aligned_cols=203  Identities=39%  Similarity=0.683  Sum_probs=188.1

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCC-cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGN-DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~-~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      .+|+++++++.++++|.+.|+.+|+++|.+++|.++.|+ |+++++|||+|||++|++|+++..... .+++++|++|++
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~-~~~~~lil~pt~   82 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPTR   82 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccc-cCcceEEEeecc
Confidence            379999999999999999999999999999999998875 999999999999999999999876554 567999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccC
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRG  205 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~  205 (258)
                      +|+.|.++.++.+....+..+....|+.....+.+.+. +++|+|+||+++.+++.++.+.+++++++|+||||++++.+
T Consensus        83 ~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~  161 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMG  161 (208)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTT
T ss_pred             ccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCC
Confidence            99999999999999999999999888887777666554 58999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEec
Q psy4698         206 FKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILVK  251 (258)
Q Consensus       206 ~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~~  251 (258)
                      +...+..+++.+++++|++++|||+|++++++++.|++||.+|++.
T Consensus       162 ~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~~  207 (208)
T d1hv8a1         162 FIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAK  207 (208)
T ss_dssp             THHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             ChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEEE
Confidence            9999999999999999999999999999999999999999999863

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=2.2e-43  Score=287.12  Aligned_cols=208  Identities=34%  Similarity=0.535  Sum_probs=192.3

Q ss_pred             cccccCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc---------c
Q psy4698          43 DHVAENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN---------I  113 (258)
Q Consensus        43 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~---------~  113 (258)
                      +....+|+++++++.+.++|.+.||..|+++|.+++|.+++|+|+++.++||||||++|++|+++.+...         .
T Consensus        17 ~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~   96 (238)
T d1wrba1          17 TNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKT   96 (238)
T ss_dssp             CSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CC
T ss_pred             CCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCC
Confidence            4455789999999999999999999999999999999999999999999999999999999999998542         3


Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF  193 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~l  193 (258)
                      .+++++|++|+++|+.|..+.+..++...++++....|+.....+.+....+++|+||||++|.+++..+...+.+++++
T Consensus        97 ~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~l  176 (238)
T d1wrba1          97 AYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYI  176 (238)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEE
T ss_pred             CCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceecccccee
Confidence            45789999999999999999999999999999999998888887777888889999999999999999999999999999


Q ss_pred             EEccchhhhccCcHHHHHHHHHhCCC----CccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         194 VLDEADEMLSRGFKDQIYDVFKHLNN----DVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       194 VvDE~h~~~~~~~~~~~~~~~~~l~~----~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      |+||+|++++.+|..++..+++.++.    ++|++++|||+|.+++++++.||++|++|.|
T Consensus       177 ViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~v  237 (238)
T d1wrba1         177 VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTV  237 (238)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEE
T ss_pred             eeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999987642    5799999999999999999999999999876

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=3.5e-41  Score=269.37  Aligned_cols=203  Identities=33%  Similarity=0.573  Sum_probs=183.7

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      +|+++++++.+.++|++.||.+|+++|.+++|.+++|+|+++++|||||||++|++|+++.+.........++++|...+
T Consensus         2 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~   81 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTREL   81 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             ccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccch
Confidence            69999999999999999999999999999999999999999999999999999999999999888888899999999999


Q ss_pred             HHHHHHHHHHhcCCC----CceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhc
Q psy4698         128 AQQIQKVVIALGDFM----SVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLS  203 (258)
Q Consensus       128 ~~q~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~  203 (258)
                      +.+.+..+.......    ...+....+.............+++|+|+||+++..++.+....+++++++|+||||++++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~  161 (209)
T d1q0ua_          82 ATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLD  161 (209)
T ss_dssp             HHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHH
T ss_pred             hHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccc
Confidence            999988877654433    3445555555555555555667799999999999999999888999999999999999999


Q ss_pred             cCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEEEe
Q psy4698         204 RGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKILV  250 (258)
Q Consensus       204 ~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v~~  250 (258)
                      .++...+..+++.+++++|++++|||+|++++++++.|+++|++|.|
T Consensus       162 ~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         162 MGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             TTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             cccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999999999999999999987

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.97  E-value=3.3e-31  Score=210.53  Aligned_cols=195  Identities=14%  Similarity=0.161  Sum_probs=144.1

Q ss_pred             CcCCCCCCHHHHHHHHHC-CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          48 NFDDMELSEELLRGIYAY-GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~-~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ..+.+++++.+.+.|++. |+..++|+|.++++++++|+|+++++|||||||++|.+|++..      ..++++++|+++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~------~~~~~~v~P~~~   76 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------NGLTVVVSPLIS   76 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------SSEEEEECSCHH
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc------cCceEEeccchh
Confidence            467888999999999875 9999999999999999999999999999999999999888753      348999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCc
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGF  206 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~  206 (258)
                      |+.|+.+.++.++...........+...............+|+++||..+.............++++|+||+|++.+++.
T Consensus        77 L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~  156 (206)
T d1oywa2          77 LMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGH  156 (206)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSS
T ss_pred             hhhhHHHHHHhhcccccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeecccc
Confidence            99999999988764321111111111111222233445589999999887654444445667899999999998876643


Q ss_pred             H-----HHHHHHHHhCCCCccEEEEEeeCChhHHH-HHHHh-cCCCeEEEe
Q psy4698         207 K-----DQIYDVFKHLNNDVQVILLSATMPADVLD-VSMKF-MRDPIKILV  250 (258)
Q Consensus       207 ~-----~~~~~~~~~l~~~~~~i~~SAT~~~~~~~-~~~~~-~~~~~~v~~  250 (258)
                      .     ..+..++..+ +++|++++|||+++++.+ +.+.+ +++|+ |.|
T Consensus       157 ~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~-v~v  205 (206)
T d1oywa2         157 DFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL-IQI  205 (206)
T ss_dssp             CCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE-EEE
T ss_pred             chHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc-EEe
Confidence            2     2223344444 579999999999998764 55554 88995 443

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.96  E-value=1.8e-30  Score=205.64  Aligned_cols=186  Identities=19%  Similarity=0.233  Sum_probs=144.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      +++.+...|++.|+..|+++|.++++.+.+|+++++++|||+|||.+++++++..+...   .++++++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~---~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG---GKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT---CCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhcc---CcceeecccHHHHHHHHH
Confidence            56788889999999999999999999999999999999999999999999988877543   479999999999999999


Q ss_pred             HHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHH-
Q psy4698         134 VVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYD-  212 (258)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~-  212 (258)
                      .++++.... ..+....++.....   .....++++++||..+..++.+....+.++++||+||+|.+.+..+...+.. 
T Consensus        87 ~~~~~~~~~-~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~  162 (202)
T d2p6ra3          87 SFKKWEKIG-LRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (202)
T ss_dssp             HHTTTTTTT-CCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHhhcc-ccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHH
Confidence            998776533 33444444433322   1223578999999999999988877888999999999999877765554443 


Q ss_pred             --HHHhCCCCccEEEEEeeCChhHHHHHHHhcCCCeEE
Q psy4698         213 --VFKHLNNDVQVILLSATMPADVLDVSMKFMRDPIKI  248 (258)
Q Consensus       213 --~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~v  248 (258)
                        .++..++++|+|+||||+++ .+++. .|++.+.++
T Consensus       163 l~~i~~~~~~~~~l~lSATl~n-~~~~~-~~l~~~~~~  198 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSATAPN-VTEIA-EWLDADYYV  198 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECCCTT-HHHHH-HHTTCEEEE
T ss_pred             HHHHHhcCCCCcEEEEcCCCCc-HHHHH-HHcCCCeee
Confidence              44555678999999999976 46665 555555444

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.96  E-value=1.1e-27  Score=188.98  Aligned_cols=180  Identities=20%  Similarity=0.204  Sum_probs=140.6

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .|+++|.+++..+. ++|+++++|||+|||+++++++...+...  +.+++|++|+++|+.|+++.++++....+..+..
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~--~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS--CSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc--CCcEEEEcCchHHHHHHHHHHHHhhcccccceee
Confidence            79999999998875 56799999999999999988877666543  3489999999999999999999998877888777


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      ..++.......... ..++++++||+.+...+....+.++++++||+||+|++........+...+.....++++++|||
T Consensus        86 ~~~~~~~~~~~~~~-~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~SA  164 (200)
T d1wp9a1          86 LTGEKSPEERSKAW-ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTA  164 (200)
T ss_dssp             ECSCSCHHHHHHHH-HHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEES
T ss_pred             eecccchhHHHHhh-hcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEEe
Confidence            66666554443333 33689999999999999888888999999999999998766655555555555567789999999


Q ss_pred             eCChhHHHHHHHhcC-CCeEEEecC
Q psy4698         229 TMPADVLDVSMKFMR-DPIKILVKK  252 (258)
Q Consensus       229 T~~~~~~~~~~~~~~-~~~~v~~~~  252 (258)
                      |++.....+.+.+.. +...|.+..
T Consensus       165 Tp~~~~~~~~~~~~~l~~~~i~~~~  189 (200)
T d1wp9a1         165 SPGSTPEKIMEVINNLGIEHIEYRS  189 (200)
T ss_dssp             CSCSSHHHHHHHHHHTTCCEEEECC
T ss_pred             cCCCcHHHHHHHHhcCCceEEEeCC
Confidence            986665555443322 344555543

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.95  E-value=1.8e-27  Score=192.76  Aligned_cols=182  Identities=15%  Similarity=0.098  Sum_probs=130.1

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHH
Q psy4698          54 LSEELLRGIYAYGFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQK  133 (258)
Q Consensus        54 ~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~  133 (258)
                      +.+.+.+.+ +.++..|+++|+++++.++.|+|+++++|||+|||++++++++.....   +.+++|++|+++|+.|+++
T Consensus        29 ~~~~~~~~~-~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~---~~rvliv~Pt~~La~Q~~~  104 (237)
T d1gkub1          29 LLKEFVEFF-RKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSLLVIQAAE  104 (237)
T ss_dssp             HHHHHHHHH-HTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT---SCCEEEEESCHHHHHHHHH
T ss_pred             hHHHHHHHH-HhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh---cCeEEEEeccHHHHHHHHH
Confidence            334444444 457779999999999999999999999999999999999988876654   3489999999999999999


Q ss_pred             HHHHhcCCCCce----EEEEECCcchHHHHHH--HhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH
Q psy4698         134 VVIALGDFMSVS----CHACIGGTIVRDDIRK--LEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK  207 (258)
Q Consensus       134 ~~~~~~~~~~~~----~~~~~~~~~~~~~~~~--~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~  207 (258)
                      .+++++...++.    +....+..........  ....++|+|+||+.+.+    ....+++++++|+||+|.+++.+..
T Consensus       105 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~----~~~~~~~~~~vVvDE~d~~l~~~~~  180 (237)
T d1gkub1         105 TIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK----HYRELGHFDFIFVDDVDAILKASKN  180 (237)
T ss_dssp             HHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH----CSTTSCCCSEEEESCHHHHHTSTHH
T ss_pred             HHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHH----hhhhcCCCCEEEEEChhhhhhcccc
Confidence            999987765543    3333343333322222  23447999999987654    3345678999999999999876533


Q ss_pred             HH-HHHHH----------HhCCCCccEEEEEeeCChhHHH-HHHHhcC
Q psy4698         208 DQ-IYDVF----------KHLNNDVQVILLSATMPADVLD-VSMKFMR  243 (258)
Q Consensus       208 ~~-~~~~~----------~~l~~~~~~i~~SAT~~~~~~~-~~~~~~~  243 (258)
                      .. ...++          ...+...|++++|||+++..+. +.+.+++
T Consensus       181 ~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r~ll~  228 (237)
T d1gkub1         181 VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLN  228 (237)
T ss_dssp             HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHC
T ss_pred             hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHHHHhC
Confidence            21 11121          1123467899999999876544 4455544

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.84  E-value=1.1e-19  Score=144.72  Aligned_cols=174  Identities=18%  Similarity=0.173  Sum_probs=132.1

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhc----CC--cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          52 MELSEELLRGIYAYGFEKPSAIQQRAIIPCVR----GN--DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        52 ~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~----g~--~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      +..+....+.+.+.-...+++-|..++..+..    ++  +.+++|.||||||.+|+..+...+.++   .++++++|+.
T Consensus        38 ~~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g---~qv~~l~Pt~  114 (233)
T d2eyqa3          38 FKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH---KQVAVLVPTT  114 (233)
T ss_dssp             CCCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT---CEEEEECSSH
T ss_pred             CCCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcC---CceEEEccHH
Confidence            44566777777665555899999999988643    33  689999999999999999998887654   3899999999


Q ss_pred             HHHHHHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhh
Q psy4698         126 ELAQQIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       126 ~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~  201 (258)
                      .|+.|.+..++++....+..+..+++......   .+..+.+| .+|+|||...+.     ..+.++++++||+||-|+.
T Consensus       115 ~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDEeH~f  189 (233)
T d2eyqa3         115 LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF  189 (233)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS
T ss_pred             HhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeechhhh
Confidence            99999999999998888899988888776543   34445444 899999985543     3356789999999999974


Q ss_pred             hccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHH
Q psy4698         202 LSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       202 ~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~  238 (258)
                      .   +.  -...++....++.++.+|||...+-...+
T Consensus       190 g---~k--Q~~~l~~~~~~~~~l~~SATPiprtl~~~  221 (233)
T d2eyqa3         190 G---VR--HKERIKAMRANVDILTLTATPIPRTLNMA  221 (233)
T ss_dssp             C---HH--HHHHHHHHHTTSEEEEEESSCCCHHHHHH
T ss_pred             h---hH--HHHHHHhhCCCCCEEEEecchhHHHHHHH
Confidence            2   22  22334444567889999999865544443

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.84  E-value=2.5e-21  Score=159.93  Aligned_cols=153  Identities=22%  Similarity=0.208  Sum_probs=112.8

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .|+++|.+++..++.++..++.+|||+|||+++...+. .+... ...++||++|+++|+.|+.+.+.+++......+..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~-~~~~~-~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~  190 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLAR-YYLEN-YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHH-HHHHH-CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHH-Hhhhc-ccceEEEEEcCchhHHHHHHHHHHhhcccccccee
Confidence            79999999999999888899999999999998754443 33332 33489999999999999999999987665555555


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      ..++......   .....+++|+|++.+....   ...++++++||+||||++.    ...+..++..+.+....+++||
T Consensus       191 ~~~g~~~~~~---~~~~~~i~i~t~qs~~~~~---~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~~~~rlGlTa  260 (282)
T d1rifa_         191 IGGGASKDDK---YKNDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCMFKFGLSG  260 (282)
T ss_dssp             CSTTCSSTTC---CCTTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCCEEEEECS
T ss_pred             ecceeccccc---ccccceEEEEeeehhhhhc---ccccCCCCEEEEECCCCCC----chhHHHHHHhccCCCeEEEEEe
Confidence            5554432211   1234789999998765332   2345689999999999863    4456667776655445699999


Q ss_pred             eCChh
Q psy4698         229 TMPAD  233 (258)
Q Consensus       229 T~~~~  233 (258)
                      |+++.
T Consensus       261 T~~~~  265 (282)
T d1rifa_         261 SLRDG  265 (282)
T ss_dssp             SCCTT
T ss_pred             ecCCC
Confidence            98764

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.82  E-value=1.7e-19  Score=146.17  Aligned_cols=170  Identities=21%  Similarity=0.266  Sum_probs=124.6

Q ss_pred             CCHHHHHHHH-HCCCCCCcHHHHHHhhhhhc----C--CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          54 LSEELLRGIY-AYGFEKPSAIQQRAIIPCVR----G--NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        54 ~~~~l~~~l~-~~~~~~~~~~Q~~~~~~l~~----g--~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      ....+.+.+. ...| .+|+-|.+++..+..    +  .+.++.|.||||||.+|+..++..+.++.   ++++++||..
T Consensus        68 ~~~~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~---q~~~m~Pt~~  143 (264)
T d1gm5a3          68 IEGKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF---QTAFMVPTSI  143 (264)
T ss_dssp             CCTHHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS---CEEEECSCHH
T ss_pred             CChHHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc---ceeEEeehHh
Confidence            3334444443 4555 899999999988753    2  36899999999999999999988877654   7999999999


Q ss_pred             HHHHHHHHHHHhcCCCCceEEEEECCcchHH---HHHHHhcC-CcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhh
Q psy4698         127 LAQQIQKVVIALGDFMSVSCHACIGGTIVRD---DIRKLEAG-AQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEML  202 (258)
Q Consensus       127 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~  202 (258)
                      |+.|.+..++++....+..+..+.++....+   .+..+.+| .+|+|||..-+.     ..+.+++++++||||-|+..
T Consensus       144 La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~-----~~~~f~~LglviiDEqH~fg  218 (264)
T d1gm5a3         144 LAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ-----EDVHFKNLGLVIIDEQHRFG  218 (264)
T ss_dssp             HHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH-----HCCCCSCCCEEEEESCCCC-
T ss_pred             hhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc-----CCCCccccceeeeccccccc
Confidence            9999999999998888899988888776543   34444444 899999985443     23467799999999999863


Q ss_pred             ccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHH
Q psy4698         203 SRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       203 ~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~  237 (258)
                      -.+.     ..+..-..++.++.||||...+-..+
T Consensus       219 v~Qr-----~~l~~~~~~~~~l~~SATPiprtl~~  248 (264)
T d1gm5a3         219 VKQR-----EALMNKGKMVDTLVMSATPIPRSMAL  248 (264)
T ss_dssp             ---------CCCCSSSSCCCEEEEESSCCCHHHHH
T ss_pred             hhhH-----HHHHHhCcCCCEEEEECCCCHHHHHH
Confidence            2221     12222335688999999965443333

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.81  E-value=4.4e-20  Score=136.03  Aligned_cols=136  Identities=19%  Similarity=0.228  Sum_probs=91.7

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR  160 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (258)
                      +..|+++++.+|||+|||.+++..++......  +.++++++|++.+++|.++.+...    ...+.......       
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--~~~vli~~p~~~l~~q~~~~~~~~----~~~~~~~~~~~-------   70 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL----DVKFHTQAFSA-------   70 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS----CEEEESSCCCC-------
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--CceeeeeecchhHHHHHHHHhhhh----hhhhccccccc-------
Confidence            56789999999999999999877776666554  358999999999999998866332    22221111111       


Q ss_pred             HHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHH-HHHHHHHhCCCCccEEEEEeeCC
Q psy4698         161 KLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKD-QIYDVFKHLNNDVQVILLSATMP  231 (258)
Q Consensus       161 ~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~-~~~~~~~~l~~~~~~i~~SAT~~  231 (258)
                      .......+.+.|...+...... ...+.++++||+||+|++...+... .+...+.. .++.++|+||||+|
T Consensus        71 ~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          71 HGSGREVIDAMCHATLTYRMLE-PTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             CCCSSCCEEEEEHHHHHHHHTS-SSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             ccccccchhhhhHHHHHHHHhc-cccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence            1112256777887776654433 4567899999999999874333221 12222322 35789999999987

>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=99.81  E-value=2.5e-20  Score=155.30  Aligned_cols=138  Identities=17%  Similarity=0.171  Sum_probs=97.1

Q ss_pred             hhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI  159 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (258)
                      .+.+|+++++.||||||||++|+.+++......  +.+++|++|+++|+.|+++.++.++.......           ..
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~-----------~~   71 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRYQTPA-----------IR   71 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBCCC---------------
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCcceeeeE-----------Ee
Confidence            356889999999999999999988888766554  35899999999999999887765532211100           00


Q ss_pred             HHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhC--CCCccEEEEEeeCChh
Q psy4698         160 RKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHL--NNDVQVILLSATMPAD  233 (258)
Q Consensus       160 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l--~~~~~~i~~SAT~~~~  233 (258)
                      ........++++|++.+..+... ...+.+++++|+||+|++..+++.  ...++..+  +...+++++|||.+..
T Consensus        72 ~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~~--~~~~l~~~~~~~~~~~v~~SAT~~~~  144 (305)
T d2bmfa2          72 AEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASIA--ARGYISTRVEMGEAAGIFMTATPPGS  144 (305)
T ss_dssp             ----CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHHH--HHHHHHHHHHHTSCEEEEECSSCTTC
T ss_pred             ecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhHH--HHHHHHHhhccccceEEEeecCCCcc
Confidence            12234468999999988766554 446788999999999988554322  22222222  3568999999999865

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.81  E-value=1.2e-19  Score=143.28  Aligned_cols=137  Identities=17%  Similarity=0.183  Sum_probs=100.1

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      .++++|.+++..+..+++.++.+|||+|||++++..+ ..+     +.++||+||+++|+.|+.+.++.++..   .+..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~-----~~~~Liv~p~~~L~~q~~~~~~~~~~~---~~~~  140 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL-----STPTLIVVPTLALAEQWKERLGIFGEE---YVGE  140 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS-----CSCEEEEESSHHHHHHHHHHHGGGCGG---GEEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh-----cCceeEEEcccchHHHHHHHHHhhccc---chhh
Confidence            6899999999999998889999999999999875443 222     347999999999999999999877532   2333


Q ss_pred             EECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         149 CIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      ..+..         ....+++|+|.+.+......   ..+++++||+||+|++...    .+..++..++ ...++++||
T Consensus       141 ~~~~~---------~~~~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a~----~~~~i~~~~~-~~~~lgLTA  203 (206)
T d2fz4a1         141 FSGRI---------KELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAE----SYVQIAQMSI-APFRLGLTA  203 (206)
T ss_dssp             ESSSC---------BCCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTT----THHHHHHTCC-CSEEEEEEE
T ss_pred             ccccc---------ccccccccceehhhhhhhHh---hCCcCCEEEEECCeeCCcH----HHHHHHhccC-CCcEEEEec
Confidence            33322         23357999999887655443   2356889999999987433    2334555543 345789999


Q ss_pred             eCC
Q psy4698         229 TMP  231 (258)
Q Consensus       229 T~~  231 (258)
                      |+.
T Consensus       204 Tl~  206 (206)
T d2fz4a1         204 TFE  206 (206)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            973

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.70  E-value=3.8e-17  Score=120.09  Aligned_cols=127  Identities=17%  Similarity=0.158  Sum_probs=84.9

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHh
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLE  163 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (258)
                      .+..++.+|||||||+++...+.    .  .+.+++|++|++.|++|+.+.+.+.....   .....++...       .
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~----~--~~~~vli~~P~~~l~~q~~~~~~~~~~~~---~~~~~~~~~~-------~   71 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA----A--QGYKVLVLNPSVAATLGFGAYMSKAHGVD---PNIRTGVRTI-------T   71 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH----T--TTCCEEEEESCHHHHHHHHHHHHHHHSCC---CEEECSSCEE-------C
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH----H--cCCcEEEEcChHHHHHHHHHHHHHHhhcc---cccccccccc-------c
Confidence            35689999999999986533322    1  34589999999999999999988764322   1222222211       1


Q ss_pred             cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCC--CCccEEEEEeeC
Q psy4698         164 AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLN--NDVQVILLSATM  230 (258)
Q Consensus       164 ~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~--~~~~~i~~SAT~  230 (258)
                      ....+.++|.+.+...   ....++++++||+||+|++. ......+..+++.+.  ++.+++++|||.
T Consensus        72 ~~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~-~~~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          72 TGSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTD-ATSILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             CCCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCS-HHHHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             cccceEEEeeeeeccc---cchhhhcCCEEEEecccccC-HHHHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            2357889998775533   33457789999999999753 223333445555543  456899999993

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=99.44  E-value=7.9e-13  Score=109.27  Aligned_cols=155  Identities=16%  Similarity=0.138  Sum_probs=97.8

Q ss_pred             CCcHHHHHHhhhhh---------cCCcEEEEcccCCCcchHhHHHHHHHhhhcc----ccceEEEEeccHHHHHHHHHHH
Q psy4698          69 KPSAIQQRAIIPCV---------RGNDVIAQAQSGTGKTATFSISILQQVDQNI----KECQALILAPTRELAQQIQKVV  135 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~---------~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~----~~~~~lil~P~~~l~~q~~~~~  135 (258)
                      .+++||.+++..+.         .+..+++.-.+|.|||+..+..+...+....    ...++||+||. .+..||.+.+
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHH
Confidence            68999999997652         3456899999999999876544333333221    12369999996 5888999999


Q ss_pred             HHhcCCCCceEEEEECCcchHHHHH--HH-h-----cCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcH
Q psy4698         136 IALGDFMSVSCHACIGGTIVRDDIR--KL-E-----AGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFK  207 (258)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~-~-----~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~  207 (258)
                      .++.... ......+++........  .. .     ...+++|+|++.+......  +.--+.++||+||+|++-+.  .
T Consensus       134 ~k~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~--l~~~~~~~vI~DEaH~ikn~--~  208 (298)
T d1z3ix2         134 GKWLGGR-VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV--LHKGKVGLVICDEGHRLKNS--D  208 (298)
T ss_dssp             HHHHGGG-CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT--TTTSCCCEEEETTGGGCCTT--C
T ss_pred             HhhcCCc-eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhc--ccccceeeeecccccccccc--c
Confidence            8876432 23334444433222111  11 1     1257999999887644332  22335679999999987433  2


Q ss_pred             HHHHHHHHhCCCCccEEEEEeeC
Q psy4698         208 DQIYDVFKHLNNDVQVILLSATM  230 (258)
Q Consensus       208 ~~~~~~~~~l~~~~~~i~~SAT~  230 (258)
                      ......+..+. ....+++|||.
T Consensus       209 s~~~~a~~~l~-~~~rllLTGTP  230 (298)
T d1z3ix2         209 NQTYLALNSMN-AQRRVLISGTP  230 (298)
T ss_dssp             HHHHHHHHHHC-CSEEEEECSSC
T ss_pred             chhhhhhhccc-cceeeeecchH
Confidence            33333444453 34578999996

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.39  E-value=6.7e-13  Score=105.59  Aligned_cols=154  Identities=14%  Similarity=0.145  Sum_probs=98.6

Q ss_pred             CCcHHHHHHhhhhh----cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCc
Q psy4698          69 KPSAIQQRAIIPCV----RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSV  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~  144 (258)
                      .+++||.+++..+.    .+..+++.-++|.|||+..+..+ ..+.......+++|+|| ..+..++.+.+.++.....+
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~-~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~~~   89 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHLRF   89 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTSCE
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhh-hhhhhcccccccceecc-hhhhhHHHHHHHhhcccccc
Confidence            58999999997643    34568999999999999975444 44444444457999999 66778888888888654332


Q ss_pred             eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEE
Q psy4698         145 SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVI  224 (258)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i  224 (258)
                        ...........     ....+|+++|.+.+.....-   .--...++|+||+|.+-+..  ......+..+.. ...+
T Consensus        90 --~~~~~~~~~~~-----~~~~~vvi~~~~~~~~~~~l---~~~~~~~vI~DEah~~k~~~--s~~~~~~~~l~a-~~r~  156 (230)
T d1z63a1          90 --AVFHEDRSKIK-----LEDYDIILTTYAVLLRDTRL---KEVEWKYIVIDEAQNIKNPQ--TKIFKAVKELKS-KYRI  156 (230)
T ss_dssp             --EECSSSTTSCC-----GGGSSEEEEEHHHHTTCHHH---HTCCEEEEEEETGGGGSCTT--SHHHHHHHTSCE-EEEE
T ss_pred             --eeeccccchhh-----ccCcCEEEeeHHHHHhHHHH---hcccceEEEEEhhhcccccc--hhhhhhhhhhcc-ceEE
Confidence              22222111111     12368999999876532221   11245789999999875432  222344445543 4478


Q ss_pred             EEEeeC-ChhHHHH
Q psy4698         225 LLSATM-PADVLDV  237 (258)
Q Consensus       225 ~~SAT~-~~~~~~~  237 (258)
                      ++|||. ++...++
T Consensus       157 ~LTgTPi~n~~~dl  170 (230)
T d1z63a1         157 ALTGTPIENKVDDL  170 (230)
T ss_dssp             EECSSCSTTCHHHH
T ss_pred             EEecchHHhHHHHH
Confidence            999996 5555554

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=99.20  E-value=3.1e-10  Score=89.99  Aligned_cols=168  Identities=15%  Similarity=0.233  Sum_probs=126.9

Q ss_pred             CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCce
Q psy4698          66 GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVS  145 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~  145 (258)
                      |. ++++.|...--.+.+|+  +..+.||-|||+++.+|++.....+.   .+-|++...-||..=.+++..+....++.
T Consensus        78 G~-RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~---~vhvvTvNdyLA~RDae~m~~iy~~lGls  151 (273)
T d1tf5a3          78 GM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIFEFLGLT  151 (273)
T ss_dssp             SC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHHHHTTCC
T ss_pred             ce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCC---CceEEecCccccchhhhHHhHHHHHcCCC
Confidence            55 88999999988888997  99999999999999888877766653   58888889999999999999999999999


Q ss_pred             EEEEECCcchHHHHHHHhcCCcEEEeChHHH-HHHHhcCC------CCCCCccEEEEccchhhhccCcH-----------
Q psy4698         146 CHACIGGTIVRDDIRKLEAGAQVVVGTPGRV-FDMISRGA------LSTKQIRMFVLDEADEMLSRGFK-----------  207 (258)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~~~~l~~lVvDE~h~~~~~~~~-----------  207 (258)
                      +.+........+.....  .|||+++|...+ +++++.+.      .....+.+.||||+|.++=+...           
T Consensus       152 vg~~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg~~~~  229 (273)
T d1tf5a3         152 VGLNLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQSMT  229 (273)
T ss_dssp             EEECCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEEEEE
T ss_pred             ccccccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEeccCccc
Confidence            98876665544433332  479999998876 56665432      23467889999999987522100           


Q ss_pred             ---HHHHHHHHhCCCCccEEEEEeeCChhHHHHHHHhcCC
Q psy4698         208 ---DQIYDVFKHLNNDVQVILLSATMPADVLDVSMKFMRD  244 (258)
Q Consensus       208 ---~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~~~~~  244 (258)
                         -.+...++..   .++.+|+.|.-.+..++.+.|--+
T Consensus       230 ~a~it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy~l~  266 (273)
T d1tf5a3         230 LATITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIYNMQ  266 (273)
T ss_dssp             EEEEEHHHHHTTS---SEEEEEESCCGGGHHHHHHHHCCC
T ss_pred             hhhhhHHHHHHHH---HHHhCCccccHHHHHHHHhccCCc
Confidence               1123344443   578999999988989999888644

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.61  E-value=1.4e-07  Score=78.97  Aligned_cols=144  Identities=18%  Similarity=0.226  Sum_probs=85.0

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh--ccccceEEEEeccHHHHHHHHHHHHHhcCCCCc--
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ--NIKECQALILAPTRELAQQIQKVVIALGDFMSV--  144 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~--~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~--  144 (258)
                      ...+.|+.|+..++.++-++|.||.|+|||.+... ++..+..  ...+.++++.+||..-+....+...........  
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~-~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~  226 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAK-LLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTD  226 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHH-HHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCS
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHH-HHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchh
Confidence            45788999999999999999999999999987532 2222222  234568999999988887776654332111110  


Q ss_pred             --eEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCcc
Q psy4698         145 --SCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQ  222 (258)
Q Consensus       145 --~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~  222 (258)
                        ...........          ...+-.+++.  ..+.++......++++||||+-++    ....+..++..+++..+
T Consensus       227 ~~~~~~~~~~~t~----------~~ll~~~~~~--~~~~~~~~~~l~~d~lIIDEaSmv----~~~l~~~ll~~~~~~~~  290 (359)
T d1w36d1         227 EQKKRIPEDASTL----------HRLLGAQPGS--QRLRHHAGNPLHLDVLVVDEASMI----DLPMMSRLIDALPDHAR  290 (359)
T ss_dssp             CCCCSCSCCCBTT----------TSCC-------------CTTSCCSCSEEEECSGGGC----BHHHHHHHHHTCCTTCE
T ss_pred             hhhhhhhhhhhHH----------HHHHhhhhcc--hHHHHhhhcccccceeeehhhhcc----CHHHHHHHHHHhcCCCE
Confidence              00000000000          0000001111  112233344557889999999965    34566788888888899


Q ss_pred             EEEEEee
Q psy4698         223 VILLSAT  229 (258)
Q Consensus       223 ~i~~SAT  229 (258)
                      +|++.-.
T Consensus       291 lILvGD~  297 (359)
T d1w36d1         291 VIFLGDR  297 (359)
T ss_dssp             EEEEECT
T ss_pred             EEEECCh
Confidence            9988643

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=98.17  E-value=2.7e-06  Score=68.85  Aligned_cols=70  Identities=17%  Similarity=0.125  Sum_probs=54.3

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhc-cccceEEEEeccHHHHHHHHHHHHHhcC
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQN-IKECQALILAPTRELAQQIQKVVIALGD  140 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~-~~~~~~lil~P~~~l~~q~~~~~~~~~~  140 (258)
                      +++|-|++++..  ...+++|.|+.|||||.+.+.-+...+... ....+++++++|++++......+.+...
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            478999999965  345699999999999998766655555442 2345899999999999999888776543

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.92  E-value=1.4e-05  Score=64.97  Aligned_cols=68  Identities=21%  Similarity=0.246  Sum_probs=53.9

Q ss_pred             CCcHHHHHHhhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhhcc-ccceEEEEeccHHHHHHHHHHHHHh
Q psy4698          69 KPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQNI-KECQALILAPTRELAQQIQKVVIAL  138 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~-~~~~~lil~P~~~l~~q~~~~~~~~  138 (258)
                      .+++-|.+++.+.  +..++|.|+.|||||.+.+--+.+.+.... ...+++++++++..+......+...
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~   79 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhh
Confidence            5899999999753  456999999999999988766666555442 3348999999999999988877654

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.76  E-value=3.5e-05  Score=58.95  Aligned_cols=50  Identities=8%  Similarity=0.139  Sum_probs=30.7

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      .+.+++|+||+|.|... ....+.+.+..-++++.+|+.+-. +..+...++
T Consensus       107 ~~~kviIide~d~l~~~-a~n~Llk~lEep~~~~~fIl~t~~-~~~ll~tI~  156 (207)
T d1a5ta2         107 GGAKVVWVTDAALLTDA-AANALLKTLEEPPAETWFFLATRE-PERLLATLR  156 (207)
T ss_dssp             SSCEEEEESCGGGBCHH-HHHHHHHHHTSCCTTEEEEEEESC-GGGSCHHHH
T ss_pred             CccceEEechhhhhhhh-hhHHHHHHHHhhcccceeeeeecC-hhhhhhhhc
Confidence            45779999999987433 455666666665566655554433 334444443

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.64  E-value=0.00018  Score=54.84  Aligned_cols=136  Identities=17%  Similarity=0.185  Sum_probs=67.7

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHH
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDD  158 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (258)
                      ..+.+-+++.||||+|||++..--+.. +...  +.++.+++-  +|.-+.++.+.+.+.   .++.+............
T Consensus         7 ~~~~~vi~lvGp~GvGKTTTiaKLA~~-~~~~--g~kV~lit~Dt~R~gA~eQL~~~a~~---l~v~~~~~~~~~~~~~~   80 (207)
T d1ls1a2           7 LKDRNLWFLVGLQGSGKTTTAAKLALY-YKGK--GRRPLLVAADTQRPAAREQLRLLGEK---VGVPVLEVMDGESPESI   80 (207)
T ss_dssp             CCSSEEEEEECCTTTTHHHHHHHHHHH-HHHT--TCCEEEEECCSSCHHHHHHHHHHHHH---HTCCEEECCTTCCHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEecccccchHHHHHHHHHHh---cCCccccccccchhhHH
Confidence            334444678999999999876443332 2222  335666664  455554444433332   23444433332222111


Q ss_pred             HHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhcc-CcHHHHHHHHHhCCCCccEEEEEeeCChhHHHH
Q psy4698         159 IRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSR-GFKDQIYDVFKHLNNDVQVILLSATMPADVLDV  237 (258)
Q Consensus       159 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~-~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~  237 (258)
                      ....              ..+     ....+.+++++|=+-+...+ ....++..+.+..+++..++.++|+...+..+.
T Consensus        81 ~~~~--------------~~~-----~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~  141 (207)
T d1ls1a2          81 RRRV--------------EEK-----ARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSV  141 (207)
T ss_dssp             HHHH--------------HHH-----HHHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHH
T ss_pred             HHHH--------------HHH-----HhhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHH
Confidence            0000              000     01122345555555433221 234555566666666666788888887776666


Q ss_pred             HHHh
Q psy4698         238 SMKF  241 (258)
Q Consensus       238 ~~~~  241 (258)
                      ++.|
T Consensus       142 ~~~f  145 (207)
T d1ls1a2         142 ARAF  145 (207)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6655

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.39  E-value=9.6e-05  Score=57.71  Aligned_cols=41  Identities=7%  Similarity=0.360  Sum_probs=27.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ....++|+||+|.+... ....+..++...+.++.+|+.+..
T Consensus       130 ~~~~iiiide~d~l~~~-~~~~l~~~~e~~~~~~~~Il~tn~  170 (252)
T d1sxje2         130 HRYKCVIINEANSLTKD-AQAALRRTMEKYSKNIRLIMVCDS  170 (252)
T ss_dssp             -CCEEEEEECTTSSCHH-HHHHHHHHHHHSTTTEEEEEEESC
T ss_pred             CCceEEEeccccccccc-cchhhhcccccccccccceeeecc
Confidence            45679999999987433 555667777777677766665443

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.28  E-value=0.00038  Score=52.62  Aligned_cols=41  Identities=5%  Similarity=0.157  Sum_probs=27.6

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      .+.+++|+||||.|. ......+.+.+..-++++.+++.|..
T Consensus        78 ~~~KviIId~ad~l~-~~aqNaLLK~LEEPp~~t~fiLit~~  118 (198)
T d2gnoa2          78 YTRKYVIVHDCERMT-QQAANAFLKALEEPPEYAVIVLNTRR  118 (198)
T ss_dssp             SSSEEEEETTGGGBC-HHHHHHTHHHHHSCCTTEEEEEEESC
T ss_pred             CCCEEEEEeCccccc-hhhhhHHHHHHhCCCCCceeeeccCC
Confidence            466899999999873 33555666667665666666655444

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.15  E-value=0.00041  Score=53.38  Aligned_cols=50  Identities=14%  Similarity=0.237  Sum_probs=29.5

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHH
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSM  239 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~  239 (258)
                      ....+|+||+|.+... ....+..++...+..+.+++.+....+-...+..
T Consensus       108 ~~~viiiDe~d~l~~~-~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~s  157 (237)
T d1sxjd2         108 PYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICNYVTRIIDPLAS  157 (237)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHH
T ss_pred             CceEEEEecccccCHH-HHHHHhhccccccccccccccccccccccccccc
Confidence            4568999999987543 3444555555555556555555444444444433

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.09  E-value=0.00046  Score=52.86  Aligned_cols=44  Identities=16%  Similarity=0.265  Sum_probs=28.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCCh
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPA  232 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~  232 (258)
                      ....++|+||+|.+... ....+...+...+..+.+++.+....+
T Consensus       100 ~~~kviiiDe~d~~~~~-~~~~ll~~~e~~~~~~~~i~~~~~~~~  143 (224)
T d1sxjb2         100 GKHKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFACNQSNK  143 (224)
T ss_dssp             TCCEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEESCGGG
T ss_pred             cceEEEEEecccccchh-HHHHHhhhccccccceeeeeccCchhh
Confidence            45679999999987544 334445566666666666666655443

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.02  E-value=0.0034  Score=47.69  Aligned_cols=62  Identities=18%  Similarity=0.322  Sum_probs=33.5

Q ss_pred             CccEEEEccchhhhccC-cHHHHHHHHHhCC-CCccEEEEEeeCChhHH---HHHHHhcCCCeEEEe
Q psy4698         189 QIRMFVLDEADEMLSRG-FKDQIYDVFKHLN-NDVQVILLSATMPADVL---DVSMKFMRDPIKILV  250 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~-~~~~~~~~~~~l~-~~~~~i~~SAT~~~~~~---~~~~~~~~~~~~v~~  250 (258)
                      ..++|++|++|.+.... ....+..++..+. .+.++|+.|...|.++.   .-++..+.-..++.+
T Consensus        97 ~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i  163 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEI  163 (213)
T ss_dssp             TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEEC
T ss_pred             hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHHHhhCceEEEE
Confidence            46799999999885432 3344555555544 44555554444443321   223334445555544

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.92  E-value=0.0014  Score=50.70  Aligned_cols=41  Identities=12%  Similarity=0.325  Sum_probs=25.9

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      ...+++|+||+|.|. ......+.+.+...++.+.+|+.+--
T Consensus       114 ~~~kviiIde~d~l~-~~~q~~Llk~lE~~~~~~~~il~tn~  154 (239)
T d1njfa_         114 GRFKVYLIDEVHMLS-RHSFNALLKTLEEPPEHVKFLLATTD  154 (239)
T ss_dssp             SSSEEEEEETGGGSC-HHHHHHHHHHHHSCCTTEEEEEEESC
T ss_pred             CCCEEEEEECcccCC-HHHHHHHHHHHhcCCCCeEEEEEcCC
Confidence            346799999999873 23344566666655555655555433

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.91  E-value=0.0011  Score=50.26  Aligned_cols=56  Identities=21%  Similarity=0.232  Sum_probs=30.5

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cHHHHHHHHHHHHHhcCCCCceEEE
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TRELAQQIQKVVIALGDFMSVSCHA  148 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~~l~~q~~~~~~~~~~~~~~~~~~  148 (258)
                      +++.||||+|||++..--+. ++...  +.++.+++-  +|.=+.++.+   .+++.+++.+..
T Consensus        12 i~lvGptGvGKTTTiAKLA~-~~~~~--g~kV~lit~Dt~R~gA~eQL~---~~a~~l~v~~~~   69 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLAR-QFEQQ--GKSVMLAAGDTFRAAAVEQLQ---VWGQRNNIPVIA   69 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-HHHTT--TCCEEEECCCTTCHHHHHHHH---HHHHHTTCCEEC
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHC--CCcEEEEecccccccchhhhh---hhhhhcCCcccc
Confidence            67899999999988654332 33332  235666653  2444444333   333333455443

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.87  E-value=0.0013  Score=50.28  Aligned_cols=42  Identities=21%  Similarity=0.445  Sum_probs=26.9

Q ss_pred             CCCCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         185 LSTKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       185 ~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      ....+..++|+||+|.+... ....+...+....+.+.+++.+
T Consensus        95 ~~~~~~kiiiiDe~d~~~~~-~~~~Ll~~le~~~~~~~~~~~~  136 (227)
T d1sxjc2          95 IFSKGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLA  136 (227)
T ss_dssp             SSSCSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             ccCCCeEEEEEeccccchhh-HHHHHHHHhhhcccceeecccc
Confidence            34456679999999987544 4455666666665555444443

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.81  E-value=0.0035  Score=47.38  Aligned_cols=47  Identities=19%  Similarity=0.117  Sum_probs=27.8

Q ss_pred             CCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cHHHHHHHHH
Q psy4698          84 GNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TRELAQQIQK  133 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~~l~~q~~~  133 (258)
                      ++-++++||||+|||.+..--+. .+...  +.++.+++-  +|.-+.++.+
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~-~~~~~--g~kV~lit~Dt~R~gA~eQL~   54 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGR-YYQNL--GKKVMFCAGDTFRAAGGTQLS   54 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHH-HHHTT--TCCEEEECCCCSSTTHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-HHHHC--CCcEEEEEeccccccchhhHh
Confidence            45578899999999988654332 33322  235665553  3554544443

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.77  E-value=0.0024  Score=48.83  Aligned_cols=40  Identities=23%  Similarity=0.408  Sum_probs=26.9

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhhhcC--CcEEEEcccCCCcchHhH
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPCVRG--NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l~~g--~~~li~~~tGsGKT~~~l  102 (258)
                      .|+++-..+.+++.|...               +..+  .++++.||+|+|||.++.
T Consensus        22 ~~~diig~~~~~~~l~~~---------------i~~~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHY---------------VKTGSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             STTTCCSCHHHHHHHHHH---------------HHHTCCCEEEEESCTTSSHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCcHHHHHH
Confidence            566666666666655431               1122  469999999999998763

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.60  E-value=0.014  Score=44.10  Aligned_cols=43  Identities=16%  Similarity=0.142  Sum_probs=20.9

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec--cHHHHHHHH
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP--TRELAQQIQ  132 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P--~~~l~~q~~  132 (258)
                      +++.||||+|||.+..--+. ++...  +.++.+++-  +|.=+.++.
T Consensus        15 i~lvGptGvGKTTTiAKLA~-~~~~~--g~kV~lit~Dt~R~ga~eQL   59 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAY-FYKKK--GFKVGLVGADVYRPAALEQL   59 (211)
T ss_dssp             EEEECSCCC----HHHHHHH-HHHHT--TCCEEEEECCCSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHC--CCceEEEEeeccccchhHHH
Confidence            67799999999988653332 33333  234555543  344444433

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=96.53  E-value=0.0089  Score=46.34  Aligned_cols=52  Identities=17%  Similarity=0.109  Sum_probs=29.1

Q ss_pred             cCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhhh--hcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAYGFEKPSAIQQRAIIPC--VRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~l--~~g~~~li~~~tGsGKT~~~  101 (258)
                      .+|.++.-.+.+++.+.+. + .+- .+.+.+..+  ...+.+++.||+|+|||..+
T Consensus         6 ~~~~di~G~~~~k~~l~~~-i-~~l-~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEI-V-EFL-KNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHH-H-HHH-HCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CcHHHHccHHHHHHHHHHH-H-HHH-HCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            5677776566666655431 0 000 011112221  12256999999999999875

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.38  E-value=0.019  Score=43.33  Aligned_cols=45  Identities=20%  Similarity=0.124  Sum_probs=25.8

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEe-c-cHHHHHHHHH
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILA-P-TRELAQQIQK  133 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~-P-~~~l~~q~~~  133 (258)
                      -++++||||+|||++..--+. ++...+  .++.+++ - +|.=+.++.+
T Consensus        13 vi~lvGptGvGKTTTiAKLAa-~~~~~~--~kV~lit~Dt~R~gA~eQL~   59 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAK-MFVDEG--KSVVLAAADTFRAAAIEQLK   59 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH-HHHHTT--CCEEEEEECTTCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHCC--CceEEEeecccccchhHHHH
Confidence            378899999999988653333 333332  2444444 3 4554444433

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=96.29  E-value=0.0032  Score=44.46  Aligned_cols=100  Identities=13%  Similarity=0.216  Sum_probs=54.5

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCC
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGA  166 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (258)
                      -++.||+.||||.-.+.-+ +++..  .+.+++++-|...-..         ..  .+  . ...+.         .. .
T Consensus         5 ~~i~GpMfsGKTteLi~~~-~~~~~--~~~kv~~ikp~~D~R~---------~~--~i--~-s~~g~---------~~-~   57 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRL-HRLEY--ADVKYLVFKPKIDTRS---------IR--NI--Q-SRTGT---------SL-P   57 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHH-HHHHH--TTCCEEEEEECCCGGG---------CS--SC--C-CCCCC---------SS-C
T ss_pred             EEEEccccCHHHHHHHHHH-HHHHH--CCCcEEEEEEcccccc---------cc--eE--E-cccCc---------ee-e
Confidence            4789999999998754433 33332  2347889988643110         00  00  0 00010         01 2


Q ss_pred             cEEEeChHHHHHHHhcCCCCCCCccEEEEccchhhhccCcHHHHHHHHHh
Q psy4698         167 QVVVGTPGRVFDMISRGALSTKQIRMFVLDEADEMLSRGFKDQIYDVFKH  216 (258)
Q Consensus       167 ~Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~  216 (258)
                      .+.+.....++..+..... ..+.++|.|||++.+.  +....+...+..
T Consensus        58 ~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf~--d~i~~~~~~~~~  104 (139)
T d2b8ta1          58 SVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFFD--DRICEVANILAE  104 (139)
T ss_dssp             CEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGSC--THHHHHHHHHHH
T ss_pred             eEEeccchhhHHHHHhhcc-ccCcCEEEechhhhcc--hhHHHHHHHHHh
Confidence            3555565555666554432 3578899999999652  233444444443

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.22  E-value=0.0073  Score=45.46  Aligned_cols=93  Identities=16%  Similarity=0.116  Sum_probs=67.3

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH---HHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR---KLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      ++.++.|+||..+-....+..+++...  +.++...+|.....+...   ... ...+|+|||.      +-...++.++
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt------vIEvGiDvpn  101 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPT  101 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTGGGSCCTT
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh------hhhhccCCCC
Confidence            455899999999888888888888754  466777888876554332   223 3489999996      2334578999


Q ss_pred             ccEEEEccchhhhccCcHHHHHHHHHhCC
Q psy4698         190 IRMFVLDEADEMLSRGFKDQIYDVFKHLN  218 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~~~~~~~~~~~l~  218 (258)
                      ..++|+.+||++    -..++..+.-+..
T Consensus       102 A~~iiI~~a~rf----GLaQLhQLRGRVG  126 (211)
T d2eyqa5         102 ANTIIIERADHF----GLAQLHQLRGRVG  126 (211)
T ss_dssp             EEEEEETTTTSS----CHHHHHHHHTTCC
T ss_pred             CcEEEEecchhc----cccccccccceee
Confidence            999999999976    3455555655554

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.05  E-value=0.0043  Score=51.88  Aligned_cols=67  Identities=31%  Similarity=0.396  Sum_probs=48.3

Q ss_pred             CCcHHHHHHhhhhh----cC-CcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          69 KPSAIQQRAIIPCV----RG-NDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        69 ~~~~~Q~~~~~~l~----~g-~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      .|.--|-+++..+.    .| ++.++.|-||||||+++. .++...     +..+|||+|+..+|.++++.++.+...
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-----~rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-----NKPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            45556666665544    44 568899999999997642 222221     235999999999999999999998644

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=95.90  E-value=0.011  Score=41.63  Aligned_cols=41  Identities=12%  Similarity=0.169  Sum_probs=26.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRE  126 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~  126 (258)
                      .|.=-++.||+.||||.-.+..+ ++...  .+.+++++-|...
T Consensus         6 ~G~l~lI~GpMfSGKTteLi~~~-~~~~~--~g~~vl~i~~~~D   46 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSEELIRRI-RRAKI--AKQKIQVFKPEID   46 (141)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHH-HHHHH--TTCCEEEEEEC--
T ss_pred             ceeEEEEEeccccHHHHHHHHHH-HHhhh--cCCcEEEEEeccc
Confidence            34446889999999998754333 33332  2347999999754

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=95.73  E-value=0.0058  Score=50.95  Aligned_cols=40  Identities=18%  Similarity=0.370  Sum_probs=26.6

Q ss_pred             cHHHHHHhhhhhcCCc--EEEEcccCCCcchHhHHHHHHHhhh
Q psy4698          71 SAIQQRAIIPCVRGND--VIAQAQSGTGKTATFSISILQQVDQ  111 (258)
Q Consensus        71 ~~~Q~~~~~~l~~g~~--~li~~~tGsGKT~~~l~~~l~~l~~  111 (258)
                      .+.|.+.+..+.....  +++.||||||||++. ..++..+..
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~~  184 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELNS  184 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHCC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhcC
Confidence            4555555555554443  899999999999885 445555543

>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=95.68  E-value=0.2  Score=36.17  Aligned_cols=115  Identities=11%  Similarity=0.120  Sum_probs=71.9

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      ++.++||.|+++.-++.....+.+.    ++.+..++|+....+..   ..+.+ ..+|+|+|.     + -..+++.++
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~-----v-~~~GiDip~   99 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----L-LREGLDIPE   99 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----C-CCTTCCCTT
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee-----e-eeeeccCCC
Confidence            4558999999999999999988776    57888888887654332   33333 489999995     2 334578999


Q ss_pred             ccEEEEccchhhhccCcHHHHHHHHHhC-C-CCccEEEEEeeCChhHHHHH
Q psy4698         190 IRMFVLDEADEMLSRGFKDQIYDVFKHL-N-NDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       190 l~~lVvDE~h~~~~~~~~~~~~~~~~~l-~-~~~~~i~~SAT~~~~~~~~~  238 (258)
                      ++++|+=.++..........+.-.+-+. + .+...+++.......+++.+
T Consensus       100 V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2         100 VSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             EEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHHH
T ss_pred             CcEEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHHHH
Confidence            9999987666422111122222222222 1 23345555555555555443

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.39  E-value=0.013  Score=40.74  Aligned_cols=36  Identities=8%  Similarity=0.205  Sum_probs=24.1

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccH
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTR  125 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~  125 (258)
                      -++.||+.||||.-.+..+ .....  .+.+++++-|..
T Consensus         5 ~li~GpMfsGKTt~Li~~~-~~~~~--~g~~v~~ikp~~   40 (133)
T d1xbta1           5 QVILGPMFSGKSTELMRRV-RRFQI--AQYKCLVIKYAK   40 (133)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHT--TTCCEEEEEETT
T ss_pred             EEEEecccCHHHHHHHHHH-HHHHH--cCCcEEEEeccc
Confidence            5889999999998653333 33332  234688888863

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.38  E-value=0.035  Score=39.65  Aligned_cols=53  Identities=21%  Similarity=0.354  Sum_probs=40.0

Q ss_pred             CCCCccEEEEccchhhhccCc--HHHHHHHHHhCCCCccEEEEEeeCChhHHHHH
Q psy4698         186 STKQIRMFVLDEADEMLSRGF--KDQIYDVFKHLNNDVQVILLSATMPADVLDVS  238 (258)
Q Consensus       186 ~~~~l~~lVvDE~h~~~~~~~--~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~  238 (258)
                      .-..+++||+||+-...+.++  ...+..+++..|...-+|+..-..|.++.+.+
T Consensus        91 ~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          91 ADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             TCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             hcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhc
Confidence            335688999999998877764  47777888887777777777666887776654

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.37  E-value=0.01  Score=47.87  Aligned_cols=52  Identities=27%  Similarity=0.357  Sum_probs=34.0

Q ss_pred             HHHHHHhhh-hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          72 AIQQRAIIP-CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        72 ~~Q~~~~~~-l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      +-+...+.. +..+++++|+|+||||||... -+++..+..   ..+++.+--+.++
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~l-~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTYI-KSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHHH-HHHGGGSCT---TCCEEEEESSCCC
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHHH-HHHhhhccc---ccceeeccchhhh
Confidence            444444444 567789999999999999863 444444332   2367777666554

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=95.28  E-value=0.042  Score=42.59  Aligned_cols=52  Identities=23%  Similarity=0.254  Sum_probs=29.2

Q ss_pred             cCcCCCCCCHHHHHHHHHC--CCCCCcHHHHHHhhhhhcCCcEEEEcccCCCcchHh
Q psy4698          47 ENFDDMELSEELLRGIYAY--GFEKPSAIQQRAIIPCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        47 ~~~~~~~~~~~l~~~l~~~--~~~~~~~~Q~~~~~~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .+|.+..-.+.+++.+.+.  .+..+..+|..-   ....+.+++.||+|+|||..+
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHHH
Confidence            4677777666666655431  011111122111   112367999999999999875

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.24  E-value=0.0066  Score=43.90  Aligned_cols=29  Identities=17%  Similarity=0.188  Sum_probs=21.3

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhccc
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNIK  114 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~~  114 (258)
                      |+++|.||+|+|||... ..++..+...+.
T Consensus         2 k~v~ItG~~GtGKTtl~-~~i~~~l~~~~~   30 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLI-HKASEVLKSSGV   30 (189)
T ss_dssp             CCEEEESCCSSCHHHHH-HHHHHHHHHTTC
T ss_pred             cEEEEECCCCCcHHHHH-HHHHHHHHHCCC
Confidence            67999999999999854 455555555433

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.89  E-value=0.061  Score=41.59  Aligned_cols=17  Identities=29%  Similarity=0.421  Sum_probs=15.0

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.||+|+|||..+
T Consensus        39 ~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             ceeEEecCCCCCchHHH
Confidence            56999999999999864

>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=94.74  E-value=0.18  Score=35.88  Aligned_cols=78  Identities=12%  Similarity=0.225  Sum_probs=54.7

Q ss_pred             hccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH---HHh-cCCcEEEeChHHHHHHHhcCCCC
Q psy4698         111 QNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR---KLE-AGAQVVVGTPGRVFDMISRGALS  186 (258)
Q Consensus       111 ~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~Tp~~l~~~l~~~~~~  186 (258)
                      ......++||.|.++..+++.+..+...    +..+..++++....+...   ... ....|+|||-     .+ ..+++
T Consensus        23 ~~~~~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v~-~rGiD   92 (162)
T d1fuka_          23 DSISVTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LL-ARGID   92 (162)
T ss_dssp             HHTTCSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GG-TTTCC
T ss_pred             HhCCCCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----cc-ccccc
Confidence            3334458999999999999998887665    466777787766544322   222 3478999995     33 34578


Q ss_pred             CCCccEEEEccc
Q psy4698         187 TKQIRMFVLDEA  198 (258)
Q Consensus       187 ~~~l~~lVvDE~  198 (258)
                      +++++++|.=+.
T Consensus        93 i~~v~~VI~~d~  104 (162)
T d1fuka_          93 VQQVSLVINYDL  104 (162)
T ss_dssp             CCSCSEEEESSC
T ss_pred             CCCceEEEEecc
Confidence            899999887553

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=94.69  E-value=0.11  Score=39.20  Aligned_cols=38  Identities=24%  Similarity=0.316  Sum_probs=27.6

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .|.-++|.|++|+|||...+..+.+.+...   ..+++++-
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~~---~~~~~is~   62 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACANK---ERAILFAY   62 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTTT---CCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc---cccceeec
Confidence            346799999999999988766666644432   35777764

>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=94.42  E-value=0.12  Score=37.57  Aligned_cols=76  Identities=17%  Similarity=0.276  Sum_probs=57.4

Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHhc-CCcEEEeChHHHHHHHhcCCCCCCCc
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLEA-GAQVVVGTPGRVFDMISRGALSTKQI  190 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~~Ilv~Tp~~l~~~l~~~~~~~~~l  190 (258)
                      +.++||.|+++.-+......+++.    ++.+..++|+....+..   ....+ ..+|+|||.     + -..+++.+++
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v-~~rGiDip~v  100 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----L-LREGLDIPEV  100 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----C-CSSSCCCTTE
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----H-HHccCCCCCC
Confidence            448999999999999888877655    68888888888765433   33333 489999994     2 3345789999


Q ss_pred             cEEEEccchh
Q psy4698         191 RMFVLDEADE  200 (258)
Q Consensus       191 ~~lVvDE~h~  200 (258)
                      ++||.-++..
T Consensus       101 ~~VI~~d~p~  110 (181)
T d1t5la2         101 SLVAILDADK  110 (181)
T ss_dssp             EEEEETTTTS
T ss_pred             CEEEEecCCc
Confidence            9999888764

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=94.11  E-value=0.0077  Score=46.82  Aligned_cols=15  Identities=27%  Similarity=0.222  Sum_probs=12.8

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      +++.||+|+|||.+.
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            466799999999876

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=94.09  E-value=0.16  Score=39.46  Aligned_cols=42  Identities=19%  Similarity=0.281  Sum_probs=25.5

Q ss_pred             EEEEccchhhhccC----cHHHHHHHHHhCC--CCccEEEEEeeCChhHH
Q psy4698         192 MFVLDEADEMLSRG----FKDQIYDVFKHLN--NDVQVILLSATMPADVL  235 (258)
Q Consensus       192 ~lVvDE~h~~~~~~----~~~~~~~~~~~l~--~~~~~i~~SAT~~~~~~  235 (258)
                      ++++||+|.++..+    -...+..+++..-  .+.|+|+  +|=|.+++
T Consensus       113 IlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIg--atT~eey~  160 (268)
T d1r6bx2         113 ILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIG--STTYQEFS  160 (268)
T ss_dssp             EEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEE--EECHHHHH
T ss_pred             eEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEE--eCCHHHHH
Confidence            78899999997542    2345666665432  3455555  55554443

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=94.07  E-value=0.013  Score=41.35  Aligned_cols=19  Identities=16%  Similarity=0.261  Sum_probs=16.5

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      .+++++.|++|+|||+++-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4689999999999998763

>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=94.07  E-value=0.25  Score=35.31  Aligned_cols=77  Identities=10%  Similarity=0.145  Sum_probs=54.8

Q ss_pred             cccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCC
Q psy4698         113 IKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTK  188 (258)
Q Consensus       113 ~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~  188 (258)
                      ..+.++||.|.++.-+......+...    +..+..++++....+..   .... ...+|+|||.-      -..++++.
T Consensus        30 ~~~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~------~~~Gid~~   99 (171)
T d1s2ma2          30 LQINQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL------LTRGIDIQ   99 (171)
T ss_dssp             SCCSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC------SSSSCCCT
T ss_pred             CCCCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchhH------hhhccccc
Confidence            34458999999999999999888776    46677777776654332   2222 34899999962      34457888


Q ss_pred             CccEEEEccch
Q psy4698         189 QIRMFVLDEAD  199 (258)
Q Consensus       189 ~l~~lVvDE~h  199 (258)
                      +++++|.=+..
T Consensus       100 ~v~~VI~~d~p  110 (171)
T d1s2ma2         100 AVNVVINFDFP  110 (171)
T ss_dssp             TEEEEEESSCC
T ss_pred             eeEEEEecCCc
Confidence            99988865554

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=94.05  E-value=0.021  Score=46.84  Aligned_cols=17  Identities=24%  Similarity=0.472  Sum_probs=15.5

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .++++.||||.|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999876

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.70  E-value=0.063  Score=44.79  Aligned_cols=53  Identities=19%  Similarity=0.191  Sum_probs=39.7

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhcc---------ccceEEEEeccHHHHHHHHHHHHH
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQNI---------KECQALILAPTRELAQQIQKVVIA  137 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~~---------~~~~~lil~P~~~l~~q~~~~~~~  137 (258)
                      .+++|.|+.|||||.+..--++..+....         ..-++|+|+=|+.-+.+..+++..
T Consensus        17 g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            35899999999999988777777765431         123699999998888887766544

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.66  E-value=0.011  Score=49.88  Aligned_cols=19  Identities=21%  Similarity=0.392  Sum_probs=16.5

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      .+|+++.||||+|||+.+-
T Consensus        49 ksNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHH
Confidence            4689999999999998763

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=93.42  E-value=0.015  Score=46.48  Aligned_cols=19  Identities=21%  Similarity=0.392  Sum_probs=16.6

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      ..+++++.||||+|||..+
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999876

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=93.36  E-value=0.061  Score=44.60  Aligned_cols=67  Identities=31%  Similarity=0.364  Sum_probs=47.1

Q ss_pred             CCcHHHHHHhhh----hhcCCc-EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCC
Q psy4698          69 KPSAIQQRAIIP----CVRGND-VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDF  141 (258)
Q Consensus        69 ~~~~~Q~~~~~~----l~~g~~-~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~  141 (258)
                      .|+.-|-+++..    +..|.. ..+.|.+||||+++.. .++.    . .+..+|||+|+...|.++++.++.+...
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~----~-~~rp~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIE----A-LGRPALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHH----H-HTCCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHH----H-hCCCEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            566666555554    445544 6889999999997532 2222    1 1225999999999999999999988644

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.31  E-value=0.021  Score=40.81  Aligned_cols=19  Identities=26%  Similarity=0.499  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .|+-+++.|++|||||+++
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4677899999999999975

>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=93.28  E-value=0.39  Score=35.28  Aligned_cols=72  Identities=17%  Similarity=0.196  Sum_probs=49.6

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHH---HHHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDI---RKLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|+|+..+......+...    ++.+..++++.......   .... ...+|+|+|-     .+ ..++++.+
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~~-~~GiD~p~   98 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AF-GMGINKPN   98 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TS-CTTTCCTT
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----hh-hhccCCCC
Confidence            4457999999999999998887765    46777778876654322   2222 3478999995     22 23467777


Q ss_pred             ccEEEE
Q psy4698         190 IRMFVL  195 (258)
Q Consensus       190 l~~lVv  195 (258)
                      +++||-
T Consensus        99 v~~VI~  104 (200)
T d1oywa3          99 VRFVVH  104 (200)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            777763

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=93.25  E-value=0.05  Score=41.60  Aligned_cols=26  Identities=23%  Similarity=0.311  Sum_probs=19.3

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhh
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQ  111 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~  111 (258)
                      .++++.||+|+|||.+. -.+.+.+..
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~~   69 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYKD   69 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHTT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHhc
Confidence            57999999999999875 344444443

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.13  E-value=0.045  Score=45.44  Aligned_cols=43  Identities=14%  Similarity=0.264  Sum_probs=26.5

Q ss_pred             hcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEeccHHH
Q psy4698          82 VRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPTREL  127 (258)
Q Consensus        82 ~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~~~l  127 (258)
                      ...+|++|.|+||||||..+ ..++..+...  +..++|+=|.-++
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~--g~~~iiiD~kge~   90 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGLLR--GDRMVIVDPNGDM   90 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHT--TCEEEEEEETTHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHHhC--CCCEEEEeCChhH
Confidence            45578999999999999875 3344443332  2245555554443

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.00  E-value=0.021  Score=44.40  Aligned_cols=39  Identities=21%  Similarity=0.343  Sum_probs=29.4

Q ss_pred             CccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEE
Q psy4698         189 QIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLS  227 (258)
Q Consensus       189 ~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~S  227 (258)
                      +-+++|+||+-.-+|......+...+..+.++..+|+.|
T Consensus       172 ~p~ililDEpts~LD~~t~~~i~~~l~~l~~~~TvI~it  210 (255)
T d2hyda1         172 NPPILILDEATSALDLESESIIQEALDVLSKDRTTLIVA  210 (255)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEEC
T ss_pred             CCCEEEEeCccccCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            345999999998888877888888888776665455544

>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=92.92  E-value=0.36  Score=34.33  Aligned_cols=76  Identities=8%  Similarity=0.116  Sum_probs=52.6

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHH---HHh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIR---KLE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      ...++||.|+++.-+..+.+.+.+.    +..+..++|+....+...   ... +..+|+|||--      ...++++++
T Consensus        26 ~~~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~------~~~Gid~~~   95 (168)
T d1t5ia_          26 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL------FGRGMDIER   95 (168)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC------CSTTCCGGG
T ss_pred             CCCeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecccc------ccchhhccc
Confidence            3458999999999999888877665    466777888766554332   223 34889999942      234567778


Q ss_pred             ccEEEEccch
Q psy4698         190 IRMFVLDEAD  199 (258)
Q Consensus       190 l~~lVvDE~h  199 (258)
                      ++++|.=+.-
T Consensus        96 ~~~vi~~~~p  105 (168)
T d1t5ia_          96 VNIAFNYDMP  105 (168)
T ss_dssp             CSEEEESSCC
T ss_pred             chhhhhhhcc
Confidence            8887765543

>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=92.81  E-value=0.47  Score=33.73  Aligned_cols=75  Identities=12%  Similarity=0.183  Sum_probs=53.0

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH---Hh-cCCcEEEeChHHHHHHHhcCCCCCCC
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK---LE-AGAQVVVGTPGRVFDMISRGALSTKQ  189 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~  189 (258)
                      .+.++||.|.++..++.....++..+    ..+..++++....+....   .. ...+|+|+|-     .+ ..++++++
T Consensus        33 ~~~k~iiF~~~~~~~~~~~~~l~~~~----~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td-----~~-~rGiDi~~  102 (168)
T d2j0sa2          33 TITQAVIFCNTKRKVDWLTEKMREAN----FTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VW-ARGLDVPQ  102 (168)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHTT----CCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GG-SSSCCCTT
T ss_pred             CCCceEEEeeeHHHHHHHHHHhhhcc----cchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc-----hh-cccccccC
Confidence            44589999999999999988887763    566677777665543222   22 3479999995     33 34678899


Q ss_pred             ccEEEEccc
Q psy4698         190 IRMFVLDEA  198 (258)
Q Consensus       190 l~~lVvDE~  198 (258)
                      ++++|.=++
T Consensus       103 v~~VIn~d~  111 (168)
T d2j0sa2         103 VSLIINYDL  111 (168)
T ss_dssp             EEEEEESSC
T ss_pred             cceEEEecC
Confidence            988875443

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {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: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=92.55  E-value=0.0048  Score=47.71  Aligned_cols=41  Identities=17%  Similarity=0.310  Sum_probs=29.8

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEe
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSA  228 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SA  228 (258)
                      .+-+++|+||+=.-+|......+...+..+.++..+|+.|-
T Consensus       156 ~~p~ililDEpts~LD~~~~~~i~~~l~~l~~~~Tvi~itH  196 (241)
T d2pmka1         156 NNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAH  196 (241)
T ss_dssp             TCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             cccchhhhhCCccccCHHHHHHHHHHHHHHhCCCEEEEEEC
Confidence            34569999999887787777778888877766555555443

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=92.53  E-value=0.018  Score=41.23  Aligned_cols=22  Identities=18%  Similarity=0.246  Sum_probs=18.6

Q ss_pred             hhhcCCcEEEEcccCCCcchHh
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ...+|..++++|.+|||||+++
T Consensus         2 ~~~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           2 RATQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TTTCCEEEEEECSTTSSHHHHH
T ss_pred             CCCCCeEEEEECCCCCCHHHHH
Confidence            3456778899999999999886

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=92.09  E-value=0.024  Score=39.64  Aligned_cols=16  Identities=19%  Similarity=0.283  Sum_probs=13.8

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -++++|++|||||+.+
T Consensus         4 lIii~G~pGsGKTTla   19 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999864

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=92.08  E-value=0.026  Score=40.32  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=15.7

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      +.++++.|++|||||++.
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            456999999999999976

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=91.86  E-value=1.3  Score=32.23  Aligned_cols=113  Identities=18%  Similarity=0.150  Sum_probs=58.2

Q ss_pred             CcEEEEcccCCCcchHhHHHHHHHhhhc-----cccceEEEEeccHHHH-----HHHHHHHHH----hcCCCCceEEEEE
Q psy4698          85 NDVIAQAQSGTGKTATFSISILQQVDQN-----IKECQALILAPTRELA-----QQIQKVVIA----LGDFMSVSCHACI  150 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~~~l~~l~~~-----~~~~~~lil~P~~~l~-----~q~~~~~~~----~~~~~~~~~~~~~  150 (258)
                      .|.++.|++|.|||....-.+. ++..+     -.+.+++-+-...-++     -++...++.    +....+ .+..+.
T Consensus        44 ~n~lLvG~pGVGKTalv~~LA~-ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~-~iILfI  121 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVEGLAQ-RIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEG-NVILFI  121 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH-HHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTT-TEEEEE
T ss_pred             CCeEEEecCCcccHHHHHHHHH-HHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCC-cEEEEc
Confidence            5799999999999987643333 33322     1223444444333221     133333433    322211 111111


Q ss_pred             -------------CCcch-HHHHHHHhcC-Cc-EEEeChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         151 -------------GGTIV-RDDIRKLEAG-AQ-VVVGTPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       151 -------------~~~~~-~~~~~~~~~~-~~-Ilv~Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                                   |+... ......+.++ .. |.-+||+...+++..+.-....+..|-|+|.+
T Consensus       122 Deih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         122 DELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             ETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             chHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence                         11111 1222233344 33 44578998888877765555678889999875

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=91.78  E-value=0.26  Score=40.30  Aligned_cols=18  Identities=33%  Similarity=0.516  Sum_probs=15.4

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .|.++.|+.|.|||...-
T Consensus        44 ~n~llvG~~GvGKtaiv~   61 (387)
T d1qvra2          44 NNPVLIGEPGVGKTAIVE   61 (387)
T ss_dssp             CCCEEEECTTSCHHHHHH
T ss_pred             CCCeEECCCCCCHHHHHH
Confidence            579999999999998753

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=91.72  E-value=0.028  Score=39.93  Aligned_cols=16  Identities=31%  Similarity=0.412  Sum_probs=14.2

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -+++.|++|||||+++
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999975

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=91.70  E-value=0.038  Score=41.88  Aligned_cols=18  Identities=28%  Similarity=0.418  Sum_probs=15.7

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|+|||..+-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            479999999999998763

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=91.51  E-value=0.041  Score=39.05  Aligned_cols=17  Identities=24%  Similarity=0.391  Sum_probs=14.8

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      .++++.|++|||||+..
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            35899999999999875

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=91.38  E-value=0.021  Score=41.11  Aligned_cols=18  Identities=17%  Similarity=0.248  Sum_probs=15.7

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      -+.++|.|++|+|||+.+
T Consensus         7 ~K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLV   24 (192)
T ss_dssp             CEEEEEECCTTSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            467999999999999865

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=91.30  E-value=0.047  Score=41.93  Aligned_cols=16  Identities=31%  Similarity=0.439  Sum_probs=14.5

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.||+|+|||..+
T Consensus        34 ~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEECCTTSCTHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5999999999999875

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=91.09  E-value=0.049  Score=41.31  Aligned_cols=18  Identities=22%  Similarity=0.320  Sum_probs=15.7

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      .++++.||+|+|||..+-
T Consensus        36 ~~~Ll~GPpG~GKTtla~   53 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH   53 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            479999999999998763

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=91.00  E-value=0.04  Score=39.24  Aligned_cols=17  Identities=18%  Similarity=0.352  Sum_probs=15.2

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      |++++.|++|+|||++.
T Consensus         1 k~I~liG~~GsGKsTi~   17 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLA   17 (161)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57899999999999876

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=90.64  E-value=0.11  Score=40.04  Aligned_cols=42  Identities=17%  Similarity=0.116  Sum_probs=28.9

Q ss_pred             hhcCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEecc
Q psy4698          81 CVRGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAPT  124 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P~  124 (258)
                      +..|.-+++.|++|+|||...+-.+.+....  .+.+++|++.-
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~--~g~~v~~~s~E   73 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAMLE   73 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHT--SCCCEEEEESS
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhh--cccceeEeeec
Confidence            4456779999999999997665555443332  23468888854

>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=90.21  E-value=1.8  Score=29.92  Aligned_cols=73  Identities=11%  Similarity=0.212  Sum_probs=50.3

Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHH---Hh-cCCcEEEeChHHHHHHHhcCCCCCCCc
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRK---LE-AGAQVVVGTPGRVFDMISRGALSTKQI  190 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~Ilv~Tp~~l~~~l~~~~~~~~~l  190 (258)
                      +.++||.|+++.-+..+...++..    +..+..++++....+....   .. ....|+|||--     +.+ ++++.++
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~-----~~~-Gid~~~v   97 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-----MSR-GIDVNDL   97 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-----HHH-HCCCSCC
T ss_pred             CCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehhH-----Hhh-hhhhccC
Confidence            347999999999999999888775    4667777777654433222   22 34799999942     222 3677888


Q ss_pred             cEEEEcc
Q psy4698         191 RMFVLDE  197 (258)
Q Consensus       191 ~~lVvDE  197 (258)
                      +++|.=+
T Consensus        98 ~~Vi~~d  104 (155)
T d1hv8a2          98 NCVINYH  104 (155)
T ss_dssp             SEEEESS
T ss_pred             cEEEEec
Confidence            8887533

>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=90.15  E-value=0.23  Score=34.27  Aligned_cols=67  Identities=21%  Similarity=0.287  Sum_probs=47.9

Q ss_pred             ccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeChHHHHHHHhcCCCCCCCccEE
Q psy4698         114 KECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTPGRVFDMISRGALSTKQIRMF  193 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~l~~l  193 (258)
                      ++.++||.|+++.-++..+..++..    ++.+..++++......   -....+|+|||-     .+.++ ++ .++++|
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaTd-----~~~~G-iD-~~v~~V   99 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVATD-----ALMTG-FT-GDFDSV   99 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEESS-----SSCSS-SC-CCBSEE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehhH-----HHHhc-cc-cccceE
Confidence            3448999999999999999988776    4677777777654332   134589999994     44444 45 577776


Q ss_pred             E
Q psy4698         194 V  194 (258)
Q Consensus       194 V  194 (258)
                      |
T Consensus       100 i  100 (138)
T d1jr6a_         100 I  100 (138)
T ss_dssp             E
T ss_pred             E
Confidence            5

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=90.07  E-value=0.12  Score=38.48  Aligned_cols=39  Identities=18%  Similarity=0.129  Sum_probs=26.8

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .|.-++|.|++|+|||...+-.+.+.+....  ..++++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~--~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFD--EPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHC--CCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcC--CCcccccc
Confidence            4567999999999999776555544444332  25777764

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=90.03  E-value=0.052  Score=38.56  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=15.4

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+-+++.|++|||||.++
T Consensus         3 ~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456889999999999876

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.34  E-value=0.069  Score=40.14  Aligned_cols=40  Identities=15%  Similarity=0.013  Sum_probs=25.3

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhh---ccccceEEEEe
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQ---NIKECQALILA  122 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~---~~~~~~~lil~  122 (258)
                      .|+-++|.|++|+|||...+-.+.+....   ...+..++++.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~   75 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID   75 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe
Confidence            45679999999999998765444333221   12234566665

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.32  E-value=0.078  Score=38.83  Aligned_cols=28  Identities=18%  Similarity=-0.006  Sum_probs=21.4

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhh
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVD  110 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~  110 (258)
                      .|.-++|.|++|+|||...+..+.+...
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~~   49 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQL   49 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTS
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            4567999999999999877665555443

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.14  E-value=0.13  Score=38.88  Aligned_cols=40  Identities=10%  Similarity=-0.075  Sum_probs=26.7

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhc---cccceEEEEe
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQN---IKECQALILA  122 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~---~~~~~~lil~  122 (258)
                      .|+-++|.|++|+|||...+..+.+...+.   +.+..++++.
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~   77 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   77 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe
Confidence            346799999999999988766665554321   2234566654

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {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: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=89.02  E-value=0.063  Score=38.06  Aligned_cols=18  Identities=33%  Similarity=0.374  Sum_probs=15.1

Q ss_pred             CcEEEEcccCCCcchHhH
Q psy4698          85 NDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l  102 (258)
                      +-+++.|++|||||+.+-
T Consensus         7 ~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEEECSTTSCHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347889999999998864

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.60  E-value=0.093  Score=39.88  Aligned_cols=53  Identities=9%  Similarity=0.064  Sum_probs=29.8

Q ss_pred             CcCCCCCCHHHHHHHHHCCCCCCcHHHHHHhhh-----hhcCCcEEEEcccCCCcchHh
Q psy4698          48 NFDDMELSEELLRGIYAYGFEKPSAIQQRAIIP-----CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        48 ~~~~~~~~~~l~~~l~~~~~~~~~~~Q~~~~~~-----l~~g~~~li~~~tGsGKT~~~  101 (258)
                      .|.++-..+..++.|+.. +..........+..     ....+.+++.||+|+|||.++
T Consensus        12 ~~~dlig~~~~~~~L~~~-l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNW-LANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHH-HHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHH-HHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            578887788777766541 00000001111111     111246999999999999875

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=88.35  E-value=0.11  Score=37.68  Aligned_cols=19  Identities=21%  Similarity=0.349  Sum_probs=15.8

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      |-.+++.||+|||||+..-
T Consensus         3 ~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHH
Confidence            4467889999999999763

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=88.34  E-value=0.11  Score=37.03  Aligned_cols=19  Identities=16%  Similarity=0.151  Sum_probs=15.9

Q ss_pred             CcEEEEcccCCCcchHhHH
Q psy4698          85 NDVIAQAQSGTGKTATFSI  103 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~l~  103 (258)
                      +.+++.|++|||||+++-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5688999999999987643

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=88.25  E-value=0.086  Score=37.65  Aligned_cols=17  Identities=24%  Similarity=0.374  Sum_probs=14.7

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +-++|.|++|||||+..
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45899999999999865

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.14  E-value=0.1  Score=37.41  Aligned_cols=17  Identities=18%  Similarity=0.366  Sum_probs=14.7

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      ++++.||+|||||+..-
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37899999999999763

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=88.10  E-value=0.069  Score=40.98  Aligned_cols=17  Identities=29%  Similarity=0.333  Sum_probs=15.0

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.+++.||+|+|||..+
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999875

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.07  E-value=0.13  Score=41.08  Aligned_cols=24  Identities=29%  Similarity=0.513  Sum_probs=19.6

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ++.+++|.+  ++..|+||||||.+.
T Consensus        68 v~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          68 VKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHcCCCcceeeecccCCCCceec
Confidence            455678876  899999999999874

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.05  E-value=0.079  Score=38.19  Aligned_cols=17  Identities=24%  Similarity=0.335  Sum_probs=14.7

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      ++++.||+|||||+..-
T Consensus         2 ~I~i~G~pGsGKsT~a~   18 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAV   18 (181)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999999764

>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=87.79  E-value=0.69  Score=36.24  Aligned_cols=55  Identities=13%  Similarity=0.064  Sum_probs=38.0

Q ss_pred             cceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcchHHHHHHHhcCCcEEEeCh
Q psy4698         115 ECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIVRDDIRKLEAGAQVVVGTP  173 (258)
Q Consensus       115 ~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp  173 (258)
                      +++++|.||+..-+++....+++.+    ..+..+++.....+..+......+|+|+|.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g----~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAG----KSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTT----CCEEECCSSSCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcC----CeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            3479999999999999999887754    567778887665555444455588999995

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=87.71  E-value=0.1  Score=38.13  Aligned_cols=21  Identities=14%  Similarity=0.257  Sum_probs=17.5

Q ss_pred             hhcCCcEEEEcccCCCcchHh
Q psy4698          81 CVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        81 l~~g~~~li~~~tGsGKT~~~  101 (258)
                      +..++-+++.||+|||||+.+
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a   25 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQC   25 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHH
Confidence            455677899999999999876

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=87.65  E-value=0.083  Score=38.40  Aligned_cols=17  Identities=18%  Similarity=0.339  Sum_probs=14.6

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .+++.||+|||||+..-
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48999999999998763

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=87.46  E-value=0.096  Score=41.87  Aligned_cols=19  Identities=26%  Similarity=0.380  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      .+.++++.|++|+|||..+
T Consensus        27 ~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          27 GIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             GGCCEEEECCGGGCTTHHH
T ss_pred             CCCeEEEECCCCccHHHHH
Confidence            4578999999999999865

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.43  E-value=0.095  Score=37.74  Aligned_cols=16  Identities=31%  Similarity=0.432  Sum_probs=13.8

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -++++|++|||||+.+
T Consensus        16 liil~G~pGsGKST~a   31 (172)
T d1yj5a2          16 VVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999754

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=87.34  E-value=0.086  Score=37.90  Aligned_cols=16  Identities=19%  Similarity=0.189  Sum_probs=14.1

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.||+|||||+..
T Consensus         2 ~I~i~G~pGSGKsT~~   17 (179)
T d1e4va1           2 RIILLGAPVAGKGTQA   17 (179)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999976

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=87.10  E-value=0.13  Score=36.99  Aligned_cols=17  Identities=18%  Similarity=0.397  Sum_probs=14.5

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .+++.||+|||||+.+-
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQAD   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37899999999999763

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {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: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.97  E-value=0.1  Score=38.08  Aligned_cols=16  Identities=19%  Similarity=0.320  Sum_probs=14.0

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -+++.||+|||||+.+
T Consensus        10 iI~i~GppGSGKsT~a   25 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQC   25 (196)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999876

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.94  E-value=0.11  Score=37.46  Aligned_cols=18  Identities=28%  Similarity=0.455  Sum_probs=15.7

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      |+-+++.||.|+|||...
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            566899999999999864

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.87  E-value=0.11  Score=37.66  Aligned_cols=17  Identities=29%  Similarity=0.577  Sum_probs=14.7

Q ss_pred             CcEEEEcccCCCcchHh
Q psy4698          85 NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        85 ~~~li~~~tGsGKT~~~  101 (258)
                      +.++++||+|+|||...
T Consensus         2 rpIvl~GpsG~GK~tl~   18 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45899999999999864

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.81  E-value=0.15  Score=38.35  Aligned_cols=43  Identities=12%  Similarity=-0.047  Sum_probs=28.0

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhhcc---ccceEEEEeccH
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQNI---KECQALILAPTR  125 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~~~---~~~~~lil~P~~  125 (258)
                      .|+-++|.|++|+|||...+..+.+......   ....++++....
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~   81 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN   81 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHH
Confidence            4567999999999999887666655443321   223455555443

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {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: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.81  E-value=0.045  Score=39.75  Aligned_cols=19  Identities=37%  Similarity=0.391  Sum_probs=15.6

Q ss_pred             CCcEEEEcccCCCcchHhH
Q psy4698          84 GNDVIAQAQSGTGKTATFS  102 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~l  102 (258)
                      |..++++|++|||||+.+-
T Consensus        19 g~vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4467799999999998763

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=86.65  E-value=0.16  Score=41.25  Aligned_cols=24  Identities=33%  Similarity=0.533  Sum_probs=18.6

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      +..++.|.+  ++..|.||||||.+.
T Consensus       106 v~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         106 VQTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCceEEeeccCCCCCceee
Confidence            345567876  777799999999875

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=86.40  E-value=0.18  Score=40.81  Aligned_cols=25  Identities=32%  Similarity=0.505  Sum_probs=19.5

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ++..+++|.+  ++..|+||||||.+.
T Consensus        71 lv~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          71 TVDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhhccCceeEEecccCCCCcceee
Confidence            3445568876  888899999999774

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=86.39  E-value=0.15  Score=36.17  Aligned_cols=63  Identities=11%  Similarity=0.075  Sum_probs=33.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEeeCChhHHHHHHH--hcCCCeEEEecC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSATMPADVLDVSMK--FMRDPIKILVKK  252 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT~~~~~~~~~~~--~~~~~~~v~~~~  252 (258)
                      .+-+++++||++..... .......+.+.+......++++..-.. ...++..  .+.+..++.+..
T Consensus        98 ~~~~vlllDE~~~~~~~-~~~~~~~l~~~l~~~~~~il~~~h~~~-~~~~~~~i~~~~~~~i~~v~~  162 (178)
T d1ye8a1          98 DRRKVIIIDEIGKMELF-SKKFRDLVRQIMHDPNVNVVATIPIRD-VHPLVKEIRRLPGAVLIELTP  162 (178)
T ss_dssp             CTTCEEEECCCSTTGGG-CHHHHHHHHHHHTCTTSEEEEECCSSC-CSHHHHHHHTCTTCEEEECCT
T ss_pred             cCCCceeecCCCccchh-hHHHHHHHHHHhccCCCEEEEEEccHH-HHHhhceEEEEeCCEEEEECC
Confidence            45679999998754332 233444455555544455665554332 2233332  345666666643

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=86.33  E-value=0.13  Score=38.14  Aligned_cols=19  Identities=37%  Similarity=0.553  Sum_probs=16.5

Q ss_pred             cCCcEEEEcccCCCcchHh
Q psy4698          83 RGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~  101 (258)
                      +|+-++++||.|+|||...
T Consensus         1 ~G~livi~GPSG~GK~tl~   19 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLI   19 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4677899999999999864

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=85.87  E-value=0.15  Score=36.95  Aligned_cols=16  Identities=25%  Similarity=0.345  Sum_probs=14.0

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -+++.||+|||||+.+
T Consensus         8 iI~i~G~pGSGKsT~a   23 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999875

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=85.74  E-value=0.17  Score=36.42  Aligned_cols=15  Identities=27%  Similarity=0.186  Sum_probs=12.8

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      +-|.|++|||||+.+
T Consensus        25 IgI~G~~GSGKSTla   39 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLA   39 (198)
T ss_dssp             EEEEECTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            449999999999865

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=85.45  E-value=0.2  Score=40.34  Aligned_cols=24  Identities=29%  Similarity=0.530  Sum_probs=19.2

Q ss_pred             hhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          78 IIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        78 ~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      ++.+++|.+  ++..|.||||||.+.
T Consensus        79 v~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          79 LQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhccCceeeeeccCCCCCceee
Confidence            344578876  889999999999774

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {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: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.44  E-value=0.18  Score=36.53  Aligned_cols=16  Identities=25%  Similarity=0.410  Sum_probs=14.1

Q ss_pred             EEEEcccCCCcchHhH
Q psy4698          87 VIAQAQSGTGKTATFS  102 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l  102 (258)
                      ++|.||+|||||+.+-
T Consensus         4 I~i~GppGSGKsT~a~   19 (194)
T d1teva_           4 VFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999998863

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.43  E-value=0.18  Score=36.19  Aligned_cols=16  Identities=19%  Similarity=0.339  Sum_probs=14.0

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      .+++.||+|||||+..
T Consensus         4 rIvl~G~pGSGKtT~a   19 (180)
T d1akya1           4 RMVLIGPPGAGKGTQA   19 (180)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788999999999876

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=85.42  E-value=0.18  Score=40.98  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=20.0

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .++.+++|.+  ++..|+||||||.+.
T Consensus        66 lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          66 LVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCceeeeccccCCCCccccc
Confidence            3556678876  788899999999875

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.14  E-value=0.16  Score=37.05  Aligned_cols=16  Identities=31%  Similarity=0.565  Sum_probs=14.1

Q ss_pred             cEEEEcccCCCcchHh
Q psy4698          86 DVIAQAQSGTGKTATF  101 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~  101 (258)
                      -+++.||+|+|||..+
T Consensus         2 pIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4799999999999864

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=85.13  E-value=0.19  Score=40.91  Aligned_cols=25  Identities=36%  Similarity=0.567  Sum_probs=20.0

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .++.+++|.+  ++..|+||||||.+.
T Consensus       116 lv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         116 LIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcccceeEEeeccCCCccceEe
Confidence            4455678876  899999999999774

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=85.05  E-value=0.17  Score=37.84  Aligned_cols=29  Identities=17%  Similarity=0.110  Sum_probs=23.2

Q ss_pred             cCCcEEEEcccCCCcchHhHHHHHHHhhh
Q psy4698          83 RGNDVIAQAQSGTGKTATFSISILQQVDQ  111 (258)
Q Consensus        83 ~g~~~li~~~tGsGKT~~~l~~~l~~l~~  111 (258)
                      .|.-++|.|++|+|||...+..+.+.+..
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~~~   61 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQNP   61 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCG
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            45679999999999998887777766543

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=85.04  E-value=0.37  Score=33.58  Aligned_cols=35  Identities=20%  Similarity=0.198  Sum_probs=22.1

Q ss_pred             cEEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          86 DVIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .+.|+|+.|||||+.. -.++..+...  +.++.++..
T Consensus         4 vi~itG~~GSGKTTL~-~~L~~~l~~~--g~~v~v~~~   38 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLL-KKLIPALCAR--GIRPGLIKH   38 (170)
T ss_dssp             EEEEECCTTSCHHHHH-HHHHHHHHHT--TCCEEEEEE
T ss_pred             EEEEEcCCCCCHHHHH-HHHHHHHHHC--CCeEEEecc
Confidence            3689999999999864 3344444433  335655553

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=84.53  E-value=0.25  Score=39.59  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=20.6

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .++.+++|.+  ++..|.||||||.+.
T Consensus        74 ~v~~~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          74 LVQSSLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             hhcchhcccccceeeeeccCCcccccc
Confidence            5566778876  788999999999876

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=84.43  E-value=0.22  Score=39.98  Aligned_cols=25  Identities=36%  Similarity=0.523  Sum_probs=19.7

Q ss_pred             HhhhhhcCCc--EEEEcccCCCcchHh
Q psy4698          77 AIIPCVRGND--VIAQAQSGTGKTATF  101 (258)
Q Consensus        77 ~~~~l~~g~~--~li~~~tGsGKT~~~  101 (258)
                      .+..+++|.+  ++..|+||||||.+.
T Consensus        72 lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          72 ILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhccCCceEEeeeeccccceEEe
Confidence            3455678876  789999999999764

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=84.27  E-value=0.22  Score=36.22  Aligned_cols=17  Identities=24%  Similarity=0.290  Sum_probs=14.7

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      .+++.||+|||||+..-
T Consensus         8 rIiliG~PGSGKtT~a~   24 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSS   24 (189)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            58899999999998763

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.07  E-value=0.24  Score=34.94  Aligned_cols=17  Identities=18%  Similarity=0.282  Sum_probs=14.5

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      ++++.|++|+|||++.-
T Consensus         3 ~IvliG~~G~GKSTig~   19 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGR   19 (165)
T ss_dssp             SEEEECSTTSSHHHHHH
T ss_pred             cEEEECCCCCCHHHHHH
Confidence            57888999999998763

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=83.61  E-value=0.18  Score=36.05  Aligned_cols=15  Identities=27%  Similarity=0.452  Sum_probs=13.1

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      ++|.|+.|+|||+..
T Consensus         4 ivi~G~~GsGKTT~~   18 (194)
T d1nksa_           4 GIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999875

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=83.54  E-value=0.43  Score=34.58  Aligned_cols=15  Identities=20%  Similarity=0.231  Sum_probs=13.6

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      ++++|.+|||||+.+
T Consensus         5 i~l~GlpgsGKSTla   19 (213)
T d1bifa1           5 IVMVGLPARGKTYIS   19 (213)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999876

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.50  E-value=0.45  Score=35.53  Aligned_cols=32  Identities=16%  Similarity=0.267  Sum_probs=20.0

Q ss_pred             EEEEcccCCCcchHhHHHHHHHhhhccccceEEEEec
Q psy4698          87 VIAQAQSGTGKTATFSISILQQVDQNIKECQALILAP  123 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l~~~l~~l~~~~~~~~~lil~P  123 (258)
                      .+|.|.-|||||+.     ++++.....+.++.||+.
T Consensus         6 ~iitGFLGaGKTTl-----l~~lL~~~~~~riaVI~N   37 (222)
T d1nija1           6 TLLTGFLGAGKTTL-----LRHILNEQHGYKIAVIEN   37 (222)
T ss_dssp             EEEEESSSSSCHHH-----HHHHHHSCCCCCEEEECS
T ss_pred             EEEeeCCCCCHHHH-----HHHHHhcCCCCcEEEEEe
Confidence            68999999999974     233333333445655553

>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=82.84  E-value=3.5  Score=31.34  Aligned_cols=86  Identities=16%  Similarity=0.256  Sum_probs=53.2

Q ss_pred             HHHHHhhhccccceEEEEeccHHHHHHHHHHHHHhcCCCCceEEEEECCcch-----------HHHHHHHhc-CCcEEEe
Q psy4698         104 SILQQVDQNIKECQALILAPTRELAQQIQKVVIALGDFMSVSCHACIGGTIV-----------RDDIRKLEA-GAQVVVG  171 (258)
Q Consensus       104 ~~l~~l~~~~~~~~~lil~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~-~~~Ilv~  171 (258)
                      -++..+.....+.++||.|.++..+..+.+.+.+.+    +.+..+.|....           ........+ .++|+|+
T Consensus       150 ~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~----~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~  225 (286)
T d1wp9a2         150 EIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDG----IKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVA  225 (286)
T ss_dssp             HHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTT----CCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEE
T ss_pred             HHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcC----CceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEE
Confidence            344444444556689999999999999998886643    444444443221           112223333 4899999


Q ss_pred             ChHHHHHHHhcCCCCCCCccEEEEccch
Q psy4698         172 TPGRVFDMISRGALSTKQIRMFVLDEAD  199 (258)
Q Consensus       172 Tp~~l~~~l~~~~~~~~~l~~lVvDE~h  199 (258)
                      |-     ... .++++.++++||.=+.+
T Consensus       226 T~-----~~~-~Gld~~~~~~Vi~~d~~  247 (286)
T d1wp9a2         226 TS-----VGE-EGLDVPEVDLVVFYEPV  247 (286)
T ss_dssp             CG-----GGG-GGGGSTTCCEEEESSCC
T ss_pred             cc-----cee-ccccCCCCCEEEEeCCC
Confidence            94     223 34678889888864443

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.53  E-value=0.57  Score=36.46  Aligned_cols=14  Identities=29%  Similarity=0.387  Sum_probs=11.5

Q ss_pred             EEEcccCCCcchHh
Q psy4698          88 IAQAQSGTGKTATF  101 (258)
Q Consensus        88 li~~~tGsGKT~~~  101 (258)
                      -|.|++|||||+..
T Consensus        31 Gi~G~qGSGKSTl~   44 (286)
T d1odfa_          31 FFSGPQGSGKSFTS   44 (286)
T ss_dssp             EEECCTTSSHHHHH
T ss_pred             EeECCCCCCHHHHH
Confidence            36899999999654

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=82.23  E-value=0.41  Score=36.42  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=17.8

Q ss_pred             hhhcCCcEEEEcccCCCcchHh
Q psy4698          80 PCVRGNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        80 ~l~~g~~~li~~~tGsGKT~~~  101 (258)
                      ....+..++|.|++|+||+.++
T Consensus        19 ~a~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          19 ISCAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             HTTCCSCEEEECSTTSSHHHHH
T ss_pred             HhCCCCCEEEECCCCcCHHHHH
Confidence            3455678999999999999754

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=82.01  E-value=0.46  Score=36.22  Aligned_cols=61  Identities=18%  Similarity=0.152  Sum_probs=35.4

Q ss_pred             hhhhhcCCcEEEEcccCCCcchHhHHHHHHHhhh-------ccccceEEEEeccHHHHHHHHHHHHHhc
Q psy4698          78 IIPCVRGNDVIAQAQSGTGKTATFSISILQQVDQ-------NIKECQALILAPTRELAQQIQKVVIALG  139 (258)
Q Consensus        78 ~~~l~~g~~~li~~~tGsGKT~~~l~~~l~~l~~-------~~~~~~~lil~P~~~l~~q~~~~~~~~~  139 (258)
                      ++-+..|.-.++.|++|+|||..++..++.....       ...+.+++|+.--. -..++..++..+.
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~-~~~~~~~Rl~~~~   90 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAED-PPTAIHHRLHALG   90 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSS-CHHHHHHHHHHHH
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccc-hHHHHHHHHHHHh
Confidence            3444567789999999999998776555432211       11234677776432 2334444454443

>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=81.75  E-value=0.14  Score=38.06  Aligned_cols=82  Identities=12%  Similarity=0.177  Sum_probs=48.1

Q ss_pred             ccceEEEEeccHHHHHHH-----HHHHHHhcCC--CCceEEEEECCcchHH---HHHHHhc-CCcEEEeChHHHHHHHhc
Q psy4698         114 KECQALILAPTRELAQQI-----QKVVIALGDF--MSVSCHACIGGTIVRD---DIRKLEA-GAQVVVGTPGRVFDMISR  182 (258)
Q Consensus       114 ~~~~~lil~P~~~l~~q~-----~~~~~~~~~~--~~~~~~~~~~~~~~~~---~~~~~~~-~~~Ilv~Tp~~l~~~l~~  182 (258)
                      ++.++.|+||..+-.+..     .+....+.+.  .+..+..++|.....+   ......+ ..+|+|||.      +-.
T Consensus        28 ~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt------ViE  101 (206)
T d1gm5a4          28 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT------VIE  101 (206)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS------CCC
T ss_pred             cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh------hhh
Confidence            345899999986533321     2222233322  2456667787765432   3334444 499999995      234


Q ss_pred             CCCCCCCccEEEEccchhh
Q psy4698         183 GALSTKQIRMFVLDEADEM  201 (258)
Q Consensus       183 ~~~~~~~l~~lVvDE~h~~  201 (258)
                      .+++.++..++|+.+++++
T Consensus       102 ~GIDip~a~~iii~~a~~f  120 (206)
T d1gm5a4         102 VGIDVPRANVMVIENPERF  120 (206)
T ss_dssp             SCSCCTTCCEEEBCSCSSS
T ss_pred             ccccccCCcEEEEEccCCc
Confidence            4578999999999999964

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=81.68  E-value=0.47  Score=38.30  Aligned_cols=36  Identities=14%  Similarity=0.019  Sum_probs=23.0

Q ss_pred             CCCCCcHHHHHHhhhhhcC----CcEEEEcccCCCcchHh
Q psy4698          66 GFEKPSAIQQRAIIPCVRG----NDVIAQAQSGTGKTATF  101 (258)
Q Consensus        66 ~~~~~~~~Q~~~~~~l~~g----~~~li~~~tGsGKT~~~  101 (258)
                      ++......-.+.+..+..|    +.+++.||+|+|||..+
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~  171 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA  171 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHH
Confidence            3444333333444444444    46999999999999865

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.43  E-value=0.27  Score=35.38  Aligned_cols=18  Identities=11%  Similarity=0.243  Sum_probs=15.3

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+-++++||+|+||+...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            356899999999999864

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.16  E-value=0.28  Score=37.55  Aligned_cols=32  Identities=16%  Similarity=0.235  Sum_probs=25.4

Q ss_pred             CCccEEEEccchhhhccCcHHHHHHHHHhCCC
Q psy4698         188 KQIRMFVLDEADEMLSRGFKDQIYDVFKHLNN  219 (258)
Q Consensus       188 ~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~  219 (258)
                      .+-+++|+||+=.-+|......+...+..+.+
T Consensus       168 ~~p~ililDEpTs~LD~~~~~~i~~~l~~l~~  199 (251)
T d1jj7a_         168 RKPCVLILDDATSALDANSQLQVEQLLYESPE  199 (251)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHTCGG
T ss_pred             cCCcEEEecCcCcccChhhHHHHHHHHHHHhh
Confidence            34569999999888887777888888877754

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=80.91  E-value=0.58  Score=34.07  Aligned_cols=34  Identities=9%  Similarity=0.054  Sum_probs=20.1

Q ss_pred             CcEEEEcc-cCCCcchHhHHHHHHHhhhccccceEEEE
Q psy4698          85 NDVIAQAQ-SGTGKTATFSISILQQVDQNIKECQALIL  121 (258)
Q Consensus        85 ~~~li~~~-tGsGKT~~~l~~~l~~l~~~~~~~~~lil  121 (258)
                      |.++|+|- ||.|||++...-+. .+.+.  +.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~-aLa~~--G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQ-AAKAA--GYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHH-HHHHT--TCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHH-HHHHC--CCeEEEE
Confidence            34566666 69999988643332 33332  3367665

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {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: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.80  E-value=0.27  Score=36.18  Aligned_cols=15  Identities=13%  Similarity=0.302  Sum_probs=12.6

Q ss_pred             EEEEcccCCCcchHh
Q psy4698          87 VIAQAQSGTGKTATF  101 (258)
Q Consensus        87 ~li~~~tGsGKT~~~  101 (258)
                      +-|.|++|||||+.+
T Consensus         5 IgI~G~~gSGKSTla   19 (213)
T d1uj2a_           5 IGVSGGTASGKSSVC   19 (213)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            458899999999865

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=80.64  E-value=0.28  Score=36.12  Aligned_cols=43  Identities=12%  Similarity=0.296  Sum_probs=29.6

Q ss_pred             CCCccEEEEccchhhhccCcHHHHHHHHHhCCCCccEEEEEee
Q psy4698         187 TKQIRMFVLDEADEMLSRGFKDQIYDVFKHLNNDVQVILLSAT  229 (258)
Q Consensus       187 ~~~l~~lVvDE~h~~~~~~~~~~~~~~~~~l~~~~~~i~~SAT  229 (258)
                      +.+-+++++||.=.-+|......+...+..+.++..+++++.+
T Consensus       141 ~~~~~llllDEPt~gLD~~~~~~i~~~l~~~~~~~~~~ii~~~  183 (200)
T d1sgwa_         141 LVNAEIYVLDDPVVAIDEDSKHKVLKSILEILKEKGIVIISSR  183 (200)
T ss_dssp             TSCCSEEEEESTTTTSCTTTHHHHHHHHHHHHHHHSEEEEEES
T ss_pred             hcCCCEEEEcCcccccCHHHHHHHHHHHHHHHhCCCEEEEEEe
Confidence            3456799999998777777776776666555444456666665

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.20  E-value=0.25  Score=38.06  Aligned_cols=18  Identities=28%  Similarity=0.331  Sum_probs=15.8

Q ss_pred             CCcEEEEcccCCCcchHh
Q psy4698          84 GNDVIAQAQSGTGKTATF  101 (258)
Q Consensus        84 g~~~li~~~tGsGKT~~~  101 (258)
                      .+.+++.||+|+|||...
T Consensus        41 ~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcchhHH
Confidence            467999999999999865

>d1ckea_ c.37.1.1 (A:) CMP kinase {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: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=80.11  E-value=0.38  Score=35.25  Aligned_cols=16  Identities=25%  Similarity=0.410  Sum_probs=13.4

Q ss_pred             EEEEcccCCCcchHhH
Q psy4698          87 VIAQAQSGTGKTATFS  102 (258)
Q Consensus        87 ~li~~~tGsGKT~~~l  102 (258)
                      +.|.||.||||++.+-
T Consensus         6 I~I~GppGSGKgT~ak   21 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCK   21 (225)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5677999999999863

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=80.05  E-value=0.28  Score=38.88  Aligned_cols=17  Identities=24%  Similarity=0.362  Sum_probs=14.8

Q ss_pred             cEEEEcccCCCcchHhH
Q psy4698          86 DVIAQAQSGTGKTATFS  102 (258)
Q Consensus        86 ~~li~~~tGsGKT~~~l  102 (258)
                      ++++.||||+|||..+-
T Consensus        54 ~~lf~Gp~GvGKT~lak   70 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTV   70 (315)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCcchhHHHHH
Confidence            58999999999998763