Psyllid ID: psy1539

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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-----
Protein Sequence
MDSMFGMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHHHccEEEEEccccccHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHccccccEEEEEEcccccHHHHHHHHccccEEEEcccccccccccHHHHHHHHcccHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHcccEEEEcccccEEEHHHHHHHHHHHHHcccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MDSMFGMFHGVTVKVLSsrnrrekedrigesqpfreqtsfqhecipqAVLGMDILCqaksgmgkTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVgvffgglpiqkdeeylkthnpqivglVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Flexible Loop (DISEMBL)
mdsmfgmfhgvtvkvlssrnrrekedrigesqpfreqtsfqHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Low Complexity Region (SEG)
MDSMFGMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Disordered region (IsUnstruct)
******MFHGVTVK*************************FQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILS***
Disordered Region (DISOPRED)
*********GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Disordered Region (DISEMBL)
MDSMFGMFHGVTVKVLS**********************FQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Disordered Region (DISPRO)
************VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDSMFGMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILSKCA
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	175	2.2.26 [Sep-21-2011]
Q27268	424	ATP-dependent RNA helicas	yes	N/A	0.6	0.247	0.783	6e-43
Q63413	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q9Z1N5	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q5RE47	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q29024	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
P60024	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q5TM17	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q13838	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q5WR10	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.771	2e-42
Q3T147	428	Spliceosome RNA helicase	yes	N/A	0.6	0.245	0.761	8e-42

>sp|Q27268|DX39B_DROME ATP-dependent RNA helicase WM6 OS=Drosophila melanogaster GN=Hel25E PE=1 SV=1

 Score =  173 bits (438), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 83/106 (78%), Positives = 90/106 (84%), Gaps = 1/106 (0%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTR 92
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTR
Sbjct: 61  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTR 120

Query: 93  ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           ELAFQISKEYERFSKYM  +KV VFFGG+ IQKDEE LK+  P IV
Sbjct: 121 ELAFQISKEYERFSKYMPTVKVAVFFGGMAIQKDEETLKSGTPHIV 166

Required for mRNA export out of the nucleus. Probable RNA helicase that may regulate entry into mitosis by down-regulating the expression of other genes whose activity may be rate-limiting for entry into mitosis during embryogenesis. Binds to salivary gland chromosomes and modifies position effect variegation. Promotes an open chromatin structure that favors transcription during development by regulating the spread of heterochromatin.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q63413|DX39B_RAT Spliceosome RNA helicase Ddx39b OS=Rattus norvegicus GN=Ddx39b PE=1 SV=3

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9Z1N5|DX39B_MOUSE Spliceosome RNA helicase Ddx39b OS=Mus musculus GN=Ddx39b PE=1 SV=1

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5RE47|DX39B_PONAB Spliceosome RNA helicase DDX39B OS=Pongo abelii GN=DDX39B PE=2 SV=1

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q29024|DX39B_PIG Spliceosome RNA helicase DDX39B OS=Sus scrofa GN=DDX39B PE=2 SV=2

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Sus scrofa (taxid: 9823)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P60024|DX39B_PANTR Spliceosome RNA helicase DDX39B OS=Pan troglodytes GN=DDX39B PE=3 SV=1

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5TM17|DX39B_MACMU Spliceosome RNA helicase DDX39B OS=Macaca mulatta GN=DDX39B PE=3 SV=1

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Macaca mulatta (taxid: 9544)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q13838|DX39B_HUMAN Spliceosome RNA helicase DDX39B OS=Homo sapiens GN=DDX39B PE=1 SV=1

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5WR10|DX39B_CANFA Spliceosome RNA helicase DDX39B OS=Canis familiaris GN=DDX39B PE=3 SV=1

 Score =  171 bits (433), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Canis familiaris (taxid: 9615)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3T147|DX39B_BOVIN Spliceosome RNA helicase DDX39B OS=Bos taurus GN=DDX39B PE=2 SV=1

 Score =  169 bits (428), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 80/105 (76%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 65  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM ++KV VFFGGL I+KDEE LK + P IV
Sbjct: 125 LAFQISKEYERFSKYMPSVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

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	175
21068659	421	HEL protein [Chironomus tentans]	0.76	0.315	0.676	2e-45
332019236	428	ATP-dependent RNA helicase WM6 [Acromyrm	0.6	0.245	0.838	8e-45
122937741	419	AAEL001216-PA [Aedes aegypti]	0.6	0.250	0.828	8e-45
307178480	425	Spliceosome RNA helicase Bat1 [Camponotu	0.6	0.247	0.838	9e-45
157115837	423	DEAD box ATP-dependent RNA helicase [Aed	0.6	0.248	0.828	9e-45
156550340	425	PREDICTED: ATP-dependent RNA helicase WM	0.6	0.247	0.828	1e-44
332376787	424	unknown [Dendroctonus ponderosae]	0.6	0.247	0.838	1e-44
170057076	423	ATP-dependent RNA helicase WM6 [Culex qu	0.6	0.248	0.828	2e-44
322789368	420	hypothetical protein SINV_13808 [Solenop	0.6	0.25	0.838	2e-44
383858684	454	PREDICTED: ATP-dependent RNA helicase WM	0.6	0.231	0.828	2e-44

>gi|21068659|emb|CAD21558.1| HEL protein [Chironomus tentans]

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 96/142 (67%), Positives = 107/142 (75%), Gaps = 9/142 (6%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   ++ QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE TD+  YVLVMCHTRE
Sbjct: 59  FEHPSAVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTDNQAYVLVMCHTRE 118

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVN 153
           LAFQISKEYERFSKYMS +KV VFFGG+PIQKDEE LKT  P IV          G V+ 
Sbjct: 119 LAFQISKEYERFSKYMSGVKVAVFFGGMPIQKDEEVLKTTTPHIV------VGTPGRVLA 172

Query: 154 VMDVRSGGWWL-DLEALILSKC 174
           +  +RS    L +L+  IL +C
Sbjct: 173 L--IRSKKLNLKNLKHFILDEC 192

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332019236|gb|EGI59746.1| ATP-dependent RNA helicase WM6 [Acromyrmex echinatior]

 Score =  184 bits (468), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 88/105 (83%), Positives = 93/105 (88%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRE
Sbjct: 62  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLELTENQVYVLVMCHTRE 121

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM ++KVGVFFGGLPIQKDEE LKT  P IV
Sbjct: 122 LAFQISKEYERFSKYMPHVKVGVFFGGLPIQKDEEMLKTVCPHIV 166

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|122937741|gb|ABM68586.1| AAEL001216-PA [Aedes aegypti]

 Score =  184 bits (468), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 92/105 (87%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++  YVLVMCHTRE
Sbjct: 61  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTENVPYVLVMCHTRE 120

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM NIKV VFFGGLPIQKDEE LK+ NP I+
Sbjct: 121 LAFQISKEYERFSKYMPNIKVAVFFGGLPIQKDEEVLKSTNPHII 165

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307178480|gb|EFN67169.1| Spliceosome RNA helicase Bat1 [Camponotus floridanus]

 Score =  184 bits (468), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 88/105 (83%), Positives = 93/105 (88%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRE
Sbjct: 63  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLELTENQVYVLVMCHTRE 122

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM ++KVGVFFGGLPIQKDEE LKT  P IV
Sbjct: 123 LAFQISKEYERFSKYMPHVKVGVFFGGLPIQKDEEVLKTVCPHIV 167

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157115837|ref|XP_001658306.1| DEAD box ATP-dependent RNA helicase [Aedes aegypti] gi|94468806|gb|ABF18252.1| ATP-dependent RNA helicase [Aedes aegypti] gi|108883476|gb|EAT47701.1| AAEL001216-PA [Aedes aegypti]

 Score =  184 bits (468), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 92/105 (87%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++  YVLVMCHTRE
Sbjct: 61  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTENVPYVLVMCHTRE 120

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM NIKV VFFGGLPIQKDEE LK+ NP I+
Sbjct: 121 LAFQISKEYERFSKYMPNIKVAVFFGGLPIQKDEEVLKSTNPHII 165

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156550340|ref|XP_001606535.1| PREDICTED: ATP-dependent RNA helicase WM6-like [Nasonia vitripennis]

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 93/105 (88%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE+T+++VYVLVMCHTRE
Sbjct: 63  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLESTENHVYVLVMCHTRE 122

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGLPIQKDEE LK   P IV
Sbjct: 123 LAFQISKEYERFSKYMQNVKVSVFFGGLPIQKDEEVLKNTCPHIV 167

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332376787|gb|AEE63533.1| unknown [Dendroctonus ponderosae]

 Score =  184 bits (466), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 88/105 (83%), Positives = 93/105 (88%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRE
Sbjct: 62  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTENVVYVLVMCHTRE 121

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM +IKVGVFFGGLPIQKDEE LK + P IV
Sbjct: 122 LAFQISKEYERFSKYMPSIKVGVFFGGLPIQKDEEMLKNNCPHIV 166

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170057076|ref|XP_001864320.1| ATP-dependent RNA helicase WM6 [Culex quinquefasciatus] gi|167876642|gb|EDS40025.1| ATP-dependent RNA helicase WM6 [Culex quinquefasciatus]

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 92/105 (87%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T+S  YVLVMCHTRE
Sbjct: 61  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTESVPYVLVMCHTRE 120

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM +IKV VFFGGLPIQKDEE LK+ NP I+
Sbjct: 121 LAFQISKEYERFSKYMPSIKVAVFFGGLPIQKDEEVLKSTNPHII 165

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322789368|gb|EFZ14680.1| hypothetical protein SINV_13808 [Solenopsis invicta]

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 88/105 (83%), Positives = 93/105 (88%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRE
Sbjct: 62  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEWTENQVYVLVMCHTRE 121

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM ++KVGVFFGGLPIQKDEE LKT  P IV
Sbjct: 122 LAFQISKEYERFSKYMQHVKVGVFFGGLPIQKDEEVLKTVCPHIV 166

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858684|ref|XP_003704829.1| PREDICTED: ATP-dependent RNA helicase WM6-like [Megachile rotundata]

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 87/105 (82%), Positives = 92/105 (87%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRE
Sbjct: 62  FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLELTENQVYVLVMCHTRE 121

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM ++KVGVFFGGLPIQKDEE LK   P IV
Sbjct: 122 LAFQISKEYERFSKYMPHVKVGVFFGGLPIQKDEEVLKNTCPHIV 166

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	175
FB|FBgn0014189	424	Hel25E "Helicase at 25E" [Dros	0.6	0.247	0.783	2.3e-39
UNIPROTKB|Q5WR10	428	DDX39B "Spliceosome RNA helica	0.6	0.245	0.771	7.8e-39
UNIPROTKB|F6S4E6	231	DDX39B "Spliceosome RNA helica	0.6	0.454	0.771	7.8e-39
UNIPROTKB|F6TRA5	238	DDX39B "Spliceosome RNA helica	0.6	0.441	0.771	7.8e-39
UNIPROTKB|F6UN21	236	DDX39B "Spliceosome RNA helica	0.6	0.444	0.771	7.8e-39
UNIPROTKB|F6WLT2	289	DDX39B "Spliceosome RNA helica	0.6	0.363	0.771	7.8e-39
UNIPROTKB|F8VZL8	323	DDX39B "Spliceosome RNA helica	0.6	0.325	0.771	7.8e-39
UNIPROTKB|Q13838	428	DDX39B "Spliceosome RNA helica	0.6	0.245	0.771	7.8e-39
UNIPROTKB|Q5STU3	425	DDX39B "Spliceosome RNA helica	0.6	0.247	0.771	7.8e-39
UNIPROTKB|Q29024	428	DDX39B "Spliceosome RNA helica	0.6	0.245	0.771	7.8e-39

FB|FBgn0014189 Hel25E "Helicase at 25E" [Drosophila melanogaster (taxid:7227)]

 Score = 420 (152.9 bits), Expect = 2.3e-39, P = 2.3e-39
 Identities = 83/106 (78%), Positives = 90/106 (84%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTR 92
             F   +  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTR
Sbjct:    61 FEHPSEVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTR 120

Query:    93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             ELAFQISKEYERFSKYM  +KV VFFGG+ IQKDEE LK+  P IV
Sbjct:   121 ELAFQISKEYERFSKYMPTVKVAVFFGGMAIQKDEETLKSGTPHIV 166

GO:0005634 "nucleus" evidence=IC;NAS;IDA

GO:0006338 "chromatin remodeling" evidence=IMP

GO:0005700 "polytene chromosome" evidence=IDA

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

GO:0003724 "RNA helicase activity" evidence=ISS

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

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0006406 "mRNA export from nucleus" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

UNIPROTKB|Q5WR10 DDX39B "Spliceosome RNA helicase DDX39B" [Canis lupus familiaris (taxid:9615)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F6S4E6 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|F6TRA5 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|F6UN21 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|F6WLT2 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|F8VZL8 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|Q13838 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0005524 "ATP binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006406 "mRNA export from nucleus" evidence=IGI;IDA

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

GO:0000346 "transcription export complex" evidence=IDA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IDA

GO:0008186 "RNA-dependent ATPase activity" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008380 "RNA splicing" evidence=IDA

GO:0000245 "spliceosomal complex assembly" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0043008 "ATP-dependent protein binding" evidence=IDA

GO:0005687 "U4 snRNP" evidence=IDA

GO:0005688 "U6 snRNP" evidence=IDA

GO:0030621 "U4 snRNA binding" evidence=IDA

GO:0017070 "U6 snRNA binding" evidence=IDA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

UNIPROTKB|Q5STU3 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q29024 DDX39B "Spliceosome RNA helicase DDX39B" [Sus scrofa (taxid:9823)]

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query:    34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct:    65 FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 124

Query:    94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
             LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct:   125 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 169

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5RE47	DX39B_PONAB	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q6CH90	SUB2_YARLI	3, ., 6, ., 4, ., 1, 3	0.5607	0.6	0.2380	yes	N/A
Q5WR10	DX39B_CANFA	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q5ZHZ0	DX39B_CHICK	3, ., 6, ., 4, ., 1, 3	0.7523	0.6	0.2453	yes	N/A
O13792	SUB2_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5887	0.6	0.2419	yes	N/A
Q18212	DX39B_CAEEL	3, ., 6, ., 4, ., 1, 3	0.5704	0.76	0.3129	yes	N/A
Q2U6P7	SUB2_ASPOR	3, ., 6, ., 4, ., 1, 3	0.5981	0.6	0.2380	yes	N/A
Q9Z1N5	DX39B_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q759L6	SUB2_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5420	0.6	0.2397	yes	N/A
Q5ASK8	SUB2_EMENI	3, ., 6, ., 4, ., 1, 3	0.5794	0.6	0.2419	yes	N/A
P0CQ96	SUB2_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.5981	0.6	0.2375	yes	N/A
Q63413	DX39B_RAT	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q9LFN6	RH56_ARATH	3, ., 6, ., 4, ., 1, 3	0.5904	0.6	0.2459	yes	N/A
Q6FL17	SUB2_CANGA	3, ., 6, ., 4, ., 1, 3	0.5514	0.6	0.2391	yes	N/A
A3LST5	SUB2_PICST	3, ., 6, ., 4, ., 1, 3	0.5794	0.6	0.2424	yes	N/A
Q5TM17	DX39B_MACMU	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q29024	DX39B_PIG	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q6BME5	SUB2_DEBHA	3, ., 6, ., 4, ., 1, 3	0.5794	0.6	0.2413	yes	N/A
Q0JM17	RH56_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6	0.6	0.2430	yes	N/A
Q56XG6	RH15_ARATH	3, ., 6, ., 4, ., 1, 3	0.5904	0.6	0.2459	yes	N/A
Q3T147	DX39B_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7619	0.6	0.2453	yes	N/A
Q27268	DX39B_DROME	3, ., 6, ., 4, ., 1, 3	0.7830	0.6	0.2476	yes	N/A
A2R0B5	SUB2_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5887	0.6	0.2386	yes	N/A
P60024	DX39B_PANTR	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q4WCW2	SUB2_ASPFU	3, ., 6, ., 4, ., 1, 3	0.5981	0.6	0.2343	yes	N/A
Q13838	DX39B_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7714	0.6	0.2453	yes	N/A
Q6CM95	SUB2_KLULA	3, ., 6, ., 4, ., 1, 3	0.5140	0.6	0.2402	yes	N/A
Q07478	SUB2_YEAST	3, ., 6, ., 4, ., 1, 3	0.5607	0.6	0.2354	yes	N/A

EC Number Prediction by EFICAz Software

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	175
cd00268	203	cd00268, DEADc, DEAD-box helicases	3e-35
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-27
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-25
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-19
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-16
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	3e-16
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-15
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-15
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-13
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-11
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	4e-10
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	5e-08
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	8e-08
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	1e-07
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-04
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	9e-04

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

 Score =  121 bits (307), Expect = 3e-35
 Identities = 39/107 (36%), Positives = 59/107 (55%), Gaps = 4/107 (3%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN--VYVLVMCHT 91
           F + T  Q   IP  + G D++ QA++G GKTA F++  L++L+ +        L++  T
Sbjct: 19  FEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPT 78

Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           RELA QI++   +  K+  N+KV V +GG  I K    LK   P IV
Sbjct: 79  RELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLK-RGPHIV 123

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 =  106 bits (266), Expect = 3e-27
 Identities = 50/134 (37%), Positives = 73/134 (54%), Gaps = 12/134 (8%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYV--LVMCHT 91
           F E T  Q   IP  + G D+L QA++G GKTA F+L  LQ++  +    YV  L++  T
Sbjct: 49  FEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT 108

Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV----G-----LVN 142
           RELA QI++E  +  K +  ++V V +GG+ I+K  E LK     IV    G     +  
Sbjct: 109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIKR 167

Query: 143 YETNLSGVVVNVMD 156
            + +LSGV   V+D
Sbjct: 168 GKLDLSGVETLVLD 181

Length = 513

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

 Score = 96.2 bits (240), Expect = 1e-25
 Identities = 35/101 (34%), Positives = 52/101 (51%), Gaps = 1/101 (0%)

Query: 38  TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ 97
           T  Q + IP  + G D+L QA +G GKT  F+L  LQ L         LV+  TRELA Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 98  ISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           I +E ++  K +  ++V +  GG  +++    LK     I+
Sbjct: 61  IYEELKKLFKIL-GLRVALLTGGTSLKEQARKLKKGKADIL 100

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

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

 Score = 83.7 bits (208), Expect = 2e-19
 Identities = 42/105 (40%), Positives = 63/105 (60%), Gaps = 1/105 (0%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           + E T  Q + +P  + G D++ QAK+G GKTA F L  LQ+L+     V  LV+C TRE
Sbjct: 24  YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE 83

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA Q++KE  R ++++ NIKV    GG+P+    + L+ H   I+
Sbjct: 84  LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE-HGAHII 127

Length = 460

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

 Score = 73.3 bits (180), Expect = 1e-16
 Identities = 29/102 (28%), Positives = 50/102 (49%), Gaps = 3/102 (2%)

Query: 38  TSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF 96
             +Q E I   + G  D++  A +G GKT   +L  L+ L+       VLV+  TRELA 
Sbjct: 10  RPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKR-GKGGRVLVLVPTRELAE 68

Query: 97  QISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           Q ++E ++    +    VG+ +GG   ++    L++    I+
Sbjct: 69  QWAEELKKLGPSLGLKVVGL-YGGDSKREQLRKLESGKTDIL 109

Length = 201

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

 Score = 74.8 bits (184), Expect = 3e-16
 Identities = 56/156 (35%), Positives = 76/156 (48%), Gaps = 29/156 (18%)

Query: 27  RIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---- 82
           R    Q +RE T  Q + IP  + G D++  A++G GKTA F L  LQ L T   +    
Sbjct: 14  RAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGR 73

Query: 83  --VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL 140
             V  L++  TRELA QI +    +SKY+ NI+  V FGG+ I          NPQ++ L
Sbjct: 74  RPVRALILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSI----------NPQMMKL 122

Query: 141 VNYETNLSGVVVNVMDVRSGGWWLDLE---ALILSK 173
                   GV V V    + G  LDLE   A+ L +
Sbjct: 123 ------RGGVDVLVA---TPGRLLDLEHQNAVKLDQ 149

Length = 456

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

 Score = 69.3 bits (170), Expect = 2e-15
 Identities = 31/87 (35%), Positives = 44/87 (50%), Gaps = 4/87 (4%)

Query: 52  MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 111
            D+L  A +G GKT   +L  L+ L++      VLV+  TRELA Q+++  +        
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGE--G 57

Query: 112 IKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           IKVG   GG  I K +E L +    IV
Sbjct: 58  IKVGYLIGGTSI-KQQEKLLSGKTDIV 83

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

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

 Score = 72.2 bits (177), Expect = 3e-15
 Identities = 45/131 (34%), Positives = 67/131 (51%), Gaps = 19/131 (14%)

Query: 41  QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK 100
           Q ECIP  + G D+L  A++G GKTA F L  L  L+       +LV+  TRELA Q+++
Sbjct: 33  QAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAE 92

Query: 101 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT--HNPQIV-------------GLVNYET 145
               FSK+M  + V   +GG   Q+ +  L+     PQIV             G ++  +
Sbjct: 93  AMTDFSKHMRGVNVVALYGG---QRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDL-S 148

Query: 146 NLSGVVVNVMD 156
            LSG+V++  D
Sbjct: 149 KLSGLVLDEAD 159

Length = 629

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

 Score = 67.3 bits (165), Expect = 1e-13
 Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 6/105 (5%)

Query: 38  TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQL----ETTDSNVYVLVMCHTRE 93
           T+ Q E IP A+ G D+L  A +G GKTA F+L  LQ L            +L++  TRE
Sbjct: 25  TAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRE 84

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA Q++ +    +K+ +++ +    GG+      E     N  IV
Sbjct: 85  LAMQVADQARELAKH-THLDIATITGGVAYMNHAEVFSE-NQDIV 127

Length = 434

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

 Score = 60.0 bits (146), Expect = 4e-11
 Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 8/98 (8%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY----- 84
           E + F   T  Q   +P  + G D+  QA++G GKT  F+ AT   L +  +        
Sbjct: 24  EKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQ 83

Query: 85  --VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGG 120
              L+M  TRELA QI  + E  ++  + +K+G+ +GG
Sbjct: 84  PRALIMAPTRELAVQIHADAEPLAQ-ATGLKLGLAYGG 120

Length = 423

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

 Score = 57.1 bits (138), Expect = 4e-10
 Identities = 35/106 (33%), Positives = 53/106 (50%), Gaps = 1/106 (0%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I   + G D + QA+SG GKTA FV+A LQ ++   +    L++  TRE
Sbjct: 48  FEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRE 107

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG 139
           LA QI K       Y+  ++     GG  ++ D   LK     +VG
Sbjct: 108 LAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAGVHMVVG 152

Length = 401

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

 Score = 51.1 bits (122), Expect = 5e-08
 Identities = 31/105 (29%), Positives = 52/105 (49%), Gaps = 8/105 (7%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVYVL 86
           F   T  Q + +   + G D + +A++G GKTA F+++ + QL  T             L
Sbjct: 107 FPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRAL 166

Query: 87  VMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
           ++  TREL  QI+K+    +KY + + V  F GG+   K  + L+
Sbjct: 167 IIAPTRELVVQIAKDAAALTKY-TGLNVMTFVGGMDFDKQLKQLE 210

Length = 475

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

 Score = 50.5 bits (121), Expect = 8e-08
 Identities = 34/94 (36%), Positives = 49/94 (52%), Gaps = 6/94 (6%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATL-----QQLETTDSNVYVLVM 88
           F E T  Q +  P A+ G D++  A++G GKT  F+L  +     Q L        VLV+
Sbjct: 150 FTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVL 209

Query: 89  CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP 122
             TRELA QI ++  +F    S I+  V +GG+P
Sbjct: 210 APTRELAEQIREQCNKFGA-SSKIRNTVAYGGVP 242

Length = 545

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

 Score = 50.3 bits (120), Expect = 1e-07
 Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 8/109 (7%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV------ 83
           ES  F   T  Q   +P A+ G D+  QA++G GKT  F++A + +L +  +        
Sbjct: 25  ESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPED 84

Query: 84  -YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
              L++  TRELA QI K+  +F   +  ++  + +GG+   K  E L+
Sbjct: 85  PRALILAPTRELAIQIHKDAVKFGADLG-LRFALVYGGVDYDKQRELLQ 132

Length = 572

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

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 35/134 (26%), Positives = 59/134 (44%), Gaps = 16/134 (11%)

Query: 38  TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVL------ATLQQLETTDS-NVYVLVMCH 90
           T  Q + IP A+ G  +L  A +G GKTA F++       T++    ++  N   +V+  
Sbjct: 145 TPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTP 204

Query: 91  TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVN 142
           TREL  Q+  + +   K +   K  +  GG  + +    ++     IVG        L  
Sbjct: 205 TRELCVQVEDQAKVLGKGLP-FKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSK 263

Query: 143 YETNLSGVVVNVMD 156
           ++  L  V V V+D
Sbjct: 264 HDIELDNVSVLVLD 277

Length = 518

>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

 Score = 38.6 bits (90), Expect = 9e-04
 Identities = 32/134 (23%), Positives = 54/134 (40%), Gaps = 23/134 (17%)

Query: 10  GVTVKVLSSRNRREKEDRI-GESQPFREQTSF-------QHECIPQAV----LGMDILCQ 57
           G   + LSS+   E  D +  E  P +   +F       Q E +   V         +  
Sbjct: 2   GDLKQYLSSKGAEELADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIV 61

Query: 58  AKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 117
             +G GKT V   A        +     LV+  T+EL  Q ++  ++F   + N ++G++
Sbjct: 62  LPTGAGKTVVAAEAI------AELKRSTLVLVPTKELLDQWAEALKKF--LLLNDEIGIY 113

Query: 118 FGGLPIQKDEEYLK 131
            GG   +K+ E  K
Sbjct: 114 GGG---EKELEPAK 124

Length = 442

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	175
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0348|consensus	708		100.0
KOG0338|consensus	691		100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0345|consensus	567		100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; 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
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0342|consensus	543		99.98
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.98
KOG0335|consensus	482		99.97
KOG0340|consensus	442		99.97
KOG0343|consensus	758		99.97
KOG0346|consensus	569		99.97
KOG0333|consensus	673		99.97
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG0328|consensus	400		99.97
PTZ00424	401	helicase 45; Provisional	99.97
KOG0339|consensus	731		99.97
KOG0334|consensus	997		99.97
KOG0347|consensus	731		99.97
KOG0336|consensus	629		99.96
KOG0341|consensus	610		99.96
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.96
KOG0326|consensus	459		99.96
KOG0337|consensus	529		99.96
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.96
KOG0329|consensus	387		99.95
KOG0327|consensus	397		99.94
KOG4284|consensus	980		99.94
KOG0350|consensus	620		99.93
PRK02362	737	ski2-like helicase; Provisional	99.93
PRK00254	720	ski2-like helicase; Provisional	99.92
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.91
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.91
PRK13767	876	ATP-dependent helicase; Provisional	99.91
COG1205	851	Distinct helicase family with a unique C-terminal	99.91
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.91
KOG0332|consensus	477		99.9
PRK01172	674	ski2-like helicase; Provisional	99.9
KOG0344|consensus	593		99.88
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.88
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.88
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.88
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.88
PRK09401	1176	reverse gyrase; Reviewed	99.88
PRK14701	1638	reverse gyrase; Provisional	99.87
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.86
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.85
PRK10689	1147	transcription-repair coupling factor; Provisional	99.84
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.83
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.82
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.82
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.8
COG1204	766	Superfamily II helicase [General function predicti	99.78
PHA02558	501	uvsW UvsW helicase; Provisional	99.76
PRK05580	679	primosome assembly protein PriA; Validated	99.76
COG1202	830	Superfamily II helicase, archaea-specific [General	99.75
KOG0349|consensus	725		99.74
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.73
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.73
KOG0952|consensus	1230		99.72
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.72
PHA02653	675	RNA helicase NPH-II; Provisional	99.7
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.7
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.69
PRK13766	773	Hef nuclease; Provisional	99.65
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.65
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.63
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.62
KOG0354|consensus	746		99.6
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.59
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.51
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.49
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.49
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.47
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.47
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.46
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.45
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.43
KOG0352|consensus	641		99.43
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.42
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.41
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.41
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.38
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.38
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.37
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.35
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.32
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.31
KOG0353|consensus	695		99.25
PRK09694	878	helicase Cas3; Provisional	99.24
KOG0951|consensus	1674		99.23
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.21
KOG0351|consensus	941		99.2
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.18
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.18
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.16
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.14
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.12
KOG0947|consensus	1248		99.08
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.04
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.04
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.02
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.94
COG4096	875	HsdR Type I site-specific restriction-modification	98.88
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.86
KOG0951|consensus	1674		98.86
KOG0948|consensus	1041		98.82
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.8
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.72
PRK14873	665	primosome assembly protein PriA; Provisional	98.71
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.65
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.58
KOG0949|consensus	1330		98.58
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.57
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.55
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.52
KOG0950|consensus	1008		98.51
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.5
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.43
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.43
PRK04914	956	ATP-dependent helicase HepA; Validated	98.4
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.4
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.39
PF13245	76	AAA_19: Part of AAA domain	98.38
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.36
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.32
KOG1802|consensus	935		98.27
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.24
COG4889	1518	Predicted helicase [General function prediction on	98.22
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.21
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.17
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.16
KOG1123|consensus	776		98.13
COG0610	962	Type I site-specific restriction-modification syst	98.09
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.07
PRK10536	262	hypothetical protein; Provisional	98.05
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.98
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.98
KOG0389|consensus	941		97.93
KOG0952|consensus	1230		97.92
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.83
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.82
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.8
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.8
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.79
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.69
KOG1805|consensus	1100		97.67
PRK15483	986	type III restriction-modification system StyLTI en	97.54
KOG0390|consensus	776		97.53
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.48
KOG0387|consensus	923		97.47
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.46
KOG0385|consensus	971		97.42
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.35
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	97.34
KOG1803|consensus	649		97.31
PRK11054	684	helD DNA helicase IV; Provisional	97.29
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	97.28
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.27
KOG1002|consensus	791		97.27
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.27
KOG0953|consensus	700		97.26
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.25
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.24
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	97.22
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.2
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.19
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	97.17
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	97.15
KOG0920|consensus	924		97.12
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	97.1
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	97.04
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.01
KOG0391|consensus	1958		97.0
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	96.98
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.94
PRK04296	190	thymidine kinase; Provisional	96.91
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	96.85
KOG4150|consensus	1034		96.8
PRK08116	268	hypothetical protein; Validated	96.79
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.79
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	96.77
PRK07952	244	DNA replication protein DnaC; Validated	96.76
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.73
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.7
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.68
PHA02533	534	17 large terminase protein; Provisional	96.67
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.64
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.62
PRK05298	652	excinuclease ABC subunit B; Provisional	96.62
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.61
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.56
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.53
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.5
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	96.45
PRK13851	344	type IV secretion system protein VirB11; Provision	96.38
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.38
PRK05973	237	replicative DNA helicase; Provisional	96.37
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.34
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.26
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.26
PRK08181	269	transposase; Validated	96.25
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.25
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.23
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.22
PRK11823	446	DNA repair protein RadA; Provisional	96.2
KOG0392|consensus	1549		96.2
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.19
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	96.18
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.17
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.17
PRK13764	602	ATPase; Provisional	96.15
PRK06921	266	hypothetical protein; Provisional	96.14
KOG0922|consensus	674		96.05
PRK00411	394	cdc6 cell division control protein 6; Reviewed	96.03
PRK08939	306	primosomal protein DnaI; Reviewed	96.03
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.02
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	95.95
PRK10436	462	hypothetical protein; Provisional	95.94
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.92
KOG1133|consensus	821		95.91
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.88
PRK06835	329	DNA replication protein DnaC; Validated	95.86
KOG0388|consensus	1185		95.86
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	95.86
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	95.85
PRK12377	248	putative replication protein; Provisional	95.84
COG3587	985	Restriction endonuclease [Defense mechanisms]	95.84
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.83
KOG0924|consensus	1042		95.82
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.81
TIGR02533	486	type_II_gspE general secretory pathway protein E.	95.79
KOG0331|consensus	519		95.73
KOG0925|consensus	699		95.7
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.67
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.67
PHA03368	738	DNA packaging terminase subunit 1; Provisional	95.56
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	95.55
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.49
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.47
PRK14974	336	cell division protein FtsY; Provisional	95.45
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	95.45
KOG4439|consensus	901		95.4
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	95.4
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.35
KOG0989|consensus	346		95.32
KOG1132|consensus	945		95.26
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.24
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	95.24
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	95.18
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.17
smart00382	148	AAA ATPases associated with a variety of cellular	95.17
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	95.15
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.13
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	95.12
PLN03025	319	replication factor C subunit; Provisional	95.1
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.07
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	95.07
PHA02535	581	P terminase ATPase subunit; Provisional	95.05
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.05
KOG0344|consensus	593		95.02
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.01
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.99
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	94.97
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	94.97
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.93
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	94.91
PRK05707	328	DNA polymerase III subunit delta'; Validated	94.9
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	94.9
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.85
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.85
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	94.83
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	94.82
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	94.82
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	94.79
TIGR02237	209	recomb_radB DNA repair and recombination protein R	94.76
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	94.74
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.72
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.71
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	94.68
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	94.65
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.62
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	94.6
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	94.59
PHA03333	752	putative ATPase subunit of terminase; Provisional	94.59
PRK10689	1147	transcription-repair coupling factor; Provisional	94.59
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	94.56
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	94.46
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	94.44
KOG0923|consensus	902		94.44
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	94.38
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	94.37
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	94.36
PF12846	304	AAA_10: AAA-like domain	94.34
PRK06526	254	transposase; Provisional	94.33
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.31
PTZ00110	545	helicase; Provisional	94.3
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	94.25
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	94.25
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.25
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	94.18
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	94.18
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.16
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	94.13
KOG1000|consensus	689		94.12
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	94.11
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	94.07
PRK08769	319	DNA polymerase III subunit delta'; Validated	94.03
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.03
PRK13897	606	type IV secretion system component VirD4; Provisio	94.02
KOG0058|consensus	716		94.02
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	94.02
PRK04328	249	hypothetical protein; Provisional	93.97
KOG0335|consensus	482		93.95
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	93.95
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	93.93
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	93.93
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	93.92
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	93.86
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	93.85
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	93.84
PRK08727	233	hypothetical protein; Validated	93.83
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.79
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	93.75
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.68
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.67
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	93.66
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	93.65
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.62
PF13555	62	AAA_29: P-loop containing region of AAA domain	93.61
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	93.55
PHA02544	316	44 clamp loader, small subunit; Provisional	93.55
PRK09183	259	transposase/IS protein; Provisional	93.51
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	93.51
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	93.5
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	93.47
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	93.47
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	93.46
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.45
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	93.42
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.42
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	93.41
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.34
KOG0333|consensus	673		93.3
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	93.25
COG4178	604	ABC-type uncharacterized transport system, permeas	93.23
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	93.12
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	93.11
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	93.1
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.1
PRK09112	351	DNA polymerase III subunit delta'; Validated	93.06
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	93.06
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	93.01
PRK06871	325	DNA polymerase III subunit delta'; Validated	92.98
cd03115	173	SRP The signal recognition particle (SRP) mediates	92.96
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	92.92
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	92.91
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	92.91
PRK05642	234	DNA replication initiation factor; Validated	92.88
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	92.87
PRK09354	349	recA recombinase A; Provisional	92.85
PRK00149	450	dnaA chromosomal replication initiation protein; R	92.84
PTZ00424	401	helicase 45; Provisional	92.83
cd00983	325	recA RecA is a bacterial enzyme which has roles in	92.82
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	92.81
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	92.8
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	92.8
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	92.73
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	92.73
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	92.69
PF05729	166	NACHT: NACHT domain	92.68
KOG1131|consensus	755		92.66
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	92.66
KOG0744|consensus	423		92.62
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.61
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	92.61
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	92.55
KOG0926|consensus	1172		92.51
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	92.42
PRK13342	413	recombination factor protein RarA; Reviewed	92.39
PRK08084	235	DNA replication initiation factor; Provisional	92.38
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	92.38
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	92.34
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	92.34
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	92.26
PRK10416	318	signal recognition particle-docking protein FtsY;	92.25
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	92.24
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.22
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	92.2
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	92.16
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.16
PRK14088	440	dnaA chromosomal replication initiation protein; P	92.13
PRK07940	394	DNA polymerase III subunit delta'; Validated	92.08
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	92.05
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	92.03
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.02
COG4604	252	CeuD ABC-type enterochelin transport system, ATPas	92.0
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	91.98
KOG1564|consensus	351		91.97
TIGR00959	428	ffh signal recognition particle protein. This mode	91.93
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	91.89
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	91.89
PTZ00301	210	uridine kinase; Provisional	91.88
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.86
COG1855	604	ATPase (PilT family) [General function prediction	91.85
COG0606	490	Predicted ATPase with chaperone activity [Posttran	91.8
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	91.77
PF09439	181	SRPRB: Signal recognition particle receptor beta s	91.74
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	91.68
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.65
KOG1806|consensus	1320		91.65
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	91.6
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	91.59
PLN03130	1622	ABC transporter C family member; Provisional	91.54
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	91.54
PRK07471	365	DNA polymerase III subunit delta'; Validated	91.49
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	91.47
PF00004	132	AAA: ATPase family associated with various cellula	91.47
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	91.45
PRK13876	663	conjugal transfer coupling protein TraG; Provision	91.43
PRK13880	636	conjugal transfer coupling protein TraG; Provision	91.42
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	91.41
PRK07993	334	DNA polymerase III subunit delta'; Validated	91.4
KOG0745|consensus	564		91.37
PRK05298	652	excinuclease ABC subunit B; Provisional	91.3
PRK06893	229	DNA replication initiation factor; Validated	91.29
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	91.19
PRK10867	433	signal recognition particle protein; Provisional	91.18
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	91.18
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	91.13
PRK13822	641	conjugal transfer coupling protein TraG; Provision	91.09
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	91.05
PRK13700	732	conjugal transfer protein TraD; Provisional	91.04
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	91.03
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	90.81
PRK08903	227	DnaA regulatory inactivator Hda; Validated	90.79
KOG2340|consensus	698		90.75
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	90.73
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	90.69
PRK06067	234	flagellar accessory protein FlaH; Validated	90.67
PRK09694	878	helicase Cas3; Provisional	90.65
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	90.64
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	90.63
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	90.58
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	90.53
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	90.52
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	90.51
KOG0060|consensus	659		90.5
PRK06964	342	DNA polymerase III subunit delta'; Validated	90.47
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	90.36
COG4626	546	Phage terminase-like protein, large subunit [Gener	90.35
PRK13531	498	regulatory ATPase RavA; Provisional	90.34
COG0593	408	DnaA ATPase involved in DNA replication initiation	90.23
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	90.2
PHA02244	383	ATPase-like protein	90.19
CHL00181	287	cbbX CbbX; Provisional	90.18
PHA00729	226	NTP-binding motif containing protein	90.17
PLN03232	1495	ABC transporter C family member; Provisional	90.05
PHA03372	668	DNA packaging terminase subunit 1; Provisional	89.95
PRK06090	319	DNA polymerase III subunit delta'; Validated	89.9
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	89.87
PRK12402	337	replication factor C small subunit 2; Reviewed	89.81
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	89.8
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	89.72
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	89.71
PRK00131	175	aroK shikimate kinase; Reviewed	89.67
PRK08058	329	DNA polymerase III subunit delta'; Validated	89.66
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	89.66
cd01394	218	radB RadB. The archaeal protein radB shares simila	89.65
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	89.63
PLN02165	334	adenylate isopentenyltransferase	89.62
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	89.62
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	89.56
KOG2228|consensus	408		89.54
KOG1533|consensus	290		89.44
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	89.39
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	89.39
PRK14530	215	adenylate kinase; Provisional	89.38
COG3972	660	Superfamily I DNA and RNA helicases [General funct	89.3
PTZ00243	1560	ABC transporter; Provisional	89.29
TIGR00957	1522	MRP_assoc_pro multi drug resistance-associated pro	89.28
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	89.22
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	89.17
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	89.16
KOG1015|consensus	1567		89.09
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	89.03
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	89.0
PRK08118	167	topology modulation protein; Reviewed	88.98
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	88.96
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	88.96
KOG0055|consensus	1228		88.94
PRK14737	186	gmk guanylate kinase; Provisional	88.92
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	88.9

>KOG0330|consensus

Probab=100.00  E-value=4.7e-37  Score=241.03  Aligned_cols=163  Identities=25%  Similarity=0.343  Sum_probs=151.9

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      .+...+|.+++++|++++++++.||..||++|+++||.++.|+|++..|.||||||.+|++|+++++..++..++++|++
T Consensus        57 ~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLt  136 (476)
T KOG0330|consen   57 DESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLT  136 (476)
T ss_pred             hhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEec
Confidence            45667899999999999999999999999999999999999999999999999999999999999999888889999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-----ccCCCCceEEEEeCC--
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVMDVR--  158 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDEa--  158 (175)
                      ||||||.|+.++++.+.... |+++..+.||.+...+...+.+.+++||+    |+++     .+++.+++++|+|||  
T Consensus       137 PtRELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADr  215 (476)
T KOG0330|consen  137 PTRELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADR  215 (476)
T ss_pred             CcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHh
Confidence            99999999999999999998 99999999999999999999999999999    3333     678899999999999  


Q ss_pred             --CCCCHHHHHHHHhhh
Q psy1539         159 --SGGWWLDLEALILSK  173 (175)
Q Consensus       159 --d~~f~~~v~~il~~~  173 (175)
                        |+.|.++++.||+..
T Consensus       216 lLd~dF~~~ld~ILk~i  232 (476)
T KOG0330|consen  216 LLDMDFEEELDYILKVI  232 (476)
T ss_pred             hhhhhhHHHHHHHHHhc
Confidence              689999999998753

>KOG0331|consensus

Probab=100.00  E-value=1.9e-36  Score=248.50  Aligned_cols=159  Identities=25%  Similarity=0.346  Sum_probs=149.2

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc------CCCCeEEEE
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET------TDSNVYVLV   87 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~------~~~~~~~li   87 (175)
                      ..|++++++++..++++..||..|||||.++||.++.|+|++..|.||||||++|++|++.++..      ..++|++||
T Consensus        91 ~~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLV  170 (519)
T KOG0331|consen   91 AAFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLV  170 (519)
T ss_pred             hhhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEE
Confidence            37899999999999999999999999999999999999999999999999999999999999975      356899999


Q ss_pred             EecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC-
Q psy1539          88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR-  158 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa-  158 (175)
                      |+||||||.|+.+.+..+.+.. .+++.+++||.+...|.+.++++++++|+        +.....+++++.|+|+||| 
T Consensus       171 L~PTRELA~QV~~~~~~~~~~~-~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEAD  249 (519)
T KOG0331|consen  171 LAPTRELAVQVQAEAREFGKSL-RLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEAD  249 (519)
T ss_pred             EcCcHHHHHHHHHHHHHHcCCC-CccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHH
Confidence            9999999999999999999988 89999999999999999999999999999        4444889999999999999 


Q ss_pred             ---CCCCHHHHHHHHhhh
Q psy1539         159 ---SGGWWLDLEALILSK  173 (175)
Q Consensus       159 ---d~~f~~~v~~il~~~  173 (175)
                         |+||.+||+.|+.+.
T Consensus       250 rMldmGFe~qI~~Il~~i  267 (519)
T KOG0331|consen  250 RMLDMGFEPQIRKILSQI  267 (519)
T ss_pred             hhhccccHHHHHHHHHhc
Confidence               699999999999865

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

Probab=100.00  E-value=1.4e-34  Score=242.61  Aligned_cols=159  Identities=33%  Similarity=0.460  Sum_probs=144.3

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc--CCCCeEEEEEecC
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHT   91 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~--~~~~~~~lil~Pt   91 (175)
                      ..|+++++++++++++.+.||..|||+|.++||.++.|+|+++.|+||||||++|++|+++++..  ......+||++||
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            67999999999999999999999999999999999999999999999999999999999999873  2222229999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eec----CccCCCCceEEEEeCC----C
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVN----YETNLSGVVVNVMDVR----S  159 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~----~~~~~~~~~~lVlDEa----d  159 (175)
                      ||||.|+++.++.+....+++++..++||.+...+.+.++.+++++|+    +++    ..+++++++++|+|||    |
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            999999999999999876568999999999999999999999999999    222    2689999999999999    6


Q ss_pred             CCCHHHHHHHHhh
Q psy1539         160 GGWWLDLEALILS  172 (175)
Q Consensus       160 ~~f~~~v~~il~~  172 (175)
                      +||.+|++.|+..
T Consensus       189 ~Gf~~~i~~I~~~  201 (513)
T COG0513         189 MGFIDDIEKILKA  201 (513)
T ss_pred             CCCHHHHHHHHHh
Confidence            9999999999864

>KOG0348|consensus

Probab=100.00  E-value=6.8e-35  Score=236.44  Aligned_cols=158  Identities=27%  Similarity=0.365  Sum_probs=144.4

Q ss_pred             cccccCCCCHHHHHHHhhC-CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC------CCCeEEE
Q psy1539          14 KVLSSRNRREKEDRIGESQ-PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT------DSNVYVL   86 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~-g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~------~~~~~~l   86 (175)
                      ..|.++||++.+...|+.. ++..||.+|+++||.+++|+|++|.++||||||++|++|+++.+...      ..|+.||
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            3489999999999998764 89999999999999999999999999999999999999999988632      5789999


Q ss_pred             EEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-----ccCCCCceEEEEeC
Q psy1539          87 VMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVMDV  157 (175)
Q Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDE  157 (175)
                      ||+||||||.|+|+.++++.+.+.++..+.+.||...+.+..++++|++|+|+    ++++     .+.+++++++|+||
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            99999999999999999999988677789999999999999999999999999    4444     67889999999999


Q ss_pred             C----CCCCHHHHHHHHh
Q psy1539         158 R----SGGWWLDLEALIL  171 (175)
Q Consensus       158 a----d~~f~~~v~~il~  171 (175)
                      |    |.||..||..||.
T Consensus       296 aDrlleLGfekdit~Il~  313 (708)
T KOG0348|consen  296 ADRLLELGFEKDITQILK  313 (708)
T ss_pred             hhHHHhccchhhHHHHHH
Confidence            9    5899999999985

>KOG0338|consensus

Probab=100.00  E-value=5.5e-35  Score=235.94  Aligned_cols=159  Identities=29%  Similarity=0.431  Sum_probs=146.9

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC---CCeEEEEEe
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD---SNVYVLVMC   89 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~---~~~~~lil~   89 (175)
                      -.+|.+|+|+.++++++..+||..|||+|..+||..+.|+|++.||.||||||.||++|++.++...+   ...++|||+
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            45799999999999999999999999999999999999999999999999999999999999986442   356899999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-----ccCCCCceEEEEeCCC-
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDEad-  159 (175)
                      |||||+.|++++.++++... ++.++++.||.+.+.|...|++.++|+|+    +++|     .+.++++..+|+|||| 
T Consensus       260 PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADR  338 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADR  338 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHH
Confidence            99999999999999999988 89999999999999999999999999999    4444     6889999999999995 


Q ss_pred             ---CCCHHHHHHHHhh
Q psy1539         160 ---GGWWLDLEALILS  172 (175)
Q Consensus       160 ---~~f~~~v~~il~~  172 (175)
                         .||.+++++||..
T Consensus       339 MLeegFademnEii~l  354 (691)
T KOG0338|consen  339 MLEEGFADEMNEIIRL  354 (691)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence               6899999999864

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.2e-33  Score=232.55  Aligned_cols=160  Identities=28%  Similarity=0.350  Sum_probs=143.1

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-------CCCeE
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-------DSNVY   84 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-------~~~~~   84 (175)
                      ...+|++++|++.+++++.+.||..|||+|.+|||.+++|+|++++||||||||++|++|+++.+...       ..+++
T Consensus         6 ~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~   85 (423)
T PRK04837          6 TEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPR   85 (423)
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCce
Confidence            34689999999999999999999999999999999999999999999999999999999999988532       23579


Q ss_pred             EEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEe
Q psy1539          85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMD  156 (175)
Q Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlD  156 (175)
                      +||++|||+||.|+++.++.+.+.. ++++..++||.+...+.+.+.++++++|++        .+..+.+++++++|+|
T Consensus        86 ~lil~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViD  164 (423)
T PRK04837         86 ALIMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLD  164 (423)
T ss_pred             EEEECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEe
Confidence            9999999999999999999999887 999999999998888888888889999992        2236678999999999


Q ss_pred             CC----CCCCHHHHHHHHhh
Q psy1539         157 VR----SGGWWLDLEALILS  172 (175)
Q Consensus       157 Ea----d~~f~~~v~~il~~  172 (175)
                      ||    +.+|..+++.|+..
T Consensus       165 Ead~l~~~~f~~~i~~i~~~  184 (423)
T PRK04837        165 EADRMFDLGFIKDIRWLFRR  184 (423)
T ss_pred             cHHHHhhcccHHHHHHHHHh
Confidence            99    46899999888754

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.8e-33  Score=237.52  Aligned_cols=166  Identities=25%  Similarity=0.303  Sum_probs=148.4

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----C
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----D   80 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~   80 (175)
                      +...+.+..+|+++++++.++++|.+.||.+|||+|.++||.+++|+|++++||||||||++|++|++.++...     .
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            44557888999999999999999999999999999999999999999999999999999999999999887542     3


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVV  152 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~  152 (175)
                      .++++|||+||||||.|+.+.++++.... ++++..++||.+...+...+.++++|+|++        .+....++++++
T Consensus       202 ~gp~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~  280 (545)
T PTZ00110        202 DGPIVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTY  280 (545)
T ss_pred             CCcEEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcE
Confidence            47899999999999999999999998877 899999999999888888999999999992        223567889999


Q ss_pred             EEEeCC----CCCCHHHHHHHHhh
Q psy1539         153 NVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       153 lVlDEa----d~~f~~~v~~il~~  172 (175)
                      +|+|||    +++|..+++.|+..
T Consensus       281 lViDEAd~mld~gf~~~i~~il~~  304 (545)
T PTZ00110        281 LVLDEADRMLDMGFEPQIRKIVSQ  304 (545)
T ss_pred             EEeehHHhhhhcchHHHHHHHHHh
Confidence            999999    57899999998754

>KOG0345|consensus

Probab=100.00  E-value=2.1e-33  Score=224.86  Aligned_cols=158  Identities=23%  Similarity=0.314  Sum_probs=138.9

Q ss_pred             ccccC--CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----CCCeEEEE
Q psy1539          15 VLSSR--NRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLV   87 (175)
Q Consensus        15 ~~~~~--~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~~li   87 (175)
                      .|+++  +|++++++++.+.||..+||+|..+||.+++++|+++.|+||||||+||++|++..+.+.     +....++|
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            45555  456999999999999999999999999999999999999999999999999999998432     22357999


Q ss_pred             EecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc-CCCeEEE-------eecC---ccCCCCceEEEEe
Q psy1539          88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT-HNPQIVG-------LVNY---ETNLSGVVVNVMD  156 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~-~~~iiv~-------l~~~---~~~~~~~~~lVlD  156 (175)
                      |+|||||+.|+.+++..|...++++++.+++||.+..++.+.+++ ++.|+||       ++++   .+++.++.++|+|
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            999999999999999999999889999999999999999988776 5568888       3333   3566799999999


Q ss_pred             CC----CCCCHHHHHHHHhh
Q psy1539         157 VR----SGGWWLDLEALILS  172 (175)
Q Consensus       157 Ea----d~~f~~~v~~il~~  172 (175)
                      ||    |+||..+++.||..
T Consensus       165 EADrLldmgFe~~~n~ILs~  184 (567)
T KOG0345|consen  165 EADRLLDMGFEASVNTILSF  184 (567)
T ss_pred             chHhHhcccHHHHHHHHHHh
Confidence            99    79999999999864

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

Probab=100.00  E-value=3.8e-33  Score=234.57  Aligned_cols=166  Identities=25%  Similarity=0.296  Sum_probs=147.8

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-------
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-------   78 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-------   78 (175)
                      +...+.+..+|+++++++.++++|.+.||..|||+|.++||.+++|+|++++||||||||++|++|++.++..       
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            4456788999999999999999999999999999999999999999999999999999999999999987642       


Q ss_pred             CCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCc
Q psy1539          79 TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGV  150 (175)
Q Consensus        79 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~  150 (175)
                      ...++++||++|||+||.|+.+.++.+.+.. ++++..++||.....+...+.++++++|+        +.++...++++
T Consensus       193 ~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v  271 (518)
T PLN00206        193 EQRNPLAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNV  271 (518)
T ss_pred             ccCCceEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchhe
Confidence            2357899999999999999999999998877 78899999999888888889899999999        33336778999


Q ss_pred             eEEEEeCCC----CCCHHHHHHHHhh
Q psy1539         151 VVNVMDVRS----GGWWLDLEALILS  172 (175)
Q Consensus       151 ~~lVlDEad----~~f~~~v~~il~~  172 (175)
                      +++|+||||    .+|.+++..|+..
T Consensus       272 ~~lViDEad~ml~~gf~~~i~~i~~~  297 (518)
T PLN00206        272 SVLVLDEVDCMLERGFRDQVMQIFQA  297 (518)
T ss_pred             eEEEeecHHHHhhcchHHHHHHHHHh
Confidence            999999994    6899999888753

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=6e-33  Score=230.64  Aligned_cols=159  Identities=31%  Similarity=0.430  Sum_probs=144.9

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .+|++++|++.+++++.++||..|||+|.+|||.+++|+|++++||||||||++|++|+++++......++++|++||++
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            57999999999999999999999999999999999999999999999999999999999999876656779999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCC----CCC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVR----SGG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEa----d~~  161 (175)
                      |+.|+.+.++.+....+++++..++||.+...+.+.+..+++++|++        .+....+++++++|+|||    +++
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            99999999999988766899999999999999999999999999992        223567889999999999    578


Q ss_pred             CHHHHHHHHhh
Q psy1539         162 WWLDLEALILS  172 (175)
Q Consensus       162 f~~~v~~il~~  172 (175)
                      |..+++.++..
T Consensus       164 ~~~~l~~i~~~  174 (460)
T PRK11776        164 FQDAIDAIIRQ  174 (460)
T ss_pred             cHHHHHHHHHh
Confidence            99999988754

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.2e-32  Score=235.27  Aligned_cols=161  Identities=27%  Similarity=0.370  Sum_probs=146.3

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ...+|++++|+++++++|.++||..|||+|.++||.+++|+|++++||||||||++|.+|+++.+.....++++||++||
T Consensus         4 ~~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PT   83 (629)
T PRK11634          4 FETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPT   83 (629)
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCc
Confidence            34569999999999999999999999999999999999999999999999999999999999998766667899999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCC----
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRS----  159 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad----  159 (175)
                      ++|+.|+.+.+..+.+..+++++..++||.+...+.+.+..+++|||++        .+..+.+++++++|+||||    
T Consensus        84 reLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~  163 (629)
T PRK11634         84 RELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLR  163 (629)
T ss_pred             HHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhh
Confidence            9999999999999988877899999999999888999999999999992        2235678999999999994    


Q ss_pred             CCCHHHHHHHHhh
Q psy1539         160 GGWWLDLEALILS  172 (175)
Q Consensus       160 ~~f~~~v~~il~~  172 (175)
                      ++|.+++..|+..
T Consensus       164 ~gf~~di~~Il~~  176 (629)
T PRK11634        164 MGFIEDVETIMAQ  176 (629)
T ss_pred             cccHHHHHHHHHh
Confidence            7899999998854

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=6.2e-32  Score=224.32  Aligned_cols=157  Identities=32%  Similarity=0.434  Sum_probs=140.0

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC------CCeEEEEE
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD------SNVYVLVM   88 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~------~~~~~lil   88 (175)
                      +|++++|+++++++|.+.||..|||+|.++||.+++|+|+++++|||||||++|++|+++.+....      ..+++||+
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            588999999999999999999999999999999999999999999999999999999999886431      23589999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCC--
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVR--  158 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEa--  158 (175)
                      +||++||.|+.+.++.+.+.. ++++..++||.+.+.+...+..+++|+|++.        .....+++++++|+|||  
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~  160 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADR  160 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHH
Confidence            999999999999999998887 8999999999998888888888899999922        23567899999999999  


Q ss_pred             --CCCCHHHHHHHHhh
Q psy1539         159 --SGGWWLDLEALILS  172 (175)
Q Consensus       159 --d~~f~~~v~~il~~  172 (175)
                        +.+|..+++.++..
T Consensus       161 ll~~~~~~~i~~il~~  176 (456)
T PRK10590        161 MLDMGFIHDIRRVLAK  176 (456)
T ss_pred             HhccccHHHHHHHHHh
Confidence              46898999888753

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=7.7e-32  Score=228.58  Aligned_cols=157  Identities=27%  Similarity=0.372  Sum_probs=140.4

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-------CCCeEEEE
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-------DSNVYVLV   87 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-------~~~~~~li   87 (175)
                      .|++++|++.++++|.+.||..|||+|.++||.+++|+|+++++|||||||++|++|+++++...       ..++++||
T Consensus        10 ~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLI   89 (572)
T PRK04537         10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALI   89 (572)
T ss_pred             ChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEE
Confidence            59999999999999999999999999999999999999999999999999999999999987532       23579999


Q ss_pred             EecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe----ec----C-ccCCCCceEEEEeCC
Q psy1539          88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL----VN----Y-ETNLSGVVVNVMDVR  158 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l----~~----~-~~~~~~~~~lVlDEa  158 (175)
                      |+||++|+.|+++.++++.... ++++..++|+.+...+.+.+.++++|||++    .+    . .+.+++++++|+|||
T Consensus        90 l~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEA  168 (572)
T PRK04537         90 LAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEA  168 (572)
T ss_pred             EeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCH
Confidence            9999999999999999999887 899999999999888888888888999992    22    1 356789999999999


Q ss_pred             ----CCCCHHHHHHHHhh
Q psy1539         159 ----SGGWWLDLEALILS  172 (175)
Q Consensus       159 ----d~~f~~~v~~il~~  172 (175)
                          +.+|..+++.|+..
T Consensus       169 h~lld~gf~~~i~~il~~  186 (572)
T PRK04537        169 DRMFDLGFIKDIRFLLRR  186 (572)
T ss_pred             HHHhhcchHHHHHHHHHh
Confidence                46899999988753

>KOG0342|consensus

Probab=99.98  E-value=2.4e-32  Score=219.68  Aligned_cols=159  Identities=27%  Similarity=0.377  Sum_probs=145.9

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeEEEEE
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVM   88 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~~lil   88 (175)
                      ...|++..|++..+++++++||..+|++|+.++|.++.|+|+++.|.||||||+||++|+++.+...    .++..++|+
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            4568889999999999999999999999999999999999999999999999999999999988642    567889999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-----ccCCCCceEEEEeCC-
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVMDVR-  158 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDEa-  158 (175)
                      +||||||.|++.+++.+.++++++.+..+.||.+...+.+.+.++|+++|+    |.++     .+.+.+++++|+||| 
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            999999999999999999998899999999999999999999999999999    4444     466778899999999 


Q ss_pred             ---CCCCHHHHHHHHh
Q psy1539         159 ---SGGWWLDLEALIL  171 (175)
Q Consensus       159 ---d~~f~~~v~~il~  171 (175)
                         |+||.+|++.|+.
T Consensus       241 rlLd~GF~~di~~Ii~  256 (543)
T KOG0342|consen  241 RLLDIGFEEDVEQIIK  256 (543)
T ss_pred             hhhhcccHHHHHHHHH
Confidence               6899999999985

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.98  E-value=6.3e-31  Score=217.10  Aligned_cols=156  Identities=25%  Similarity=0.360  Sum_probs=140.0

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeEEEEEec
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVMCH   90 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~~lil~P   90 (175)
                      .|+++++++.+++++.+.||..||++|.++||.+++|+|+++++|||+|||++|++|+++++...    ...+++||++|
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            58999999999999999999999999999999999999999999999999999999999987532    23468999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCC----
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVR----  158 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEa----  158 (175)
                      |++|+.|+.+.++.+.... ++++..++||.....+...+.++++++|++.        +..+.+++++++|+|||    
T Consensus        82 t~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l  160 (434)
T PRK11192         82 TRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRML  160 (434)
T ss_pred             cHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHh
Confidence            9999999999999999887 8999999999998888888888889999922        23567889999999999    


Q ss_pred             CCCCHHHHHHHHh
Q psy1539         159 SGGWWLDLEALIL  171 (175)
Q Consensus       159 d~~f~~~v~~il~  171 (175)
                      +++|..++..|..
T Consensus       161 ~~~~~~~~~~i~~  173 (434)
T PRK11192        161 DMGFAQDIETIAA  173 (434)
T ss_pred             CCCcHHHHHHHHH
Confidence            4789999988864

>KOG0335|consensus

Probab=99.97  E-value=2.8e-32  Score=221.07  Aligned_cols=165  Identities=21%  Similarity=0.247  Sum_probs=149.6

Q ss_pred             CcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-------
Q psy1539           7 MFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-------   79 (175)
Q Consensus         7 ~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-------   79 (175)
                      ..-+++...|++-.+...+..+++..||..|||+|+.+||.+..|+|++++|+||||||.+|++|++.++...       
T Consensus        67 ~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~  146 (482)
T KOG0335|consen   67 RDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGE  146 (482)
T ss_pred             CccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcc
Confidence            3445666789999999999999999999999999999999999999999999999999999999999998643       


Q ss_pred             ---CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCC
Q psy1539          80 ---DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLS  148 (175)
Q Consensus        80 ---~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~  148 (175)
                         ...|+++|++||||||.|+++..+++.... ++++...+||.+...+.+.+.++|+|+++        +.+..+.++
T Consensus       147 ~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s-~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~  225 (482)
T KOG0335|consen  147 SGGGVYPRALILAPTRELVDQIYNEARKFSYLS-GMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLD  225 (482)
T ss_pred             cCCCCCCceEEEeCcHHHhhHHHHHHHhhcccc-cceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehh
Confidence               136899999999999999999999998877 99999999999999999999999999999        333378899


Q ss_pred             CceEEEEeCC----C-CCCHHHHHHHHhh
Q psy1539         149 GVVVNVMDVR----S-GGWWLDLEALILS  172 (175)
Q Consensus       149 ~~~~lVlDEa----d-~~f~~~v~~il~~  172 (175)
                      +++++|||||    | ++|.++|+.|+.+
T Consensus       226 ~~k~~vLDEADrMlD~mgF~p~Ir~iv~~  254 (482)
T KOG0335|consen  226 NCKFLVLDEADRMLDEMGFEPQIRKIVEQ  254 (482)
T ss_pred             hCcEEEecchHHhhhhccccccHHHHhcc
Confidence            9999999999    5 9999999999865

>KOG0340|consensus

Probab=99.97  E-value=1.1e-31  Score=208.93  Aligned_cols=161  Identities=27%  Similarity=0.339  Sum_probs=145.4

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      ..+.+.|+.+||++.+.+.++++|.+.|||+|..+||.++.|+|++-+|.||||||.+|.+|++++|...+.+..++|++
T Consensus         3 ~~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlT   82 (442)
T KOG0340|consen    3 RKTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLT   82 (442)
T ss_pred             ccccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEec
Confidence            45678899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee-------cC-----ccCCCCceEEEEeC
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV-------NY-----ETNLSGVVVNVMDV  157 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~-------~~-----~~~~~~~~~lVlDE  157 (175)
                      |||||+.|+.++|..+++.. ++++.+++||.+.-.+...|...++++|+..       ..     ...+++++++|+||
T Consensus        83 PTrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDE  161 (442)
T KOG0340|consen   83 PTRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDE  161 (442)
T ss_pred             chHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecc
Confidence            99999999999999999988 9999999999998888888888888888811       11     35578999999999


Q ss_pred             CC----CCCHHHHHHHHh
Q psy1539         158 RS----GGWWLDLEALIL  171 (175)
Q Consensus       158 ad----~~f~~~v~~il~  171 (175)
                      ||    ..|.++++.|..
T Consensus       162 ADrvL~~~f~d~L~~i~e  179 (442)
T KOG0340|consen  162 ADRVLAGCFPDILEGIEE  179 (442)
T ss_pred             hhhhhccchhhHHhhhhc
Confidence            96    567777776654

>KOG0343|consensus

Probab=99.97  E-value=3.6e-32  Score=221.47  Aligned_cols=160  Identities=26%  Similarity=0.350  Sum_probs=146.9

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeEEE
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVL   86 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~~l   86 (175)
                      .....|++++|+..++++|++.+|..+|.+|+.+||..+.|+|++-.|.||||||+||++|+++++.+.    ..|..+|
T Consensus        66 ~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGal  145 (758)
T KOG0343|consen   66 TTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGAL  145 (758)
T ss_pred             hhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeE
Confidence            455679999999999999999999999999999999999999999999999999999999999998753    5688999


Q ss_pred             EEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-----ccCCCCceEEEEeC
Q psy1539          87 VMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVMDV  157 (175)
Q Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDE  157 (175)
                      ||+||||||.|+++++.+.++++ .+..+++.||.+.+.+..++.+ ++|+||    |++|     .++.+++.++|+||
T Consensus       146 IISPTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi~~-mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDE  223 (758)
T KOG0343|consen  146 IISPTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERISQ-MNILVCTPGRLLQHMDENPNFSTSNLQMLVLDE  223 (758)
T ss_pred             EecchHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhhhc-CCeEEechHHHHHHhhhcCCCCCCcceEEEecc
Confidence            99999999999999999999998 9999999999998888888754 799999    5555     57778999999999


Q ss_pred             C----CCCCHHHHHHHHhh
Q psy1539         158 R----SGGWWLDLEALILS  172 (175)
Q Consensus       158 a----d~~f~~~v~~il~~  172 (175)
                      |    ||||...++.|+.+
T Consensus       224 ADR~LDMGFk~tL~~Ii~~  242 (758)
T KOG0343|consen  224 ADRMLDMGFKKTLNAIIEN  242 (758)
T ss_pred             HHHHHHHhHHHHHHHHHHh
Confidence            9    79999999999875

>KOG0346|consensus

Probab=99.97  E-value=5.9e-32  Score=215.21  Aligned_cols=160  Identities=23%  Similarity=0.275  Sum_probs=138.8

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc------CCCCeEE
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET------TDSNVYV   85 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~------~~~~~~~   85 (175)
                      ....|+++||.+.+++++.+.||.+||-+|+.|||.+++|+|++..|.||||||.+|++|+++.+..      ...++.+
T Consensus        17 ~~ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa   96 (569)
T KOG0346|consen   17 KEKTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSA   96 (569)
T ss_pred             hhccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhccccccccee
Confidence            3478999999999999999999999999999999999999999999999999999999999998853      3568899


Q ss_pred             EEEecCHHHHHHHHHHHHHHHhhCC-CeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-----ccCCCCceEEEE
Q psy1539          86 LVMCHTRELAFQISKEYERFSKYMS-NIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVM  155 (175)
Q Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~~-~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVl  155 (175)
                      +|++||||||+|++..+.++..+++ .++++-+..+.+.......+...++|+|+    ++.+     ...+..++++|+
T Consensus        97 ~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVv  176 (569)
T KOG0346|consen   97 VILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVV  176 (569)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEe
Confidence            9999999999999999999988773 57777777676656666677777888888    2222     367789999999


Q ss_pred             eCCC----CCCHHHHHHHHh
Q psy1539         156 DVRS----GGWWLDLEALIL  171 (175)
Q Consensus       156 DEad----~~f~~~v~~il~  171 (175)
                      ||||    +||.+|++.|..
T Consensus       177 DEADLllsfGYeedlk~l~~  196 (569)
T KOG0346|consen  177 DEADLLLSFGYEEDLKKLRS  196 (569)
T ss_pred             chhhhhhhcccHHHHHHHHH
Confidence            9995    899999998865

>KOG0333|consensus

Probab=99.97  E-value=1.3e-31  Score=217.05  Aligned_cols=169  Identities=23%  Similarity=0.291  Sum_probs=155.5

Q ss_pred             CccCCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc----
Q psy1539           3 SMFGMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET----   78 (175)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~----   78 (175)
                      ++.+..-+.|+++|++.+++.++++.+.+.||..|||+|+.|||..++.+|++..+.||||||++|++|++..+..    
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            4556777899999999999999999999999999999999999999999999999999999999999999987642    


Q ss_pred             -----CCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCcc
Q psy1539          79 -----TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYET  145 (175)
Q Consensus        79 -----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~  145 (175)
                           ...+|++++++|||+|++|+.+...+|++.. +++++.++||.+..++--.+..||.++|+        |.++.+
T Consensus       314 ~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~l  392 (673)
T KOG0333|consen  314 ARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYL  392 (673)
T ss_pred             chhhhcccCceeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHH
Confidence                 2468999999999999999999999999998 99999999999999998899999999999        555577


Q ss_pred             CCCCceEEEEeCC----CCCCHHHHHHHHhh
Q psy1539         146 NLSGVVVNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       146 ~~~~~~~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      -++++.++|+|||    |+||.+|+..||.+
T Consensus       393 vl~qctyvvldeadrmiDmgfE~dv~~iL~~  423 (673)
T KOG0333|consen  393 VLNQCTYVVLDEADRMIDMGFEPDVQKILEQ  423 (673)
T ss_pred             HhccCceEeccchhhhhcccccHHHHHHHHh
Confidence            8899999999999    79999999999864

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=2.8e-30  Score=215.46  Aligned_cols=160  Identities=26%  Similarity=0.327  Sum_probs=139.3

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC-------CCeE
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVY   84 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~-------~~~~   84 (175)
                      ....|.+++|++.++++|.+.||..||++|.++|+.+++|+|+++++|||||||++|++|+++.+....       +.++
T Consensus        85 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~  164 (475)
T PRK01297         85 GKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPR  164 (475)
T ss_pred             CCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCce
Confidence            345688999999999999999999999999999999999999999999999999999999999886532       2579


Q ss_pred             EEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc-CCCeEEEe--------ecCccCCCCceEEEE
Q psy1539          85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT-HNPQIVGL--------VNYETNLSGVVVNVM  155 (175)
Q Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~-~~~iiv~l--------~~~~~~~~~~~~lVl  155 (175)
                      +|||+||++|+.|+++.++.+.+.. ++++..++||.+...+.+.+.+ .++++|++        .+....+++++++|+
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lVi  243 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVL  243 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEe
Confidence            9999999999999999999998887 8999999999887777777654 57888882        222567889999999


Q ss_pred             eCC----CCCCHHHHHHHHhh
Q psy1539         156 DVR----SGGWWLDLEALILS  172 (175)
Q Consensus       156 DEa----d~~f~~~v~~il~~  172 (175)
                      ||+    +.+|..+++.|+..
T Consensus       244 DEah~l~~~~~~~~l~~i~~~  264 (475)
T PRK01297        244 DEADRMLDMGFIPQVRQIIRQ  264 (475)
T ss_pred             chHHHHHhcccHHHHHHHHHh
Confidence            999    46788889888754

>KOG0328|consensus

Probab=99.97  E-value=1.4e-31  Score=203.18  Aligned_cols=160  Identities=26%  Similarity=0.362  Sum_probs=148.2

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .+.++|++|||++++++++.+.||++|+.+|++|+|.+++|+|++++|.+|+|||.+|.+.+++.+....+..+++|++|
T Consensus        24 ~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsP  103 (400)
T KOG0328|consen   24 KVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSP  103 (400)
T ss_pred             ccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecC
Confidence            56678999999999999999999999999999999999999999999999999999999999999887777889999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC----
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR----  158 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa----  158 (175)
                      ||||+.|+.+.+..++.++ ++++..+.||.+..++++.+.-|++++.|        +.++.+..+.++++|+|||    
T Consensus       104 TRELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL  182 (400)
T KOG0328|consen  104 TRELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEML  182 (400)
T ss_pred             hHHHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHH
Confidence            9999999999999999999 99999999999999999999988888887        3333778889999999999    


Q ss_pred             CCCCHHHHHHHHh
Q psy1539         159 SGGWWLDLEALIL  171 (175)
Q Consensus       159 d~~f~~~v~~il~  171 (175)
                      +.||.+++..|.+
T Consensus       183 ~kgfk~Qiydiyr  195 (400)
T KOG0328|consen  183 NKGFKEQIYDIYR  195 (400)
T ss_pred             HhhHHHHHHHHHH
Confidence            5799999988865

>PTZ00424 helicase 45; Provisional

Probab=99.97  E-value=9.2e-30  Score=207.97  Aligned_cols=161  Identities=25%  Similarity=0.311  Sum_probs=142.6

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      +.+++|+++++++.+.+++.+.||..|+|+|.++|+.+++|+|+++++|||||||++|++|+++.+....++.++||++|
T Consensus        25 ~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~P  104 (401)
T PTZ00424         25 EIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAP  104 (401)
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECC
Confidence            35788999999999999999999999999999999999999999999999999999999999998876556779999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------CccCCCCceEEEEeCCC---
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------YETNLSGVVVNVMDVRS---  159 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~~~~~~~~~~lVlDEad---  159 (175)
                      |++|+.|+.+.++.+.... ++.+..+.|+....++...+.++++++|++..        ....+++++++|+||+|   
T Consensus       105 t~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~  183 (401)
T PTZ00424        105 TRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEML  183 (401)
T ss_pred             CHHHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHH
Confidence            9999999999999998776 88888899999888888888888899999332        24568899999999995   


Q ss_pred             -CCCHHHHHHHHhh
Q psy1539         160 -GGWWLDLEALILS  172 (175)
Q Consensus       160 -~~f~~~v~~il~~  172 (175)
                       .+|...+..++.+
T Consensus       184 ~~~~~~~~~~i~~~  197 (401)
T PTZ00424        184 SRGFKGQIYDVFKK  197 (401)
T ss_pred             hcchHHHHHHHHhh
Confidence             5788888777654

>KOG0339|consensus

Probab=99.97  E-value=1e-30  Score=211.30  Aligned_cols=164  Identities=24%  Similarity=0.306  Sum_probs=151.8

Q ss_pred             CcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----CC
Q psy1539           7 MFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----DS   81 (175)
Q Consensus         7 ~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~~   81 (175)
                      -.++.++++|+.+|+...+..+..+..|++|||+|.+++|..+.|+|++-.|.||||||.||+.|++.++...     .+
T Consensus       216 ~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~  295 (731)
T KOG0339|consen  216 SSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGE  295 (731)
T ss_pred             CCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCC
Confidence            3457899999999999999999999999999999999999999999999999999999999999999988643     57


Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eecC----ccCCCCceEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY----ETNLSGVVVN  153 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~----~~~~~~~~~l  153 (175)
                      +|.++|+||||+||.|++..+++|++.+ +++++.+|||.+..+|...|+.++.+||+    |++.    ..+++++.+|
T Consensus       296 gPi~vilvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~L  374 (731)
T KOG0339|consen  296 GPIGVILVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYL  374 (731)
T ss_pred             CCeEEEEeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEE
Confidence            8999999999999999999999999998 99999999999999999999999999999    2222    6789999999


Q ss_pred             EEeCC----CCCCHHHHHHHHh
Q psy1539         154 VMDVR----SGGWWLDLEALIL  171 (175)
Q Consensus       154 VlDEa----d~~f~~~v~~il~  171 (175)
                      |+|||    |+||..+|++|-.
T Consensus       375 V~DEadrmfdmGfe~qVrSI~~  396 (731)
T KOG0339|consen  375 VLDEADRMFDMGFEPQVRSIKQ  396 (731)
T ss_pred             EEechhhhhccccHHHHHHHHh
Confidence            99999    6899999999854

>KOG0334|consensus

Probab=99.97  E-value=4.2e-30  Score=221.36  Aligned_cols=167  Identities=26%  Similarity=0.337  Sum_probs=151.0

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----C
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----D   80 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~   80 (175)
                      +..-+.|+++|.+-|++..++..++++||.+|+|||.+|||.++.|+|+|..|.||||||++|++|++.+...+     .
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            56678999999999999999999999999999999999999999999999999999999999999999877533     4


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC-----------ccCCCC
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY-----------ETNLSG  149 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----------~~~~~~  149 (175)
                      .||-++|++|||+|+.|+.+.+++|.+.. +++++.++||....+++..+++|++|+|++..+           ..++.+
T Consensus       437 dGPi~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR  515 (997)
T KOG0334|consen  437 DGPIALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRR  515 (997)
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccc
Confidence            69999999999999999999999999997 999999999999999999999999999993222           345666


Q ss_pred             ceEEEEeCC----CCCCHHHHHHHHhhh
Q psy1539         150 VVVNVMDVR----SGGWWLDLEALILSK  173 (175)
Q Consensus       150 ~~~lVlDEa----d~~f~~~v~~il~~~  173 (175)
                      +.++|+|||    |++|.+++-.||.+.
T Consensus       516 ~t~lv~deaDrmfdmgfePq~~~Ii~nl  543 (997)
T KOG0334|consen  516 VTYLVLDEADRMFDMGFEPQITRILQNL  543 (997)
T ss_pred             cceeeechhhhhheeccCcccchHHhhc
Confidence            779999999    689999998877653

>KOG0347|consensus

Probab=99.97  E-value=1.9e-30  Score=211.30  Aligned_cols=164  Identities=27%  Similarity=0.338  Sum_probs=143.7

Q ss_pred             CcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcC------
Q psy1539           7 MFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETT------   79 (175)
Q Consensus         7 ~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~------   79 (175)
                      ..+++.++.|..++|+.+++++|.++||..||++|..++|++..| .|++-.|.||||||+||.+|+++++...      
T Consensus       174 ~~~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e  253 (731)
T KOG0347|consen  174 DSSKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQE  253 (731)
T ss_pred             cccccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhh
Confidence            345667777999999999999999999999999999999999999 8999999999999999999999966421      


Q ss_pred             -----CCCeE--EEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe-------ecC--
Q psy1539          80 -----DSNVY--VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL-------VNY--  143 (175)
Q Consensus        80 -----~~~~~--~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l-------~~~--  143 (175)
                           ..+++  +||++||||||.|+.+.+..+.... ++++..++||.....|.+.+...++|+|++       +..  
T Consensus       254 ~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t-~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n  332 (731)
T KOG0347|consen  254 LSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKT-QIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDN  332 (731)
T ss_pred             hhhHHhccCcceeEEecChHHHHHHHHHHHHHhcccc-CeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhh
Confidence                 23445  9999999999999999999999876 999999999999999999999988888882       221  


Q ss_pred             --ccCCCCceEEEEeCCC----CCCHHHHHHHHh
Q psy1539         144 --ETNLSGVVVNVMDVRS----GGWWLDLEALIL  171 (175)
Q Consensus       144 --~~~~~~~~~lVlDEad----~~f~~~v~~il~  171 (175)
                        .-+|++++++|+||||    .|+.+++..||.
T Consensus       333 ~~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~  366 (731)
T KOG0347|consen  333 THLGNFKKVKCLVLDEADRMVEKGHFEELSKLLK  366 (731)
T ss_pred             hhhhhhhhceEEEEccHHHHhhhccHHHHHHHHH
Confidence              4578999999999996    578888888875

>KOG0336|consensus

Probab=99.96  E-value=3.9e-30  Score=203.81  Aligned_cols=162  Identities=24%  Similarity=0.316  Sum_probs=143.1

Q ss_pred             ccccccccc-CCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc------CCCC
Q psy1539          10 GVTVKVLSS-RNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET------TDSN   82 (175)
Q Consensus        10 ~~~~~~~~~-~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~------~~~~   82 (175)
                      |.|.-+|++ ++-.+++++.+.+.||.+|||+|++|||.+++|.|++..|.||+|||++|++|.+.++..      ...+
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            344445655 677899999999999999999999999999999999999999999999999999887753      3578


Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNV  154 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lV  154 (175)
                      +.+|+++|||+|+.|+.-.+.++.-.  +.+..+++||.+..++.+.++.+.++|++        ..+..+++..+.++|
T Consensus       295 p~~lvl~ptreLalqie~e~~kysyn--g~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlV  372 (629)
T KOG0336|consen  295 PGVLVLTPTRELALQIEGEVKKYSYN--GLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLV  372 (629)
T ss_pred             CceEEEeccHHHHHHHHhHHhHhhhc--CcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEE
Confidence            89999999999999999888877643  88999999999999999999999999999        223368899999999


Q ss_pred             EeCC----CCCCHHHHHHHHhhh
Q psy1539         155 MDVR----SGGWWLDLEALILSK  173 (175)
Q Consensus       155 lDEa----d~~f~~~v~~il~~~  173 (175)
                      +|||    ||||.++|+.||...
T Consensus       373 lDEADrMLDMgFEpqIrkilldi  395 (629)
T KOG0336|consen  373 LDEADRMLDMGFEPQIRKILLDI  395 (629)
T ss_pred             ecchhhhhcccccHHHHHHhhhc
Confidence            9999    799999999999764

>KOG0341|consensus

Probab=99.96  E-value=1e-30  Score=205.92  Aligned_cols=165  Identities=21%  Similarity=0.272  Sum_probs=149.1

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-------
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-------   78 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-------   78 (175)
                      ++--++|.++|.+|.++..+++.|++.|+.+|||+|.+-+|.+++|+|.+-.|-||||||++|.+|++.....       
T Consensus       162 Gd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf  241 (610)
T KOG0341|consen  162 GDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPF  241 (610)
T ss_pred             CCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCcc
Confidence            4556889999999999999999999999999999999999999999999999999999999999999876542       


Q ss_pred             -CCCCeEEEEEecCHHHHHHHHHHHHHHHhh-----CCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCc
Q psy1539          79 -TDSNVYVLVMCHTRELAFQISKEYERFSKY-----MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYE  144 (175)
Q Consensus        79 -~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~-----~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~  144 (175)
                       ...||..||+||+||||.|+++.+..+...     +|.+++.++.||.+..++...++.|.+++|+        |....
T Consensus       242 ~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~  321 (610)
T KOG0341|consen  242 ARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKI  321 (610)
T ss_pred             ccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhh
Confidence             357899999999999999999998888654     3789999999999999999999999999999        23336


Q ss_pred             cCCCCceEEEEeCC----CCCCHHHHHHHH
Q psy1539         145 TNLSGVVVNVMDVR----SGGWWLDLEALI  170 (175)
Q Consensus       145 ~~~~~~~~lVlDEa----d~~f~~~v~~il  170 (175)
                      +.+.-++++++|||    |+||.+|++.|.
T Consensus       322 ~sLd~CRyL~lDEADRmiDmGFEddir~iF  351 (610)
T KOG0341|consen  322 MSLDACRYLTLDEADRMIDMGFEDDIRTIF  351 (610)
T ss_pred             ccHHHHHHhhhhhHHHHhhccchhhHHHHH
Confidence            77889999999999    799999999985

>cd00268 DEADc DEAD-box helicases

Probab=99.96  E-value=8.1e-28  Score=179.57  Aligned_cols=155  Identities=28%  Similarity=0.370  Sum_probs=136.1

Q ss_pred             cccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC--CCCeEEEEEecCHH
Q psy1539          16 LSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT--DSNVYVLVMCHTRE   93 (175)
Q Consensus        16 ~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~--~~~~~~lil~Pt~~   93 (175)
                      |+++++++.+.+.+.+.|+..|+++|.++++.+.+|+|+++++|||+|||++|++|+++++...  .++++++|++|+++
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            6789999999999999999999999999999999999999999999999999999999998875  56789999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC----CC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS----GG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad----~~  161 (175)
                      |+.|+.+.++.+.... ++++..++|+.+..+....+.++++++|++.        +....+++++++|+||++    .+
T Consensus        81 L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~  159 (203)
T cd00268          81 LALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMG  159 (203)
T ss_pred             HHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccC
Confidence            9999999999998776 8899999999987777777776889999932        225677899999999994    45


Q ss_pred             CHHHHHHHHh
Q psy1539         162 WWLDLEALIL  171 (175)
Q Consensus       162 f~~~v~~il~  171 (175)
                      |..++..++.
T Consensus       160 ~~~~~~~~~~  169 (203)
T cd00268         160 FEDQIREILK  169 (203)
T ss_pred             hHHHHHHHHH
Confidence            7777776654

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.

>KOG0326|consensus

Probab=99.96  E-value=5.1e-30  Score=197.61  Aligned_cols=157  Identities=30%  Similarity=0.383  Sum_probs=143.0

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      -..|+++.|.++++..+.+.||++|+|+|.++||..+.|+|++..|.+|+|||.+|.+|+++++..+.+..+++|++|||
T Consensus        84 G~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtr  163 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTR  163 (459)
T ss_pred             CccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecc
Confidence            34599999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eecC-ccCCCCceEEEEeCCCC----
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVNY-ETNLSGVVVNVMDVRSG----  160 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~-~~~~~~~~~lVlDEad~----  160 (175)
                      |||.|+.+.++++.+.. ++++...+||++..+++-++.+.++++|+       |... ...+++..++|+||||.    
T Consensus       164 elALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~  242 (459)
T KOG0326|consen  164 ELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSV  242 (459)
T ss_pred             hhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhch
Confidence            99999999999999999 99999999999999999999999999998       3333 56789999999999964    


Q ss_pred             CCHHHHHHHH
Q psy1539         161 GWWLDLEALI  170 (175)
Q Consensus       161 ~f~~~v~~il  170 (175)
                      .|.+-++.++
T Consensus       243 ~F~~~~e~li  252 (459)
T KOG0326|consen  243 DFQPIVEKLI  252 (459)
T ss_pred             hhhhHHHHHH
Confidence            4555555544

>KOG0337|consensus

Probab=99.96  E-value=9.3e-29  Score=196.13  Aligned_cols=158  Identities=25%  Similarity=0.352  Sum_probs=144.5

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTR   92 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~   92 (175)
                      -.|.++||+..+++++.+.||..|||+|+.++|.+++|+|++..|.||||||.||++|+++++... ..+.++++++|||
T Consensus        21 g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilsptr  100 (529)
T KOG0337|consen   21 GGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTR  100 (529)
T ss_pred             CCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcH
Confidence            569999999999999999999999999999999999999999999999999999999999998643 4578999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eec----CccCCCCceEEEEeCCC----C
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVN----YETNLSGVVVNVMDVRS----G  160 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~----~~~~~~~~~~lVlDEad----~  160 (175)
                      +|+.|..+.++.+++.. ++++.+++||.+..++...+..++++|++    +..    ..+.++.+.|+|+||||    +
T Consensus       101 eLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfem  179 (529)
T KOG0337|consen  101 ELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEM  179 (529)
T ss_pred             HHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhh
Confidence            99999999999999988 99999999999999999999888999997    222    25778999999999995    7


Q ss_pred             CCHHHHHHHHhh
Q psy1539         161 GWWLDLEALILS  172 (175)
Q Consensus       161 ~f~~~v~~il~~  172 (175)
                      ||.+++.+|+.+
T Consensus       180 gfqeql~e~l~r  191 (529)
T KOG0337|consen  180 GFQEQLHEILSR  191 (529)
T ss_pred             hhHHHHHHHHHh
Confidence            899999999865

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

Probab=99.96  E-value=1.5e-27  Score=207.39  Aligned_cols=149  Identities=13%  Similarity=0.162  Sum_probs=126.0

Q ss_pred             CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          20 NRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        20 ~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      .+++++.++|++.||..||++|.++||.+++|+|+++++|||||||+||.+|+++.+..+ .+.++|||+|||+|++|+.
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-~~~~aL~l~PtraLa~q~~   98 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-PRATALYLAPTKALAADQL   98 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-CCcEEEEEcChHHHHHHHH
Confidence            489999999999999999999999999999999999999999999999999999998753 4679999999999999999


Q ss_pred             HHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC------------ccCCCCceEEEEeCCCC---CCHH
Q psy1539         100 KEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY------------ETNLSGVVVNVMDVRSG---GWWL  164 (175)
Q Consensus       100 ~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~------------~~~~~~~~~lVlDEad~---~f~~  164 (175)
                      +.++++. . .++++..+.|+.+ .++.+.+++++++|++..+.            ...+++++++|+||||.   .|..
T Consensus        99 ~~l~~l~-~-~~i~v~~~~Gdt~-~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g~fg~  175 (742)
T TIGR03817        99 RAVRELT-L-RGVRPATYDGDTP-TEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRGVFGS  175 (742)
T ss_pred             HHHHHhc-c-CCeEEEEEeCCCC-HHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccCccHH
Confidence            9999987 3 3788988888877 45556677778999882111            12378999999999963   4777


Q ss_pred             HHHHHHhh
Q psy1539         165 DLEALILS  172 (175)
Q Consensus       165 ~v~~il~~  172 (175)
                      ++..++.+
T Consensus       176 ~~~~il~r  183 (742)
T TIGR03817       176 HVALVLRR  183 (742)
T ss_pred             HHHHHHHH
Confidence            87777654

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.

>KOG0329|consensus

Probab=99.95  E-value=2.5e-28  Score=183.54  Aligned_cols=159  Identities=55%  Similarity=0.760  Sum_probs=144.2

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      -+.|.++-|.|++++++...||.+|+++|.++||...-|.|++.+|.+|.|||..|.++-++.+.+..+...++++|.||
T Consensus        41 ssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtr  120 (387)
T KOG0329|consen   41 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTR  120 (387)
T ss_pred             ccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccH
Confidence            34588899999999999999999999999999999999999999999999999999999999999888888999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eec-CccCCCCceEEEEeCCC-----
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVN-YETNLSGVVVNVMDVRS-----  159 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~-~~~~~~~~~~lVlDEad-----  159 (175)
                      |||-|+.+...+|.+++|++++.+++||.+++.+.+.+++.++|+||       +.+ +.+++++++++|+||+|     
T Consensus       121 elafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~  200 (387)
T KOG0329|consen  121 ELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQ  200 (387)
T ss_pred             HHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHH
Confidence            99999999999999999999999999999999999999996666666       333 37889999999999996     


Q ss_pred             CCCHHHHHHHHh
Q psy1539         160 GGWWLDLEALIL  171 (175)
Q Consensus       160 ~~f~~~v~~il~  171 (175)
                      ...+.|+++|.+
T Consensus       201 lDMrRDvQEifr  212 (387)
T KOG0329|consen  201 LDMRRDVQEIFR  212 (387)
T ss_pred             HHHHHHHHHHhh
Confidence            456677777753

>KOG0327|consensus

Probab=99.94  E-value=6.6e-27  Score=183.68  Aligned_cols=162  Identities=26%  Similarity=0.391  Sum_probs=141.5

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      .+.+.+|++|+|++++++.+...||.+|+.+|++||+++..|.|+.+++.+|+|||.+|.+++++.+..+....+|++++
T Consensus        22 ~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalila  101 (397)
T KOG0327|consen   22 NEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILA  101 (397)
T ss_pred             HHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhc
Confidence            45567899999999999999999999999999999999999999999999999999999999999998777788999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc-CCCeEEE-------eecC-ccCCCCceEEEEeCCC-
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT-HNPQIVG-------LVNY-ETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~-~~~iiv~-------l~~~-~~~~~~~~~lVlDEad-  159 (175)
                      |||+|+.|+..+...+.... +.++..+.||.....+...+.. +++++++       +++. .+....++++|+|||| 
T Consensus       102 PtreLa~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDE  180 (397)
T KOG0327|consen  102 PTRELAQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADE  180 (397)
T ss_pred             chHHHHHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHh
Confidence            99999999999999999888 9999999999887755555554 4666776       2222 4556679999999995 


Q ss_pred             ---CCCHHHHHHHHhh
Q psy1539         160 ---GGWWLDLEALILS  172 (175)
Q Consensus       160 ---~~f~~~v~~il~~  172 (175)
                         .||+++++.|...
T Consensus       181 mLs~gfkdqI~~if~~  196 (397)
T KOG0327|consen  181 MLSRGFKDQIYDIFQE  196 (397)
T ss_pred             hhccchHHHHHHHHHH
Confidence               6999999998754

>KOG4284|consensus

Probab=99.94  E-value=4.4e-27  Score=194.79  Aligned_cols=162  Identities=27%  Similarity=0.335  Sum_probs=147.5

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +--...|+++-|-.+++..|+..+|..||++|..|||.++.+.|++|+|..|+|||++|...+++.+......++++|++
T Consensus        21 ~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~  100 (980)
T KOG4284|consen   21 SNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVT  100 (980)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEe
Confidence            34456799999999999999999999999999999999999999999999999999999999999998888889999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eec-CccCCCCceEEEEeCCC--
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVN-YETNLSGVVVNVMDVRS--  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~-~~~~~~~~~~lVlDEad--  159 (175)
                      ||||++.|+.+.+..++..+.|.+|.+++||+..+.+..++++ +.|+||       |.. ..++.++++++||||||  
T Consensus       101 PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~-~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL  179 (980)
T KOG4284|consen  101 PTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ-TRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKL  179 (980)
T ss_pred             cchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh-ceEEecCchHHHHHHHhcCCCccceeEEEeccHHhh
Confidence            9999999999999999998889999999999999999988877 689998       222 26889999999999995  


Q ss_pred             ---CCCHHHHHHHHhh
Q psy1539         160 ---GGWWLDLEALILS  172 (175)
Q Consensus       160 ---~~f~~~v~~il~~  172 (175)
                         ..|.++|..|+.+
T Consensus       180 ~~t~sfq~~In~ii~s  195 (980)
T KOG4284|consen  180 MDTESFQDDINIIINS  195 (980)
T ss_pred             hchhhHHHHHHHHHHh
Confidence               5799999988765

>KOG0350|consensus

Probab=99.93  E-value=1.3e-25  Score=181.44  Aligned_cols=146  Identities=21%  Similarity=0.287  Sum_probs=125.1

Q ss_pred             cccccCCCCHHHHHH----------HhhCCCCCCcHHHHHhHHHHhc---------CCcEEEEcCCCChHHHHHHHHHHH
Q psy1539          14 KVLSSRNRREKEDRI----------GESQPFREQTSFQHECIPQAVL---------GMDILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~----------l~~~g~~~~t~~Q~~~i~~~~~---------g~~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      ..|+.++.+......          +.+++.....|+|..++|.++.         ++|++|.||||||||++|.+|+++
T Consensus       127 q~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ  206 (620)
T KOG0350|consen  127 QIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQ  206 (620)
T ss_pred             eeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHH
Confidence            447777776655544          8999999999999999998852         589999999999999999999999


Q ss_pred             hhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCC-----CeEEE----eecC-
Q psy1539          75 QLETT-DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN-----PQIVG----LVNY-  143 (175)
Q Consensus        75 ~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~-----~iiv~----l~~~-  143 (175)
                      .+... -+..+++||+||++|+.|+++.+.++.... ++.|+.+.|..+...+.+.|.+..     +|+|+    |++| 
T Consensus       207 ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl  285 (620)
T KOG0350|consen  207 LLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHL  285 (620)
T ss_pred             HHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhc
Confidence            88654 455899999999999999999999999988 999999999999988888887654     57777    5554 


Q ss_pred             ----ccCCCCceEEEEeCCCC
Q psy1539         144 ----ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       144 ----~~~~~~~~~lVlDEad~  160 (175)
                          .+++++++|+|+||||.
T Consensus       286 ~~~k~f~Lk~LrfLVIDEADR  306 (620)
T KOG0350|consen  286 NNTKSFDLKHLRFLVIDEADR  306 (620)
T ss_pred             cCCCCcchhhceEEEechHHH
Confidence                68899999999999964

>PRK02362 ski2-like helicase; Provisional

Probab=99.93  E-value=7.7e-25  Score=191.04  Aligned_cols=149  Identities=23%  Similarity=0.263  Sum_probs=123.8

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHH-HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQ-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~-~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .|++++|++.+++++.+.||.+|+|+|.+|++. +.+|+|+++++|||||||++|.+|+++.+.   ++.+++|++|+++
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 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA---RGGKALYIVPLRA   78 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh---cCCcEEEEeChHH
Confidence            478899999999999999999999999999998 678999999999999999999999999886   3458999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe-------ecC-ccCCCCceEEEEeCCC----CC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL-------VNY-ETNLSGVVVNVMDVRS----GG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l-------~~~-~~~~~~~~~lVlDEad----~~  161 (175)
                      |+.|+++.++++.. . ++++..++|+.+...  +.+ ...+++|++       .++ ...+++++++|+||+|    .+
T Consensus        79 La~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~--~~l-~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~  153 (737)
T PRK02362         79 LASEKFEEFERFEE-L-GVRVGISTGDYDSRD--EWL-GDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSAN  153 (737)
T ss_pred             HHHHHHHHHHHhhc-C-CCEEEEEeCCcCccc--ccc-CCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCc
Confidence            99999999998754 4 889999999876433  223 346899983       222 3456899999999995    45


Q ss_pred             CHHHHHHHHh
Q psy1539         162 WWLDLEALIL  171 (175)
Q Consensus       162 f~~~v~~il~  171 (175)
                      +...++.++.
T Consensus       154 rg~~le~il~  163 (737)
T PRK02362        154 RGPTLEVTLA  163 (737)
T ss_pred             chHHHHHHHH
Confidence            6677776654

>PRK00254 ski2-like helicase; Provisional

Probab=99.92  E-value=2.9e-24  Score=187.01  Aligned_cols=151  Identities=16%  Similarity=0.182  Sum_probs=125.2

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHH-HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQ-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~-~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .|+++++++.+.+.+++.||..|+|+|.++++. +++|+|+++++|||||||++|.+|+++++..  .+.+++|++|+++
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 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR--EGGKAVYLVPLKA   79 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh--cCCeEEEEeChHH
Confidence            467899999999999999999999999999986 7899999999999999999999999998764  3458999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee-------c-CccCCCCceEEEEeCCC----CC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV-------N-YETNLSGVVVNVMDVRS----GG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~-------~-~~~~~~~~~~lVlDEad----~~  161 (175)
                      |+.|+++.++.+. .. ++++..++|+.+...  +.+ ..++++|++.       + ....+++++++|+||+|    .+
T Consensus        80 La~q~~~~~~~~~-~~-g~~v~~~~Gd~~~~~--~~~-~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~  154 (720)
T PRK00254         80 LAEEKYREFKDWE-KL-GLRVAMTTGDYDSTD--EWL-GKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYD  154 (720)
T ss_pred             HHHHHHHHHHHHh-hc-CCEEEEEeCCCCCch--hhh-ccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCcc
Confidence            9999999998864 34 899999999876432  223 4578999832       2 23567899999999995    45


Q ss_pred             CHHHHHHHHhh
Q psy1539         162 WWLDLEALILS  172 (175)
Q Consensus       162 f~~~v~~il~~  172 (175)
                      +...++.++.+
T Consensus       155 rg~~le~il~~  165 (720)
T PRK00254        155 RGATLEMILTH  165 (720)
T ss_pred             chHHHHHHHHh
Confidence            66777777653

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

Probab=99.91  E-value=4.1e-24  Score=184.23  Aligned_cols=137  Identities=22%  Similarity=0.273  Sum_probs=123.2

Q ss_pred             CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----CCCeEEEEEecCHHH
Q psy1539          20 NRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTREL   94 (175)
Q Consensus        20 ~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~~lil~Pt~~L   94 (175)
                      -|+|.+.+.+.+. |..|||.|.+|||.+.+|+|+++.||||||||+++++|++..+...     ..+..+|||+|.|+|
T Consensus         7 ~l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkAL   85 (814)
T COG1201           7 ILDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKAL   85 (814)
T ss_pred             hcCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHH
Confidence            3688999999988 9999999999999999999999999999999999999999998755     456899999999999


Q ss_pred             HHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecC--ccCCCCceEEEEeCC
Q psy1539          95 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNY--ETNLSGVVVNVMDVR  158 (175)
Q Consensus        95 ~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~--~~~~~~~~~lVlDEa  158 (175)
                      .+++.+.++.+.+.+ |+.+.+.+|+++..+..+..++.++|+++        +...  ...|++++++|+||.
T Consensus        86 n~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEi  158 (814)
T COG1201          86 NNDIRRRLEEPLREL-GIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEI  158 (814)
T ss_pred             HHHHHHHHHHHHHHc-CCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehh
Confidence            999999999999998 99999999999988888888887788887        2221  567899999999999

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

Probab=99.91  E-value=1.3e-23  Score=181.86  Aligned_cols=139  Identities=18%  Similarity=0.201  Sum_probs=114.8

Q ss_pred             CCCCCCcHHHHHhHHHHhcCC-cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEE-EecCHHHHHHHHHHHHHHHhhC
Q psy1539          32 QPFREQTSFQHECIPQAVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLV-MCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~-~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~li-l~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      .||. |||+|.+++|.+++|+ ++++++|||||||.++.++++.. ......++.|+ ++|||+|+.|+++.++++.+.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            4887 9999999999999998 68888999999999766555432 33344566666 6699999999999999998865


Q ss_pred             C----------------------CeEEEEEECCCchHHhHHHHhcCCCeEEEeecC----cc----------------CC
Q psy1539         110 S----------------------NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY----ET----------------NL  147 (175)
Q Consensus       110 ~----------------------~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~----~~----------------~~  147 (175)
                      +                      .+++..++||.+.+.+.+.+..+++|||++.++    .+                .+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~L  169 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGFL  169 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCccccccccccccccchhhhh
Confidence            2                      488999999999999999999999999993322    22                26


Q ss_pred             CCceEEEEeCC--CCCCHHHHHHHHhh
Q psy1539         148 SGVVVNVMDVR--SGGWWLDLEALILS  172 (175)
Q Consensus       148 ~~~~~lVlDEa--d~~f~~~v~~il~~  172 (175)
                      ++++++|+|||  +++|.++++.|+..
T Consensus       170 ~~v~~LVLDEADLd~gF~~~l~~Il~~  196 (844)
T TIGR02621       170 GQDALIVHDEAHLEPAFQELLKQIMNE  196 (844)
T ss_pred             ccceEEEEehhhhccccHHHHHHHHHh
Confidence            88999999999  58999999999984

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.91  E-value=2.2e-23  Score=184.33  Aligned_cols=139  Identities=22%  Similarity=0.244  Sum_probs=113.6

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC------CCCeEEEEEecCHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT------DSNVYVLVMCHTREL   94 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~------~~~~~~lil~Pt~~L   94 (175)
                      +++.+.+.+.+ +|..|||+|.+|||.+++|+|++++||||||||++|.+|+++++...      .+++++||++|||+|
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            56777776665 79999999999999999999999999999999999999999987532      346789999999999


Q ss_pred             HHHHHHHHHHH-------H----hhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee-------cC---ccCCCCceEE
Q psy1539          95 AFQISKEYERF-------S----KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV-------NY---ETNLSGVVVN  153 (175)
Q Consensus        95 ~~q~~~~~~~~-------~----~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~-------~~---~~~~~~~~~l  153 (175)
                      +.|+++.+...       .    ...+++++..++|+.+..+..+.+.+.++|+|++.       ..   ...+++++++
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            99998876532       2    22347889999999988877778888888998822       21   1257899999


Q ss_pred             EEeCCCC
Q psy1539         154 VMDVRSG  160 (175)
Q Consensus       154 VlDEad~  160 (175)
                      |+||+|.
T Consensus       177 VIDE~H~  183 (876)
T PRK13767        177 IVDEIHS  183 (876)
T ss_pred             EEechhh
Confidence            9999963

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

Probab=99.91  E-value=3.2e-23  Score=181.70  Aligned_cols=150  Identities=17%  Similarity=0.198  Sum_probs=130.1

Q ss_pred             CHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          22 REKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        22 ~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      ...+..++.+.|...++++|.+|+..+.+|+|++|++|||||||.+|++|+++++..+... ++|+|.||++|++.+.+.
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            4456888889999999999999999999999999999999999999999999999876554 899999999999999999


Q ss_pred             HHHHHhhCC-CeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecC----ccCCCCceEEEEeCC---CCCCHHH
Q psy1539         102 YERFSKYMS-NIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNY----ETNLSGVVVNVMDVR---SGGWWLD  165 (175)
Q Consensus       102 ~~~~~~~~~-~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~----~~~~~~~~~lVlDEa---d~~f~~~  165 (175)
                      ++++...++ ++++..+.|++...+....+.+.++|+++        ++++    ...+++++++|+||+   +..|..+
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~GS~  214 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQGSE  214 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccchhH
Confidence            999999985 58889999999876666778887888888        2222    456778999999999   4678899


Q ss_pred             HHHHHhh
Q psy1539         166 LEALILS  172 (175)
Q Consensus       166 v~~il~~  172 (175)
                      |..++++
T Consensus       215 vA~llRR  221 (851)
T COG1205         215 VALLLRR  221 (851)
T ss_pred             HHHHHHH
Confidence            9888875

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

Probab=99.91  E-value=4.3e-23  Score=149.39  Aligned_cols=133  Identities=26%  Similarity=0.397  Sum_probs=109.9

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEE
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF  117 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~  117 (175)
                      ||+|.++++.+.+|+++++.+|||+|||++|.+|+++.+... +..++++++|+++|++|+.+.++++.... ++++..+
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~-~~~~~~~   78 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNT-NVRVVLL   78 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTT-TSSEEEE
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccc-ccccccc
Confidence            799999999999999999999999999999999999988775 44599999999999999999999998874 7899999


Q ss_pred             ECCCchH-HhHHHHhcCCCeEEEeec--------CccCCCCceEEEEeCCC----CCCHHHHHHHHhh
Q psy1539         118 FGGLPIQ-KDEEYLKTHNPQIVGLVN--------YETNLSGVVVNVMDVRS----GGWWLDLEALILS  172 (175)
Q Consensus       118 ~g~~~~~-~~~~~l~~~~~iiv~l~~--------~~~~~~~~~~lVlDEad----~~f~~~v~~il~~  172 (175)
                      +|+.+.. .....+.++++++|+...        ...++.+++++|+||+|    ..|...+..|+..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~  146 (169)
T PF00270_consen   79 HGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRR  146 (169)
T ss_dssp             STTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHH
Confidence            9998865 444455567899998222        12366779999999993    3667777777654

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 ....

>KOG0332|consensus

Probab=99.90  E-value=3.2e-24  Score=168.35  Aligned_cols=158  Identities=21%  Similarity=0.283  Sum_probs=134.0

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      ...++|++++|.|++++++..++|.+|+.+|..|+|.++..  +|++.++.+|+|||.||.+.++.+.......|+++.|
T Consensus        87 yS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCL  166 (477)
T KOG0332|consen   87 YSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICL  166 (477)
T ss_pred             cccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceee
Confidence            46788999999999999999999999999999999999986  8999999999999999999999999988888999999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eec--CccCCCCceEEEEeCCC
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVN--YETNLSGVVVNVMDVRS  159 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~--~~~~~~~~~~lVlDEad  159 (175)
                      +||||||.|..+++.++++.. +++.....-|...+.. +.+  ..+|+++       +..  ..++++.++.+|+||||
T Consensus       167 aPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~rG-~~i--~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD  242 (477)
T KOG0332|consen  167 APTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKRG-NKL--TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEAD  242 (477)
T ss_pred             CchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccccC-Ccc--hhheeeCCCccHHHHHHHHHhhChhhceEEEecchh
Confidence            999999999999999999988 8888887776632221 112  2467777       222  25778899999999994


Q ss_pred             -----CCCHHHHHHHHhh
Q psy1539         160 -----GGWWLDLEALILS  172 (175)
Q Consensus       160 -----~~f~~~v~~il~~  172 (175)
                           .||.++--.|+..
T Consensus       243 ~Mi~tqG~~D~S~rI~~~  260 (477)
T KOG0332|consen  243 VMIDTQGFQDQSIRIMRS  260 (477)
T ss_pred             hhhhcccccccchhhhhh
Confidence                 6888887776654

>PRK01172 ski2-like helicase; Provisional

Probab=99.90  E-value=1.1e-22  Score=176.18  Aligned_cols=148  Identities=15%  Similarity=0.165  Sum_probs=121.1

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      .|+++++++++++.+.+.+|. ++++|.++++.+.+|+|+++++|||||||+++.+++++.+..   +.++++++|+++|
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~---~~k~v~i~P~raL   77 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA---GLKSIYIVPLRSL   77 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh---CCcEEEEechHHH
Confidence            477899999999999999986 999999999999999999999999999999999999988764   3589999999999


Q ss_pred             HHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee-------cC-ccCCCCceEEEEeCCC----CCC
Q psy1539          95 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV-------NY-ETNLSGVVVNVMDVRS----GGW  162 (175)
Q Consensus        95 ~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~-------~~-~~~~~~~~~lVlDEad----~~f  162 (175)
                      +.|+++.++++.. . +.++...+|+.....  ..+ +.++++|++.       ++ ...+++++++|+||+|    .++
T Consensus        78 a~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~--~~~-~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~r  152 (674)
T PRK01172         78 AMEKYEELSRLRS-L-GMRVKISIGDYDDPP--DFI-KRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDR  152 (674)
T ss_pred             HHHHHHHHHHHhh-c-CCeEEEEeCCCCCCh--hhh-ccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCc
Confidence            9999999998753 4 888988898875332  223 4578999833       22 3457899999999995    345


Q ss_pred             HHHHHHHHh
Q psy1539         163 WLDLEALIL  171 (175)
Q Consensus       163 ~~~v~~il~  171 (175)
                      ...++.++.
T Consensus       153 g~~le~ll~  161 (674)
T PRK01172        153 GPTLETVLS  161 (674)
T ss_pred             cHHHHHHHH
Confidence            556666543

>KOG0344|consensus

Probab=99.88  E-value=6.7e-23  Score=168.32  Aligned_cols=160  Identities=24%  Similarity=0.242  Sum_probs=124.1

Q ss_pred             ccccccccc----CCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----C
Q psy1539          10 GVTVKVLSS----RNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----D   80 (175)
Q Consensus        10 ~~~~~~~~~----~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~   80 (175)
                      +.++.+|++    ...++.+++.+...+|..|+|+|.+|+|.+++++|++.|+|||||||++|.+|++.++...     .
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            677777876    6789999999999999999999999999999999999999999999999999999998532     4


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHH--hhCCCeEEEEEECCCchH-HhHHHHhcCCCeEEE-------eecC---ccCC
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFS--KYMSNIKVGVFFGGLPIQ-KDEEYLKTHNPQIVG-------LVNY---ETNL  147 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~--~~~~~i~v~~~~g~~~~~-~~~~~l~~~~~iiv~-------l~~~---~~~~  147 (175)
                      .|.+++|+.|||+|+.|++..+.++.  ... +.++..+....... ..........+++++       ++..   .+++
T Consensus       208 ~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t-~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl  286 (593)
T KOG0344|consen  208 VGLRALILSPTRELAAQIYREMRKYSIDEGT-SLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDL  286 (593)
T ss_pred             cceEEEEecchHHHHHHHHHHHHhcCCCCCC-chhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchh
Confidence            67899999999999999999999998  444 55555554432211 111122223455555       3333   4689


Q ss_pred             CCceEEEEeCCCCC-----CHHHHHHHH
Q psy1539         148 SGVVVNVMDVRSGG-----WWLDLEALI  170 (175)
Q Consensus       148 ~~~~~lVlDEad~~-----f~~~v~~il  170 (175)
                      +++.++|+||||..     |..+...|+
T Consensus       287 ~~V~~lV~dEaD~lfe~~~f~~Qla~I~  314 (593)
T KOG0344|consen  287 SKVEWLVVDEADLLFEPEFFVEQLADIY  314 (593)
T ss_pred             heeeeEeechHHhhhChhhHHHHHHHHH
Confidence            99999999999754     445666655

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.88  E-value=1.6e-21  Score=172.16  Aligned_cols=145  Identities=18%  Similarity=0.177  Sum_probs=115.2

Q ss_pred             CCCHHHHHHHhh-CCCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          20 NRREKEDRIGES-QPFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        20 ~l~~~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      +.+....+.+.+ .+| .|||+|.+||+.++++      +|++++++||||||.+|+.|++..+..   +.+++|++||+
T Consensus       435 ~~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~---g~qvlvLvPT~  510 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD---GKQVAVLVPTT  510 (926)
T ss_pred             CCCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh---CCeEEEEeCcH
Confidence            344566666555 578 5999999999999975      799999999999999999999988763   46999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhcC-CCeEEE---eecCccCCCCceEEEEeCCCCCCHHH
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad~~f~~~  165 (175)
                      +||.|+++.++++...+ ++++..++|+.+.++.   .+.+.+| +++||+   +.+....+++++++|+||+|. |..+
T Consensus       511 ~LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llVIDEahr-fgv~  588 (926)
T TIGR00580       511 LLAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQR-FGVK  588 (926)
T ss_pred             HHHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEEeecccc-cchh
Confidence            99999999999988877 8899999888765443   3345554 788888   555567889999999999975 3333


Q ss_pred             HHHHH
Q psy1539         166 LEALI  170 (175)
Q Consensus       166 v~~il  170 (175)
                      .+..+
T Consensus       589 ~~~~L  593 (926)
T TIGR00580       589 QKEKL  593 (926)
T ss_pred             HHHHH
Confidence            44444

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.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=9.9e-22  Score=170.44  Aligned_cols=144  Identities=14%  Similarity=0.163  Sum_probs=121.9

Q ss_pred             cccCCCCHHHHHHHh-----hCCCCCC---cHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEE
Q psy1539          16 LSSRNRREKEDRIGE-----SQPFREQ---TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLV   87 (175)
Q Consensus        16 ~~~~~l~~~l~~~l~-----~~g~~~~---t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~li   87 (175)
                      .+.+++.+++.+.+.     ..||..|   +|+|.+++|.+..+++++..++||+|||++|++|++..+....   .++|
T Consensus        64 ~eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~---~v~I  140 (970)
T PRK12899         64 PEAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK---PVHL  140 (970)
T ss_pred             HHHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC---CeEE
Confidence            456888999998877     6799988   9999999999999999999999999999999999998876422   4899


Q ss_pred             EecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC---------ccCCC-------Cce
Q psy1539          88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY---------ETNLS-------GVV  151 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~---------~~~~~-------~~~  151 (175)
                      ++||++||.|..+++..+.+.. ++++..++||.+..++.+.+  +++|++|+...         .+.++       .+.
T Consensus       141 VTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~  217 (970)
T PRK12899        141 VTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFY  217 (970)
T ss_pred             EeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhccccc
Confidence            9999999999999999999988 99999999999988777665  48999992222         23444       568


Q ss_pred             EEEEeCCCCCCHHH
Q psy1539         152 VNVMDVRSGGWWLD  165 (175)
Q Consensus       152 ~lVlDEad~~f~~~  165 (175)
                      ++|+||||..+.++
T Consensus       218 ~~IIDEADsmLiDE  231 (970)
T PRK12899        218 FAIIDEVDSILIDE  231 (970)
T ss_pred             EEEEechhhhhhhc
Confidence            99999998666544

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.88  E-value=2e-21  Score=168.20  Aligned_cols=133  Identities=23%  Similarity=0.308  Sum_probs=110.5

Q ss_pred             HHHHHH-HhhCCCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          23 EKEDRI-GESQPFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        23 ~~l~~~-l~~~g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      ..+.+. ...++| .||++|.+|++.+.++      +|+++++|||||||++|++|++..+.   ++.+++|++||++||
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~---~g~q~lilaPT~~LA  323 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE---AGYQAALMAPTEILA  323 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH---cCCeEEEEeccHHHH
Confidence            344444 455677 5999999999999886      48999999999999999999998875   467999999999999


Q ss_pred             HHHHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhcC-CCeEEE---eecCccCCCCceEEEEeCCCC
Q psy1539          96 FQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus        96 ~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad~  160 (175)
                      .|+++.++++.... ++++..++|+.+..+.   .+.+.+| ++++|+   +++....+++++++|+||+|.
T Consensus       324 ~Q~~~~l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVIDE~Hr  394 (681)
T PRK10917        324 EQHYENLKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHR  394 (681)
T ss_pred             HHHHHHHHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEEEechhh
Confidence            99999999999887 8999999999885443   3445554 788888   455566789999999999974

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.88  E-value=1.6e-21  Score=167.67  Aligned_cols=132  Identities=24%  Similarity=0.286  Sum_probs=110.5

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      .+.+.+..++| .||++|++|++.++++      .+.+++++||||||++|++|++..+.   ++.++++++||++||.|
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~---~g~qvlilaPT~~LA~Q  299 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE---AGYQVALMAPTEILAEQ  299 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH---cCCcEEEECCHHHHHHH
Confidence            34556778888 6999999999999876      36899999999999999999998876   45689999999999999


Q ss_pred             HHHHHHHHHhhCCCeEEEEEECCCchHH---hHHHHhcC-CCeEEE---eecCccCCCCceEEEEeCCCC
Q psy1539          98 ISKEYERFSKYMSNIKVGVFFGGLPIQK---DEEYLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus        98 ~~~~~~~~~~~~~~i~v~~~~g~~~~~~---~~~~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad~  160 (175)
                      +++.++++.... ++++..++|+.+.++   ..+.+.++ ++++|+   ++.....+.+++++|+||+|.
T Consensus       300 ~~~~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvVIDEaH~  368 (630)
T TIGR00643       300 HYNSLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHR  368 (630)
T ss_pred             HHHHHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEEEechhh
Confidence            999999998877 899999999987654   33444443 588888   444467789999999999974

>PRK09401 reverse gyrase; Reviewed

Probab=99.88  E-value=1.7e-21  Score=175.46  Aligned_cols=135  Identities=21%  Similarity=0.185  Sum_probs=105.4

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .|+ .||++|+.++|.++.|+|++++||||||||. |.++++..+..  ++.+++||+|||+|+.|+.+.++.+.... +
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~~~~-~  151 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGEKV-G  151 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHhhhc-C
Confidence            377 7999999999999999999999999999995 55666555443  46799999999999999999999999887 8


Q ss_pred             eEEEEEECCCch-----HHhHHHHhc-CCCeEEEee----cC--ccCCCCceEEEEeCCC---------------CCCH-
Q psy1539         112 IKVGVFFGGLPI-----QKDEEYLKT-HNPQIVGLV----NY--ETNLSGVVVNVMDVRS---------------GGWW-  163 (175)
Q Consensus       112 i~v~~~~g~~~~-----~~~~~~l~~-~~~iiv~l~----~~--~~~~~~~~~lVlDEad---------------~~f~-  163 (175)
                      +.+..++|+.+.     .+..+.+.+ +++|+|++.    ++  .+...+++++|+||||               +||. 
T Consensus       152 ~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~lGF~~  231 (1176)
T PRK09401        152 CGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSE  231 (1176)
T ss_pred             ceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccCEEEEEChHHhhhcccchhhHHHhCCCCH
Confidence            888877776542     233445554 478999833    22  2444569999999995               5785 


Q ss_pred             HHHHHHHh
Q psy1539         164 LDLEALIL  171 (175)
Q Consensus       164 ~~v~~il~  171 (175)
                      ++++.++.
T Consensus       232 ~~i~~i~~  239 (1176)
T PRK09401        232 EDIEKAME  239 (1176)
T ss_pred             HHHHHHHH
Confidence            67877763

>PRK14701 reverse gyrase; Provisional

Probab=99.87  E-value=6.5e-21  Score=175.25  Aligned_cols=141  Identities=16%  Similarity=0.150  Sum_probs=110.4

Q ss_pred             HHHHHHhh-CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHH
Q psy1539          24 KEDRIGES-QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        24 ~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      ++.+.+++ .|| .||++|++++|.+++|+|+++.||||||||++++++.+...   .++.+++|++||++|+.|+.+.+
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~---~~g~~aLVl~PTreLa~Qi~~~l  142 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLA---LKGKKCYIILPTTLLVKQTVEKI  142 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH---hcCCeEEEEECHHHHHHHHHHHH
Confidence            44555665 799 69999999999999999999999999999996666555432   24568999999999999999999


Q ss_pred             HHHHhhC-CCeEEEEEECCCchHHhH---HHHhcC-CCeEEEeecCc------cCCCCceEEEEeCCC------------
Q psy1539         103 ERFSKYM-SNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVGLVNYE------TNLSGVVVNVMDVRS------------  159 (175)
Q Consensus       103 ~~~~~~~-~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~l~~~~------~~~~~~~~lVlDEad------------  159 (175)
                      +.+.+.. .++++..++|+.+.+++.   +.+.++ ++|+|++....      ....+++++|+||||            
T Consensus       143 ~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l~~~~i~~iVVDEAD~ml~~~knid~~  222 (1638)
T PRK14701        143 ESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEMKHLKFDFIFVDDVDAFLKASKNIDRS  222 (1638)
T ss_pred             HHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHHhhCCCCEEEEECceeccccccccchh
Confidence            9998765 256778889998876653   345554 78888833321      112579999999996            


Q ss_pred             ---CCCHHHHHH
Q psy1539         160 ---GGWWLDLEA  168 (175)
Q Consensus       160 ---~~f~~~v~~  168 (175)
                         +||.+++..
T Consensus       223 L~llGF~~e~~~  234 (1638)
T PRK14701        223 LQLLGFYEEIIE  234 (1638)
T ss_pred             hhcCCChHHHHH
Confidence               489999875

>TIGR01054 rgy reverse gyrase

Probab=99.86  E-value=7e-21  Score=171.63  Aligned_cols=143  Identities=17%  Similarity=0.174  Sum_probs=107.9

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      ++.+.+.+.....|+++|+.++|.++.|+|++++||||||||. |.+|++..+..  .+++++|++|||+|+.|+.+.++
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~  142 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKIS  142 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHH
Confidence            4455555544447999999999999999999999999999996 66777766543  46799999999999999999999


Q ss_pred             HHHhhCCCeEE---EEEECCCchHHh---HHHHhc-CCCeEEEee----cCccCCC-CceEEEEeCCC------------
Q psy1539         104 RFSKYMSNIKV---GVFFGGLPIQKD---EEYLKT-HNPQIVGLV----NYETNLS-GVVVNVMDVRS------------  159 (175)
Q Consensus       104 ~~~~~~~~i~v---~~~~g~~~~~~~---~~~l~~-~~~iiv~l~----~~~~~~~-~~~~lVlDEad------------  159 (175)
                      ++.... ++.+   ..++|+.+..++   .+.+.+ +++|+|++.    ++...+. +++++|+||||            
T Consensus       143 ~l~~~~-~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~~~~~~iVvDEaD~~L~~~k~vd~i  221 (1171)
T TIGR01054       143 SLAEKA-GVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFVDDVDALLKASKNVDKL  221 (1171)
T ss_pred             HHHHhc-CCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhcCCCCEEEEeChHhhhhccccHHHH
Confidence            998876 5544   356788876554   334554 478999832    2222233 89999999994            


Q ss_pred             ---CCCHHH-HHHHH
Q psy1539         160 ---GGWWLD-LEALI  170 (175)
Q Consensus       160 ---~~f~~~-v~~il  170 (175)
                         +||.++ ++.|+
T Consensus       222 l~llGF~~e~i~~il  236 (1171)
T TIGR01054       222 LKLLGFSEELIEKAW  236 (1171)
T ss_pred             HHHcCCCHHHHHHHH
Confidence               578764 66654

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.85  E-value=2e-20  Score=156.14  Aligned_cols=129  Identities=17%  Similarity=0.146  Sum_probs=99.0

Q ss_pred             hhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC
Q psy1539          30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        30 ~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      ..+||..|+|+|.++|+.+++|+|+++.+|||||||++|.+|++..      +..+||++||++|+.|+.+.++.+    
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~~~l~~~----   74 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQVLQLKAS----   74 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHHHHHHHc----
Confidence            3469999999999999999999999999999999999999999753      237999999999999987777643    


Q ss_pred             CCeEEEEEECCCchHHhHH---HHhcC-CCeEEE----eecC-----cc-CCCCceEEEEeCCCC------CCHHHHHHH
Q psy1539         110 SNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG----LVNY-----ET-NLSGVVVNVMDVRSG------GWWLDLEAL  169 (175)
Q Consensus       110 ~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~----l~~~-----~~-~~~~~~~lVlDEad~------~f~~~v~~i  169 (175)
                       ++.+..+.|+....+...   .+.++ .+++++    +...     .+ ...+++++|+||||.      .|.++...+
T Consensus        75 -gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l  153 (470)
T TIGR00614        75 -GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKAL  153 (470)
T ss_pred             -CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHH
Confidence             777888888776543332   23333 567766    2111     12 567899999999962      477776654

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

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.84  E-value=5.7e-20  Score=165.37  Aligned_cols=132  Identities=20%  Similarity=0.235  Sum_probs=108.2

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      ...+...+++| .||+.|.+||+.++++      +|++++++||+|||.+|+.++...+.   ++.+++|++||++||.|
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~---~g~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE---NHKQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHH
Confidence            33444677778 6999999999999987      89999999999999999888876654   46799999999999999


Q ss_pred             HHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh---c-CCCeEEE---eecCccCCCCceEEEEeCCCC
Q psy1539          98 ISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK---T-HNPQIVG---LVNYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus        98 ~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~---~-~~~iiv~---l~~~~~~~~~~~~lVlDEad~  160 (175)
                      +++.+++....+ ++++..+.|+.+.+++.+.+.   + .++|+|+   +.+....+++++++|+||+|.
T Consensus       665 ~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLVIDEahr  733 (1147)
T PRK10689        665 HYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHR  733 (1147)
T ss_pred             HHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEEEechhh
Confidence            999999877766 788888998887766655443   3 4788998   444456788999999999964

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.83  E-value=1.9e-19  Score=153.95  Aligned_cols=127  Identities=13%  Similarity=0.137  Sum_probs=99.5

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      +||..++|+|.++|+.+++|+|+++++|||+|||++|.+|++..      +..++|++|+++|+.|+.+.++.+     +
T Consensus         9 fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l~~~-----g   77 (591)
T TIGR01389         9 FGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQLRAA-----G   77 (591)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHHHHc-----C
Confidence            69999999999999999999999999999999999999999853      226899999999999988877654     7


Q ss_pred             eEEEEEECCCchHHhHHH---Hhc-CCCeEEE----eecC----ccCCCCceEEEEeCCC------CCCHHHHHHH
Q psy1539         112 IKVGVFFGGLPIQKDEEY---LKT-HNPQIVG----LVNY----ETNLSGVVVNVMDVRS------GGWWLDLEAL  169 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~---l~~-~~~iiv~----l~~~----~~~~~~~~~lVlDEad------~~f~~~v~~i  169 (175)
                      +.+..+.++.+..+..+.   +.+ ..+++++    +...    .....+++++|+||||      ..|.++...+
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            788888888876554332   333 3566665    2221    3456789999999995      3477776655

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.

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

Probab=99.82  E-value=2.4e-19  Score=158.45  Aligned_cols=141  Identities=16%  Similarity=0.112  Sum_probs=106.7

Q ss_pred             cCCCCHHHHHHHhh-CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHH
Q psy1539          18 SRNRREKEDRIGES-QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF   96 (175)
Q Consensus        18 ~~~l~~~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~   96 (175)
                      .++....+...+++ +||..++|+|.++|+.++.|+|+++.+|||+|||+||.+|++..      +..+|||+|+++|++
T Consensus       441 ~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPLiSLmq  514 (1195)
T PLN03137        441 NFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPLVSLIQ  514 (1195)
T ss_pred             CCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCHHHHHH
Confidence            35556666666555 58999999999999999999999999999999999999999864      237999999999998


Q ss_pred             HHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc------CCCeEEE----eecC------c---cCCCCceEEEEeC
Q psy1539          97 QISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT------HNPQIVG----LVNY------E---TNLSGVVVNVMDV  157 (175)
Q Consensus        97 q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~------~~~iiv~----l~~~------~---~~~~~~~~lVlDE  157 (175)
                      ++...+..    . +++...+.|+.+..++.+.+..      ..+++++    +...      .   .....+.++|+||
T Consensus       515 DQV~~L~~----~-GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDE  589 (1195)
T PLN03137        515 DQIMNLLQ----A-NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDE  589 (1195)
T ss_pred             HHHHHHHh----C-CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCc
Confidence            64444432    2 8899999999887766655542      4577777    2211      1   1224589999999


Q ss_pred             CC----C--CCHHHHHHH
Q psy1539         158 RS----G--GWWLDLEAL  169 (175)
Q Consensus       158 ad----~--~f~~~v~~i  169 (175)
                      ||    .  .|+++.+.+
T Consensus       590 AHcVSqWGhDFRpdYr~L  607 (1195)
T PLN03137        590 AHCVSQWGHDFRPDYQGL  607 (1195)
T ss_pred             chhhhhcccchHHHHHHH
Confidence            95    3  488888764

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.82  E-value=3.5e-19  Score=152.61  Aligned_cols=138  Identities=14%  Similarity=0.076  Sum_probs=101.2

Q ss_pred             CCHHHHHHHhh-CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          21 RREKEDRIGES-QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        21 l~~~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      ..+...+.|++ +||..|+|+|.++++.+++|+|+++.+|||+|||++|.+|++..      ...++|++|+++|+.|+.
T Consensus         9 ~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dqv   82 (607)
T PRK11057          9 LESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQV   82 (607)
T ss_pred             chhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHHH
Confidence            33344444444 59999999999999999999999999999999999999999854      226899999999999988


Q ss_pred             HHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE----eecC----ccCCCCceEEEEeCCC------CC
Q psy1539         100 KEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG----LVNY----ETNLSGVVVNVMDVRS------GG  161 (175)
Q Consensus       100 ~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~----l~~~----~~~~~~~~~lVlDEad------~~  161 (175)
                      +.++.+     ++.+..+.++.+..+...   .+.++ .+++++    +...    .+...+++++|+||||      ..
T Consensus        83 ~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~  157 (607)
T PRK11057         83 DQLLAN-----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHD  157 (607)
T ss_pred             HHHHHc-----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCc
Confidence            877654     677777777776554433   23333 355555    2211    2334579999999996      34


Q ss_pred             CHHHHHHH
Q psy1539         162 WWLDLEAL  169 (175)
Q Consensus       162 f~~~v~~i  169 (175)
                      |.+++..+
T Consensus       158 fr~~y~~L  165 (607)
T PRK11057        158 FRPEYAAL  165 (607)
T ss_pred             ccHHHHHH
Confidence            77776544

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.80  E-value=1e-18  Score=148.63  Aligned_cols=99  Identities=16%  Similarity=0.048  Sum_probs=87.8

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .|. .|+++|..++|.+++|+  +..+.||+|||++|.+|++....   .+.+++|++||++||.|.++++..+.+.+ +
T Consensus       100 lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al---~G~~v~VvTptreLA~qdae~~~~l~~~l-G  172 (656)
T PRK12898        100 LGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL---AGLPVHVITVNDYLAERDAELMRPLYEAL-G  172 (656)
T ss_pred             hCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh---cCCeEEEEcCcHHHHHHHHHHHHHHHhhc-C
Confidence            344 68999999999999999  99999999999999999998765   45689999999999999999999999988 9


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEE
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVG  139 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~  139 (175)
                      +++++++||.+.  +.+....+++|+++
T Consensus       173 lsv~~i~gg~~~--~~r~~~y~~dIvyg  198 (656)
T PRK12898        173 LTVGCVVEDQSP--DERRAAYGADITYC  198 (656)
T ss_pred             CEEEEEeCCCCH--HHHHHHcCCCEEEE
Confidence            999999999863  34555567899998

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.78  E-value=2e-18  Score=150.10  Aligned_cols=135  Identities=23%  Similarity=0.270  Sum_probs=110.5

Q ss_pred             cCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHh-cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHH
Q psy1539          18 SRNRREKEDRIGESQPFREQTSFQHECIPQAV-LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF   96 (175)
Q Consensus        18 ~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~-~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~   96 (175)
                      ...+.+.+.+.+...|+..+.+.|+.++.... +|+|+++++|||||||+.+++.+++.+...  +.+++|+||+|+||.
T Consensus        13 ~~~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~   90 (766)
T COG1204          13 KVKLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAE   90 (766)
T ss_pred             cccccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHH
Confidence            34578899999999999888888888886555 569999999999999999999999998763  568999999999999


Q ss_pred             HHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eecC-ccCCCCceEEEEeCCC
Q psy1539          97 QISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVNY-ETNLSGVVVNVMDVRS  159 (175)
Q Consensus        97 q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~-~~~~~~~~~lVlDEad  159 (175)
                      |.++.++++ +.+ |++|...+|+.....  +.+ .+++|||+       +.++ ......++++|+||++
T Consensus        91 Ek~~~~~~~-~~~-GirV~~~TgD~~~~~--~~l-~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH  156 (766)
T COG1204          91 EKYEEFSRL-EEL-GIRVGISTGDYDLDD--ERL-ARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIH  156 (766)
T ss_pred             HHHHHhhhH-Hhc-CCEEEEecCCcccch--hhh-ccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeee
Confidence            999999955 445 999999999987433  233 35799998       3333 4466799999999994

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.76  E-value=9.2e-18  Score=141.07  Aligned_cols=129  Identities=14%  Similarity=0.130  Sum_probs=97.3

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      ...|+++|.+|++.++.+++.++++|||+|||+++...+ ..... ....++||++||++|+.|+.+.++++.... ...
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~-~~~~~-~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~-~~~  188 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLS-RYYLE-NYEGKVLIIVPTTSLVTQMIDDFVDYRLFP-REA  188 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHH-HHHHh-cCCCeEEEEECcHHHHHHHHHHHHHhcccc-ccc
Confidence            357999999999999999999999999999998764422 22222 233489999999999999999999887543 445


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      +..+.||....       .+.+++|++.+.     ...+++++++|+||||.....+++.++..
T Consensus       189 ~~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~~~~~~~~~iIvDEaH~~~~~~~~~il~~  245 (501)
T PHA02558        189 MHKIYSGTAKD-------TDAPIVVSTWQSAVKQPKEWFDQFGMVIVDECHLFTGKSLTSIITK  245 (501)
T ss_pred             eeEEecCcccC-------CCCCEEEeeHHHHhhchhhhccccCEEEEEchhcccchhHHHHHHh
Confidence            55566665422       346888884443     23468999999999988777888887754

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.76  E-value=2.9e-17  Score=142.14  Aligned_cols=121  Identities=17%  Similarity=0.183  Sum_probs=96.4

Q ss_pred             CCcHHHHHhHHHHhcC---CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          36 EQTSFQHECIPQAVLG---MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g---~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      .+|+.|+++++.+.++   +++++.++||||||.+|+.++...+..   +.++|+++||++|+.|+.+.+++.   + +.
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---g~~vLvLvPt~~L~~Q~~~~l~~~---f-g~  216 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---GKQALVLVPEIALTPQMLARFRAR---F-GA  216 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHH---h-CC
Confidence            5899999999999874   889999999999999999888776653   458999999999999998888764   3 67


Q ss_pred             EEEEEECCCchHHhHHH---Hhc-CCCeEEEeecC-ccCCCCceEEEEeCC-CCCCH
Q psy1539         113 KVGVFFGGLPIQKDEEY---LKT-HNPQIVGLVNY-ETNLSGVVVNVMDVR-SGGWW  163 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~---l~~-~~~iiv~l~~~-~~~~~~~~~lVlDEa-d~~f~  163 (175)
                      ++..++|+.+..+..+.   +.+ ..+++|++... ...+++++++|+||+ +.+|.
T Consensus       217 ~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~~p~~~l~liVvDEeh~~s~~  273 (679)
T PRK05580        217 PVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDEEHDSSYK  273 (679)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhcccccCCCEEEEECCCccccc
Confidence            89999999876554433   333 46888885443 456889999999999 44444

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

Probab=99.75  E-value=5e-18  Score=140.04  Aligned_cols=145  Identities=21%  Similarity=0.214  Sum_probs=121.1

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHH-HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQ-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~-~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      .+--..+++++++++.+.|+..|++.+.|+|..|+.. +++|+|.+|.++|+||||+...++-+.++..  .+.+.|+++
T Consensus       191 ~~r~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~--~g~KmlfLv  268 (830)
T COG1202         191 VERVPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS--GGKKMLFLV  268 (830)
T ss_pred             cccccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh--CCCeEEEEe
Confidence            3334577899999999999999999999999999975 5689999999999999999999999988875  455899999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH----HHhcCCCeEEE-------eecCccCCCCceEEEEeCC
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE----YLKTHNPQIVG-------LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~----~l~~~~~iiv~-------l~~~~~~~~~~~~lVlDEa  158 (175)
                      |..+||+|.++.|++-.... ++++..-+|-...+...+    .-...++||||       +++...++.++..+|+||.
T Consensus       269 PLVALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEi  347 (830)
T COG1202         269 PLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEI  347 (830)
T ss_pred             hhHHhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcCCcccccceEEeeee
Confidence            99999999999998877777 888888888765544322    11235799999       4444678899999999999

>KOG0349|consensus

Probab=99.74  E-value=2.4e-18  Score=138.07  Aligned_cols=87  Identities=20%  Similarity=0.211  Sum_probs=72.5

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhC--CCeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------CccCCCCceE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYM--SNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------YETNLSGVVV  152 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~--~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~~~~~~~~~~  152 (175)
                      ++++|+-|+|||++|.++++++|..+.  |.++..++.||.....|...+.+|.+|+|+...        ....+.++++
T Consensus       287 p~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crF  366 (725)
T KOG0349|consen  287 PEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRF  366 (725)
T ss_pred             cceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEE
Confidence            789999999999999999999987765  677888999999889999999999999999222        2567889999


Q ss_pred             EEEeCCC----CCCHHHHHHH
Q psy1539         153 NVMDVRS----GGWWLDLEAL  169 (175)
Q Consensus       153 lVlDEad----~~f~~~v~~i  169 (175)
                      +|+||||    .++-+-|+..
T Consensus       367 lvlDead~lL~qgy~d~I~r~  387 (725)
T KOG0349|consen  367 LVLDEADLLLGQGYDDKIYRF  387 (725)
T ss_pred             EEecchhhhhhcccHHHHHHH
Confidence            9999995    4555555543

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.73  E-value=3.9e-17  Score=141.64  Aligned_cols=125  Identities=12%  Similarity=0.082  Sum_probs=102.7

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          33 PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      |. .|+++|..+++.+.+|+  +..+.||+|||++|.+|++....   .|.+++|++||++||.|.++++..+.+.+ |+
T Consensus        76 g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al---~G~~v~VvTpt~~LA~qd~e~~~~l~~~l-Gl  148 (790)
T PRK09200         76 GM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL---EGKGVHLITVNDYLAKRDAEEMGQVYEFL-GL  148 (790)
T ss_pred             CC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHH---cCCCeEEEeCCHHHHHHHHHHHHHHHhhc-CC
Confidence            55 79999999999998887  99999999999999999986655   45689999999999999999999999998 99


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEEe---------ecC------ccCCCCceEEEEeCCCCCCHHH
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVGL---------VNY------ETNLSGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~l---------~~~------~~~~~~~~~lVlDEad~~f~~~  165 (175)
                      +++++.|+.+..++.+.. .+++|++++         .++      ....+++.++|+||||..+.++
T Consensus       149 ~v~~i~g~~~~~~~r~~~-y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDe  215 (790)
T PRK09200        149 TVGLNFSDIDDASEKKAI-YEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDE  215 (790)
T ss_pred             eEEEEeCCCCcHHHHHHh-cCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceecc
Confidence            999999998743343333 458999992         222      1355789999999998665554

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.73  E-value=4.4e-17  Score=139.79  Aligned_cols=128  Identities=16%  Similarity=0.099  Sum_probs=104.0

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          33 PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      |. .|+++|..+.+.+.+|+  +..++||+|||++|.+|++-....   +.++.|++||++||.|..+++.++.+.+ ++
T Consensus        54 g~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~VvTpt~~LA~qdae~~~~l~~~L-GL  126 (745)
T TIGR00963        54 GM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAEWMGQVYRFL-GL  126 (745)
T ss_pred             CC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh---CCCEEEEcCCHHHHHHHHHHHHHHhccC-CC
Confidence            54 68999999999888887  999999999999999999644332   3469999999999999999999999998 99


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEEeecC---------------ccCCCCceEEEEeCCCCCCHHHHHHH
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY---------------ETNLSGVVVNVMDVRSGGWWLDLEAL  169 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~---------------~~~~~~~~~lVlDEad~~f~~~v~~i  169 (175)
                      ++++++|+.+..+.....  .++|++|+...               ...++++.++|+||+|..+.++-+.-
T Consensus       127 sv~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtp  196 (745)
T TIGR00963       127 SVGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTP  196 (745)
T ss_pred             eEEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhH
Confidence            999999998865444444  47999992221               34678999999999987777555543

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.

>KOG0952|consensus

Probab=99.72  E-value=2.9e-17  Score=142.48  Aligned_cols=124  Identities=21%  Similarity=0.294  Sum_probs=101.9

Q ss_pred             CCCCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhhc-------CCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          32 QPFREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLET-------TDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~~-------~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      ++|..++.+|++++|.+++ +.|.+||||||||||..|++.+++.+..       ..++.+++||+|+++||.++.+.+.
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            4678899999999999986 5899999999999999999999998864       2567899999999999988777776


Q ss_pred             HHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eecC----ccCCCCceEEEEeCCC
Q psy1539         104 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVNY----ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       104 ~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~----~~~~~~~~~lVlDEad  159 (175)
                      +-+... |++|..++|+....+..  + ..+++||.       +.++    ...++.++++|+||++
T Consensus       186 kkl~~~-gi~v~ELTGD~ql~~te--i-~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVH  248 (1230)
T KOG0952|consen  186 KKLAPL-GISVRELTGDTQLTKTE--I-ADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVH  248 (1230)
T ss_pred             hhcccc-cceEEEecCcchhhHHH--H-HhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeeh
Confidence            665555 99999999998765443  3 24799998       2222    4567899999999993

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.72  E-value=5.2e-16  Score=113.69  Aligned_cols=139  Identities=27%  Similarity=0.356  Sum_probs=105.9

Q ss_pred             hCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC
Q psy1539          31 SQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      ..++..++++|.++++.+.++ +++++.++||+|||.++..+++..+.... ..++++++|+++++.|+.+.+..+....
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            346778999999999999999 99999999999999999999988876532 3479999999999999999988887654


Q ss_pred             CCeEEEEEECCCchHHhHHHHhcCC-CeEEEeec----C----ccCCCCceEEEEeCCCC----CCHHHHHHHHh
Q psy1539         110 SNIKVGVFFGGLPIQKDEEYLKTHN-PQIVGLVN----Y----ETNLSGVVVNVMDVRSG----GWWLDLEALIL  171 (175)
Q Consensus       110 ~~i~v~~~~g~~~~~~~~~~l~~~~-~iiv~l~~----~----~~~~~~~~~lVlDEad~----~f~~~v~~il~  171 (175)
                       ........++....+....+.++. +++++..+    .    .....+++++|+||++.    .+...+..++.
T Consensus        82 -~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~  155 (201)
T smart00487       82 -GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLK  155 (201)
T ss_pred             -CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHH
Confidence             323444455555455666666666 77777221    1    24556788999999953    66677777765

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.70  E-value=1.6e-16  Score=136.63  Aligned_cols=122  Identities=10%  Similarity=0.101  Sum_probs=92.6

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHH---------HHHHHHHhhh---cCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAV---------FVLATLQQLE---TTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~---------~~~~~l~~l~---~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      ..+|.++++.+++|++++++|+||||||.+         |++|.+..+.   ....+.++++++|||+||.|+...+.+.
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            348999999999999999999999999987         5556665543   2334568999999999999999988776


Q ss_pred             Hhh--CCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC-ccCCCCceEEEEeCCCC
Q psy1539         106 SKY--MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY-ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       106 ~~~--~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-~~~~~~~~~lVlDEad~  160 (175)
                      ...  +.+..+...+||.+ +.......++.++++++..- ...+++++++|+||||.
T Consensus       246 vg~~~~~g~~v~v~~Gg~~-~~~~~t~~k~~~Ilv~T~~L~l~~L~~v~~VVIDEaHE  302 (675)
T PHA02653        246 LGFDEIDGSPISLKYGSIP-DELINTNPKPYGLVFSTHKLTLNKLFDYGTVIIDEVHE  302 (675)
T ss_pred             hCccccCCceEEEEECCcc-hHHhhcccCCCCEEEEeCcccccccccCCEEEcccccc
Confidence            544  34677888999987 23223333356788884332 33688999999999963

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.70  E-value=1.4e-16  Score=145.32  Aligned_cols=104  Identities=20%  Similarity=0.284  Sum_probs=84.7

Q ss_pred             EEcCCCChHHHHHHHHHHHhhhcC----------CCCeEEEEEecCHHHHHHHHHHHHHHHh-----------hCCCeEE
Q psy1539          56 CQAKSGMGKTAVFVLATLQQLETT----------DSNVYVLVMCHTRELAFQISKEYERFSK-----------YMSNIKV  114 (175)
Q Consensus        56 i~a~TGsGKT~~~~~~~l~~l~~~----------~~~~~~lil~Pt~~L~~q~~~~~~~~~~-----------~~~~i~v  114 (175)
                      |+||||||||++|.+|++.++...          .++.++|||+|+++|+.|+.+.++....           ...++++
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            579999999999999999988642          2467999999999999999998875221           1237899


Q ss_pred             EEEECCCchHHhHHHHhcCCCeEEE-------e-ecC-ccCCCCceEEEEeCCC
Q psy1539         115 GVFFGGLPIQKDEEYLKTHNPQIVG-------L-VNY-ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       115 ~~~~g~~~~~~~~~~l~~~~~iiv~-------l-~~~-~~~~~~~~~lVlDEad  159 (175)
                      ..++|+.+.+++.+.+++.++|||+       + .++ ...+++++++|+||+|
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H  134 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVH  134 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHH
Confidence            9999999988877778878899998       2 222 3468999999999995

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.69  E-value=3.2e-16  Score=135.20  Aligned_cols=123  Identities=13%  Similarity=0.015  Sum_probs=91.8

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|......+.+|  .++.++||+|||++|.+|++.....   +..++|++|+++||.|..+++..+.+.+ |+++.
T Consensus        70 rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~---g~~V~VVTpn~yLA~Rdae~m~~l~~~L-GLsv~  143 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKRDAEEMGPVYEWL-GLTVS  143 (762)
T ss_pred             CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc---CCceEEeCCCHHHHHHHHHHHHHHHhhc-CCcEE
Confidence            4455555555444444  7999999999999999998766553   4469999999999999999999999998 99999


Q ss_pred             EEECCCc---hHHhHHHHhcCCCeEEEeecC---------------ccCCCCceEEEEeCCCCCCHH
Q psy1539         116 VFFGGLP---IQKDEEYLKTHNPQIVGLVNY---------------ETNLSGVVVNVMDVRSGGWWL  164 (175)
Q Consensus       116 ~~~g~~~---~~~~~~~l~~~~~iiv~l~~~---------------~~~~~~~~~lVlDEad~~f~~  164 (175)
                      .++++..   ...+.+....+++|++++...               ...++++.++|+||||..+.+
T Consensus       144 ~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiD  210 (762)
T TIGR03714       144 LGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLD  210 (762)
T ss_pred             EEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhc
Confidence            8877622   233444555679999992221               234678999999999754443

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.65  E-value=2.6e-15  Score=132.14  Aligned_cols=122  Identities=23%  Similarity=0.267  Sum_probs=97.1

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      ...++++|.++...++.+ |.++++|||+|||+++++++...+..  .+.++||++||++|+.|+.+.++++.... +.+
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~--~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~-~~~   88 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK--KGGKVLILAPTKPLVEQHAEFFRKFLNIP-EEK   88 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh--CCCeEEEEeCcHHHHHHHHHHHHHHhCCC-Cce
Confidence            447899999999888887 99999999999999999999887742  44589999999999999999998876432 457


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCCC
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad~  160 (175)
                      +..+.|+.+..+.. .+..+.++++++        ......+.+++++|+|||+.
T Consensus        89 v~~~~g~~~~~~r~-~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~  142 (773)
T PRK13766         89 IVVFTGEVSPEKRA-ELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHR  142 (773)
T ss_pred             EEEEeCCCCHHHHH-HHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcc
Confidence            88888888755443 344456888882        23356778999999999963

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

Probab=99.65  E-value=2.7e-15  Score=122.37  Aligned_cols=136  Identities=17%  Similarity=0.207  Sum_probs=110.9

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      ...++.+|.......+.+ |.+++.|||-|||+.+++-+..++...+ + ++|+++||+.|+.|+...++++..- |.-.
T Consensus        13 ~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~-~-kvlfLAPTKPLV~Qh~~~~~~v~~i-p~~~   88 (542)
T COG1111          13 TIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFG-G-KVLFLAPTKPLVLQHAEFCRKVTGI-PEDE   88 (542)
T ss_pred             cccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcC-C-eEEEecCCchHHHHHHHHHHHHhCC-Chhh
Confidence            346788888887766666 9999999999999999998888877643 3 8999999999999999999998754 3668


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC-----CCCCHHHHHHHHhhhc
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR-----SGGWWLDLEALILSKC  174 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa-----d~~f~~~v~~il~~~~  174 (175)
                      ++.++|..+.++....+.+ ..++++        +..+.+++.++.++|+|||     ++.|..=.+..+.+++
T Consensus        89 i~~ltGev~p~~R~~~w~~-~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k  161 (542)
T COG1111          89 IAALTGEVRPEEREELWAK-KKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAK  161 (542)
T ss_pred             eeeecCCCChHHHHHHHhh-CCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhcc
Confidence            8899999998777777776 488888        5555899999999999999     4667666666666543

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.63  E-value=2.2e-15  Score=131.28  Aligned_cols=122  Identities=15%  Similarity=0.125  Sum_probs=94.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|.++|...--.+.  ..-+..++||+|||++|.+|++.....   +..++|++||++||.|..+++..+.+.+ ++++.
T Consensus        82 ~~ydvQliGg~~Lh--~G~Iaem~TGeGKTL~a~Lpa~~~al~---G~~V~VvTpn~yLA~qd~e~m~~l~~~l-GLtv~  155 (896)
T PRK13104         82 RHFDVQLIGGMVLH--EGNIAEMRTGEGKTLVATLPAYLNAIS---GRGVHIVTVNDYLAKRDSQWMKPIYEFL-GLTVG  155 (896)
T ss_pred             CcchHHHhhhhhhc--cCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEcCCHHHHHHHHHHHHHHhccc-CceEE
Confidence            45666655444443  444889999999999999999977654   3469999999999999999999999988 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE----e----ecCc--cCC-----CCceEEEEeCCCCCCHHH
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG----L----VNYE--TNL-----SGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~----l----~~~~--~~~-----~~~~~lVlDEad~~f~~~  165 (175)
                      +++||.+..+....+  .++|++|    +    ++..  .++     +.+.++|+||||..+.++
T Consensus       156 ~i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDe  218 (896)
T PRK13104        156 VIYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDE  218 (896)
T ss_pred             EEeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhc
Confidence            999998866655544  5799999    2    2222  223     589999999997655544

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

Probab=99.62  E-value=7.3e-15  Score=123.87  Aligned_cols=136  Identities=24%  Similarity=0.268  Sum_probs=115.3

Q ss_pred             CCCCHHHHHH-HhhCCCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          19 RNRREKEDRI-GESQPFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        19 ~~l~~~l~~~-l~~~g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ++...++++. +..+.| ++|..|++++..|...      .+.++++.-|||||++++++++..+.   .|.|+..++||
T Consensus       245 ~~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~---~G~Q~ALMAPT  320 (677)
T COG1200         245 LPANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE---AGYQAALMAPT  320 (677)
T ss_pred             CCccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHH---cCCeeEEeccH
Confidence            3444555555 567777 6999999999999864      68899999999999999999998876   56699999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchH---HhHHHHhcC-CCeEEE---eecCccCCCCceEEEEeCCC
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ---KDEEYLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~---~~~~~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad  159 (175)
                      .-||.|.++.+.++...+ ++++..++|....+   +..+.+.+| .+++||   |.+....|.++.++|+||-+
T Consensus       321 EILA~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVIiDEQH  394 (677)
T COG1200         321 EILAEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVIIDEQH  394 (677)
T ss_pred             HHHHHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEEEeccc
Confidence            999999999999999998 99999999987644   344566677 788998   88889999999999999984

>KOG0354|consensus

Probab=99.60  E-value=1.2e-14  Score=124.14  Aligned_cols=134  Identities=17%  Similarity=0.120  Sum_probs=96.8

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      +.+.......=-..-.++.+|.+.....+ |+|++|++|||+|||.+++..+.+++...++ .++++++||+-|+.|+..
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a  124 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIA  124 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHH
Confidence            34444333322233468999999998888 9999999999999999999999999887554 599999999999999887


Q ss_pred             HHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecC-ccCCCCceEEEEeCCC
Q psy1539         101 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNY-ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       101 ~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~-~~~~~~~~~lVlDEad  159 (175)
                      .+..++..   -++....||.........+-...++++.        |.+. ...++.+.++|+|||+
T Consensus       125 ~~~~~~~~---~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~H  189 (746)
T KOG0354|consen  125 CFSIYLIP---YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECH  189 (746)
T ss_pred             HHhhccCc---ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccc
Confidence            77766643   3444455554333333344455788887        2222 2236899999999994

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.59  E-value=1.5e-14  Score=116.96  Aligned_cols=75  Identities=15%  Similarity=0.148  Sum_probs=62.9

Q ss_pred             HHHHhHHHHhcCCc--EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC---CCeEE
Q psy1539          40 FQHECIPQAVLGMD--ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM---SNIKV  114 (175)
Q Consensus        40 ~Q~~~i~~~~~g~~--~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~---~~i~v  114 (175)
                      +|.++++.+.++.+  +++++|||||||.+|++|++..      ..++++++|+++|++|+++.++++...+   .+..+
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            59999999999864  8899999999999999999852      2368999999999999999999987544   25667


Q ss_pred             EEEECC
Q psy1539         115 GVFFGG  120 (175)
Q Consensus       115 ~~~~g~  120 (175)
                      ..+.|.
T Consensus        75 ~~~~g~   80 (357)
T TIGR03158        75 LHVSKA   80 (357)
T ss_pred             EEecCC
Confidence            777775

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.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=1e-13  Score=120.60  Aligned_cols=122  Identities=18%  Similarity=0.142  Sum_probs=96.1

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|-...-.+.+|+  +..+.||+|||+++.+|++-....   +.++-|++||..||.|..+++..+.+.+ |++++
T Consensus        81 ~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~IvTpn~yLA~rd~e~~~~l~~~L-Glsv~  154 (830)
T PRK12904         81 RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT---GKGVHVVTVNDYLAKRDAEWMGPLYEFL-GLSVG  154 (830)
T ss_pred             CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc---CCCEEEEecCHHHHHHHHHHHHHHHhhc-CCeEE
Confidence            57888888776666664  899999999999999999633332   2257799999999999999999999998 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE----e----ecCc-------cCCCCceEEEEeCCCCCCHHH
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG----L----VNYE-------TNLSGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~----l----~~~~-------~~~~~~~~lVlDEad~~f~~~  165 (175)
                      +++|+.+..++.+.+  .++|+++    +    ++..       ...+.+.++|+||||....++
T Consensus       155 ~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDe  217 (830)
T PRK12904        155 VILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDE  217 (830)
T ss_pred             EEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheecc
Confidence            999999877666665  3799998    1    1111       346789999999997554443

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.49  E-value=3.6e-13  Score=118.50  Aligned_cols=109  Identities=18%  Similarity=0.169  Sum_probs=81.7

Q ss_pred             HHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH-HhhCCCeEEEEEECC
Q psy1539          42 HECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF-SKYMSNIKVGVFFGG  120 (175)
Q Consensus        42 ~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~-~~~~~~i~v~~~~g~  120 (175)
                      .+.+..+.++++++++|+||||||++|.+++++....   ..+++++.|||++|.|+.+.+.+. .... +..++..+++
T Consensus        11 ~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~-g~~VGy~vr~   86 (812)
T PRK11664         11 PELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKP-GETVGYRMRA   86 (812)
T ss_pred             HHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCccc-CceEEEEecC
Confidence            3445566678999999999999999999999976432   248999999999999999988554 3434 7778877776


Q ss_pred             CchHHhHHHHhcCCCeEEE-------eecCccCCCCceEEEEeCCCC
Q psy1539         121 LPIQKDEEYLKTHNPQIVG-------LVNYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       121 ~~~~~~~~~l~~~~~iiv~-------l~~~~~~~~~~~~lVlDEad~  160 (175)
                      .+...      +...++|+       +......+++++++|+||+|.
T Consensus        87 ~~~~~------~~t~I~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHE  127 (812)
T PRK11664         87 ESKVG------PNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHE  127 (812)
T ss_pred             ccccC------CCCcEEEEChhHHHHHHhhCCCcCcCcEEEEcCCCc
Confidence            54221      23467777       222245789999999999974

>TIGR00595 priA primosomal protein N'

Probab=99.49  E-value=2.2e-13  Score=114.58  Aligned_cols=102  Identities=20%  Similarity=0.210  Sum_probs=74.6

Q ss_pred             EEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHh
Q psy1539          55 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLK  131 (175)
Q Consensus        55 ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~  131 (175)
                      ++.++||||||.+|+..+...+.   .+.++||++|+++|+.|+.+.+++..    +.++..++|+.+..+..+   .+.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~---~g~~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er~~~~~~~~   73 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLA---LGKSVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEKLQAWRKVK   73 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHHHHHHHHHH
Confidence            46899999999999766555543   34589999999999999988887643    567888999887554433   333


Q ss_pred             cC-CCeEEEeecC-ccCCCCceEEEEeCC-CCCCH
Q psy1539         132 TH-NPQIVGLVNY-ETNLSGVVVNVMDVR-SGGWW  163 (175)
Q Consensus       132 ~~-~~iiv~l~~~-~~~~~~~~~lVlDEa-d~~f~  163 (175)
                      ++ .++|||+... ...+++++++|+||. |.+|.
T Consensus        74 ~g~~~IVVGTrsalf~p~~~l~lIIVDEeh~~syk  108 (505)
T TIGR00595        74 NGEILVVIGTRSALFLPFKNLGLIIVDEEHDSSYK  108 (505)
T ss_pred             cCCCCEEECChHHHcCcccCCCEEEEECCCccccc
Confidence            33 5788874333 346889999999999 34443

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).

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.47  E-value=1.1e-12  Score=90.69  Aligned_cols=106  Identities=30%  Similarity=0.412  Sum_probs=79.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  131 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~  131 (175)
                      +++++.+|||+|||..++..+...... ....++++++|++.++.|..+.+......  +..+..+.++...........
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~-~~~~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~   77 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS-LKGGQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQEKLLS   77 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc-ccCCCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhHHHHHhc
Confidence            478999999999999988888777654 23458999999999999999988887653  466777777766555544555


Q ss_pred             cCCCeEEEeecC--------ccCCCCceEEEEeCCCC
Q psy1539         132 THNPQIVGLVNY--------ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       132 ~~~~iiv~l~~~--------~~~~~~~~~lVlDEad~  160 (175)
                      .+.+++++..+.        ........++|+||++.
T Consensus        78 ~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~  114 (144)
T cd00046          78 GKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHR  114 (144)
T ss_pred             CCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHH
Confidence            667888872222        22345789999999953

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

>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=99.47  E-value=3.4e-13  Score=98.34  Aligned_cols=130  Identities=17%  Similarity=0.105  Sum_probs=82.3

Q ss_pred             CCcHHHHHhHHHHhc-------CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          36 EQTSFQHECIPQAVL-------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~-------g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      +++++|.+++..+.+       .+++++.+|||||||.+++..+.....      ++++++|+..|+.|..+.+..+...
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            579999999988874       589999999999999988754544432      8999999999999999999766544


Q ss_pred             CCCeEEE----------EEECCCchHHhHHHHhcCCCeEEEeecC-------------------ccCCCCceEEEEeCCC
Q psy1539         109 MSNIKVG----------VFFGGLPIQKDEEYLKTHNPQIVGLVNY-------------------ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       109 ~~~i~v~----------~~~g~~~~~~~~~~l~~~~~iiv~l~~~-------------------~~~~~~~~~lVlDEad  159 (175)
                      .......          ..............-.....+++...+.                   ........++|+|||+
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            2111000          0011111111122223344556551111                   1233467899999998


Q ss_pred             CCCHHH-HHHHHh
Q psy1539         160 GGWWLD-LEALIL  171 (175)
Q Consensus       160 ~~f~~~-v~~il~  171 (175)
                      ...... .+.|+.
T Consensus       157 ~~~~~~~~~~i~~  169 (184)
T PF04851_consen  157 HYPSDSSYREIIE  169 (184)
T ss_dssp             CTHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHc
Confidence            777766 666654

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 ....

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.46  E-value=9.3e-13  Score=115.88  Aligned_cols=108  Identities=17%  Similarity=0.131  Sum_probs=80.7

Q ss_pred             HHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH-HhhCCCeEEEEEECC
Q psy1539          42 HECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF-SKYMSNIKVGVFFGG  120 (175)
Q Consensus        42 ~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~-~~~~~~i~v~~~~g~  120 (175)
                      .+.+..+.++.+++++|+||||||.+|.+++++...   .+.+++++.|+|++|.|+.+.+.+. .... +..++..+++
T Consensus         8 ~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~-g~~VGy~vr~   83 (819)
T TIGR01970         8 PALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAV-GQTVGYRVRG   83 (819)
T ss_pred             HHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCc-CcEEEEEEcc
Confidence            344566667899999999999999999999998763   3458999999999999999987544 3333 6667666555


Q ss_pred             CchHHhHHHHhcCCCeEEE----e---ecCccCCCCceEEEEeCCC
Q psy1539         121 LPIQKDEEYLKTHNPQIVG----L---VNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       121 ~~~~~~~~~l~~~~~iiv~----l---~~~~~~~~~~~~lVlDEad  159 (175)
                      .+.      ..++..|+++    +   +.....+++++++|+||+|
T Consensus        84 ~~~------~s~~t~I~v~T~G~Llr~l~~d~~L~~v~~VIiDEaH  123 (819)
T TIGR01970        84 ENK------VSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFH  123 (819)
T ss_pred             ccc------cCCCCcEEEECCcHHHHHHhhCcccccCCEEEEeccc
Confidence            431      2234577777    2   2224568999999999997

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.45  E-value=7.3e-13  Score=106.97  Aligned_cols=53  Identities=19%  Similarity=0.258  Sum_probs=46.9

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      ++++.+|||||||.+|++|++..+.. ..+.+++|++|+++|+.|+++.+..+.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~-~~~~~ii~v~P~~~L~~q~~~~l~~~f   53 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS-QKADRVIIALPTRATINAMYRRAKELF   53 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh-CCCCeEEEEeehHHHHHHHHHHHHHHh
Confidence            58999999999999999999988654 345689999999999999999998875

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.

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

Probab=99.43  E-value=1.8e-12  Score=107.61  Aligned_cols=120  Identities=21%  Similarity=0.177  Sum_probs=83.2

Q ss_pred             CCcHHHHHhHHHHhc----CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQAVL----GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~----g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .++++|++|+..+.+    ++..+++.|||+|||..++..+... ..     .+|||||+++|+.|+.+.+.+....  .
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~-~~-----~~Lvlv~~~~L~~Qw~~~~~~~~~~--~  107 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL-KR-----STLVLVPTKELLDQWAEALKKFLLL--N  107 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh-cC-----CEEEEECcHHHHHHHHHHHHHhcCC--c
Confidence            589999999999998    8999999999999998876655443 21     3999999999999998766665432  2


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEEeecC--------ccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY--------ETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~--------~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      ..++.+.|+.. ...     . ..+.|+..+.        .+...+..++|+||++..-.+..+.++
T Consensus       108 ~~~g~~~~~~~-~~~-----~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~  167 (442)
T COG1061         108 DEIGIYGGGEK-ELE-----P-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRIL  167 (442)
T ss_pred             cccceecCcee-ccC-----C-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHH
Confidence            23444444432 111     0 2477772222        223336999999999877665554443

>KOG0352|consensus

Probab=99.43  E-value=6.1e-13  Score=107.07  Aligned_cols=134  Identities=16%  Similarity=0.136  Sum_probs=95.2

Q ss_pred             HHHHHHhhC-CCCCC-cHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          24 KEDRIGESQ-PFREQ-TSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        24 ~l~~~l~~~-g~~~~-t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      .+.++|++. |+.++ ++.|..|+..+..+ +|+.|+.|||+||++||-+|.|-+     ++ ..|++.|..+|.+.+.+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-----~g-ITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-----GG-ITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-----CC-eEEEehHHHHHHHHHHH
Confidence            445555554 55543 89999999988876 899999999999999999999865     33 78999999999998888


Q ss_pred             HHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC---CCeEEE------------eecCccCCCCceEEEEeCC----
Q psy1539         101 EYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH---NPQIVG------------LVNYETNLSGVVVNVMDVR----  158 (175)
Q Consensus       101 ~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~---~~iiv~------------l~~~~~~~~~~~~lVlDEa----  158 (175)
                      .+.++     .+.+..+.+..+..+..+   .|...   ..++..            +++...+-..++++|+|||    
T Consensus        80 HL~~L-----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVS  154 (641)
T KOG0352|consen   80 HLKRL-----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVS  154 (641)
T ss_pred             HHHhc-----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHh
Confidence            87766     455555656555444333   22222   223333            4444555668999999999    


Q ss_pred             --CCCCHHHHHH
Q psy1539         159 --SGGWWLDLEA  168 (175)
Q Consensus       159 --d~~f~~~v~~  168 (175)
                        ...|++|.-.
T Consensus       155 QWGHDFRPDYL~  166 (641)
T KOG0352|consen  155 QWGHDFRPDYLT  166 (641)
T ss_pred             hhccccCcchhh
Confidence              4567777543

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

Probab=99.42  E-value=1.2e-12  Score=115.61  Aligned_cols=118  Identities=25%  Similarity=0.243  Sum_probs=94.7

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      -...+| .+.++|++|+-.+.+|.+++++||||||||+...+++...+..   +.+++|.+|.++|.+|.++.+......
T Consensus       113 ~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~---~qrviYTsPIKALsNQKyrdl~~~fgd  188 (1041)
T COG4581         113 AREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD---GQRVIYTSPIKALSNQKYRDLLAKFGD  188 (1041)
T ss_pred             HHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc---CCceEeccchhhhhhhHHHHHHHHhhh
Confidence            345667 5899999999999999999999999999999998888777664   346999999999999988887665543


Q ss_pred             CCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC
Q psy1539         109 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       109 ~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa  158 (175)
                      . .-.+++++|+.+...       +++++|.        +.+....+..+..+|+||+
T Consensus       189 v-~~~vGL~TGDv~IN~-------~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEv  238 (1041)
T COG4581         189 V-ADMVGLMTGDVSINP-------DAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEV  238 (1041)
T ss_pred             h-hhhccceecceeeCC-------CCceEEeeHHHHHHHhccCcccccccceEEEEee
Confidence            2 334788899887654       3566666        3333677889999999999

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.41  E-value=1.5e-12  Score=113.61  Aligned_cols=122  Identities=15%  Similarity=0.083  Sum_probs=91.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|-..--.+.  ..-+..++||.|||+++.+|++.+...   +..+.|++|+..||.|..+++..+.+.+ |+++.
T Consensus        82 ~~ydVQliGgl~L~--~G~IaEm~TGEGKTL~a~lp~~l~al~---g~~VhIvT~ndyLA~RD~e~m~~l~~~l-Glsv~  155 (908)
T PRK13107         82 RHFDVQLLGGMVLD--SNRIAEMRTGEGKTLTATLPAYLNALT---GKGVHVITVNDYLARRDAENNRPLFEFL-GLTVG  155 (908)
T ss_pred             CcCchHHhcchHhc--CCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEeCCHHHHHHHHHHHHHHHHhc-CCeEE
Confidence            45666655433333  455889999999999999999877664   3359999999999999999999999998 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEee---------cC-ccCC-----CCceEEEEeCCCCCCHHH
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLV---------NY-ETNL-----SGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~---------~~-~~~~-----~~~~~lVlDEad~~f~~~  165 (175)
                      ++.++.+..+..+..  +++|++++.         ++ ....     +.+.+.|+||+|..+.++
T Consensus       156 ~i~~~~~~~~r~~~Y--~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDE  218 (908)
T PRK13107        156 INVAGLGQQEKKAAY--NADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDE  218 (908)
T ss_pred             EecCCCCHHHHHhcC--CCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhcccc
Confidence            999988753332222  579999821         11 1222     678999999997655544

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

Probab=99.41  E-value=1.6e-12  Score=109.57  Aligned_cols=128  Identities=17%  Similarity=0.145  Sum_probs=98.8

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      +||..+++-|.++|..+++|+|+++..|||.||++||-+|.+-.     .| -+|||+|..+|.+...+.++..     |
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-----~G-~TLVVSPLiSLM~DQV~~l~~~-----G   81 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-----EG-LTLVVSPLISLMKDQVDQLEAA-----G   81 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-----CC-CEEEECchHHHHHHHHHHHHHc-----C
Confidence            48999999999999999999999999999999999999999765     33 6899999999998877766654     7


Q ss_pred             eEEEEEECCCchHHhHHH---HhcC-CCeEEE----eecC----ccCCCCceEEEEeCC------CCCCHHHHHHHH
Q psy1539         112 IKVGVFFGGLPIQKDEEY---LKTH-NPQIVG----LVNY----ETNLSGVVVNVMDVR------SGGWWLDLEALI  170 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~---l~~~-~~iiv~----l~~~----~~~~~~~~~lVlDEa------d~~f~~~v~~il  170 (175)
                      +.+..+.+..+.++....   +..+ .+++..    +.+.    .+.-..+.++|+|||      ...|+++...+-
T Consensus        82 i~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg  158 (590)
T COG0514          82 IRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLG  158 (590)
T ss_pred             ceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHH
Confidence            888888888775554433   3333 244433    2222    233558999999999      345999888763

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

Probab=99.38  E-value=1.8e-11  Score=108.66  Aligned_cols=145  Identities=19%  Similarity=0.166  Sum_probs=111.3

Q ss_pred             CCCCHHHHHHHhhC-CCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          19 RNRREKEDRIGESQ-PFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        19 ~~l~~~l~~~l~~~-g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ++.+.+..+.+.+. +|. -|+-|..||..+.+.      .|.++|+--|-|||-+++=++.....   +|.|+.++|||
T Consensus       577 f~~d~~~q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~---~GKQVAvLVPT  652 (1139)
T COG1197         577 FPPDTEWQEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM---DGKQVAVLVPT  652 (1139)
T ss_pred             CCCChHHHHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc---CCCeEEEEccc
Confidence            34444555555443 554 599999999998853      79999999999999988777766655   56799999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE---eecCccCCCCceEEEEeCCC-C--C
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRS-G--G  161 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad-~--~  161 (175)
                      .-||+|+++.+++-.+.+ .++|..+.-=.+.+++.+   .+++| .+||||   |++..+.|.++.++|+||-. +  .
T Consensus       653 TlLA~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlIIDEEqRFGVk  731 (1139)
T COG1197         653 TLLAQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVK  731 (1139)
T ss_pred             HHhHHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEEEechhhcCcc
Confidence            999999999999888888 888888766555555544   44554 689999   88889999999999999982 2  3


Q ss_pred             CHHHHHH
Q psy1539         162 WWLDLEA  168 (175)
Q Consensus       162 f~~~v~~  168 (175)
                      .++.+++
T Consensus       732 ~KEkLK~  738 (1139)
T COG1197         732 HKEKLKE  738 (1139)
T ss_pred             HHHHHHH
Confidence            4444444

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

Probab=99.38  E-value=5.3e-12  Score=112.28  Aligned_cols=97  Identities=16%  Similarity=0.143  Sum_probs=77.5

Q ss_pred             CHHHHHHHhhCCCCCCcHHHHHhHH----HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          22 REKEDRIGESQPFREQTSFQHECIP----QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        22 ~~~l~~~l~~~g~~~~t~~Q~~~i~----~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      .+.+.+.+...||. ++|.|.+.+.    .+.+|+++++.||||+|||++|++|++....   ++.+++|.+||++|..|
T Consensus       232 ~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq~Q  307 (850)
T TIGR01407       232 SSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQSQ  307 (850)
T ss_pred             cHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHHHH
Confidence            34677778888986 7999998665    5556899999999999999999999988765   23489999999999999


Q ss_pred             HHH-HHHHHHhhCC-CeEEEEEECCCc
Q psy1539          98 ISK-EYERFSKYMS-NIKVGVFFGGLP  122 (175)
Q Consensus        98 ~~~-~~~~~~~~~~-~i~v~~~~g~~~  122 (175)
                      +.. .+..+.+.++ .++++.+.|+.+
T Consensus       308 l~~~~~~~l~~~~~~~~~~~~~kG~~~  334 (850)
T TIGR01407       308 LLEKDIPLLNEILNFKINAALIKGKSN  334 (850)
T ss_pred             HHHHHHHHHHHHcCCCceEEEEEcchh
Confidence            865 5666666541 488888888754

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.

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

Probab=99.37  E-value=8.4e-12  Score=112.87  Aligned_cols=123  Identities=15%  Similarity=0.177  Sum_probs=81.3

Q ss_pred             CCcHHHHHhHHHHh----cC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          36 EQTSFQHECIPQAV----LG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .++++|.+|+..+.    +| ++.+++.+||||||.+.+ .++.++.......++|+|+|+++|+.|..+.+..+.-.. 
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai-~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~-  490 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI-ALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEG-  490 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH-HHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhccccc-
Confidence            58999999998765    34 689999999999998743 444555444445689999999999999999888763221 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEeecC-------------ccCCCCceEEEEeCCCCCC
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY-------------ETNLSGVVVNVMDVRSGGW  162 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-------------~~~~~~~~~lVlDEad~~f  162 (175)
                      ......+++.....+.  .......++|++.+.             ...+.+++++|+|||+.+.
T Consensus       491 ~~~~~~i~~i~~L~~~--~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~  553 (1123)
T PRK11448        491 DQTFASIYDIKGLEDK--FPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGY  553 (1123)
T ss_pred             ccchhhhhchhhhhhh--cccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCC
Confidence            1111112221111111  112346788884332             1345678899999998765

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.35  E-value=1.8e-11  Score=105.87  Aligned_cols=124  Identities=13%  Similarity=0.095  Sum_probs=87.3

Q ss_pred             CCcHHHHHhHHHHh-cC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          36 EQTSFQHECIPQAV-LG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~-~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      .++|+|.+|+..+. +|  +..+++.|||+|||+..+..+.. +.     .++|||||+.+|+.|+.+.+.++.... ..
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l~-----k~tLILvps~~Lv~QW~~ef~~~~~l~-~~  327 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-VK-----KSCLVLCTSAVSVEQWKQQFKMWSTID-DS  327 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-hC-----CCEEEEeCcHHHHHHHHHHHHHhcCCC-Cc
Confidence            47999999998877 34  47899999999999988765543 21     259999999999999999999886432 45


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEEeecC----------------ccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY----------------ETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~----------------~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+..++|+....     .....+++|++.+.                .+.-....++|+||++..-....+.++.
T Consensus       328 ~I~~~tg~~k~~-----~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~~fr~il~  397 (732)
T TIGR00603       328 QICRFTSDAKER-----FHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAAMFRRVLT  397 (732)
T ss_pred             eEEEEecCcccc-----cccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHHHHHHHHH
Confidence            667777764321     11235788872211                1112367899999998766666666554

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).

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

Probab=99.32  E-value=2.1e-11  Score=105.41  Aligned_cols=121  Identities=17%  Similarity=0.216  Sum_probs=93.2

Q ss_pred             CCcHHHHHhHHHHhcC----CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQAVLG----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g----~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .+++-|+.|...+...    +..++.+.||||||.+|+-.+-..+..   |.++|+|+|..+|..|+.+.++..   + +
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~---GkqvLvLVPEI~Ltpq~~~rf~~r---F-g  270 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ---GKQVLVLVPEIALTPQLLARFKAR---F-G  270 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc---CCEEEEEeccccchHHHHHHHHHH---h-C
Confidence            5688999999888754    789999999999999998877777663   458999999999999977766654   4 6


Q ss_pred             eEEEEEECCCchHHhHHH---Hhc-CCCeEEEeecC-ccCCCCceEEEEeCC-CCCCH
Q psy1539         112 IKVGVFFGGLPIQKDEEY---LKT-HNPQIVGLVNY-ETNLSGVVVNVMDVR-SGGWW  163 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~---l~~-~~~iiv~l~~~-~~~~~~~~~lVlDEa-d~~f~  163 (175)
                      .++..++++.+..+..+.   ..+ ...++||.-+. ...|+++.++|+||- |..|+
T Consensus       271 ~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~Pf~~LGLIIvDEEHD~sYK  328 (730)
T COG1198         271 AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFLPFKNLGLIIVDEEHDSSYK  328 (730)
T ss_pred             CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhcCchhhccEEEEecccccccc
Confidence            789999999876544433   333 35677775444 557899999999998 44443

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

Probab=99.31  E-value=4.1e-11  Score=104.85  Aligned_cols=128  Identities=20%  Similarity=0.219  Sum_probs=91.6

Q ss_pred             HHhhC-CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          28 IGESQ-PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        28 ~l~~~-g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .+.+. || .|+..|+-+...+..|++.-+.||||.|||..-++..+-.   ...+.++++|+||+.|+.|+++.++++.
T Consensus        74 fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~---a~kgkr~yii~PT~~Lv~Q~~~kl~~~~  149 (1187)
T COG1110          74 FFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYL---AKKGKRVYIIVPTTTLVRQVYERLKKFA  149 (1187)
T ss_pred             HHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHH---HhcCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            34444 55 8999999999999999999999999999996444333222   2245689999999999999999999999


Q ss_pred             hhCCCeEEEE-EECCCchHH---hHHHHhc-CCCeEEE----eecCccCCC--CceEEEEeCCC
Q psy1539         107 KYMSNIKVGV-FFGGLPIQK---DEEYLKT-HNPQIVG----LVNYETNLS--GVVVNVMDVRS  159 (175)
Q Consensus       107 ~~~~~i~v~~-~~g~~~~~~---~~~~l~~-~~~iiv~----l~~~~~~~~--~~~~lVlDEad  159 (175)
                      ....+..+-. .+|..+.++   ..+.+.+ +-+|+|+    +..+.-.++  +++++.+|++|
T Consensus       150 e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~~~kFdfifVDDVD  213 (1187)
T COG1110         150 EDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSKLKFDFIFVDDVD  213 (1187)
T ss_pred             hhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhcccCCCEEEEccHH
Confidence            7762244433 566655433   3445555 4678887    333333344  68999999985

>KOG0353|consensus

Probab=99.25  E-value=4.9e-11  Score=95.17  Aligned_cols=150  Identities=14%  Similarity=0.145  Sum_probs=107.9

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhC-CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeE
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQ-PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY   84 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~-g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~   84 (175)
                      ++++|..|.. ++++.+.+..+.|++. ...+++|.|..+|...+.|++.++..|||-||++||-+|.+-.     +| .
T Consensus        64 yd~spaawdk-d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a-----dg-~  136 (695)
T KOG0353|consen   64 YDRSPAAWDK-DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA-----DG-F  136 (695)
T ss_pred             ccCCcccccc-CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc-----CC-c
Confidence            4455555544 5688888888877765 4568999999999999999999999999999999999999754     33 6


Q ss_pred             EEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh----c-CC--CeEEE----------eecC---c
Q psy1539          85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK----T-HN--PQIVG----------LVNY---E  144 (175)
Q Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~----~-~~--~iiv~----------l~~~---~  144 (175)
                      +|+++|...|.+...-+++.+     |+....+...++. +..+.+.    + +.  ..|..          +++.   .
T Consensus       137 alvi~plislmedqil~lkql-----gi~as~lnanssk-e~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka  210 (695)
T KOG0353|consen  137 ALVICPLISLMEDQILQLKQL-----GIDASMLNANSSK-EEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKA  210 (695)
T ss_pred             eEeechhHHHHHHHHHHHHHh-----CcchhhccCcccH-HHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHH
Confidence            999999999998877777766     6666666666653 3333222    1 11  12222          1111   3


Q ss_pred             cCCCCceEEEEeCC------CCCCHHHHHH
Q psy1539         145 TNLSGVVVNVMDVR------SGGWWLDLEA  168 (175)
Q Consensus       145 ~~~~~~~~lVlDEa------d~~f~~~v~~  168 (175)
                      .....++++.+||+      ...|++|.+.
T Consensus       211 ~~~~~~~~iaidevhccsqwghdfr~dy~~  240 (695)
T KOG0353|consen  211 LEAGFFKLIAIDEVHCCSQWGHDFRPDYKA  240 (695)
T ss_pred             hhcceeEEEeecceeehhhhCcccCcchHH
Confidence            45567899999999      3567777654

>PRK09694 helicase Cas3; Provisional

Probab=99.24  E-value=9.7e-11  Score=103.64  Aligned_cols=87  Identities=11%  Similarity=0.057  Sum_probs=65.5

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh-CCCeE
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY-MSNIK  113 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~-~~~i~  113 (175)
                      ..|+|+|+.+.........+++.+|||+|||.+++..+.... ......++++..||++.++|+++.++++.+. ++...
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~-~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~  363 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLI-DQGLADSIIFALPTQATANAMLSRLEALASKLFPSPN  363 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHH-HhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            379999998864434457799999999999999877655433 3333458999999999999999999876553 33456


Q ss_pred             EEEEECCCc
Q psy1539         114 VGVFFGGLP  122 (175)
Q Consensus       114 v~~~~g~~~  122 (175)
                      +.+.+|...
T Consensus       364 v~L~Hg~a~  372 (878)
T PRK09694        364 LILAHGNSR  372 (878)
T ss_pred             eEeecCcch
Confidence            777787654

>KOG0951|consensus

Probab=99.23  E-value=2e-11  Score=108.34  Aligned_cols=134  Identities=18%  Similarity=0.152  Sum_probs=103.8

Q ss_pred             CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcC--------CCCeEEEEEec
Q psy1539          20 NRREKEDRIGESQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETT--------DSNVYVLVMCH   90 (175)
Q Consensus        20 ~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~--------~~~~~~lil~P   90 (175)
                      .++..-..++.  |...++++|....+..+.+ .|+++|||||+|||-.+++.+++.+...        ....+.+|++|
T Consensus       295 elP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAP  372 (1674)
T KOG0951|consen  295 ELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAP  372 (1674)
T ss_pred             CCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEee
Confidence            44444555554  4567999999999998877 8999999999999999999999988643        23458999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC----------ccCCCCceEEEEeCCC
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY----------ETNLSGVVVNVMDVRS  159 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~----------~~~~~~~~~lVlDEad  159 (175)
                      +++|++.+...+.+....+ |++|.-.+|+.....+  .+ .+..+||++...          ....+-++++|+||.+
T Consensus       373 mKaLvqE~VgsfSkRla~~-GI~V~ElTgD~~l~~~--qi-eeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIH  447 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPL-GITVLELTGDSQLGKE--QI-EETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIH  447 (1674)
T ss_pred             HHHHHHHHHHHHHhhcccc-CcEEEEecccccchhh--hh-hcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhh
Confidence            9999999999888888888 9999999999763221  12 346888883332          2344568999999994

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

Probab=99.21  E-value=1.1e-10  Score=103.24  Aligned_cols=85  Identities=22%  Similarity=0.230  Sum_probs=68.7

Q ss_pred             CCCCCCcHHHHHhHHH----HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH-HHHHHHHH
Q psy1539          32 QPFREQTSFQHECIPQ----AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI-SKEYERFS  106 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~----~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~-~~~~~~~~  106 (175)
                      .|| ++++-|.+....    +.++..+++.|+||+|||++|++|++...    .+.+++|++||++|++|+ .+.+..+.
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            356 579999995543    33578999999999999999999988754    346899999999999999 46688887


Q ss_pred             hhCCCeEEEEEECCCc
Q psy1539         107 KYMSNIKVGVFFGGLP  122 (175)
Q Consensus       107 ~~~~~i~v~~~~g~~~  122 (175)
                      +.+ ++++..+.|+.+
T Consensus       317 ~~~-~~~~~~~kg~~~  331 (820)
T PRK07246        317 EVF-HIDCHSLKGPQN  331 (820)
T ss_pred             Hhc-CCcEEEEECCcc
Confidence            776 788888887754

>KOG0351|consensus

Probab=99.20  E-value=4.7e-11  Score=105.75  Aligned_cols=135  Identities=19%  Similarity=0.144  Sum_probs=100.1

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      ........+|...+++-|.++|...+.|+|.++..|||.||++||-+|++-.      +.-.++|.|..+|.+.+...+ 
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L-  324 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHL-  324 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhh-
Confidence            3333455668999999999999999999999999999999999999988643      227899999999997754444 


Q ss_pred             HHHhhCCCeEEEEEECCCchHHhH---HHHhcCCCeE---EE----------eecCccCCCC---ceEEEEeCC------
Q psy1539         104 RFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQI---VG----------LVNYETNLSG---VVVNVMDVR------  158 (175)
Q Consensus       104 ~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~~~ii---v~----------l~~~~~~~~~---~~~lVlDEa------  158 (175)
                        ...  ++....+.++....++.   +.+.++.+.+   ..          +.+....+..   +.++|+|||      
T Consensus       325 --~~~--~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqW  400 (941)
T KOG0351|consen  325 --SKK--GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQW  400 (941)
T ss_pred             --hhc--CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhh
Confidence              322  88889999988765433   4455553332   22          3333445555   899999999      


Q ss_pred             CCCCHHHHHHH
Q psy1539         159 SGGWWLDLEAL  169 (175)
Q Consensus       159 d~~f~~~v~~i  169 (175)
                      ...|+++.+.+
T Consensus       401 gHdFRp~Yk~l  411 (941)
T KOG0351|consen  401 GHDFRPSYKRL  411 (941)
T ss_pred             cccccHHHHHH
Confidence            46788887765

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.18  E-value=3.2e-10  Score=97.40  Aligned_cols=122  Identities=13%  Similarity=0.016  Sum_probs=96.4

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          33 PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      |. .|+++|....-.+++|+  +....||+|||++..+|+.....   .|.++.+++|+--||.|-++++..+.+.+ |+
T Consensus        76 g~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL---~G~~VhvvT~NdyLA~RDae~m~~ly~~L-GL  148 (764)
T PRK12326         76 GL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYAL---QGRRVHVITVNDYLARRDAEWMGPLYEAL-GL  148 (764)
T ss_pred             CC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHH---cCCCeEEEcCCHHHHHHHHHHHHHHHHhc-CC
Confidence            44 58999999988888774  67999999999999999887765   45579999999999999999999999998 99


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCCH
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGWW  163 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f~  163 (175)
                      +++++.++.+.++..+..  .|+|..+         |-++      ....+.+.+.|+||+|....
T Consensus       149 svg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLI  212 (764)
T PRK12326        149 TVGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLV  212 (764)
T ss_pred             EEEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhee
Confidence            999999988755444444  4788887         2221      22335688999999974443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.18  E-value=2e-10  Score=100.03  Aligned_cols=121  Identities=14%  Similarity=0.065  Sum_probs=95.3

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|..+--.+.+|+  +....||+|||++..+|++-....   |.++-+++||--||.|-++.+..+.+.+ |++++
T Consensus        80 ~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~---G~~v~vvT~neyLA~Rd~e~~~~~~~~L-Gl~vg  153 (796)
T PRK12906         80 RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT---GKGVHVVTVNEYLSSRDATEMGELYRWL-GLTVG  153 (796)
T ss_pred             CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc---CCCeEEEeccHHHHHhhHHHHHHHHHhc-CCeEE
Confidence            57889988876666776  899999999999999998877664   5579999999999999999999999999 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCCHH
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGWWL  164 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f~~  164 (175)
                      ++.|+.+.++..+..  .|+|+.+         |.++      ....+.+.+.|+||+|....+
T Consensus       154 ~i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiD  215 (796)
T PRK12906        154 LNLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILID  215 (796)
T ss_pred             EeCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeec
Confidence            999988765554444  4689888         2221      122357889999999754443

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

Probab=99.16  E-value=2.8e-10  Score=97.53  Aligned_cols=76  Identities=22%  Similarity=0.293  Sum_probs=62.1

Q ss_pred             HHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH-hhC-CCeEEEEEECCCc
Q psy1539          46 PQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS-KYM-SNIKVGVFFGGLP  122 (175)
Q Consensus        46 ~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~-~~i~v~~~~g~~~  122 (175)
                      ..+.+++.+++.|+||+|||++|++|++..+... .+.+++|.+||++|..|+.+.+..+. +.. ..+++..+.|+.+
T Consensus        11 ~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~lkGr~n   88 (636)
T TIGR03117        11 TSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPGSQE   88 (636)
T ss_pred             HHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEEECCcc
Confidence            3445678999999999999999999999876532 34689999999999999999999887 432 2678888888754

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.

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.14  E-value=3.5e-10  Score=99.12  Aligned_cols=121  Identities=16%  Similarity=0.056  Sum_probs=92.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|-..--.+  ...-+....||+|||+++.+|++-...   .|.++.+++|+--||.|-++++..+.+.+ |+++.
T Consensus        82 ~~ydVQliGg~~L--h~G~iaEM~TGEGKTLvA~l~a~l~al---~G~~VhvvT~ndyLA~RD~e~m~~l~~~l-Gl~v~  155 (913)
T PRK13103         82 RHFDVQLIGGMTL--HEGKIAEMRTGEGKTLVGTLAVYLNAL---SGKGVHVVTVNDYLARRDANWMRPLYEFL-GLSVG  155 (913)
T ss_pred             CcchhHHHhhhHh--ccCccccccCCCCChHHHHHHHHHHHH---cCCCEEEEeCCHHHHHHHHHHHHHHhccc-CCEEE
Confidence            4666776544333  355678999999999999999976655   45579999999999999999999999998 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE---e-----ecCccCC-------CCceEEEEeCCCCCCHH
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG---L-----VNYETNL-------SGVVVNVMDVRSGGWWL  164 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~---l-----~~~~~~~-------~~~~~lVlDEad~~f~~  164 (175)
                      ++.++.+.++..+.+.  ++|++|   .     ++..+.+       +++.+.|+||+|....+
T Consensus       156 ~i~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLID  217 (913)
T PRK13103        156 IVTPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILID  217 (913)
T ss_pred             EECCCCCHHHHHHHhc--CCEEEEcccccccchhhccceechhhhcccccceeEechhhheecc
Confidence            9998887555544443  799998   1     2223334       78999999999644433

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

Probab=99.12  E-value=9.4e-10  Score=95.62  Aligned_cols=127  Identities=20%  Similarity=0.196  Sum_probs=82.1

Q ss_pred             CcHHHHHhHHHHh----c------CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          37 QTSFQHECIPQAV----L------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~------g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      +..+|.+|+..+.    +      .+..+++.+||||||++.+..+...+ .....+++|+|+|+++|..|+.+.+..+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            6889999987653    2      25789999999999988765544333 33456799999999999999999988875


Q ss_pred             hhCCCeEEEEEECCCchHHhHHHHhc-CCCeEEEeecCcc--------CCC--C-ceEEEEeCCCCCCHHHHHHHHh
Q psy1539         107 KYMSNIKVGVFFGGLPIQKDEEYLKT-HNPQIVGLVNYET--------NLS--G-VVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       107 ~~~~~i~v~~~~g~~~~~~~~~~l~~-~~~iiv~l~~~~~--------~~~--~-~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ...  .     .+..+...-...+.+ ..+++|++.+...        .+.  + -.++|+|||+.+...+....|.
T Consensus       318 ~~~--~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~~~~~~l~  387 (667)
T TIGR00348       318 KDC--A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYGELAKNLK  387 (667)
T ss_pred             CCC--C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccchHHHHHHH
Confidence            321  1     111122222233333 3578888444411        111  1 1379999998776666655554

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

>KOG0947|consensus

Probab=99.08  E-value=3.8e-10  Score=98.27  Aligned_cols=112  Identities=21%  Similarity=0.249  Sum_probs=85.4

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .+| ++...|++||-++..|.+++|.|+|.+|||+++..++.-.   ..+..+++|-+|-++|.+|.++.|+.-...   
T Consensus       294 ~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAiala---q~h~TR~iYTSPIKALSNQKfRDFk~tF~D---  366 (1248)
T KOG0947|consen  294 YPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALA---QKHMTRTIYTSPIKALSNQKFRDFKETFGD---  366 (1248)
T ss_pred             CCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHH---HhhccceEecchhhhhccchHHHHHHhccc---
Confidence            344 5899999999999999999999999999999876655432   235679999999999999977777665443   


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEad  159 (175)
                        +.+++|+.....+       +.++|.        |.+..-.++++.++|+||++
T Consensus       367 --vgLlTGDvqinPe-------AsCLIMTTEILRsMLYrgadliRDvE~VIFDEVH  413 (1248)
T KOG0947|consen  367 --VGLLTGDVQINPE-------ASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVH  413 (1248)
T ss_pred             --cceeecceeeCCC-------cceEeehHHHHHHHHhcccchhhccceEEEeeee
Confidence              3478888765433       345554        33334556799999999993

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.04  E-value=1.7e-09  Score=85.20  Aligned_cols=70  Identities=17%  Similarity=0.145  Sum_probs=56.9

Q ss_pred             CcHHHHHhH----HHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCC---CeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          37 QTSFQHECI----PQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        37 ~t~~Q~~~i----~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      |+|.|.+.+    ..+.+|.++++.||||+|||++|++|++..+.....   +.++++.++|..+..|....++++.
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~~   85 (289)
T smart00489        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhcc
Confidence            699999954    455578999999999999999999999977654322   2489999999999999877777653

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.04  E-value=1.7e-09  Score=85.20  Aligned_cols=70  Identities=17%  Similarity=0.145  Sum_probs=56.9

Q ss_pred             CcHHHHHhH----HHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCC---CeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          37 QTSFQHECI----PQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        37 ~t~~Q~~~i----~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      |+|.|.+.+    ..+.+|.++++.||||+|||++|++|++..+.....   +.++++.++|..+..|....++++.
T Consensus         9 ~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~~   85 (289)
T smart00488        9 PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKLM   85 (289)
T ss_pred             CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhcc
Confidence            699999954    455578999999999999999999999977654322   2489999999999999877777653

>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=99.02  E-value=8.4e-09  Score=80.01  Aligned_cols=123  Identities=19%  Similarity=0.190  Sum_probs=89.9

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      ..|+ .|+++|..++-.+.+|+  ++.-.||-|||++..+|+.-...   .|..+-|++.+..||..=.+++..+.+.+ 
T Consensus        73 ~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL---~G~~V~vvT~NdyLA~RD~~~~~~~y~~L-  145 (266)
T PF07517_consen   73 TLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNAL---QGKGVHVVTSNDYLAKRDAEEMRPFYEFL-  145 (266)
T ss_dssp             HTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHT---TSS-EEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHH---hcCCcEEEeccHHHhhccHHHHHHHHHHh-
Confidence            3444 68999999997776766  89999999999998887766655   34578999999999999999999999999 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCC
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGW  162 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f  162 (175)
                      |+++....++.+..+..+...  ++|+.+         |.++      ....+.+.++|+||+|..+
T Consensus       146 Glsv~~~~~~~~~~~r~~~Y~--~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  146 GLSVGIITSDMSSEERREAYA--ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             T--EEEEETTTEHHHHHHHHH--SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             hhccccCccccCHHHHHHHHh--CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            999999999987554444443  578888         2111      2225789999999997443

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 ....

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

Probab=98.94  E-value=5.9e-09  Score=82.31  Aligned_cols=111  Identities=15%  Similarity=0.189  Sum_probs=85.4

Q ss_pred             CCcHHHHHhHHHH----hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQA----VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~----~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .+||.|+.+-..+    .+.++.+++|-||+|||.- +++.++....  .|.++.+.+|..+.|.+++..++.-   +++
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~--~G~~vciASPRvDVclEl~~Rlk~a---F~~  170 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALN--QGGRVCIASPRVDVCLELYPRLKQA---FSN  170 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHh--cCCeEEEecCcccchHHHHHHHHHh---hcc
Confidence            6899999886544    4569999999999999964 4555555443  4558999999999998888877654   346


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCC-CCceEEEEeCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNL-SGVVVNVMDVRS  159 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~-~~~~~lVlDEad  159 (175)
                      ..+..++|+++..-+       .+.+|++..+.+.| +.++++++||+|
T Consensus       171 ~~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk~aFD~liIDEVD  212 (441)
T COG4098         171 CDIDLLYGDSDSYFR-------APLVVATTHQLLRFKQAFDLLIIDEVD  212 (441)
T ss_pred             CCeeeEecCCchhcc-------ccEEEEehHHHHHHHhhccEEEEeccc
Confidence            788999999864332       58999977775555 479999999997

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

Probab=98.88  E-value=9.8e-09  Score=88.76  Aligned_cols=124  Identities=15%  Similarity=0.096  Sum_probs=86.0

Q ss_pred             CCcHHHHHhHHHHh----cC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          36 EQTSFQHECIPQAV----LG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .++.+|..||..+.    +| +..+++..||+|||.++ ++++.+|.+...-.++|+|+-+++|+.|.+..+..+.-   
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P---  240 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLP---  240 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCC---
Confidence            57889999987554    45 45899999999999775 66777777766666899999999999998888776653   


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEeecC-------------ccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY-------------ETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-------------~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      .-.......+.....       ++.+.+++.+.             .+....++++|+|||+.|...+-++|+
T Consensus       241 ~~~~~n~i~~~~~~~-------s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi~~~~~~I~  306 (875)
T COG4096         241 FGTKMNKIEDKKGDT-------SSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGIYSEWSSIL  306 (875)
T ss_pred             CccceeeeecccCCc-------ceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhHHhhhHHHH
Confidence            333332222222111       35666662221             344556999999999877666555554

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.86  E-value=1.3e-08  Score=89.03  Aligned_cols=124  Identities=13%  Similarity=0.065  Sum_probs=92.6

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          33 PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      |. .|+++|....-.+  .++-+....||.|||+++.+|+.-...   .|..+.|++++..||.+-.+++..+.+.+ |+
T Consensus        74 G~-r~ydvQlig~l~L--~~G~IaEm~TGEGKTL~a~l~ayl~aL---~G~~VhVvT~NdyLA~RD~e~m~pvy~~L-GL  146 (870)
T CHL00122         74 GL-RHFDVQLIGGLVL--NDGKIAEMKTGEGKTLVATLPAYLNAL---TGKGVHIVTVNDYLAKRDQEWMGQIYRFL-GL  146 (870)
T ss_pred             CC-CCCchHhhhhHhh--cCCccccccCCCCchHHHHHHHHHHHh---cCCceEEEeCCHHHHHHHHHHHHHHHHHc-CC
Confidence            44 4677777654333  456789999999999999999864433   34578999999999999999999999999 99


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCCHHH
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f~~~  165 (175)
                      +++++.++.+..+..+..  .|+|..+         |.++      ....+.+.+.|+||+|....++
T Consensus       147 svg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDe  212 (870)
T CHL00122        147 TVGLIQEGMSSEERKKNY--LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDE  212 (870)
T ss_pred             ceeeeCCCCChHHHHHhc--CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheecc
Confidence            999998888765544444  3688887         2222      1234678999999997554443

>KOG0951|consensus

Probab=98.86  E-value=1.4e-09  Score=96.95  Aligned_cols=118  Identities=19%  Similarity=0.237  Sum_probs=91.3

Q ss_pred             CCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          34 FREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      |...+|+|.++++.+.+ +.++++.+|+|||||.++.++++.    .....+++++.|..+.+...++.+.+-....-|.
T Consensus      1141 f~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~ 1216 (1674)
T KOG0951|consen 1141 FQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGL 1216 (1674)
T ss_pred             ccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCc
Confidence            44559999999998886 488999999999999999999887    2355689999999999998888776544433488


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEEeecC---ccCCCCceEEEEeCC
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY---ETNLSGVVVNVMDVR  158 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~---~~~~~~~~~lVlDEa  158 (175)
                      ++..+.|..+.  +.+.+.. .+++|++..+   .-..+++++.|.||+
T Consensus      1217 ~~~~l~ge~s~--~lkl~~~-~~vii~tpe~~d~lq~iQ~v~l~i~d~l 1262 (1674)
T KOG0951|consen 1217 RIVKLTGETSL--DLKLLQK-GQVIISTPEQWDLLQSIQQVDLFIVDEL 1262 (1674)
T ss_pred             eEEecCCcccc--chHHhhh-cceEEechhHHHHHhhhhhcceEeeehh
Confidence            89888888764  3334444 4888883222   226789999999999

>KOG0948|consensus

Probab=98.82  E-value=1.1e-08  Score=87.72  Aligned_cols=109  Identities=24%  Similarity=0.228  Sum_probs=85.7

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .+.|.|+.||..+-++.+++|+|-|.+|||.++..++...+..++   ++||-+|-++|.+|.|+.+..=.+     .|+
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ---RVIYTSPIKALSNQKYREl~~EF~-----DVG  200 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ---RVIYTSPIKALSNQKYRELLEEFK-----DVG  200 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC---eEEeeChhhhhcchhHHHHHHHhc-----ccc
Confidence            478999999999999999999999999999999999988887533   899999999999998777654332     367


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCCC
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEad  159 (175)
                      +.+|+......       +..+|.        +.+...-.+.+.-+|+||.+
T Consensus       201 LMTGDVTInP~-------ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIH  245 (1041)
T KOG0948|consen  201 LMTGDVTINPD-------ASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIH  245 (1041)
T ss_pred             eeecceeeCCC-------CceeeeHHHHHHHHHhccchHhheeeeEEeeeeh
Confidence            78888765433       344444        33335556788899999984

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

Probab=98.80  E-value=4e-08  Score=88.41  Aligned_cols=87  Identities=17%  Similarity=0.219  Sum_probs=64.3

Q ss_pred             CCCCCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH-HHHHHh
Q psy1539          33 PFREQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE-YERFSK  107 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~-~~~~~~  107 (175)
                      || +++|-|.+.+..+.    +++.+++.||||+|||++|++|++.....  ++.+++|-++|+.|-+|+.+. +-.+.+
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~--~~~~vvIsT~T~~LQ~Ql~~kDiP~L~~  331 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK--KEEPVVISTYTIQLQQQLLEKDIPLLQK  331 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc--cCCeEEEEcCCHHHHHHHHHhhHHHHHH
Confidence            45 57999999665443    57899999999999999999999865543  445899999999999998764 333333


Q ss_pred             hCC-CeEEEEEECCCc
Q psy1539         108 YMS-NIKVGVFFGGLP  122 (175)
Q Consensus       108 ~~~-~i~v~~~~g~~~  122 (175)
                      .++ .++++++-|..+
T Consensus       332 ~~~~~~~~~~lKGr~n  347 (928)
T PRK08074        332 IFPFPVEAALLKGRSH  347 (928)
T ss_pred             HcCCCceEEEEEcccc
Confidence            221 567777776543

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.72  E-value=1.6e-07  Score=82.62  Aligned_cols=120  Identities=15%  Similarity=0.065  Sum_probs=89.7

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|-..--.+  ...-+....||-|||+++.+|+.-...   .|..+.|++++-.||..=.+++..+.+.+ |++|+
T Consensus        85 r~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL---~GkgVhVVTvNdYLA~RDae~m~~vy~~L-GLtvg  158 (939)
T PRK12902         85 RHFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNAL---TGKGVHVVTVNDYLARRDAEWMGQVHRFL-GLSVG  158 (939)
T ss_pred             CcchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhh---cCCCeEEEeCCHHHHHhHHHHHHHHHHHh-CCeEE
Confidence            4566666554333  455678999999999999999876554   34469999999999999999999999998 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCCH
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGWW  163 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f~  163 (175)
                      ++.++.+..+.....  .|+|+.+         |.++      ....+.+.+.|+||+|....
T Consensus       159 ~i~~~~~~~err~aY--~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILI  219 (939)
T PRK12902        159 LIQQDMSPEERKKNY--ACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILI  219 (939)
T ss_pred             EECCCCChHHHHHhc--CCCeEEecCCcccccchhhhhcccccccccCccceEEEecccceee
Confidence            998877654433333  5799988         2222      23446789999999974433

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.71  E-value=7.9e-08  Score=83.37  Aligned_cols=102  Identities=13%  Similarity=-0.003  Sum_probs=74.8

Q ss_pred             EEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc
Q psy1539          56 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT  132 (175)
Q Consensus        56 i~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~  132 (175)
                      ..+.+|||||..|+-.+-..+..   |.++|+++|...|..|+.+.++....   +..+..++++.+..+..+   .+.+
T Consensus       165 ~~~~~GSGKTevyl~~i~~~l~~---Gk~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~w~~~~~  238 (665)
T PRK14873        165 WQALPGEDWARRLAAAAAATLRA---GRGALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRRWLAVLR  238 (665)
T ss_pred             hhcCCCCcHHHHHHHHHHHHHHc---CCeEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHHHHHHhC
Confidence            33446999999998777666553   45899999999999998888775542   256888999887665443   3444


Q ss_pred             C-CCeEEEeecC-ccCCCCceEEEEeCC-CCCCH
Q psy1539         133 H-NPQIVGLVNY-ETNLSGVVVNVMDVR-SGGWW  163 (175)
Q Consensus       133 ~-~~iiv~l~~~-~~~~~~~~~lVlDEa-d~~f~  163 (175)
                      | ..|+||.-.. ...++++.++|+||- |..|+
T Consensus       239 G~~~IViGtRSAvFaP~~~LgLIIvdEEhd~syk  272 (665)
T PRK14873        239 GQARVVVGTRSAVFAPVEDLGLVAIWDDGDDLLA  272 (665)
T ss_pred             CCCcEEEEcceeEEeccCCCCEEEEEcCCchhhc
Confidence            5 5788885444 567899999999987 44444

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.65  E-value=3.2e-07  Score=80.36  Aligned_cols=84  Identities=20%  Similarity=0.237  Sum_probs=60.2

Q ss_pred             CCCCCcHHHHHhHHHHh---c------CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH-H
Q psy1539          33 PFREQTSFQHECIPQAV---L------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE-Y  102 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~---~------g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~-~  102 (175)
                      || ++++-|.+....+.   +      ++.++|.||||+|||++|++|++-....  .+.+++|-+.|+.|-+|+.+. +
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~--~~k~vVIST~T~~LQeQL~~kDl   99 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA--EKKKLVISTATVALQEQLVSKDL   99 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH--cCCeEEEEcCCHHHHHHHHhhhh
Confidence            56 57999999665554   3      2678999999999999999999875543  344799999999999998654 3


Q ss_pred             HHHHhhC-CCeEEEEEEC
Q psy1539         103 ERFSKYM-SNIKVGVFFG  119 (175)
Q Consensus       103 ~~~~~~~-~~i~v~~~~g  119 (175)
                      -.+.+.. ..++++++-|
T Consensus       100 P~l~~~l~~~~~~~llKG  117 (697)
T PRK11747        100 PLLLKISGLDFKFTLAKG  117 (697)
T ss_pred             hHHHHHcCCCceEEEEcC
Confidence            3333322 1455555544

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.58  E-value=3.8e-07  Score=80.08  Aligned_cols=74  Identities=16%  Similarity=0.191  Sum_probs=62.7

Q ss_pred             CCCCCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          33 PFREQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|..++|.|.+.+..+.    +|.+.++.+|||+|||++.+.|.+......+...++++.+.|..-..|..+.++++.
T Consensus         7 Py~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         7 PYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             CCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            46667999999876554    579999999999999999999999976654445789999999999999999998864

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).

>KOG0949|consensus

Probab=98.58  E-value=1.3e-07  Score=83.08  Aligned_cols=119  Identities=14%  Similarity=0.087  Sum_probs=82.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe-EE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI-KV  114 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i-~v  114 (175)
                      .|..+|++.+..+-.++..+|.|||-+|||.+-...+=..+.. .+.-.+++++||++|++|+........... .+ +.
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLRe-sD~~VVIyvaPtKaLVnQvsa~VyaRF~~~-t~~rg  588 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRE-SDSDVVIYVAPTKALVNQVSANVYARFDTK-TFLRG  588 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhh-cCCCEEEEecchHHHhhhhhHHHHHhhccC-ccccc
Confidence            5788999999999999999999999999997654444334433 344479999999999999887766554221 11 22


Q ss_pred             EEEECCCchHHhHHHHhcCCCeEEE--------eec---CccCCCCceEEEEeCC
Q psy1539         115 GVFFGGLPIQKDEEYLKTHNPQIVG--------LVN---YETNLSGVVVNVMDVR  158 (175)
Q Consensus       115 ~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~---~~~~~~~~~~lVlDEa  158 (175)
                      ..+.|....+=+...  -+|+++|+        |..   +....++++++|+||+
T Consensus       589 ~sl~g~ltqEYsinp--~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEV  641 (1330)
T KOG0949|consen  589 VSLLGDLTQEYSINP--WNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEV  641 (1330)
T ss_pred             hhhHhhhhHHhcCCc--hhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechh
Confidence            233343321111111  15788887        444   3567789999999999

>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=98.57  E-value=2.2e-07  Score=72.79  Aligned_cols=107  Identities=14%  Similarity=0.080  Sum_probs=61.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCC---eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  126 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~---~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~  126 (175)
                      ..+..+++...|+|||+..+..+. .+......   ..+||++|. .+..|+.+.+.++.... ..++..+.|+......
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~-~~~v~~~~~~~~~~~~  100 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPD-SLRVIIYDGDSERRRL  100 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT--TS-EEEESSSCHHHHT
T ss_pred             CCCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhccccccc-cccccccccccccccc
Confidence            347899999999999977654443 33322221   259999999 78889999999987543 5677776666512222


Q ss_pred             HHHHhcCCCeEEE----ee-----cC--ccCCCCceEEEEeCCC
Q psy1539         127 EEYLKTHNPQIVG----LV-----NY--ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       127 ~~~l~~~~~iiv~----l~-----~~--~~~~~~~~~lVlDEad  159 (175)
                      ........+++|+    +.     ..  .+.--+.+++|+||++
T Consensus       101 ~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH  144 (299)
T PF00176_consen  101 SKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAH  144 (299)
T ss_dssp             TSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGG
T ss_pred             cccccccceeeeccccccccccccccccccccccceeEEEeccc
Confidence            2222234566666    22     11  1222358999999994

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.55  E-value=7.8e-07  Score=81.48  Aligned_cols=106  Identities=16%  Similarity=0.100  Sum_probs=61.8

Q ss_pred             HHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE--ec----CHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          40 FQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM--CH----TRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        40 ~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil--~P----t~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .-.+.+..+.++..++++|+||||||.  .+|.+-...  ..+....|+  -|    +++||.|+.+.+..-.    |-.
T Consensus        78 ~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~--g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~l----G~~  149 (1294)
T PRK11131         78 KKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLEL--GRGVKGLIGHTQPRRLAARTVANRIAEELETEL----GGC  149 (1294)
T ss_pred             HHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHc--CCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhh----cce
Confidence            333445566667788899999999998  467433211  112222333  35    5788888888776421    222


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEE----ee---cCccCCCCceEEEEeCCC
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVG----LV---NYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~----l~---~~~~~~~~~~~lVlDEad  159 (175)
                      ++.-+.   ...+   ..+++.|+++    +.   .....+++++++|+||||
T Consensus       150 VGY~vr---f~~~---~s~~t~I~v~TpG~LL~~l~~d~~Ls~~~~IIIDEAH  196 (1294)
T PRK11131        150 VGYKVR---FNDQ---VSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAH  196 (1294)
T ss_pred             eceeec---Cccc---cCCCCCEEEEChHHHHHHHhcCCccccCcEEEecCcc
Confidence            222111   1111   1245678887    22   224458999999999996

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

Probab=98.52  E-value=4.8e-07  Score=78.75  Aligned_cols=73  Identities=25%  Similarity=0.257  Sum_probs=59.3

Q ss_pred             hCCCCCCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          31 SQPFREQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      ......|++.|.+.+..+.    +|+.+++.||||+|||++|+.|++.....  .+.+++|.++|+.|-.|+.+....+
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~--~~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYARE--EGKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHH--cCCcEEEECCCHHHHHHHHHhhcch
Confidence            3345579999999985443    45779999999999999999999987654  3358999999999999988886554

>KOG0950|consensus

Probab=98.51  E-value=2.5e-07  Score=81.15  Aligned_cols=140  Identities=19%  Similarity=0.237  Sum_probs=103.2

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhH--HHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECI--PQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i--~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      ...-..+..|...+..+|.+++  |.+++++|.+...||+.|||++..+-++.....  ....++.+.|....++.....
T Consensus       211 ~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~--~rr~~llilp~vsiv~Ek~~~  288 (1008)
T KOG0950|consen  211 VSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLC--RRRNVLLILPYVSIVQEKISA  288 (1008)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHH--HhhceeEecceeehhHHHHhh
Confidence            3333456668888999999997  788899999999999999999999888887654  233688999999999988888


Q ss_pred             HHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eecC---ccCCCCceEEEEeCCC----CCCHHHHH
Q psy1539         102 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVNY---ETNLSGVVVNVMDVRS----GGWWLDLE  167 (175)
Q Consensus       102 ~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~---~~~~~~~~~lVlDEad----~~f~~~v~  167 (175)
                      +..+.... |+.+...+|........    +...+-|+       +.+.   .-++..+.++|+||.+    .+-..+++
T Consensus       289 l~~~~~~~-G~~ve~y~g~~~p~~~~----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE  363 (1008)
T KOG0950|consen  289 LSPFSIDL-GFPVEEYAGRFPPEKRR----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILE  363 (1008)
T ss_pred             hhhhcccc-CCcchhhcccCCCCCcc----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHH
Confidence            88888887 99888887776543332    22356666       2222   2356688999999993    33334444


Q ss_pred             HHH
Q psy1539         168 ALI  170 (175)
Q Consensus       168 ~il  170 (175)
                      .++
T Consensus       364 ~~l  366 (1008)
T KOG0950|consen  364 LLL  366 (1008)
T ss_pred             HHH
Confidence            444

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

Probab=98.50  E-value=1.4e-06  Score=64.94  Aligned_cols=113  Identities=19%  Similarity=0.142  Sum_probs=65.7

Q ss_pred             CCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .+++-|.+++..++.+  +-.++.++.|+|||.+ +-.+...+..  .+.++++++||..-+..+.+..        ++.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~--~g~~v~~~apT~~Aa~~L~~~~--------~~~   69 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEA--AGKRVIGLAPTNKAAKELREKT--------GIE   69 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHH--TT--EEEEESSHHHHHHHHHHH--------TS-
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHh--CCCeEEEECCcHHHHHHHHHhh--------Ccc
Confidence            3689999999999754  3577889999999965 3345555544  3568999999998887755542        222


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      +..+.          .+....+.  .-......+.+..++|+|||.+.-..++..++.
T Consensus        70 a~Ti~----------~~l~~~~~--~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~  115 (196)
T PF13604_consen   70 AQTIH----------SFLYRIPN--GDDEGRPELPKKDVLIVDEASMVDSRQLARLLR  115 (196)
T ss_dssp             EEEHH----------HHTTEECC--EECCSSCC-TSTSEEEESSGGG-BHHHHHHHHH
T ss_pred             hhhHH----------HHHhcCCc--ccccccccCCcccEEEEecccccCHHHHHHHHH
Confidence            21111          01000000  000001114566799999998887777777765

>TIGR00376 DNA helicase, putative

Probab=98.43  E-value=8.7e-06  Score=70.73  Aligned_cols=67  Identities=19%  Similarity=0.151  Sum_probs=51.1

Q ss_pred             CCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          35 REQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      ..+++.|.+|+..++.. ...+|.+|+|+|||.+..--+.+.+.   .+.++++++||..-+.++.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~---~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVK---RGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHH---cCCCEEEEcCcHHHHHHHHHHHHh
Confidence            35799999999988876 77889999999999655433333332   344899999999888887776654

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.

>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=98.43  E-value=1.8e-06  Score=64.64  Aligned_cols=127  Identities=11%  Similarity=0.133  Sum_probs=67.4

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH-------HHHHHHH--
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI-------SKEYERF--  105 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~-------~~~~~~~--  105 (175)
                      ...|+.|..++..+++..-+++.+|.|||||+..+...++.+.. ....+.++.-|..+....+       .+.+..+  
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            45689999999999988999999999999999998888888766 3445778888876532221       1111111  


Q ss_pred             --HhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC--ccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         106 --SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY--ETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       106 --~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~--~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                        ...+..+-     +    ....+.+.+...+-+.-...  ...|+ -.++|+|||...-..+++.+|-+
T Consensus        82 p~~d~l~~~~-----~----~~~~~~~~~~~~Ie~~~~~~iRGrt~~-~~~iIvDEaQN~t~~~~k~ilTR  142 (205)
T PF02562_consen   82 PIYDALEELF-----G----KEKLEELIQNGKIEIEPLAFIRGRTFD-NAFIIVDEAQNLTPEELKMILTR  142 (205)
T ss_dssp             HHHHHHTTTS----------TTCHHHHHHTTSEEEEEGGGGTT--B--SEEEEE-SGGG--HHHHHHHHTT
T ss_pred             HHHHHHHHHh-----C----hHhHHHHhhcCeEEEEehhhhcCcccc-ceEEEEecccCCCHHHHHHHHcc
Confidence              11110110     1    22333333333444441111  22233 38999999977777888888765

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

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.40  E-value=2.7e-06  Score=76.41  Aligned_cols=118  Identities=19%  Similarity=0.104  Sum_probs=74.6

Q ss_pred             CCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .|.|+|.++...+++.  ..+++.-..|.|||+-..+.+...+... ...++||+||. .|..|+...+.+..    ++.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~kF----~l~  225 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRRF----NLR  225 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHHh----CCC
Confidence            4899999998776643  5789999999999988766555444433 33479999998 89999887775433    444


Q ss_pred             EEEEECCCchHH--h-HHHHhcCCCeEEE----eecC-----ccCCCCceEEEEeCCCC
Q psy1539         114 VGVFFGGLPIQK--D-EEYLKTHNPQIVG----LVNY-----ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       114 v~~~~g~~~~~~--~-~~~l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDEad~  160 (175)
                      ..++.++.....  . ...+ ...+++|+    +.+.     .+.-.+.+++|+|||++
T Consensus       226 ~~i~~~~~~~~~~~~~~~pf-~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~  283 (956)
T PRK04914        226 FSLFDEERYAEAQHDADNPF-ETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHH  283 (956)
T ss_pred             eEEEcCcchhhhcccccCcc-ccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhh
Confidence            444433321100  0 0111 12466666    2221     12234789999999953

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.40  E-value=4e-06  Score=75.82  Aligned_cols=120  Identities=14%  Similarity=0.114  Sum_probs=77.4

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .+.++|.+++..+.    +|.+.++.-..|.|||+-.+ .++..+.. .......|||||. .+..|+.+.++++.   |
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaI-alL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~---p  243 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTI-SLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFC---P  243 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHH-HHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHC---C
Confidence            57899999997664    57889999999999998643 33443332 1222358999997 56678888888775   5


Q ss_pred             CeEEEEEECCCchHHhHH--HHh-cCCCeEEE----eecC--ccCCCCceEEEEeCCCC
Q psy1539         111 NIKVGVFFGGLPIQKDEE--YLK-THNPQIVG----LVNY--ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~--~l~-~~~~iiv~----l~~~--~~~~~~~~~lVlDEad~  160 (175)
                      .+++..++|.........  .+. ...+++|+    +.+.  .+.--+..++|+|||+.
T Consensus       244 ~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~L~k~~W~~VIvDEAHr  302 (1033)
T PLN03142        244 VLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHR  302 (1033)
T ss_pred             CCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHHhccCCCCEEEEcCccc
Confidence            678888887654322211  111 23466666    2221  12222567999999953

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.39  E-value=2.7e-06  Score=74.91  Aligned_cols=123  Identities=16%  Similarity=0.070  Sum_probs=90.8

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          33 PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      |. .|+++|...--.+..|  -+....||-|||++..+|+.-...   .|..+-|++..--||..=.+++..+.+.+ |+
T Consensus        76 G~-r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL---~GkgVhVVTvNdYLA~RDae~mg~vy~fL-GL  148 (925)
T PRK12903         76 GK-RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNAL---TGKGVIVSTVNEYLAERDAEEMGKVFNFL-GL  148 (925)
T ss_pred             CC-CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHh---cCCceEEEecchhhhhhhHHHHHHHHHHh-CC
Confidence            44 5788888777666666  479999999999999998865444   34468888999999998888899998888 99


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCCHH
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGWWL  164 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f~~  164 (175)
                      +|++...+.+..+..+..  .|+|..+         |.++      ....+.+.+.|+||+|....+
T Consensus       149 svG~i~~~~~~~~rr~aY--~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILID  213 (925)
T PRK12903        149 SVGINKANMDPNLKREAY--ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILID  213 (925)
T ss_pred             ceeeeCCCCChHHHHHhc--cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeec
Confidence            999998887655444444  4799988         1111      122467889999999644433

>PF13245 AAA_19: Part of AAA domain

Probab=98.38  E-value=2.5e-06  Score=53.87  Aligned_cols=59  Identities=25%  Similarity=0.369  Sum_probs=40.2

Q ss_pred             hHHHHhcCCc-EEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHH
Q psy1539          44 CIPQAVLGMD-ILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        44 ~i~~~~~g~~-~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      ++...+++.+ ++|.+|+|||||....--+...+.. ...+.++++++||+..+.++.+.+
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            4443333444 5569999999996665555444421 122568999999999999887777

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

Probab=98.36  E-value=3.2e-06  Score=63.55  Aligned_cols=68  Identities=24%  Similarity=0.317  Sum_probs=50.3

Q ss_pred             CCcHHHHHhHHHHhcCCc-EEEEcCCCChHHHHHHHHHHHhh------hcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLGMD-ILCQAKSGMGKTAVFVLATLQQL------ETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~-~ii~a~TGsGKT~~~~~~~l~~l------~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      ++++-|.+|+..+++... .+|.||+|+|||.+.. .++..+      .....+.++|+++|+..-+.++.+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            368899999999999998 9999999999995443 344443      1234566899999999999998888777

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.32  E-value=1.1e-05  Score=74.28  Aligned_cols=120  Identities=12%  Similarity=0.081  Sum_probs=65.5

Q ss_pred             hCCCCCCcHHHH---HhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          31 SQPFREQTSFQH---ECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        31 ~~g~~~~t~~Q~---~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ...|...-|+..   +.+..+.++..++++|+||||||.  .+|.+-.-.......++++.-|.|--|..+...+.+-  
T Consensus        59 ~~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~e--  134 (1283)
T TIGR01967        59 EIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTT--QLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEE--  134 (1283)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHH--
Confidence            345655556554   344555567888999999999998  3464432211111223444457776665555444332  


Q ss_pred             hCCCeEEEEEECC-CchHHhHHHHhcCCCeEEE----ee---cCccCCCCceEEEEeCCC
Q psy1539         108 YMSNIKVGVFFGG-LPIQKDEEYLKTHNPQIVG----LV---NYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       108 ~~~~i~v~~~~g~-~~~~~~~~~l~~~~~iiv~----l~---~~~~~~~~~~~lVlDEad  159 (175)
                       . +..++..+|. .....+.   .++..|+++    ++   .....+++++++|+||||
T Consensus       135 -l-g~~lG~~VGY~vR~~~~~---s~~T~I~~~TdGiLLr~l~~d~~L~~~~~IIIDEaH  189 (1283)
T TIGR01967       135 -L-GTPLGEKVGYKVRFHDQV---SSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAH  189 (1283)
T ss_pred             -h-CCCcceEEeeEEcCCccc---CCCceeeeccccHHHHHhhhCcccccCcEEEEcCcc
Confidence             2 3444444442 1111111   223456555    22   223458899999999996

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.

>KOG1802|consensus

Probab=98.27  E-value=9e-06  Score=69.47  Aligned_cols=85  Identities=15%  Similarity=0.074  Sum_probs=65.0

Q ss_pred             HHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          28 IGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        28 ~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .+...++.+++.-|..|...+++..=.+|++|+|+|||.+-.--+.+....  ....+|+.+|+.--+.|+.+.+.+-  
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLaeKIh~t--  477 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAEKIHKT--  477 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHHHHHhc--
Confidence            566678889999999999999999999999999999997754444443333  4447999999998888877665543  


Q ss_pred             hCCCeEEEEEEC
Q psy1539         108 YMSNIKVGVFFG  119 (175)
Q Consensus       108 ~~~~i~v~~~~g  119 (175)
                         +++|..+..
T Consensus       478 ---gLKVvRl~a  486 (935)
T KOG1802|consen  478 ---GLKVVRLCA  486 (935)
T ss_pred             ---CceEeeeeh
Confidence               556655544

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.24  E-value=1.3e-05  Score=68.86  Aligned_cols=126  Identities=17%  Similarity=0.177  Sum_probs=71.5

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHH--HHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVF--VLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~--~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      ...|+.|+...+.++-.++.++.|+|||...  ++..+..........++++.+||-.=+..+.+.+..-.... ...-.
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l-~~~~~  225 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNL-AAAEA  225 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhccc-ccchh
Confidence            3789999999999999999999999999653  23333222221123578999999877777666554432211 00000


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEe-------ecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGL-------VNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l-------~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ... ...  ....    ..+-+++.       .....+...++++|+|||.|.=...+..++.
T Consensus       226 ~~~-~~~--~~a~----TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd~~l~~~ll~  281 (586)
T TIGR01447       226 LIA-ALP--SEAV----TIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVDLPLMAKLLK  281 (586)
T ss_pred             hhh-ccc--cccc----hhhhhhcccCCcchhhhcccCCCcccEEEEcccccCCHHHHHHHHH
Confidence            000 000  0000    00011110       0011223468999999998887777777765

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.

>COG4889 Predicted helicase [General function prediction only]

Probab=98.22  E-value=5.7e-06  Score=72.69  Aligned_cols=128  Identities=15%  Similarity=0.128  Sum_probs=80.1

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcC-----CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLG-----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g-----~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ++...+.-..-.+|+|+|+.|+....+|     +.-+|. .+|+|||.+.+ -+.+.+-.    .++|+++|+..|..|.
T Consensus       149 e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIM-AcGTGKTfTsL-kisEala~----~~iL~LvPSIsLLsQT  222 (1518)
T COG4889         149 ELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIM-ACGTGKTFTSL-KISEALAA----ARILFLVPSISLLSQT  222 (1518)
T ss_pred             ccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEE-ecCCCccchHH-HHHHHHhh----hheEeecchHHHHHHH
Confidence            4444454445568999999999988865     444544 47999998753 33333322    5899999999999996


Q ss_pred             HHHHHHHHhhCCCeEEEEEECCCchHHh-----------------------HHHHhcCCC--eEEEeecC--------cc
Q psy1539          99 SKEYERFSKYMSNIKVGVFFGGLPIQKD-----------------------EEYLKTHNP--QIVGLVNY--------ET  145 (175)
Q Consensus        99 ~~~~~~~~~~~~~i~v~~~~g~~~~~~~-----------------------~~~l~~~~~--iiv~l~~~--------~~  145 (175)
                      .+.+..=.+.  .++...++++......                       ++..++...  ++.++.+.        ..
T Consensus       223 lrew~~~~~l--~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~  300 (1518)
T COG4889         223 LREWTAQKEL--DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEA  300 (1518)
T ss_pred             HHHHhhccCc--cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHHHHc
Confidence            6665443222  5666666666443221                       111122222  33333332        45


Q ss_pred             CCCCceEEEEeCCC
Q psy1539         146 NLSGVVVNVMDVRS  159 (175)
Q Consensus       146 ~~~~~~~lVlDEad  159 (175)
                      -+..++++|.|||+
T Consensus       301 G~~~fDliicDEAH  314 (1518)
T COG4889         301 GLDEFDLIICDEAH  314 (1518)
T ss_pred             CCCCccEEEecchh
Confidence            67889999999993

>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=98.21  E-value=7.9e-06  Score=64.29  Aligned_cols=70  Identities=20%  Similarity=0.153  Sum_probs=53.9

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      +|+-|.+++..  ...+++|.|+.|||||.+.+.-++..+... -...+.+++++|+..+.++.+.+......
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            47889999877  788999999999999988766665555443 34457999999999999999998887544

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 ....

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.17  E-value=8.9e-06  Score=71.80  Aligned_cols=73  Identities=14%  Similarity=0.158  Sum_probs=62.4

Q ss_pred             CcHHHHHhHHHHhcC---C-cEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHhhC
Q psy1539          37 QTSFQHECIPQAVLG---M-DILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g---~-~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      ..+.|..++..+.+.   . .+++.+|||.|||.+.+.++...... .....+.+++.|++.+++++++.++.+....
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~  273 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF  273 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccc
Confidence            488999999877754   4 88999999999999999988887765 3467799999999999999999999887654

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

Probab=98.16  E-value=3.3e-06  Score=59.44  Aligned_cols=95  Identities=19%  Similarity=0.158  Sum_probs=54.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  129 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~  129 (175)
                      +|+-.++-..+|+|||--.+.-++.....  .+.++|+|.|||.++..+.+.++..     .+++..   ... ..   .
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~--~~~rvLvL~PTRvva~em~~aL~~~-----~~~~~t---~~~-~~---~   68 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK--RRLRVLVLAPTRVVAEEMYEALKGL-----PVRFHT---NAR-MR---T   68 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH--TT--EEEEESSHHHHHHHHHHTTTS-----SEEEES---TTS-S-----
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH--ccCeEEEecccHHHHHHHHHHHhcC-----CcccCc---eee-ec---c
Confidence            45667788999999998776666665443  4558999999999998877766532     333321   110 00   0


Q ss_pred             HhcCCCeEEE--------eecCccCCCCceEEEEeCCC
Q psy1539         130 LKTHNPQIVG--------LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       130 l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEad  159 (175)
                      -..+..+-+.        +.+ .....+.+++|+||++
T Consensus        69 ~~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH  105 (148)
T PF07652_consen   69 HFGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECH  105 (148)
T ss_dssp             --SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT
T ss_pred             ccCCCcccccccHHHHHHhcC-cccccCccEEEEeccc
Confidence            1112222222        222 4556799999999994

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 ....

>KOG1123|consensus

Probab=98.13  E-value=3.1e-06  Score=70.27  Aligned_cols=128  Identities=14%  Similarity=0.137  Sum_probs=89.2

Q ss_pred             CCcHHHHHhHHHHhc-C--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          36 EQTSFQHECIPQAVL-G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~-g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      .++|+|..++..+.. |  ++-+|..|.|+|||++-+-+++..      ...+|++|.+---+.|+..++..+..-- .-
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~ti------kK~clvLcts~VSVeQWkqQfk~wsti~-d~  374 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTI------KKSCLVLCTSAVSVEQWKQQFKQWSTIQ-DD  374 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeee------cccEEEEecCccCHHHHHHHHHhhcccC-cc
Confidence            578999999998884 4  788999999999998765544322      1268999999999999999999887654 45


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEEeecC----------------ccCCCCceEEEEeCCCCC---CHHHHHHHHhhh
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY----------------ETNLSGVVVNVMDVRSGG---WWLDLEALILSK  173 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~----------------~~~~~~~~~lVlDEad~~---f~~~v~~il~~~  173 (175)
                      .++.++++...     ....++.++|.+...                .+.-+.-.++++||++-.   ...-|-.|+.++
T Consensus       375 ~i~rFTsd~Ke-----~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv~aH  449 (776)
T KOG1123|consen  375 QICRFTSDAKE-----RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIVQAH  449 (776)
T ss_pred             ceEEeeccccc-----cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHHHHH
Confidence            57777766532     233577888872111                122245689999999532   223455666666


Q ss_pred             cC
Q psy1539         174 CA  175 (175)
Q Consensus       174 ~~  175 (175)
                      |+
T Consensus       450 cK  451 (776)
T KOG1123|consen  450 CK  451 (776)
T ss_pred             hh
Confidence            63

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.09  E-value=7.7e-05  Score=67.63  Aligned_cols=112  Identities=21%  Similarity=0.132  Sum_probs=74.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  131 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~  131 (175)
                      +.-+|+--+|||||++-+..+-. +......+.+++|+-.++|-.|+.+.+..+.... ....    ...+..+-.+.+.
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~-l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~-~~~~----~~~s~~~Lk~~l~  347 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARL-LLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVA-FNDP----KAESTSELKELLE  347 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHH-HHhccCCCeEEEEechHHHHHHHHHHHHHHHHhh-hhcc----cccCHHHHHHHHh
Confidence            56899999999999876544332 2233677899999999999999999999998764 1111    2334344445555


Q ss_pred             cCC-CeEEEeecCc----------cCCCCceEEEEeCCCCCCHHHHHHH
Q psy1539         132 THN-PQIVGLVNYE----------TNLSGVVVNVMDVRSGGWWLDLEAL  169 (175)
Q Consensus       132 ~~~-~iiv~l~~~~----------~~~~~~~~lVlDEad~~f~~~v~~i  169 (175)
                      .+. .+|+++++..          ..-.+=-.+|+|||+.+..+.....
T Consensus       348 ~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~G~~~~~  396 (962)
T COG0610         348 DGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQYGELAKL  396 (962)
T ss_pred             cCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhccccHHHHH
Confidence            443 6888866650          1123445679999975544444433

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.07  E-value=8.6e-05  Score=64.22  Aligned_cols=131  Identities=18%  Similarity=0.090  Sum_probs=72.1

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHHH--HHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFV--LATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~--~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .+.|+.|+-..+.++-.+|.+++|+|||.+..  +..+.... .....++.+.+||..=+..+.+.+....... ++.-.
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~-~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~-~~~~~  231 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLA-DGERCRIRLAAPTGKAAARLTESLGKALRQL-PLTDE  231 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhc-CCCCcEEEEECCcHHHHHHHHHHHHhhhhcc-ccchh
Confidence            58999999999999999999999999996532  22222221 1223578888999888887777665433322 11000


Q ss_pred             EEECCCc-hHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         116 VFFGGLP-IQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       116 ~~~g~~~-~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      . ..... ...-+..+..-.+.=-....+..+.-..+++|+||++|.-...+..++.
T Consensus       232 ~-~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~  287 (615)
T PRK10875        232 Q-KKRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLID  287 (615)
T ss_pred             h-hhcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHH
Confidence            0 00000 0011111110000000000011223356899999998877777776665

>PRK10536 hypothetical protein; Provisional

Probab=98.05  E-value=0.00012  Score=56.56  Aligned_cols=61  Identities=15%  Similarity=0.124  Sum_probs=45.1

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .++...+..|...+..+.++..+++.+|+|+|||+......++.+..+ .-.++++.-|+.+
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~  115 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQ  115 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCC
Confidence            344556889999999999989999999999999988777676665442 2334555556644

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.98  E-value=3.2e-05  Score=69.14  Aligned_cols=119  Identities=18%  Similarity=0.079  Sum_probs=84.2

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEE
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGV  116 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~  116 (175)
                      |+++|...--.+  ...-+....||-|||++..+|+.-....   |..+-+++..--||..=.+++..+.+.+ |++|++
T Consensus       139 ~ydVQLiGgivL--h~G~IAEM~TGEGKTLvatlp~yLnAL~---G~gVHvVTvNDYLA~RDaewm~p~y~fl-GLtVg~  212 (1025)
T PRK12900        139 PYDVQLIGGIVL--HSGKISEMATGEGKTLVSTLPTFLNALT---GRGVHVVTVNDYLAQRDKEWMNPVFEFH-GLSVGV  212 (1025)
T ss_pred             ccchHHhhhHHh--hcCCccccCCCCCcchHhHHHHHHHHHc---CCCcEEEeechHhhhhhHHHHHHHHHHh-CCeeee
Confidence            555665543333  3455789999999999999998765554   3357788888899998888899998888 999999


Q ss_pred             EECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCCH
Q psy1539         117 FFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGWW  163 (175)
Q Consensus       117 ~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f~  163 (175)
                      +..+.+..+..+..  .|+|..|         |.++      ....+.+.+.|+||+|....
T Consensus       213 i~~~~~~~~Rr~aY--~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvLI  272 (1025)
T PRK12900        213 ILNTMRPEERREQY--LCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVLI  272 (1025)
T ss_pred             eCCCCCHHHHHHhC--CCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhhh
Confidence            87766544333333  5799988         2222      22346788999999964333

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.98  E-value=8.3e-05  Score=65.59  Aligned_cols=119  Identities=13%  Similarity=0.021  Sum_probs=70.4

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .++ .+++-|++|+..+..++-.++.++.|+|||... -.++..+....+...+++.+||-.-+..+.+..        +
T Consensus       320 ~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~--------g  389 (720)
T TIGR01448       320 LRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEVT--------G  389 (720)
T ss_pred             cCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHhc--------C
Confidence            444 689999999999998899999999999999643 344444443221246888899987776543321        1


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .....+      -   +.+.....-..  ..........+++|+|||.|.-...+..++.
T Consensus       390 ~~a~Ti------h---~lL~~~~~~~~--~~~~~~~~~~~llIvDEaSMvd~~~~~~Ll~  438 (720)
T TIGR01448       390 LTASTI------H---RLLGYGPDTFR--HNHLEDPIDCDLLIVDESSMMDTWLALSLLA  438 (720)
T ss_pred             CccccH------H---HHhhccCCccc--hhhhhccccCCEEEEeccccCCHHHHHHHHH
Confidence            111000      0   00000000000  0000112457899999998877777777765

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.

>KOG0389|consensus

Probab=97.93  E-value=7.8e-05  Score=64.85  Aligned_cols=118  Identities=16%  Similarity=0.159  Sum_probs=82.3

Q ss_pred             CcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          37 QTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      +-++|.--+..+.    .+-+.|+.-.-|-|||. =+++.+..+.......--||+||...|-    .+++.+.+-+|.+
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTi-QvIaFlayLkq~g~~gpHLVVvPsSTle----NWlrEf~kwCPsl  474 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTI-QVIAFLAYLKQIGNPGPHLVVVPSSTLE----NWLREFAKWCPSL  474 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchh-HHHHHHHHHHHcCCCCCcEEEecchhHH----HHHHHHHHhCCce
Confidence            7789988876543    46777999999999994 3455566655443333479999987763    5666676667899


Q ss_pred             EEEEEECCCchHHhHHHHhc----CCCeEEEeec---C------ccCCCCceEEEEeCCC
Q psy1539         113 KVGVFFGGLPIQKDEEYLKT----HNPQIVGLVN---Y------ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~----~~~iiv~l~~---~------~~~~~~~~~lVlDEad  159 (175)
                      +|...+|.....++++...+    +-++++++.+   .      .+.-.++.++|.||++
T Consensus       475 ~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgH  534 (941)
T KOG0389|consen  475 KVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGH  534 (941)
T ss_pred             EEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchh
Confidence            99999999876666654332    3467776222   1      2344589999999994

>KOG0952|consensus

Probab=97.92  E-value=5.4e-06  Score=73.69  Aligned_cols=120  Identities=18%  Similarity=0.225  Sum_probs=91.2

Q ss_pred             CCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCe
Q psy1539          34 FREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  112 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i  112 (175)
                      ++...|+|.+.+-.... ..+.++-+|||+|||++|.+++...+... .+.++++++|..+|+....+.+.+.... +|+
T Consensus       925 ~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~-p~~kvvyIap~kalvker~~Dw~~r~~~-~g~ 1002 (1230)
T KOG0952|consen  925 YKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYY-PGSKVVYIAPDKALVKERSDDWSKRDEL-PGI 1002 (1230)
T ss_pred             hcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccC-CCccEEEEcCCchhhcccccchhhhccc-CCc
Confidence            44667788887755554 47899999999999999999988776654 3469999999999998877777665544 499


Q ss_pred             EEEEEECCCchHHhHHHHhcCCCeEEE-------eec---CccCCCCceEEEEeCC
Q psy1539         113 KVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVN---YETNLSGVVVNVMDVR  158 (175)
Q Consensus       113 ~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~---~~~~~~~~~~lVlDEa  158 (175)
                      ++.-+.|+...+  ...+.. .+++|.       ..+   ....++++..+|+||.
T Consensus      1003 k~ie~tgd~~pd--~~~v~~-~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~ 1055 (1230)
T KOG0952|consen 1003 KVIELTGDVTPD--VKAVRE-ADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEI 1055 (1230)
T ss_pred             eeEeccCccCCC--hhheec-CceEEcccccccCccccccchhhhccccceeeccc
Confidence            999999987643  444443 467776       222   2567889999999998

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.83  E-value=0.00065  Score=61.66  Aligned_cols=113  Identities=16%  Similarity=0.020  Sum_probs=72.3

Q ss_pred             CCCCCCcHHHHHhHHHHhcCC-cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~-~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .|+ .+++-|.+|+..++.++ -+++.++.|+|||.. +-++...+..  .+.+++.++||-.-+..+.+       .. 
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~--~G~~V~~~ApTGkAA~~L~e-------~t-  410 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA--AGYEVRGAALSGIAAENLEG-------GS-  410 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH--cCCeEEEecCcHHHHHHHhh-------cc-
Confidence            454 58999999999999865 478999999999975 3444444443  45689999999766544322       11 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      ++...      ........+..+          ...+....++|+||+.|.-..++..+|..
T Consensus       411 Gi~a~------TI~sll~~~~~~----------~~~l~~~~vlIVDEASMv~~~~m~~LL~~  456 (988)
T PRK13889        411 GIASR------TIASLEHGWGQG----------RDLLTSRDVLVIDEAGMVGTRQLERVLSH  456 (988)
T ss_pred             Ccchh------hHHHHHhhhccc----------ccccccCcEEEEECcccCCHHHHHHHHHh
Confidence            22211      111111111111          12345778999999998888888888753

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

Probab=97.82  E-value=6.2e-05  Score=63.07  Aligned_cols=67  Identities=25%  Similarity=0.296  Sum_probs=52.3

Q ss_pred             CCcHHHHHhHHHHhcC-----CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          36 EQTSFQHECIPQAVLG-----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g-----~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      .|+.-|-+||..+.+|     +.-.+.+.||||||.+..--+. ...     .-+||++|.+.||-|++..++.|...
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI~-~~~-----rPtLV~AhNKTLAaQLy~Efk~fFP~   83 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIA-KVQ-----RPTLVLAHNKTLAAQLYSEFKEFFPE   83 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHHH-HhC-----CCeEEEecchhHHHHHHHHHHHhCcC
Confidence            5788888898777654     6788899999999987544332 222     14899999999999999999988644

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.80  E-value=0.00096  Score=59.21  Aligned_cols=123  Identities=14%  Similarity=0.021  Sum_probs=75.1

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      +++..++.....++ .+++-|.+|+..++.+ +-+++.++.|+|||... -++...+..  .+.+++.++||-.-+..+.
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~--~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEA--AGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHh--CCCeEEEEeCcHHHHHHHH
Confidence            44444443333333 5899999999998874 67899999999999643 334444433  3567999999976655433


Q ss_pred             HHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         100 KEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       100 ~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      +       .. ++....+      ......+..          ....+...+++|+||+.|.=..++..++.
T Consensus       414 ~-------~~-g~~a~Ti------~~~~~~~~~----------~~~~~~~~~llIvDEasMv~~~~~~~Ll~  461 (744)
T TIGR02768       414 A-------ES-GIESRTL------ASLEYAWAN----------GRDLLSDKDVLVIDEAGMVGSRQMARVLK  461 (744)
T ss_pred             h-------cc-CCceeeH------HHHHhhhcc----------CcccCCCCcEEEEECcccCCHHHHHHHHH
Confidence            2       11 3222111      111011111          11234678999999998877777777765

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.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.80  E-value=9.8e-05  Score=66.34  Aligned_cols=118  Identities=16%  Similarity=0.040  Sum_probs=82.0

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEE
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGV  116 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~  116 (175)
                      |.++|..  -.+.-...-+....||-|||++..+|+.-....   |..+-+++..--||..=.+++..+.+.+ |+++++
T Consensus       170 ~yDVQli--GgivLh~G~IAEM~TGEGKTLvAtlp~yLnAL~---GkgVHvVTVNDYLA~RDaewmgply~fL-GLsvg~  243 (1112)
T PRK12901        170 HYDVQLI--GGVVLHQGKIAEMATGEGKTLVATLPVYLNALT---GNGVHVVTVNDYLAKRDSEWMGPLYEFH-GLSVDC  243 (1112)
T ss_pred             ccchHHh--hhhhhcCCceeeecCCCCchhHHHHHHHHHHHc---CCCcEEEEechhhhhccHHHHHHHHHHh-CCceee
Confidence            4555544  444445566789999999999999998766554   3357788888899988888888888888 999998


Q ss_pred             EEC-CCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCCCCC
Q psy1539         117 FFG-GLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRSGGW  162 (175)
Q Consensus       117 ~~g-~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad~~f  162 (175)
                      +.. +.+. ++.+.. =.|+|..+         |.++      ....+.+.+.|+||+|...
T Consensus       244 i~~~~~~~-~~rr~a-Y~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        244 IDKHQPNS-EARRKA-YNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             cCCCCCCH-HHHHHh-CCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            866 3333 333222 24799888         2222      2234568899999996433

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.79  E-value=0.00011  Score=59.92  Aligned_cols=59  Identities=20%  Similarity=0.273  Sum_probs=42.3

Q ss_pred             CcHHHHHhHHHH------hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          37 QTSFQHECIPQA------VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        37 ~t~~Q~~~i~~~------~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      +++-|++++..+      .++.++++.++-|+|||..  +-.+...... .+..+++.+||-.=|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l--~~~i~~~~~~-~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFL--IKAIIDYLRS-RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHH--HHHHHHHhcc-ccceEEEecchHHHHHhc
Confidence            678899998888      6789999999999999864  3333333322 345788888986555444

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.69  E-value=0.00015  Score=58.84  Aligned_cols=52  Identities=21%  Similarity=0.375  Sum_probs=38.0

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      -++|.+..|||||+..+ -++..+.....+.+++++++...|...+++.+..-
T Consensus         3 v~~I~G~aGTGKTvla~-~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    3 VILITGGAGTGKTVLAL-NLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEEecCCcCHHHHHH-HHHHHhhccccCCceEEEEecchHHHHHHHHHhhh
Confidence            47899999999997654 34444422335568999999999998877776544

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG1805|consensus

Probab=97.67  E-value=0.00056  Score=60.92  Aligned_cols=130  Identities=16%  Similarity=0.077  Sum_probs=74.7

Q ss_pred             CCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCc-EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          19 RNRREKEDRIGESQPFREQTSFQHECIPQAVLGMD-ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        19 ~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~-~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      ..+.|.+.+.    -+..++.-|++|+-.++..+| .+|.+=+|+|||..-. .++..+..  .+.++|..+-|..=+.-
T Consensus       656 ~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~-~LIkiL~~--~gkkVLLtsyThsAVDN  728 (1100)
T KOG1805|consen  656 KVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTIS-LLIKILVA--LGKKVLLTSYTHSAVDN  728 (1100)
T ss_pred             cccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHH-HHHHHHHH--cCCeEEEEehhhHHHHH
Confidence            3444454443    234789999999998887754 6888999999996532 23333332  34467777777655544


Q ss_pred             HHHHHHHHHhhCCCeEEEEEECCCchHHhH-----------------HHHhcCCCeEEE----eecCccCCCCceEEEEe
Q psy1539          98 ISKEYERFSKYMSNIKVGVFFGGLPIQKDE-----------------EYLKTHNPQIVG----LVNYETNLSGVVVNVMD  156 (175)
Q Consensus        98 ~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~-----------------~~l~~~~~iiv~----l~~~~~~~~~~~~lVlD  156 (175)
                      +.-.++.+     ++.+..+..+.....+.                 +...+...|+.+    +.+..+..+++++.|+|
T Consensus       729 ILiKL~~~-----~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf~~R~FD~cIiD  803 (1100)
T KOG1805|consen  729 ILIKLKGF-----GIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLFVNRQFDYCIID  803 (1100)
T ss_pred             HHHHHhcc-----CcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhhhccccCEEEEc
Confidence            43333333     33333333332222222                 233333444444    22225666789999999


Q ss_pred             CCCC
Q psy1539         157 VRSG  160 (175)
Q Consensus       157 Ead~  160 (175)
                      ||.+
T Consensus       804 EASQ  807 (1100)
T KOG1805|consen  804 EASQ  807 (1100)
T ss_pred             cccc
Confidence            9953

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

Probab=97.54  E-value=0.00047  Score=62.08  Aligned_cols=51  Identities=14%  Similarity=0.120  Sum_probs=41.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .|+.+..+||+|||.+|+-.++... ...+..+.||+||+.+.-..+.+.++
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~-~~~~~~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELH-QKYGLFKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHH-HHcCCcEEEEEeCCHHHHHHHHHHhh
Confidence            4889999999999999987776543 33455689999999999888876655

>KOG0390|consensus

Probab=97.53  E-value=0.0011  Score=58.45  Aligned_cols=121  Identities=18%  Similarity=0.115  Sum_probs=78.7

Q ss_pred             CCcHHHHHhHHHHhc---C-------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCC-----eEEEEEecCHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVL---G-------MDILCQAKSGMGKTAVFVLATLQQLETTDSN-----VYVLVMCHTRELAFQISK  100 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~---g-------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~-----~~~lil~Pt~~L~~q~~~  100 (175)
                      .+.|+|++.+.-+++   |       ...++.-..|+|||+- .++.+..+.+....     .++||++|. .|+.-+++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq-~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQ-CISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHH-HHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHH
Confidence            579999999987764   2       2467777889999964 35566655554444     579999997 58888999


Q ss_pred             HHHHHHhhCCCeEEEEEECCCch--HHhHHHHhcC---C--CeEEE----eecC--ccCCCCceEEEEeCCC
Q psy1539         101 EYERFSKYMSNIKVGVFFGGLPI--QKDEEYLKTH---N--PQIVG----LVNY--ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       101 ~~~~~~~~~~~i~v~~~~g~~~~--~~~~~~l~~~---~--~iiv~----l~~~--~~~~~~~~~lVlDEad  159 (175)
                      .+.++.... .+....++|..+.  ......+.-+   .  ++.+.    +.++  .+....+.++|+||.+
T Consensus       316 EF~KWl~~~-~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~il~~~~glLVcDEGH  386 (776)
T KOG0390|consen  316 EFGKWLGNH-RINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRKILLIRPGLLVCDEGH  386 (776)
T ss_pred             HHHHhcccc-ccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHHHhcCCCCeEEECCCC
Confidence            999987653 6677777777652  0111111111   1  12121    1111  4566789999999993

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.48  E-value=0.0048  Score=56.68  Aligned_cols=125  Identities=15%  Similarity=0.030  Sum_probs=78.4

Q ss_pred             CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          20 NRREKEDRIGESQPFREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        20 ~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ++++..++.....++ .+++-|.+|+..+.. ++-.++.++.|+|||... -++...+..  .+.+++-++||-.=+..+
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-KAAREAWEA--AGYRVVGGALAGKAAEGL  441 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHH--cCCeEEEEcCcHHHHHHH
Confidence            455666665544444 689999999998764 467899999999999643 344444443  456889999996665443


Q ss_pred             HHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539          99 SKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus        99 ~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      .+       .. ++....+.      .....+..+          ...+..-.++|+||+.|.=..++..++..
T Consensus       442 ~e-------~~-Gi~a~TIa------s~ll~~~~~----------~~~l~~~~vlVIDEAsMv~~~~m~~Ll~~  491 (1102)
T PRK13826        442 EK-------EA-GIQSRTLS------SWELRWNQG----------RDQLDNKTVFVLDEAGMVASRQMALFVEA  491 (1102)
T ss_pred             HH-------hh-CCCeeeHH------HHHhhhccC----------ccCCCCCcEEEEECcccCCHHHHHHHHHH
Confidence            22       22 43332211      111111111          12355677999999998888888877653

>KOG0387|consensus

Probab=97.47  E-value=0.00091  Score=58.50  Aligned_cols=80  Identities=19%  Similarity=0.253  Sum_probs=56.4

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHH---HHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTA---VFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~---~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      .+.++|++.+..++    ++..-|+--.-|-|||+   +|+-++.+. .  +-...+|||||.. +..|+.+.+..+.  
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S-~--k~~~paLIVCP~T-ii~qW~~E~~~w~--  278 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHS-G--KLTKPALIVCPAT-IIHQWMKEFQTWW--  278 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhc-c--cccCceEEEccHH-HHHHHHHHHHHhC--
Confidence            56789999987766    46788889999999994   333333222 1  1223699999984 6678777777775  


Q ss_pred             CCCeEEEEEECCCc
Q psy1539         109 MSNIKVGVFFGGLP  122 (175)
Q Consensus       109 ~~~i~v~~~~g~~~  122 (175)
                       |.+++..++|..+
T Consensus       279 -p~~rv~ilh~t~s  291 (923)
T KOG0387|consen  279 -PPFRVFILHGTGS  291 (923)
T ss_pred             -cceEEEEEecCCc
Confidence             5678888887655

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=97.46  E-value=0.00073  Score=59.52  Aligned_cols=52  Identities=21%  Similarity=0.371  Sum_probs=38.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .-.+|.||.|||||.+..-.+-+.+.  ....++++++..+.|+.+....++..
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~--~~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALK--NPDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhcc--CCCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            44689999999999766444333332  24458999999999999988877654

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

>KOG0385|consensus

Probab=97.42  E-value=0.0014  Score=57.36  Aligned_cols=118  Identities=16%  Similarity=0.172  Sum_probs=76.5

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhc--CCCCeEEEEEecCHHHHHHHHHHHHHHHhhC
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~--~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      .++++|.+-+..+.    +|-|.++.-.-|-|||+- .++++.++..  +..|| -||++|...|.    .+.+.+.+..
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQ-tIs~l~yl~~~~~~~GP-fLVi~P~StL~----NW~~Ef~rf~  240 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQ-TISLLGYLKGRKGIPGP-FLVIAPKSTLD----NWMNEFKRFT  240 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHH-HHHHHHHHHHhcCCCCC-eEEEeeHhhHH----HHHHHHHHhC
Confidence            57899999876554    688999999999999954 3444444432  23444 68899988775    3455555556


Q ss_pred             CCeEEEEEECCCchHHhH-HH-Hhc-CCCeEEE-----eecC-ccCCCCceEEEEeCCC
Q psy1539         110 SNIKVGVFFGGLPIQKDE-EY-LKT-HNPQIVG-----LVNY-ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       110 ~~i~v~~~~g~~~~~~~~-~~-l~~-~~~iiv~-----l~~~-~~~~~~~~~lVlDEad  159 (175)
                      |++++..++|+....... +. +.. .-+++|+     +.+. .+.--+=+++|+|||+
T Consensus       241 P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk~~lk~~~W~ylvIDEaH  299 (971)
T KOG0385|consen  241 PSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDKSFLKKFNWRYLVIDEAH  299 (971)
T ss_pred             CCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhHHHHhcCCceEEEechhh
Confidence            899999999987432222 11 222 3456665     2222 2223356999999994

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.35  E-value=0.00069  Score=59.50  Aligned_cols=70  Identities=14%  Similarity=0.080  Sum_probs=52.9

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .+++-|++|+..  ....++|.|+.|||||.+...-+...+.. .-...++++++.|+.-|.++.+.+.+...
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            478999998864  34577889999999998866555555543 22234799999999999999988877643

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

Probab=97.34  E-value=0.00044  Score=61.61  Aligned_cols=113  Identities=15%  Similarity=0.023  Sum_probs=59.9

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEE
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF  117 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~  117 (175)
                      +....+.+..+.+..-++|+++||||||...-.-+++.-.  ..+.+..+.=|.|-=|.-+.+.+.+-...-.|-.|+.-
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~  129 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYS  129 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEE
Confidence            4445555666777889999999999999754333333322  12224555558775554444443332221123334332


Q ss_pred             ECCCchHHhHHHHhcCCCeEEE-------eecCccCCCCceEEEEeCC
Q psy1539         118 FGGLPIQKDEEYLKTHNPQIVG-------LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       118 ~g~~~~~~~~~~l~~~~~iiv~-------l~~~~~~~~~~~~lVlDEa  158 (175)
                      .-..+....      ...+-+.       .+.....++..+++|+|||
T Consensus       130 iRfe~~~s~------~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEa  171 (845)
T COG1643         130 IRFESKVSP------RTRIKVMTDGILLREIQNDPLLSGYSVVIIDEA  171 (845)
T ss_pred             EEeeccCCC------CceeEEeccHHHHHHHhhCcccccCCEEEEcch
Confidence            221111110      1122222       2222456899999999999

>KOG1803|consensus

Probab=97.31  E-value=0.00077  Score=57.33  Aligned_cols=63  Identities=21%  Similarity=0.176  Sum_probs=50.7

Q ss_pred             CCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      .+.+-|++|+....+. .-.++++|+|+|||.+...-+.+.+..   +.++|+.+||.+-+.-+.+.
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~---~k~VLVcaPSn~AVdNiver  248 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ---KKRVLVCAPSNVAVDNIVER  248 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc---CCeEEEEcCchHHHHHHHHH
Confidence            5788999999888877 557899999999998876666665554   34899999999888777774

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.29  E-value=0.0019  Score=56.73  Aligned_cols=71  Identities=18%  Similarity=0.147  Sum_probs=51.6

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ..+++-|++|+-.  ...+++|.|..|||||.+..--+...+... -...++++++.|+..|..+.+.+.....
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            4689999998853  335689999999999987654443333222 2334799999999999999888776543

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=97.28  E-value=0.0012  Score=52.89  Aligned_cols=68  Identities=24%  Similarity=0.212  Sum_probs=43.1

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHH-HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQ-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~-~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      .-++.+.+.|+  +++.|.+.+.. +..+++++++++|||||| +++-+++..+.......+.+++=.+.|+
T Consensus       122 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        122 FTLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            34555666564  56778887764 446799999999999999 5556666554211222345555555554

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.27  E-value=0.0032  Score=48.81  Aligned_cols=71  Identities=15%  Similarity=0.263  Sum_probs=45.5

Q ss_pred             HhhCCCCCCcHHHHHhHHHHh-------cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          29 GESQPFREQTSFQHECIPQAV-------LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~-------~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      +....|......+..++..+.       ++.++++.||+|+|||..+ .++...+..  .+ ..++++++.+++.++...
T Consensus        76 ~~~~d~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa-~Ai~~~l~~--~g-~sv~f~~~~el~~~Lk~~  151 (254)
T COG1484          76 FEEFDFEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLA-IAIGNELLK--AG-ISVLFITAPDLLSKLKAA  151 (254)
T ss_pred             cccccccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH-HHHHHHHHH--cC-CeEEEEEHHHHHHHHHHH
Confidence            344445555666666554333       5789999999999999643 344444442  34 455666888888776665


Q ss_pred             HH
Q psy1539         102 YE  103 (175)
Q Consensus       102 ~~  103 (175)
                      +.
T Consensus       152 ~~  153 (254)
T COG1484         152 FD  153 (254)
T ss_pred             Hh
Confidence            44

>KOG1002|consensus

Probab=97.27  E-value=0.0027  Score=53.25  Aligned_cols=95  Identities=23%  Similarity=0.232  Sum_probs=65.3

Q ss_pred             CCcHHHHHhHHHHhcC-----CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          36 EQTSFQHECIPQAVLG-----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g-----~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .+-|+|.+.+-.+...     ..-++.-.-|.|||+-.+.-++..    ..+...|+++|+.+|. |+.+.+.+....  
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae----~~ra~tLVvaP~VAlm-QW~nEI~~~T~g--  256 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAE----VDRAPTLVVAPTVALM-QWKNEIERHTSG--  256 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhc----cccCCeeEEccHHHHH-HHHHHHHHhccC--
Confidence            4678999887555432     355677789999997655444443    2334599999999985 778888877663  


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEE
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVG  139 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~  139 (175)
                      ..++-..+|... ....+.+.+ .++++.
T Consensus       257 slkv~~YhG~~R-~~nikel~~-YDvVLT  283 (791)
T KOG1002|consen  257 SLKVYIYHGAKR-DKNIKELMN-YDVVLT  283 (791)
T ss_pred             ceEEEEEecccc-cCCHHHhhc-CcEEEE
Confidence            566766666543 566666654 577776

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.27  E-value=0.0022  Score=52.42  Aligned_cols=83  Identities=16%  Similarity=0.129  Sum_probs=45.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec-C-HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-T-RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  128 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~  128 (175)
                      |..+++.+|||+|||....--....... .+..++.++.. + |.=+   .++++.+.+.+ ++.+.....+........
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~-~G~~~V~lit~D~~R~ga---~EqL~~~a~~~-gv~~~~~~~~~~l~~~l~  211 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMR-FGASKVALLTTDSYRIGG---HEQLRIFGKIL-GVPVHAVKDGGDLQLALA  211 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCeEEEEecccccccH---HHHHHHHHHHc-CCceEecCCcccHHHHHH
Confidence            5789999999999997654322222222 12124444432 2 2222   34566666666 777766655555555444


Q ss_pred             HHhcCCCeEEE
Q psy1539         129 YLKTHNPQIVG  139 (175)
Q Consensus       129 ~l~~~~~iiv~  139 (175)
                      .+.+ +++|+.
T Consensus       212 ~l~~-~DlVLI  221 (374)
T PRK14722        212 ELRN-KHMVLI  221 (374)
T ss_pred             HhcC-CCEEEE
Confidence            4443 455544

>KOG0953|consensus

Probab=97.26  E-value=0.00049  Score=58.05  Aligned_cols=93  Identities=17%  Similarity=0.115  Sum_probs=60.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  131 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~  131 (175)
                      +=++=++||.||||.-    +++++...+   .+++-.|.|-||.++++.++..     |+.|-+++|.......-.  -
T Consensus       192 kIi~H~GPTNSGKTy~----ALqrl~~ak---sGvycGPLrLLA~EV~~r~na~-----gipCdL~TGeE~~~~~~~--~  257 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYR----ALQRLKSAK---SGVYCGPLRLLAHEVYDRLNAL-----GIPCDLLTGEERRFVLDN--G  257 (700)
T ss_pred             eEEEEeCCCCCchhHH----HHHHHhhhc---cceecchHHHHHHHHHHHhhhc-----CCCccccccceeeecCCC--C
Confidence            3466688999999964    466776544   4678889999999999988766     788888888643211100  0


Q ss_pred             cCCCeEEEeecCccCCCCceEEEEeCC
Q psy1539         132 THNPQIVGLVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       132 ~~~~iiv~l~~~~~~~~~~~~lVlDEa  158 (175)
                      +.+.++=+++...---...+..|+||.
T Consensus       258 ~~a~hvScTVEM~sv~~~yeVAViDEI  284 (700)
T KOG0953|consen  258 NPAQHVSCTVEMVSVNTPYEVAVIDEI  284 (700)
T ss_pred             CcccceEEEEEEeecCCceEEEEehhH
Confidence            112333333433222356788999998

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.25  E-value=0.0015  Score=52.34  Aligned_cols=65  Identities=18%  Similarity=0.250  Sum_probs=39.7

Q ss_pred             HHHhhCCCCCCcHHHHHhHHHHh-cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          27 RIGESQPFREQTSFQHECIPQAV-LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        27 ~~l~~~g~~~~t~~Q~~~i~~~~-~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      +.+.+.|.  +++.|...+..+. .+.|++++++||||||. ++-+++..+.....+-+.+.+=.+.||
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTT-ll~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTT-LANAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHHHhcCCCCceEEEecCCccc
Confidence            34555554  5777887775544 56899999999999995 445666655321122244444444443

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.24  E-value=0.0023  Score=51.72  Aligned_cols=66  Identities=18%  Similarity=0.106  Sum_probs=51.1

Q ss_pred             CCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          32 QPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      .|...-+..|.-|+..++..  .=+.+.++-|||||+.++.+.+......+...+.++--|+..+.+.
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~d  291 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGED  291 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccc
Confidence            36666677899999988875  5577889999999999888888877665566677777787766644

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=97.22  E-value=0.0087  Score=49.09  Aligned_cols=84  Identities=15%  Similarity=0.196  Sum_probs=54.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC-HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT-RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  129 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~  129 (175)
                      ++.+.+.||||-|||.+..=-+.......++..-+||=.-| |-=|   .++++.+++.+ ++.+.++.......+.+..
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA---~EQLk~Ya~im-~vp~~vv~~~~el~~ai~~  278 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGA---VEQLKTYADIM-GVPLEVVYSPKELAEAIEA  278 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhH---HHHHHHHHHHh-CCceEEecCHHHHHHHHHH
Confidence            78899999999999977542222222122233345555544 4444   34567777777 8888888887777777777


Q ss_pred             HhcCCCeEEE
Q psy1539         130 LKTHNPQIVG  139 (175)
Q Consensus       130 l~~~~~iiv~  139 (175)
                      +.+ +++|+.
T Consensus       279 l~~-~d~ILV  287 (407)
T COG1419         279 LRD-CDVILV  287 (407)
T ss_pred             hhc-CCEEEE
Confidence            765 577665

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.20  E-value=0.0019  Score=56.46  Aligned_cols=66  Identities=27%  Similarity=0.343  Sum_probs=51.4

Q ss_pred             CCcHHHHHhHHHHhcC-----CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVLG-----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g-----~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|+..|..++..+.++     +..++.+.||||||+...- ++..+     +..+|||+|+..+|.|+++.++.|..
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~~-----~~p~Lvi~~n~~~A~ql~~el~~f~p   79 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQV-----NRPTLVIAHNKTLAAQLYNEFKEFFP   79 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHHh-----CCCEEEEECCHHHHHHHHHHHHHhCC
Confidence            5899999999887654     3667999999999976432 33332     12589999999999999999998863

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

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.19  E-value=0.0021  Score=51.04  Aligned_cols=68  Identities=26%  Similarity=0.270  Sum_probs=42.4

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHh-cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAV-LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~-~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      .-++.+.+.|.  +++-|.+.+..+. .+.+++++++||||||. ++-.++..+.......+++.+=.+.|+
T Consensus       106 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTT-ll~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       106 FTLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTT-LANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHHhhccCCCceEEEECCchhh
Confidence            34555555553  5666666665444 56899999999999995 445566655432223355555555555

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.

>TIGR01075 uvrD DNA helicase II

Probab=97.17  E-value=0.0014  Score=58.05  Aligned_cols=71  Identities=18%  Similarity=0.167  Sum_probs=53.7

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ..+++-|++|+..  ...+++|.|..|||||.+...=+...+.. .-...++|+++.|+.-|.+..+.+.++..
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            3589999998854  34679999999999998765544444432 22334789999999999999998887754

Designed to identify uvrD members of the uvrD/rep subfamily.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=97.15  E-value=0.0018  Score=56.71  Aligned_cols=69  Identities=16%  Similarity=0.114  Sum_probs=52.5

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      +++-|++++..  ...+++|.|+.|||||.+..--+...+.. .....+.++++.|+.-+.+..+.+.+...
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            68999998754  35689999999999998766655555533 22334689999999999999988877543

Designed to identify rep members of the uvrD/rep subfamily.

>KOG0920|consensus

Probab=97.12  E-value=0.0055  Score=55.04  Aligned_cols=116  Identities=13%  Similarity=0.107  Sum_probs=73.2

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEE
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGV  116 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~  116 (175)
                      .+..+.+.+..+.+...++|++.||+|||.=.-.-+++.........+.++=-|.|--|.-+.+.+..=.....+-.|+.
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGY  253 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGY  253 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeE
Confidence            36677777888999999999999999999865555565543333444555555888877777776544332222544444


Q ss_pred             EECCCchHHhHHHHhcCCCeEEE----eecC---ccCCCCceEEEEeCC
Q psy1539         117 FFGGLPIQKDEEYLKTHNPQIVG----LVNY---ETNLSGVVVNVMDVR  158 (175)
Q Consensus       117 ~~g~~~~~~~~~~l~~~~~iiv~----l~~~---~~~~~~~~~lVlDEa  158 (175)
                      -.+..+....      ...+..+    +++.   ...+.++.++|+||+
T Consensus       254 qvrl~~~~s~------~t~L~fcTtGvLLr~L~~~~~l~~vthiivDEV  296 (924)
T KOG0920|consen  254 QVRLESKRSR------ETRLLFCTTGVLLRRLQSDPTLSGVTHIIVDEV  296 (924)
T ss_pred             EEeeecccCC------ceeEEEecHHHHHHHhccCcccccCceeeeeeE
Confidence            3333221111      1234444    2222   566789999999999

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=97.10  E-value=0.0019  Score=57.17  Aligned_cols=71  Identities=20%  Similarity=0.209  Sum_probs=53.3

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ..+++-|++|+..  ....++|.|+.|||||.+...=+...+.. .-...++|+++-|+.-|.++.+.+.++..
T Consensus         8 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          8 DSLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HhcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            3589999998864  34688999999999998765544444432 22334699999999999999998887754

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=97.04  E-value=0.0031  Score=59.02  Aligned_cols=69  Identities=28%  Similarity=0.269  Sum_probs=54.9

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|+-|.++|.  ..|++++|.|.-|||||.+..--++..+.....--+.++++=|+.-+.+..+.+++-..
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~   70 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQ   70 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHH
Confidence            5899999997  46899999999999999887766666665432223689999999999998888776544

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.

>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=97.01  E-value=0.027  Score=38.39  Aligned_cols=25  Identities=28%  Similarity=0.384  Sum_probs=18.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ++.+++.+|+|+|||.. +-.+...+
T Consensus        19 ~~~v~i~G~~G~GKT~l-~~~i~~~~   43 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL-ARAIANEL   43 (151)
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHh
Confidence            68899999999999953 33344433

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.

>KOG0391|consensus

Probab=97.00  E-value=0.0023  Score=58.45  Aligned_cols=123  Identities=15%  Similarity=0.171  Sum_probs=78.3

Q ss_pred             CcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhh-cCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          37 QTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLE-TTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~-~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      ++.||..-+..+.    ++-|-|+.-.-|-|||+- .+.++.++- .+.+..--||+|||.-+. -+.-.+++|+   |+
T Consensus       616 LReYQkiGLdWLatLYeknlNGILADEmGLGKTIQ-tISllAhLACeegnWGPHLIVVpTsviL-nWEMElKRwc---Pg  690 (1958)
T KOG0391|consen  616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQ-TISLLAHLACEEGNWGPHLIVVPTSVIL-NWEMELKRWC---PG  690 (1958)
T ss_pred             HHHHHHhhHHHHHHHHHhcccceehhhhcccchhH-HHHHHHHHHhcccCCCCceEEeechhhh-hhhHHHhhhC---Cc
Confidence            4678888776543    356889999999999954 345555542 334444578999997654 3344466664   79


Q ss_pred             eEEEEEECCCchH-HhHHHHhcCCCeEEEeecC--------ccCCCCceEEEEeCCC--CCCHH
Q psy1539         112 IKVGVFFGGLPIQ-KDEEYLKTHNPQIVGLVNY--------ETNLSGVVVNVMDVRS--GGWWL  164 (175)
Q Consensus       112 i~v~~~~g~~~~~-~~~~~l~~~~~iiv~l~~~--------~~~~~~~~~lVlDEad--~~f~~  164 (175)
                      +++..++|..... +..+.+.+-...-||+..+        .+.-.+-+|+|+|||.  .+|..
T Consensus       691 lKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~AFkrkrWqyLvLDEaqnIKnfks  754 (1958)
T KOG0391|consen  691 LKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTAFKRKRWQYLVLDEAQNIKNFKS  754 (1958)
T ss_pred             ceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHHHHhhccceeehhhhhhhcchhH
Confidence            9999999976432 3333444433444554443        3334467899999993  34443

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

Probab=96.98  E-value=0.0065  Score=53.91  Aligned_cols=112  Identities=19%  Similarity=0.212  Sum_probs=81.3

Q ss_pred             HHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCC
Q psy1539          42 HECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL  121 (175)
Q Consensus        42 ~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~  121 (175)
                      .+.+..+.....-+....||-|||++..+|+.-....   +..+.+++-.--|+.-=..+...+.+.. |+++++...+.
T Consensus        84 VQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~---gkgVhvVTvNdYLA~RDae~m~~l~~~L-GlsvG~~~~~m  159 (822)
T COG0653          84 VQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALA---GKGVHVVTVNDYLARRDAEWMGPLYEFL-GLSVGVILAGM  159 (822)
T ss_pred             HHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcC---CCCcEEeeehHHhhhhCHHHHHHHHHHc-CCceeeccCCC
Confidence            3334444445666789999999999999988655443   3357888888889888888888888888 99999999998


Q ss_pred             chHHhHHHHhcCCCeEEEeec---------C------ccCCCCceEEEEeCCC
Q psy1539         122 PIQKDEEYLKTHNPQIVGLVN---------Y------ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       122 ~~~~~~~~l~~~~~iiv~l~~---------~------~~~~~~~~~lVlDEad  159 (175)
                      +..+..+...  |+|..++.+         .      ......+.+.|+||+|
T Consensus       160 ~~~ek~~aY~--~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvD  210 (822)
T COG0653         160 SPEEKRAAYA--CDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVD  210 (822)
T ss_pred             ChHHHHHHHh--cCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchh
Confidence            7666666663  688887111         1      2233467888888884

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.94  E-value=0.0075  Score=49.60  Aligned_cols=61  Identities=16%  Similarity=0.186  Sum_probs=33.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGV  116 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~  116 (175)
                      ..+++.+|||+|||.+..--+...... ...+.++.++.  +.|.-+..   +++.+.+.. ++.+..
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~e---QL~~~a~~l-gvpv~~  238 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKK---QIQTYGDIM-GIPVKA  238 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHH---HHHHHhhcC-CcceEe
Confidence            578999999999997754322221111 12233454444  33444433   366666655 665543

>PRK04296 thymidine kinase; Provisional

Probab=96.91  E-value=0.0027  Score=46.97  Aligned_cols=37  Identities=16%  Similarity=0.112  Sum_probs=24.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      |.=.++.+|+|+|||...+ -.+.++..  .+.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l-~~~~~~~~--~g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELL-QRAYNYEE--RGMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHH-HHHHHHHH--cCCeEEEEec
Confidence            3446889999999996554 33444332  3457888876

>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=96.85  E-value=0.033  Score=42.43  Aligned_cols=97  Identities=19%  Similarity=0.069  Sum_probs=64.2

Q ss_pred             cccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhc---CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          16 LSSRNRREKEDRIGESQPFREQTSFQHECIPQAVL---GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        16 ~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~---g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      |+...-+..++=.+.. ++ -.++.|.+....+.+   |+|.+.+.-.|.|||.+ ++|++.....+.+ .-+.+++|. 
T Consensus         5 w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~-~LvrviVpk-   79 (229)
T PF12340_consen    5 WDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGS-RLVRVIVPK-   79 (229)
T ss_pred             CCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCC-cEEEEEcCH-
Confidence            3334444444443433 23 579999999888775   68999999999999954 6888887776433 345666664 


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEE
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVF  117 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~  117 (175)
                      +|..|..+.++.-....-+-++..+
T Consensus        80 ~Ll~q~~~~L~~~lg~l~~r~i~~l  104 (229)
T PF12340_consen   80 ALLEQMRQMLRSRLGGLLNRRIYHL  104 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhCCeeEEe
Confidence            6889988887765443324444333

There are two conserved sequence motifs: LLE and NMG.

>KOG4150|consensus

Probab=96.80  E-value=0.00034  Score=59.33  Aligned_cols=130  Identities=9%  Similarity=-0.085  Sum_probs=86.5

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      ++++.-.....+|.+++..+.+|+++++...|.+||.++|-......+... .....+++.|+.++++...+-+.-..+.
T Consensus       279 ~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~-~~s~~~~~~~~~~~~~~~~~~~~V~~~~  357 (1034)
T KOG4150|consen  279 LNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLC-HATNSLLPSEMVEHLRNGSKGQVVHVEV  357 (1034)
T ss_pred             HhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcC-cccceecchhHHHHhhccCCceEEEEEe
Confidence            344444567899999999999999999999999999999988777655443 3346788999999987655443222222


Q ss_pred             CCCeEE--EEEECCCchHHhHHHHhcCCCeEEE---------eecC---ccCCCCceEEEEeCCC
Q psy1539         109 MSNIKV--GVFFGGLPIQKDEEYLKTHNPQIVG---------LVNY---ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       109 ~~~i~v--~~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~---~~~~~~~~~lVlDEad  159 (175)
                      .|..+.  +-.+.+.+..+.....+.+...+..         |.++   ...+-...+++.||+.
T Consensus       358 I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~  422 (1034)
T KOG4150|consen  358 IKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCA  422 (1034)
T ss_pred             hhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhccccee
Confidence            222222  2224444445566666677777766         2222   3334467788899983

>PRK08116 hypothetical protein; Validated

Probab=96.79  E-value=0.026  Score=44.11  Aligned_cols=44  Identities=23%  Similarity=0.280  Sum_probs=27.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      ..+++.|++|+|||.. +.++.+.+...  +..++ ..+..++..++.
T Consensus       115 ~gl~l~G~~GtGKThL-a~aia~~l~~~--~~~v~-~~~~~~ll~~i~  158 (268)
T PRK08116        115 VGLLLWGSVGTGKTYL-AACIANELIEK--GVPVI-FVNFPQLLNRIK  158 (268)
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHHHHHc--CCeEE-EEEHHHHHHHHH
Confidence            4599999999999954 34566666543  33344 445555655443

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.79  E-value=0.0086  Score=56.91  Aligned_cols=62  Identities=21%  Similarity=0.187  Sum_probs=45.4

Q ss_pred             CCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHH--HHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVF--VLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~--~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      .+++-|++|+..++.+  +-++|.+..|+|||...  ++.++..+.. ..+..++.++||-.=+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-SERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-ccCceEEEEechHHHHHHH
Confidence            6899999999999865  78999999999999763  2333333222 2455788899997666554

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=96.77  E-value=0.0076  Score=49.56  Aligned_cols=116  Identities=15%  Similarity=0.157  Sum_probs=67.8

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH-HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE-LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  131 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~-L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~  131 (175)
                      -.++.++.|||||.+...-++..+.....+.+++++.|+.. +-.-++..+......+ ++....-....+.  .+. +.
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~-g~~~~~~~~~~~~--~i~-~~   78 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIE-GINYEFKKSKSSM--EIK-IL   78 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHc-CChhheeecCCcc--EEE-ec
Confidence            35789999999999988877777665424568899989865 6666777777665554 4332111111110  111 11


Q ss_pred             c-CCCeEEE-eecC---ccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         132 T-HNPQIVG-LVNY---ETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       132 ~-~~~iiv~-l~~~---~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      + |..++.. +-+.   ......+.++.+|||+..-.+.++.++.+
T Consensus        79 ~~g~~i~f~g~~d~~~~ik~~~~~~~~~idEa~~~~~~~~~~l~~r  124 (396)
T TIGR01547        79 NTGKKFIFKGLNDKPNKLKSGAGIAIIWFEEASQLTFEDIKELIPR  124 (396)
T ss_pred             CCCeEEEeecccCChhHhhCcceeeeehhhhhhhcCHHHHHHHHHH
Confidence            2 3233333 3122   22233468999999975555566666543

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.76  E-value=0.026  Score=43.50  Aligned_cols=43  Identities=19%  Similarity=0.303  Sum_probs=26.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ..+++.+++|+|||.. +.++...+..  .+..++++ +..++...+
T Consensus       100 ~~~~l~G~~GtGKThL-a~aia~~l~~--~g~~v~~i-t~~~l~~~l  142 (244)
T PRK07952        100 ASFIFSGKPGTGKNHL-AAAICNELLL--RGKSVLII-TVADIMSAM  142 (244)
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHHHHh--cCCeEEEE-EHHHHHHHH
Confidence            4799999999999954 3455555543  23345554 444554443

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.73  E-value=0.024  Score=55.44  Aligned_cols=120  Identities=14%  Similarity=0.109  Sum_probs=71.8

Q ss_pred             CCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .+++-|++|+..++..  +-.++.++.|+|||.. +-.++..+..  .+.+++.++||..-+.++.+....-.     -+
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~-l~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~~g~~A-----~T  500 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI-AQLLLHLASE--QGYEIQIITAGSLSAQELRQKIPRLA-----ST  500 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH-HHHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHhcchh-----hh
Confidence            5799999999988875  6789999999999964 3344444433  45689999999876655544321100     00


Q ss_pred             EEEEECCCchHHhHHHHhcCCC-eEE-EeecCccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNP-QIV-GLVNYETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~-iiv-~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      +         -.....+.++.. .-+ ++.+....+..-+++|+|||.|.=..++..++..
T Consensus       501 i---------~~~l~~l~~~~~~~tv~~fl~~~~~l~~~~vlIVDEAsMl~~~~~~~Ll~~  552 (1960)
T TIGR02760       501 F---------ITWVKNLFNDDQDHTVQGLLDKSSPFSNKDIFVVDEANKLSNNELLKLIDK  552 (1960)
T ss_pred             H---------HHHHHhhcccccchhHHHhhcccCCCCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            0         000000000000 000 0111122345678999999998888888888763

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.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.70  E-value=0.027  Score=55.06  Aligned_cols=112  Identities=17%  Similarity=0.110  Sum_probs=68.6

Q ss_pred             CCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHH---HHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC
Q psy1539          35 REQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFV---LATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~---~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      ..+++.|++|+..++.+  +-++|.++.|+|||...-   -++.+.+..  .+.+++.++||..=+.++.+        .
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L~~--------~ 1087 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGELKS--------A 1087 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHHHh--------c
Confidence            36899999999998865  567889999999996541   233343332  45678889999766655432        1


Q ss_pred             CCeEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         110 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       110 ~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                       ++...          -+..+..+..    ............++|+||+.|.=..++..++.
T Consensus      1088 -g~~a~----------Ti~s~l~~~~----~~~~~~~~~~~~v~ivDEasMv~~~~~~~l~~ 1134 (1960)
T TIGR02760      1088 -GVQAQ----------TLDSFLTDIS----LYRNSGGDFRNTLFILDESSMVSNFQLTHATE 1134 (1960)
T ss_pred             -CCchH----------hHHHHhcCcc----cccccCCCCcccEEEEEccccccHHHHHHHHH
Confidence             22211          0111110000    00001113456899999998887888877764

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.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.68  E-value=0.0062  Score=49.83  Aligned_cols=27  Identities=19%  Similarity=0.137  Sum_probs=19.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+..+++++|||||||.. +-.+++.+.
T Consensus       148 ~~GlilI~G~TGSGKTT~-l~al~~~i~  174 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTL-AASIYQHCG  174 (372)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHH
Confidence            345789999999999954 456666654

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).

>PHA02533 17 large terminase protein; Provisional

Probab=96.67  E-value=0.018  Score=49.33  Aligned_cols=119  Identities=11%  Similarity=0.081  Sum_probs=73.6

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .+.|.|...+..+..++-.++..+-..|||.+...-++..... ..+.++++++|+++-+..+++.++.+.+..|.+.-.
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 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCF-NKDKNVGILAHKASMAAEVLDRTKQAIELLPDFLQP  137 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHh-CCCCEEEEEeCCHHHHHHHHHHHHHHHHhCHHHhhc
Confidence            4789999998877666666788888999998766444433322 234589999999999999999888877765443110


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEeecC--ccCCCCceEEEEeCCC
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLVNY--ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~~~--~~~~~~~~~lVlDEad  159 (175)
                      .+....   ...-.+.+|.-+.+ +...  ...=.+..++++||+.
T Consensus       138 ~i~~~~---~~~I~l~NGS~I~~-lss~~~t~rG~~~~~liiDE~a  179 (534)
T PHA02533        138 GIVEWN---KGSIELENGSKIGA-YASSPDAVRGNSFAMIYIDECA  179 (534)
T ss_pred             ceeecC---ccEEEeCCCCEEEE-EeCCCCccCCCCCceEEEeccc
Confidence            011110   11111234433322 2222  2222356789999984

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

Probab=96.64  E-value=0.0081  Score=48.25  Aligned_cols=63  Identities=22%  Similarity=0.164  Sum_probs=41.3

Q ss_pred             HHHhhCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          27 RIGESQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        27 ~~l~~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      ..+-+  |...++-|...+..+..+ .|+++++.||||||.. +-+++..+...  . +++.+=-|.||-
T Consensus       150 ~dli~--~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~--e-RvItiEDtaELq  213 (355)
T COG4962         150 LDLII--FGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSD--E-RVITIEDTAELQ  213 (355)
T ss_pred             HHHHH--cCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCc--c-cEEEEeehhhhc
Confidence            34444  567899999998877776 5999999999999953 33443333221  1 555555555543

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.62  E-value=0.0078  Score=53.41  Aligned_cols=71  Identities=18%  Similarity=0.193  Sum_probs=52.9

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ..++|-|.+|+..  ...+++|.|+.|||||.+...=+...+... -..-++|+++-|+.-+..+.+.+.++..
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            3589999999864  346799999999999987665555544322 1223689999999999998888877643

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.62  E-value=0.01  Score=52.03  Aligned_cols=66  Identities=26%  Similarity=0.341  Sum_probs=51.3

Q ss_pred             CCcHHHHHhHHHHhcC-----CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVLG-----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g-----~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|++.|..++..+.++     +..++.+.+|||||+... .++...     +..+|||+|+...+.|+++.++.+..
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~-----~r~vLIVt~~~~~A~~l~~dL~~~~~   82 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL-----QRPTLVLAHNKTLAAQLYSEFKEFFP   82 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh-----CCCEEEEECCHHHHHHHHHHHHHhcC
Confidence            6899999999887643     257799999999997643 233322     23599999999999999999988853

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.61  E-value=0.039  Score=53.17  Aligned_cols=62  Identities=19%  Similarity=0.147  Sum_probs=45.0

Q ss_pred             CCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhh--cCCCCeEEEEEecCHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLE--TTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~--~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      .+++-|++|+..++.+  +-++|.+..|+|||... -.++..+.  ....+.+++.++||-.=+.++
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHHH
Confidence            6899999999999975  67899999999999653 23333332  123455788899997666553

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.56  E-value=0.034  Score=47.46  Aligned_cols=20  Identities=30%  Similarity=0.320  Sum_probs=16.8

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~   69 (175)
                      .|..+.+.+|||+|||....
T Consensus       349 ~G~vIaLVGPtGvGKTTtaa  368 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIA  368 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            46789999999999997653

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=96.53  E-value=0.028  Score=47.53  Aligned_cols=134  Identities=13%  Similarity=0.062  Sum_probs=75.4

Q ss_pred             HHHHHhHHHHh-----cC----CcEEEEcCCCChHHHHHHHHHHHhh-hcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          39 SFQHECIPQAV-----LG----MDILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        39 ~~Q~~~i~~~~-----~g----~~~ii~a~TGsGKT~~~~~~~l~~l-~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      |+|+-.+-.++     .|    +.+++.-|-+.|||.....-.+-.+ .....+..+++.+++++-|..+++.++.+.+.
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            45666655554     22    4688888999999975544333333 33345678999999999999999999999877


Q ss_pred             CCCeEEEEEECCCc-hHHhHHHHhcCCCeEEEeecC--ccCCCCceEEEEeCCCCCCHHHHHHHHhhh
Q psy1539         109 MSNIKVGVFFGGLP-IQKDEEYLKTHNPQIVGLVNY--ETNLSGVVVNVMDVRSGGWWLDLEALILSK  173 (175)
Q Consensus       109 ~~~i~v~~~~g~~~-~~~~~~~l~~~~~iiv~l~~~--~~~~~~~~~lVlDEad~~f~~~v~~il~~~  173 (175)
                      .|......-..-.. ....+....++ ..+..+...  ..+=.+..++|+||++..-..++...|.+.
T Consensus        81 ~~~l~~~~~~~~~~~~~~~i~~~~~~-s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g  147 (477)
T PF03354_consen   81 SPELRKRKKPKIIKSNKKEIEFPKTG-SFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESG  147 (477)
T ss_pred             ChhhccchhhhhhhhhceEEEEcCCC-cEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhh
Confidence            64443211000000 00000001111 122222222  233336789999999533334455555543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=96.50  E-value=0.0098  Score=47.07  Aligned_cols=25  Identities=24%  Similarity=0.460  Sum_probs=19.8

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcC
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETT   79 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~   79 (175)
                      ++|.+|||||||.+ +.+++.+++..
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            78899999999965 46777777653

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=96.45  E-value=0.0069  Score=52.16  Aligned_cols=121  Identities=9%  Similarity=-0.014  Sum_probs=75.7

Q ss_pred             CCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH-HHHHHHHhhCCCe
Q psy1539          36 EQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS-KEYERFSKYMSNI  112 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~-~~~~~~~~~~~~i  112 (175)
                      ..+|+|.+.+..+..-  +.++++.++-+|||...+..+...+...+  .-++++.||.+.+.... ..+..+.+..|.+
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 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDP--GPMLYVQPTDDAAKDFSKERLDPMIRASPVL   93 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCC--CCEEEEEEcHHHHHHHHHHHHHHHHHhCHHH
Confidence            5689999988877764  78999999999999854443333333322  35899999999999877 4477777766554


Q ss_pred             EEEEEE---CCCchHHhHHHHhcCCCeEEEeecC--ccCCCCceEEEEeCCC
Q psy1539         113 KVGVFF---GGLPIQKDEEYLKTHNPQIVGLVNY--ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       113 ~v~~~~---g~~~~~~~~~~l~~~~~iiv~l~~~--~~~~~~~~~lVlDEad  159 (175)
                      +-.+--   .+...+...+.+. |..+.++-.+.  .+.-..++++++||.|
T Consensus        94 ~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S~~~l~s~~~r~~~~DEvD  144 (557)
T PF05876_consen   94 RRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANSPSNLRSRPARYLLLDEVD  144 (557)
T ss_pred             HHHhCchhhcccCCchhheecC-CCEEEEEeCCCCcccccCCcCEEEEechh
Confidence            421111   0111112222222 33444443333  4444579999999996

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 [].

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=96.38  E-value=0.0073  Score=48.90  Aligned_cols=44  Identities=20%  Similarity=0.246  Sum_probs=28.0

Q ss_pred             HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      .+..+.++++++|||||||. ++-+++..+...   .+.+.+=.+.||
T Consensus       158 ~v~~~~nilI~G~tGSGKTT-ll~aLl~~i~~~---~rivtiEd~~El  201 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTT-MSKTLISAIPPQ---ERLITIEDTLEL  201 (344)
T ss_pred             HHHcCCeEEEECCCCccHHH-HHHHHHcccCCC---CCEEEECCCccc
Confidence            34467999999999999995 455566555321   234444444444

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.38  E-value=0.039  Score=46.00  Aligned_cols=63  Identities=21%  Similarity=0.256  Sum_probs=32.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEEEE
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFF  118 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~  118 (175)
                      |+.+++.+|||+|||.+..--+. .+.....+.++.++.  |.|.-+   .++++.+.+.. ++.+....
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~-~~~~~~~g~~V~li~~D~~r~~a---~eqL~~~a~~~-~vp~~~~~  285 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAA-RYALLYGKKKVALITLDTYRIGA---VEQLKTYAKIM-GIPVEVVY  285 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH-HHHHhcCCCeEEEEECCccHHHH---HHHHHHHHHHh-CCceEccC
Confidence            56789999999999976542222 221011233455554  333322   23455555444 55554433

>PRK05973 replicative DNA helicase; Provisional

Probab=96.37  E-value=0.016  Score=44.46  Aligned_cols=83  Identities=18%  Similarity=0.172  Sum_probs=51.4

Q ss_pred             cCCCCHHHHHHHhhCCCCC----------CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEE
Q psy1539          18 SRNRREKEDRIGESQPFRE----------QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLV   87 (175)
Q Consensus        18 ~~~l~~~l~~~l~~~g~~~----------~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~li   87 (175)
                      ..+++..+-+.-.+.||..          +||... ...-+..|.-++|.|++|+|||...+.-+.+...   ++.+++|
T Consensus        22 ~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~---~Ge~vly   97 (237)
T PRK05973         22 NIPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEE-LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMK---SGRTGVF   97 (237)
T ss_pred             CCcHHHHHHHHHHHhccchHHHHHHhccCCCCHHH-hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHh---cCCeEEE
Confidence            4567777777777778763          455322 3334456788999999999999655444443332   3446777


Q ss_pred             EecCHHHHHHHHHHHHHH
Q psy1539          88 MCHTRELAFQISKEYERF  105 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~  105 (175)
                      ++-- +=..|+.+.+..+
T Consensus        98 fSlE-es~~~i~~R~~s~  114 (237)
T PRK05973         98 FTLE-YTEQDVRDRLRAL  114 (237)
T ss_pred             EEEe-CCHHHHHHHHHHc
Confidence            7643 2245666666655

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.041  Score=45.47  Aligned_cols=81  Identities=17%  Similarity=0.194  Sum_probs=41.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  129 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~  129 (175)
                      +.+.+.+|||+|||.....-. ..+..  .+.++.++.  |.|.-+   .++++.+.+.. ++.+..........+.++.
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA-~~L~~--~GkkVglI~aDt~RiaA---vEQLk~yae~l-gipv~v~~d~~~L~~aL~~  314 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMA-WQFHG--KKKTVGFITTDHSRIGT---VQQLQDYVKTI-GFEVIAVRDEAAMTRALTY  314 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHH-HHHHH--cCCcEEEEecCCcchHH---HHHHHHHhhhc-CCcEEecCCHHHHHHHHHH
Confidence            578899999999997644322 23332  233444444  334222   22344555544 6665543332233333444


Q ss_pred             Hhc--CCCeEEE
Q psy1539         130 LKT--HNPQIVG  139 (175)
Q Consensus       130 l~~--~~~iiv~  139 (175)
                      +..  +.++|+.
T Consensus       315 lk~~~~~DvVLI  326 (436)
T PRK11889        315 FKEEARVDYILI  326 (436)
T ss_pred             HHhccCCCEEEE
Confidence            443  4566665

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.26  E-value=0.02  Score=46.15  Aligned_cols=29  Identities=24%  Similarity=0.424  Sum_probs=22.2

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +..+.+++++++||||||. ++-+++..+.
T Consensus       157 v~~~~nili~G~tgSGKTT-ll~aL~~~ip  185 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTT-FTNAALREIP  185 (332)
T ss_pred             HHcCCcEEEECCCCCCHHH-HHHHHHhhCC
Confidence            3467999999999999995 4556666553

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.26  E-value=0.014  Score=42.72  Aligned_cols=46  Identities=20%  Similarity=0.232  Sum_probs=27.8

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      .+++++++.+++|+|||..+ .++...+..  .+..+++ ++..+|..++
T Consensus        45 ~~~~~l~l~G~~G~GKThLa-~ai~~~~~~--~g~~v~f-~~~~~L~~~l   90 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLA-VAIANEAIR--KGYSVLF-ITASDLLDEL   90 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHH-HHHHHHHHH--TT--EEE-EEHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHH-HHHHHHhcc--CCcceeE-eecCceeccc
Confidence            35799999999999999654 444444443  3434555 4666676554

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.

>PRK08181 transposase; Validated

Probab=96.25  E-value=0.024  Score=44.39  Aligned_cols=60  Identities=22%  Similarity=0.171  Sum_probs=36.8

Q ss_pred             CcHHHHHhHH----HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          37 QTSFQHECIP----QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        37 ~t~~Q~~~i~----~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      +++.|..++.    .+-.++++++.||+|+|||... .++...+..  .+..++ ..+..+|..++..
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa-~Aia~~a~~--~g~~v~-f~~~~~L~~~l~~  151 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLA-AAIGLALIE--NGWRVL-FTRTTDLVQKLQV  151 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHH-HHHHHHHHH--cCCcee-eeeHHHHHHHHHH
Confidence            4566666653    3346799999999999999533 333333332  233444 4456777776543

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.25  E-value=0.028  Score=48.36  Aligned_cols=91  Identities=18%  Similarity=0.088  Sum_probs=58.7

Q ss_pred             cCCCCHHHHH-HHhhCCCCCCcH----HHHHhHHHHh--cCCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEE
Q psy1539          18 SRNRREKEDR-IGESQPFREQTS----FQHECIPQAV--LGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLV   87 (175)
Q Consensus        18 ~~~l~~~l~~-~l~~~g~~~~t~----~Q~~~i~~~~--~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~li   87 (175)
                      +.+...+++. +|.+.--.++..    +|.+==..+.  .++-++|++..|||||.+++.-+.-.++.-   ..+..+++
T Consensus       186 d~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlv  265 (747)
T COG3973         186 DTGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLV  265 (747)
T ss_pred             CCchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEE
Confidence            4555555554 465543333322    3333322333  357789999999999988876554444321   22334999


Q ss_pred             EecCHHHHHHHHHHHHHHHhh
Q psy1539          88 MCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      +.|.+-+...+.+++-.++..
T Consensus       266 l~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         266 LGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             EcCcHHHHHHHHHhchhhccC
Confidence            999999999999999888764

>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=0.016  Score=48.73  Aligned_cols=41  Identities=29%  Similarity=0.370  Sum_probs=30.8

Q ss_pred             cHHHHHhHHHHhcCC--cEEEEcCCCChHHHHHHHHHHHhhhcC
Q psy1539          38 TSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETT   79 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~--~~ii~a~TGsGKT~~~~~~~l~~l~~~   79 (175)
                      ++.|...+..+++..  =+++.+|||||||.+ +..+++.+...
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            778888887777653  367899999999965 56777777643

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.22  E-value=0.036  Score=46.53  Aligned_cols=49  Identities=27%  Similarity=0.275  Sum_probs=31.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      ..+++.|++|+|||. .+.++.+.+.....+.+++++.+ .++..+....+
T Consensus       142 npl~i~G~~G~GKTH-Ll~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l  190 (450)
T PRK14087        142 NPLFIYGESGMGKTH-LLKAAKNYIESNFSDLKVSYMSG-DEFARKAVDIL  190 (450)
T ss_pred             CceEEECCCCCcHHH-HHHHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHH
Confidence            459999999999994 34566665554344556766654 56665544443

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.20  E-value=0.026  Score=47.31  Aligned_cols=87  Identities=20%  Similarity=0.197  Sum_probs=49.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  130 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l  130 (175)
                      |.-+++.+++|+|||...+. ++.....  .+.+++|+.- .+-..|+....+++.....+   ..+....+..+..+.+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq-~a~~~a~--~g~~vlYvs~-Ees~~qi~~ra~rlg~~~~~---l~~~~e~~l~~i~~~i  152 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQ-VAARLAA--AGGKVLYVSG-EESASQIKLRAERLGLPSDN---LYLLAETNLEAILATI  152 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHH-HHHHHHh--cCCeEEEEEc-cccHHHHHHHHHHcCCChhc---EEEeCCCCHHHHHHHH
Confidence            46789999999999965433 3333222  3447888874 44556776666665432212   2233444443333333


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCC
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad  159 (175)
                      .+               .+.+++|+|+..
T Consensus       153 ~~---------------~~~~lVVIDSIq  166 (446)
T PRK11823        153 EE---------------EKPDLVVIDSIQ  166 (446)
T ss_pred             Hh---------------hCCCEEEEechh
Confidence            22               356788899873

>KOG0392|consensus

Probab=96.20  E-value=0.013  Score=53.77  Aligned_cols=119  Identities=17%  Similarity=0.131  Sum_probs=76.6

Q ss_pred             CcHHHHHhHHHH--hc--CCcEEEEcCCCChHHHHHHHHHHHhhhcC-----CCCeE-EEEEecCHHHHHHHHHHHHHHH
Q psy1539          37 QTSFQHECIPQA--VL--GMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVY-VLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        37 ~t~~Q~~~i~~~--~~--g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~-~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      ++.+|++-+..+  ++  +-+-++|-.-|-|||+--+.-+.......     +-... +||+||. .|+-.+...+.+|.
T Consensus       976 LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf~ 1054 (1549)
T KOG0392|consen  976 LRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKFF 1054 (1549)
T ss_pred             HHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHhc
Confidence            467899987543  33  35778999999999976554443332221     11223 8999997 57767666666654


Q ss_pred             hhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE---eecC---ccCCCCceEEEEeCCC
Q psy1539         107 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG---LVNY---ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       107 ~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~---l~~~---~~~~~~~~~lVlDEad  159 (175)
                         |-+++...+|+...+...+.--++.+|||+   ..++   .+.=..-.|.|+||-+
T Consensus      1055 ---pfL~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~l~~~~wNYcVLDEGH 1110 (1549)
T KOG0392|consen 1055 ---PFLKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDYLIKIDWNYCVLDEGH 1110 (1549)
T ss_pred             ---chhhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHHHHhcccceEEecCcc
Confidence               557888888876555555554455788887   3333   1122356789999973

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.19  E-value=0.17  Score=44.89  Aligned_cols=136  Identities=14%  Similarity=0.039  Sum_probs=77.7

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          29 GESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      +.+...+.+..-|.+.+..++++  +-+++.|.-|-|||.+.-+.+........ ...+++-+|+.+=++.+.+.+.+-.
T Consensus       207 l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~-~~~iiVTAP~~~nv~~Lf~fa~~~l  285 (758)
T COG1444         207 LYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAG-SVRIIVTAPTPANVQTLFEFAGKGL  285 (758)
T ss_pred             HhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcC-CceEEEeCCCHHHHHHHHHHHHHhH
Confidence            44443444455555556666654  46899999999999887766643333221 4578999999999988887766555


Q ss_pred             hhCCCeEEEEEECC-CchHHhHHHHhcCCCeEEEeecC-ccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         107 KYMSNIKVGVFFGG-LPIQKDEEYLKTHNPQIVGLVNY-ETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       107 ~~~~~i~v~~~~g~-~~~~~~~~~l~~~~~iiv~l~~~-~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      +.. |.+-.+.... ......     ++....|-.... ... ..-+.+|+|||...-.+=++.++.+
T Consensus       286 ~~l-g~~~~v~~d~~g~~~~~-----~~~~~~i~y~~P~~a~-~~~DllvVDEAAaIplplL~~l~~~  346 (758)
T COG1444         286 EFL-GYKRKVAPDALGEIREV-----SGDGFRIEYVPPDDAQ-EEADLLVVDEAAAIPLPLLHKLLRR  346 (758)
T ss_pred             HHh-CCccccccccccceeee-----cCCceeEEeeCcchhc-ccCCEEEEehhhcCChHHHHHHHhh
Confidence            544 4332111111 000000     011112221221 111 2278899999977777777666654

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=96.18  E-value=0.093  Score=40.47  Aligned_cols=34  Identities=18%  Similarity=0.096  Sum_probs=24.8

Q ss_pred             CCCcHHHHHhHHHHh----cC-CcEEEEcCCCChHHHHH
Q psy1539          35 REQTSFQHECIPQAV----LG-MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~----~g-~~~ii~a~TGsGKT~~~   68 (175)
                      -.+++.+.+++..+.    .+ ..+++.||+|+|||...
T Consensus        22 ~~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        22 FYPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             hCCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            356777777776553    23 36889999999999654

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.17  E-value=0.033  Score=46.97  Aligned_cols=24  Identities=17%  Similarity=-0.039  Sum_probs=17.7

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.+|+||+|+.-....+.+|+
T Consensus       120 g~~KV~IIDEah~Ls~~A~NALLK  143 (484)
T PRK14956        120 GKYKVYIIDEVHMLTDQSFNALLK  143 (484)
T ss_pred             CCCEEEEEechhhcCHHHHHHHHH
Confidence            367899999998776666666554

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.17  E-value=0.02  Score=46.72  Aligned_cols=25  Identities=32%  Similarity=0.549  Sum_probs=18.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .|+++.++||+|||.+.-. ++..+.
T Consensus        43 ~n~~iyG~~GTGKT~~~~~-v~~~l~   67 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKF-VMEELE   67 (366)
T ss_pred             ccEEEECCCCCCHhHHHHH-HHHHHH
Confidence            5799999999999976433 334443

>PRK13764 ATPase; Provisional

Probab=96.15  E-value=0.013  Score=50.74  Aligned_cols=27  Identities=26%  Similarity=0.321  Sum_probs=21.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+.++++++|||||||. ++.+++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTT-ll~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKST-FAQALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHH-HHHHHHHHHh
Confidence            46889999999999995 4566666664

>PRK06921 hypothetical protein; Provisional

Probab=96.14  E-value=0.08  Score=41.34  Aligned_cols=49  Identities=22%  Similarity=0.167  Sum_probs=30.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      .+.++++.+++|+|||.. +.+++..+... .+..++++ +..++..++...
T Consensus       116 ~~~~l~l~G~~G~GKThL-a~aia~~l~~~-~g~~v~y~-~~~~l~~~l~~~  164 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHL-LTAAANELMRK-KGVPVLYF-PFVEGFGDLKDD  164 (266)
T ss_pred             CCCeEEEECCCCCcHHHH-HHHHHHHHhhh-cCceEEEE-EHHHHHHHHHHH
Confidence            367899999999999953 34555555432 14455555 455666555443

>KOG0922|consensus

Probab=96.05  E-value=0.064  Score=46.44  Aligned_cols=107  Identities=15%  Similarity=0.130  Sum_probs=54.6

Q ss_pred             HHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH-HHHhhCCCeEEEEE--E
Q psy1539          42 HECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE-RFSKYMSNIKVGVF--F  118 (175)
Q Consensus        42 ~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~-~~~~~~~~i~v~~~--~  118 (175)
                      .+.+..+-+++-++|.+.||||||.= +.-.|........| +.-+--|.|-=|.-+.+... ++.... |-.|+.-  +
T Consensus        57 ~~il~~ve~nqvlIviGeTGsGKSTQ-ipQyL~eaG~~~~g-~I~~TQPRRVAavslA~RVAeE~~~~l-G~~VGY~IRF  133 (674)
T KOG0922|consen   57 DQILYAVEDNQVLIVIGETGSGKSTQ-IPQYLAEAGFASSG-KIACTQPRRVAAVSLAKRVAEEMGCQL-GEEVGYTIRF  133 (674)
T ss_pred             HHHHHHHHHCCEEEEEcCCCCCcccc-HhHHHHhcccccCC-cEEeecCchHHHHHHHHHHHHHhCCCc-CceeeeEEEe
Confidence            34455666788999999999999952 22122221122233 24444477766655444432 232222 3333322  2


Q ss_pred             CCCchHHhHHHHhcCCCeEEE----eecC---ccCCCCceEEEEeCCC
Q psy1539         119 GGLPIQKDEEYLKTHNPQIVG----LVNY---ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       119 g~~~~~~~~~~l~~~~~iiv~----l~~~---~~~~~~~~~lVlDEad  159 (175)
                      -+..  ..      ...+..-    |++.   .-.+++-..+|+|||+
T Consensus       134 ed~t--s~------~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAH  173 (674)
T KOG0922|consen  134 EDST--SK------DTRIKYMTDGMLLREILKDPLLSKYSVIILDEAH  173 (674)
T ss_pred             cccC--CC------ceeEEEecchHHHHHHhcCCccccccEEEEechh
Confidence            2221  00      0112221    2332   3457899999999993

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=96.03  E-value=0.024  Score=46.35  Aligned_cols=36  Identities=22%  Similarity=0.393  Sum_probs=22.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      .++++.||+|+|||... --++..+.....+...+++
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            68999999999999653 3444444332223445554

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.03  E-value=0.12  Score=41.23  Aligned_cols=44  Identities=18%  Similarity=0.255  Sum_probs=26.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ++++++.|++|+|||... .++.+.+..  .+..+.++ ..-+++.++
T Consensus       156 ~~gl~L~G~~G~GKThLa-~Aia~~l~~--~g~~v~~~-~~~~l~~~l  199 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLL-AAIANELAK--KGVSSTLL-HFPEFIREL  199 (306)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHH--cCCCEEEE-EHHHHHHHH
Confidence            468999999999999543 344444442  33344444 333455443

>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=96.02  E-value=0.1  Score=38.86  Aligned_cols=60  Identities=17%  Similarity=0.192  Sum_probs=33.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEEEECC
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGG  120 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~  120 (175)
                      +++.+|||+|||.+.. -+..++...  +.++.+++  ..|.=+   .++++.+.+.+ ++.+......
T Consensus         4 i~lvGptGvGKTTt~a-KLAa~~~~~--~~~v~lis~D~~R~ga---~eQL~~~a~~l-~vp~~~~~~~   65 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIA-KLAARLKLK--GKKVALISADTYRIGA---VEQLKTYAEIL-GVPFYVARTE   65 (196)
T ss_dssp             EEEEESTTSSHHHHHH-HHHHHHHHT--T--EEEEEESTSSTHH---HHHHHHHHHHH-TEEEEESSTT
T ss_pred             EEEECCCCCchHhHHH-HHHHHHhhc--cccceeecCCCCCccH---HHHHHHHHHHh-ccccchhhcc
Confidence            6789999999997643 222233222  33444444  345444   34566666666 7776554433

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 ....

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.95  E-value=0.093  Score=44.55  Aligned_cols=102  Identities=17%  Similarity=0.041  Sum_probs=50.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCc-hHHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP-IQKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~-~~~~~~~l  130 (175)
                      +.++++||.|+|||.++.+-. ..+.- ..+       |+.+-|.+ -..|+.+.... ...+..+.+... .-++.+.+
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilA-k~LnC-~~~-------~~~~pCg~-C~~C~~i~~~~-~~Dv~eidaas~~~vddIR~I  104 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIIS-LCLNC-SNG-------PTSDPCGT-CHNCISIKNSN-HPDVIEIDAASNTSVDDIKVI  104 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHH-HHHcC-cCC-------CCCCCccc-cHHHHHHhccC-CCCEEEEecccCCCHHHHHHH
Confidence            579999999999997654322 22211 111       22222222 12244443332 334444444321 12334433


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ...       ....-...+.+.+|+||+|+.-....+.+++
T Consensus       105 ie~-------~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK  138 (491)
T PRK14964        105 LEN-------SCYLPISSKFKVYIIDEVHMLSNSAFNALLK  138 (491)
T ss_pred             HHH-------HHhccccCCceEEEEeChHhCCHHHHHHHHH
Confidence            321       1111124688999999998766555555543

>PRK10436 hypothetical protein; Provisional

Probab=95.94  E-value=0.02  Score=48.22  Aligned_cols=45  Identities=31%  Similarity=0.278  Sum_probs=29.8

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhc--CCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVL--GMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~--g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      |.++|+   .+.|.+.+..+..  +--+++++|||||||... .+++..+.
T Consensus       197 L~~LG~---~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        197 LETLGM---TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             HHHcCc---CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            444553   5556666665543  346889999999999754 45666654

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.92  E-value=0.048  Score=44.69  Aligned_cols=86  Identities=17%  Similarity=0.205  Sum_probs=48.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  130 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l  130 (175)
                      |.-+++.+++|+|||...+. ++..+..  .+.+++|+.-. +-..|+....+++.-...++   .+....+..+-.+.+
T Consensus        82 GslvLI~G~pG~GKStLllq-~a~~~a~--~g~~VlYvs~E-Es~~qi~~Ra~rlg~~~~~l---~l~~e~~le~I~~~i  154 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQ-VAARLAK--RGGKVLYVSGE-ESPEQIKLRADRLGISTENL---YLLAETNLEDILASI  154 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHH-HHHHHHh--cCCeEEEEECC-cCHHHHHHHHHHcCCCcccE---EEEccCcHHHHHHHH
Confidence            46789999999999965443 3333322  23468887654 33456666565554322122   233344433333333


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCC
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEa  158 (175)
                      ..               .+.+++|+|++
T Consensus       155 ~~---------------~~~~lVVIDSI  167 (372)
T cd01121         155 EE---------------LKPDLVIIDSI  167 (372)
T ss_pred             Hh---------------cCCcEEEEcch
Confidence            22               36678899987

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.

>KOG1133|consensus

Probab=95.91  E-value=0.013  Score=50.92  Aligned_cols=41  Identities=20%  Similarity=0.257  Sum_probs=34.8

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +|+.+|.+.+..++    +|+=-+..+|||+|||+..+.+.+.-+
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            58999999887655    589889999999999999888887655

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.88  E-value=0.028  Score=45.83  Aligned_cols=27  Identities=19%  Similarity=0.340  Sum_probs=20.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+..+++++|||||||... -.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            5678999999999999653 55555553

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.86  E-value=0.059  Score=43.41  Aligned_cols=47  Identities=19%  Similarity=0.186  Sum_probs=30.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      .+.++++.|+||+|||.. +.++...+..  .+..+++ .+..+|..++..
T Consensus       182 ~~~~Lll~G~~GtGKThL-a~aIa~~l~~--~g~~V~y-~t~~~l~~~l~~  228 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFL-SNCIAKELLD--RGKSVIY-RTADELIEILRE  228 (329)
T ss_pred             cCCcEEEECCCCCcHHHH-HHHHHHHHHH--CCCeEEE-EEHHHHHHHHHH
Confidence            358999999999999963 3455555543  3445555 455667665543

>KOG0388|consensus

Probab=95.86  E-value=0.026  Score=49.52  Aligned_cols=117  Identities=19%  Similarity=0.227  Sum_probs=73.4

Q ss_pred             CcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCC-CeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          37 QTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDS-NVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~-~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      +-++|...+..+.    +|-|-++.-.-|-|||.- .++++.++....+ ..--|+++|...|-    .+.+.+.+..|.
T Consensus       568 LKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQ-sisvlAhLaE~~nIwGPFLVVtpaStL~----NWaqEisrFlP~  642 (1185)
T KOG0388|consen  568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQ-SISVLAHLAETHNIWGPFLVVTPASTLH----NWAQEISRFLPS  642 (1185)
T ss_pred             hHHHhhccHHHHHHHHHccccceehhhhccchhHH-HHHHHHHHHHhccCCCceEEeehHHHHh----HHHHHHHHhCcc
Confidence            3467777765543    588999999999999965 4566666644322 12368888876663    445566666689


Q ss_pred             eEEEEEECCCchHHhHHHH---------hcCCCeEEE----eecCccCCC--CceEEEEeCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYL---------KTHNPQIVG----LVNYETNLS--GVVVNVMDVR  158 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l---------~~~~~iiv~----l~~~~~~~~--~~~~lVlDEa  158 (175)
                      +++.-+-|+.+....++..         ..+.+++|+    ++.....|+  +-.+.|+|||
T Consensus       643 ~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qkvKWQYMILDEA  704 (1185)
T KOG0388|consen  643 FKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQKVKWQYMILDEA  704 (1185)
T ss_pred             ceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHHhhhhhheehhHH
Confidence            9999888887644444431         123355555    222222333  3468899998

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

Probab=95.86  E-value=0.017  Score=42.51  Aligned_cols=45  Identities=27%  Similarity=0.226  Sum_probs=31.1

Q ss_pred             HhhCCCCCCcHHHHHhHHHHh-cCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          29 GESQPFREQTSFQHECIPQAV-LGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~-~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      |.+.|  ..++-|...+.... .|.++++.+|||||||... -.++..+
T Consensus         4 l~~~g--~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll-~aL~~~i   49 (186)
T cd01130           4 LIAQG--TFSPLQAAYLWLAVEARKNILISGGTGSGKTTLL-NALLAFI   49 (186)
T ss_pred             HHHcC--CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhc
Confidence            44444  45777777776544 6899999999999999643 3344443

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.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=95.85  E-value=0.11  Score=44.97  Aligned_cols=74  Identities=19%  Similarity=0.290  Sum_probs=55.7

Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEE
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVN  153 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~l  153 (175)
                      ..+.++||.|+|++.++++.+.+.+.     ++.+..++|+.+..+..   +.++++ ..++|+  +....+++.+++++
T Consensus       255 ~~~~k~LVF~nt~~~ae~l~~~L~~~-----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~V  329 (572)
T PRK04537        255 SEGARTMVFVNTKAFVERVARTLERH-----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYV  329 (572)
T ss_pred             ccCCcEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEE
Confidence            34568999999999999988777543     77899999998755443   344444 467777  66668899999999


Q ss_pred             EEeCC
Q psy1539         154 VMDVR  158 (175)
Q Consensus       154 VlDEa  158 (175)
                      |.-+.
T Consensus       330 Inyd~  334 (572)
T PRK04537        330 YNYDL  334 (572)
T ss_pred             EEcCC
Confidence            88665

>PRK12377 putative replication protein; Provisional

Probab=95.84  E-value=0.033  Score=43.09  Aligned_cols=46  Identities=15%  Similarity=0.259  Sum_probs=30.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      .++++.+|+|+|||.. +.++.+.+..  .+..+ +.++..+|..++...
T Consensus       102 ~~l~l~G~~GtGKThL-a~AIa~~l~~--~g~~v-~~i~~~~l~~~l~~~  147 (248)
T PRK12377        102 TNFVFSGKPGTGKNHL-AAAIGNRLLA--KGRSV-IVVTVPDVMSRLHES  147 (248)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHH--cCCCe-EEEEHHHHHHHHHHH
Confidence            6899999999999953 3455555543  23334 445666777766543

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=95.84  E-value=0.013  Score=51.99  Aligned_cols=54  Identities=11%  Similarity=0.165  Sum_probs=39.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      -|+=|...||+|||.+|+--+.. +.+.-+-.+-||+|||.+.-.-++...+...
T Consensus        75 lNiDI~METGTGKTy~Ylrtmfe-Lhk~YG~~KFIivVPs~AIkeGv~~~s~~~~  128 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFE-LHKKYGLFKFIIVVPSLAIKEGVFLTSKETT  128 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHH-HHHHhCceeEEEEeccHHHHhhhHHHHHHHH
Confidence            57889999999999999765543 3333456789999999887666555544443

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.83  E-value=0.14  Score=36.88  Aligned_cols=31  Identities=29%  Similarity=0.238  Sum_probs=22.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEE
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLV   87 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~li   87 (175)
                      +.|..++|.|||.+.+--.+..+.   .+.++++
T Consensus         5 i~vy~g~G~Gkt~~a~g~~~ra~~---~g~~v~~   35 (159)
T cd00561           5 IQVYTGNGKGKTTAALGLALRALG---HGYRVGV   35 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH---CCCeEEE
Confidence            567788899999887666666554   3446666

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.

>KOG0924|consensus

Probab=95.82  E-value=0.066  Score=46.86  Aligned_cols=62  Identities=16%  Similarity=0.178  Sum_probs=39.1

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHH
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYE  103 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~  103 (175)
                      ...+.+.+..+..+.-++|.+.||||||.-.    .+.++....+...+|-|  |.|.-|.-+.+.+.
T Consensus       358 f~~R~~ll~~ir~n~vvvivgETGSGKTTQl----~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa  421 (1042)
T KOG0924|consen  358 FACRDQLLSVIRENQVVVIVGETGSGKTTQL----AQYLYEDGYADNGMIGCTQPRRVAAISVAKRVA  421 (1042)
T ss_pred             HHHHHHHHHHHhhCcEEEEEecCCCCchhhh----HHHHHhcccccCCeeeecCchHHHHHHHHHHHH
Confidence            4455666666667888999999999999743    33343332222234444  88877776655543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.81  E-value=0.17  Score=35.29  Aligned_cols=39  Identities=23%  Similarity=0.258  Sum_probs=23.4

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      +++.+++|+|||.... .++.....  .+..++++.......
T Consensus         2 ~~i~G~~G~GKT~l~~-~i~~~~~~--~~~~v~~~~~e~~~~   40 (165)
T cd01120           2 ILVFGPTGSGKTTLAL-QLALNIAT--KGGKVVYVDIEEEIE   40 (165)
T ss_pred             eeEeCCCCCCHHHHHH-HHHHHHHh--cCCEEEEEECCcchH
Confidence            5789999999996443 23333222  344677776554443

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=95.79  E-value=0.029  Score=47.53  Aligned_cols=45  Identities=22%  Similarity=0.255  Sum_probs=30.4

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcC-Cc-EEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVLG-MD-ILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g-~~-~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      |.++||   ++-|.+.+..+... +. +++++|||||||... ..++..+.
T Consensus       221 l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       221 LETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             HHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            455554   56677777666543 43 689999999999654 44566654

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.

>KOG0331|consensus

Probab=95.73  E-value=0.093  Score=44.59  Aligned_cols=83  Identities=16%  Similarity=0.221  Sum_probs=60.7

Q ss_pred             HHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh---c-CCCeEEE--eecC
Q psy1539          70 LATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK---T-HNPQIVG--LVNY  143 (175)
Q Consensus        70 ~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~---~-~~~iiv~--l~~~  143 (175)
                      .+++.... ...+.++||.|-|+.-|.++.+.++..     ++.+..++|+.+..+....|+   + .++++|+  +.-+
T Consensus       330 ~~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~-----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaR  403 (519)
T KOG0331|consen  330 GKLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRK-----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAAR  403 (519)
T ss_pred             HHHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhc-----CcceeeecccccHHHHHHHHHhcccCCcceEEEcccccc
Confidence            34444444 345569999999999998876666543     578899999998665554443   3 4688998  6677


Q ss_pred             ccCCCCceEEEEeCC
Q psy1539         144 ETNLSGVVVNVMDVR  158 (175)
Q Consensus       144 ~~~~~~~~~lVlDEa  158 (175)
                      .+++.++++||-=+.
T Consensus       404 GLDi~dV~lVInydf  418 (519)
T KOG0331|consen  404 GLDVPDVDLVINYDF  418 (519)
T ss_pred             cCCCccccEEEeCCC
Confidence            899999999997555

>KOG0925|consensus

Probab=95.70  E-value=0.029  Score=47.16  Aligned_cols=90  Identities=12%  Similarity=0.028  Sum_probs=56.9

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .....|...+.++.-.+.+++..=-.-+..+.+.+..+.++.-+++.+.||||||.---.=.+.......  ..+..--|
T Consensus        22 k~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--~~v~CTQp   99 (699)
T KOG0925|consen   22 KAINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--TGVACTQP   99 (699)
T ss_pred             hhcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--cceeecCc
Confidence            4466788899999888888776332335555555666777899999999999999531111112211111  23455558


Q ss_pred             CHHHHHHHHHHH
Q psy1539          91 TRELAFQISKEY  102 (175)
Q Consensus        91 t~~L~~q~~~~~  102 (175)
                      .|--+.++....
T Consensus       100 rrvaamsva~RV  111 (699)
T KOG0925|consen  100 RRVAAMSVAQRV  111 (699)
T ss_pred             hHHHHHHHHHHH
Confidence            887777755443

>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=95.67  E-value=0.016  Score=45.12  Aligned_cols=44  Identities=23%  Similarity=0.295  Sum_probs=29.7

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      ..+.+++++|+||||||.. +-.++..+...  ..+++.+=.+.|+-
T Consensus       125 ~~~~~ili~G~tGSGKTT~-l~all~~i~~~--~~~iv~iEd~~E~~  168 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTL-LNALLEEIPPE--DERIVTIEDPPELR  168 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHH-HHHHHHHCHTT--TSEEEEEESSS-S-
T ss_pred             ccceEEEEECCCccccchH-HHHHhhhcccc--ccceEEecccccee
Confidence            4578999999999999954 46666666543  23666666665553

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 ....

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.67  E-value=0.07  Score=42.00  Aligned_cols=19  Identities=32%  Similarity=0.433  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~   69 (175)
                      ++.+.+.+|||+|||....
T Consensus       194 ~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3578899999999997543

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=95.56  E-value=0.15  Score=44.72  Aligned_cols=116  Identities=10%  Similarity=-0.030  Sum_probs=72.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC-CCeEEEEEECCCchHHhHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM-SNIKVGVFFGGLPIQKDEE  128 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~i~v~~~~g~~~~~~~~~  128 (175)
                      +.+-.++..|--.|||+... +++..+.....+.++++.+|.+.-++.+++.+..+.+.. ++-.+....| ...   .-
T Consensus       253 kqk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i  327 (738)
T PHA03368        253 RQRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SF  327 (738)
T ss_pred             hccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EE
Confidence            34567788899999998665 666665554467899999999999999999988876642 2212222222 111   00


Q ss_pred             HHhcCC--CeEEEeec--CccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         129 YLKTHN--PQIVGLVN--YETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       129 ~l~~~~--~iiv~l~~--~~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      .+.+|.  -+..+-.+  +...=.+++++|+|||...-.+.+..+|
T Consensus       328 ~f~nG~kstI~FaSarntNsiRGqtfDLLIVDEAqFIk~~al~~il  373 (738)
T PHA03368        328 SFPDGSRSTIVFASSHNTNGIRGQDFNLLFVDEANFIRPDAVQTIM  373 (738)
T ss_pred             EecCCCccEEEEEeccCCCCccCCcccEEEEechhhCCHHHHHHHH
Confidence            122232  22222111  1234457999999999766556666665

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=95.55  E-value=0.044  Score=44.34  Aligned_cols=50  Identities=16%  Similarity=0.032  Sum_probs=33.4

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHh-cCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAV-LGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~-~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .-++.+.+.|+  +++.+.+.+..+. .+.+++++++||||||.. +-.++..+
T Consensus       152 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl-l~al~~~i  202 (340)
T TIGR03819       152 FTLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL-LSALLALV  202 (340)
T ss_pred             CCHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH-HHHHHccC
Confidence            34555666665  4566666665554 568999999999999953 34444444

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

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.49  E-value=0.033  Score=42.56  Aligned_cols=53  Identities=15%  Similarity=0.141  Sum_probs=35.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|..+++.+++|+|||....--+...+.   ++-++++++ +.+-..|+.+.+..+.
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~---~ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQ---MGEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHH---cCCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            3688999999999999755444444443   344677777 4455666666666553

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=95.47  E-value=0.045  Score=42.69  Aligned_cols=46  Identities=22%  Similarity=0.179  Sum_probs=30.8

Q ss_pred             HHhhCCCCCCcHHHHHhHHHHhc-C-CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          28 IGESQPFREQTSFQHECIPQAVL-G-MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        28 ~l~~~g~~~~t~~Q~~~i~~~~~-g-~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+.+.|+   .+-|.+.+..+.. . ..+++.++||||||.. +..++..+.
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~-l~all~~i~  105 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTT-LYSALSELN  105 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHH-HHHHHhhhC
Confidence            3556664   5667777765553 3 4689999999999964 455555553

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=95.45  E-value=0.23  Score=40.14  Aligned_cols=56  Identities=21%  Similarity=0.249  Sum_probs=30.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC--HH-HHHHHHHHHHHHHhhCCCeEEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT--RE-LAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt--~~-L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .-+++.+++|+|||.+..--+ ..+..  .+.+++++...  |. -..|    ++.+.... ++.+.
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA-~~l~~--~g~~V~li~~Dt~R~~a~eq----L~~~a~~l-gv~v~  199 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLA-YYLKK--NGFSVVIAAGDTFRAGAIEQ----LEEHAERL-GVKVI  199 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHH-HHHHH--cCCeEEEecCCcCcHHHHHH----HHHHHHHc-CCcee
Confidence            457889999999997543222 23332  33355555532  33 3334    44444444 55544

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=95.45  E-value=0.042  Score=47.50  Aligned_cols=45  Identities=22%  Similarity=0.239  Sum_probs=31.1

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +.++||   .+.|.+.+..+...  -.+++++|||||||.+. ..++..+.
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            455665   56677777665543  45789999999999764 56666664

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.

>KOG4439|consensus

Probab=95.40  E-value=0.11  Score=45.64  Aligned_cols=101  Identities=18%  Similarity=0.212  Sum_probs=70.4

Q ss_pred             CCcHHHHHhHHHHhc-----CCcEEEEcCCCChHHHHHHHHHHHhh-----hcC--CCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVL-----GMDILCQAKSGMGKTAVFVLATLQQL-----ETT--DSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~-----g~~~ii~a~TGsGKT~~~~~~~l~~l-----~~~--~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .+-|+|..++..+.-     +..-++...-|-|||+..+--+++.-     ..+  ......|||||- .|..|+...+.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHHH
Confidence            356799998866552     36778888999999987554444321     111  112258999997 47789998888


Q ss_pred             HHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE
Q psy1539         104 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG  139 (175)
Q Consensus       104 ~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~  139 (175)
                      +-.... -++|.+++|........+.+++ .+++|.
T Consensus       404 ~rl~~n-~LsV~~~HG~n~r~i~~~~L~~-YDvViT  437 (901)
T KOG4439|consen  404 RRLEQN-ALSVYLYHGPNKREISAKELRK-YDVVIT  437 (901)
T ss_pred             HHHhhc-ceEEEEecCCccccCCHHHHhh-cceEEE
Confidence            776665 7888888888755556666765 588887

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=95.40  E-value=0.19  Score=46.00  Aligned_cols=77  Identities=8%  Similarity=0.132  Sum_probs=59.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.+++|++|+++-+..+.+.++++   .|+.++..++|+.+..+..+   .+.+| .+++|+  +....++++++.++|
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~---~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~iie~GIDIp~v~~VI  735 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLREL---VPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII  735 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHh---CCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcccccccCCEEE
Confidence            3458999999998888877777655   35789999999987554433   34443 578888  777899999999999


Q ss_pred             EeCCCC
Q psy1539         155 MDVRSG  160 (175)
Q Consensus       155 lDEad~  160 (175)
                      ++.++.
T Consensus       736 i~~a~~  741 (926)
T TIGR00580       736 IERADK  741 (926)
T ss_pred             EecCCC
Confidence            999964

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.35  E-value=0.077  Score=46.12  Aligned_cols=45  Identities=18%  Similarity=0.193  Sum_probs=28.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ..+++.+++|+|||. .+.++.+.+.....+.+++++ +..+++.+.
T Consensus       315 NpL~LyG~sGsGKTH-LL~AIa~~a~~~~~g~~V~Yi-taeef~~el  359 (617)
T PRK14086        315 NPLFIYGESGLGKTH-LLHAIGHYARRLYPGTRVRYV-SSEEFTNEF  359 (617)
T ss_pred             CcEEEECCCCCCHHH-HHHHHHHHHHHhCCCCeEEEe-eHHHHHHHH
Confidence            349999999999994 345556655443334466665 445555543

>KOG0989|consensus

Probab=95.32  E-value=0.033  Score=44.23  Aligned_cols=33  Identities=18%  Similarity=0.048  Sum_probs=22.7

Q ss_pred             HHHHhHHHHhc------CCcEEEEcCCCChHHHHHHHHH
Q psy1539          40 FQHECIPQAVL------GMDILCQAKSGMGKTAVFVLAT   72 (175)
Q Consensus        40 ~Q~~~i~~~~~------g~~~ii~a~TGsGKT~~~~~~~   72 (175)
                      .|..+...+.+      +.+.+..+|+|+|||-+..+..
T Consensus        40 gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafa   78 (346)
T KOG0989|consen   40 GQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFA   78 (346)
T ss_pred             chHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHH
Confidence            45555544332      3689999999999997765443

>KOG1132|consensus

Probab=95.26  E-value=0.013  Score=52.07  Aligned_cols=39  Identities=18%  Similarity=0.244  Sum_probs=32.2

Q ss_pred             CCcHHHHHhHHHHhc----CCcEEEEcCCCChHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVL----GMDILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~----g~~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      .|++.|...+..++.    ..+.++.+|||+|||++.+...+.
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LA   63 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLA   63 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHH
Confidence            589999988876664    578999999999999998866654

>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=95.24  E-value=0.049  Score=39.54  Aligned_cols=48  Identities=19%  Similarity=0.129  Sum_probs=30.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      +++.+|+|+|||...+--+...+.   ++.++++++. .+-..++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~---~g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA---RGEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH---CCCcEEEEEC-CCCHHHHHHHHHHc
Confidence            689999999999654433333332   3446777754 45556666666554

A related protein is found in archaea.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.24  E-value=0.16  Score=43.42  Aligned_cols=25  Identities=20%  Similarity=0.066  Sum_probs=17.3

Q ss_pred             CCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         147 LSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       147 ~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      +.+.+++|+||+|..-....+.++.
T Consensus       114 ~~~~kVVIIDEad~ls~~a~naLLk  138 (504)
T PRK14963        114 RGGRKVYILDEAHMMSKSAFNALLK  138 (504)
T ss_pred             cCCCeEEEEECccccCHHHHHHHHH
Confidence            3578899999998655555555543

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=95.18  E-value=0.089  Score=48.19  Aligned_cols=84  Identities=18%  Similarity=0.209  Sum_probs=61.1

Q ss_pred             cHHHHHhHHHHhc--------CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC
Q psy1539          38 TSFQHECIPQAVL--------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  109 (175)
Q Consensus        38 t~~Q~~~i~~~~~--------g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  109 (175)
                      ..+|-.|+..+..        |--++-.|.||+|||++=. =++..+.....+.+..|-.-.|.|-.|..+.+++-....
T Consensus       410 F~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA-RImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~L~  488 (1110)
T TIGR02562       410 FRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA-RAMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLNLS  488 (1110)
T ss_pred             cchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH-HHHHHhCCCCCCceEEEEccccceeccchHHHHHhcCCC
Confidence            5588888876653        3456778999999997632 223334444667788888899999999999998876554


Q ss_pred             CCeEEEEEECCCch
Q psy1539         110 SNIKVGVFFGGLPI  123 (175)
Q Consensus       110 ~~i~v~~~~g~~~~  123 (175)
                       +-..++++|+...
T Consensus       489 -~ddLAVlIGs~Av  501 (1110)
T TIGR02562       489 -DDDLAVLIGGTAV  501 (1110)
T ss_pred             -ccceEEEECHHHH
Confidence             5677888887543

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.17  E-value=0.05  Score=41.07  Aligned_cols=53  Identities=21%  Similarity=0.248  Sum_probs=32.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .|..+++.+++|+|||...+--+.+.+...  +-++++++- .+-..++.+.++.+
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs~-ee~~~~l~~~~~s~   70 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVSF-EEPPEELIENMKSF   70 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEES-SS-HHHHHHHHHTT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEEe-cCCHHHHHHHHHHc
Confidence            458899999999999966544444444430  336777763 34445656665554

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 ....

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.17  E-value=0.035  Score=37.44  Aligned_cols=40  Identities=25%  Similarity=0.185  Sum_probs=24.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      +..+++.+|+|+|||... ..++..+....  ..++++.+...
T Consensus         2 ~~~~~l~G~~G~GKTtl~-~~l~~~~~~~~--~~~~~~~~~~~   41 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA-RALARELGPPG--GGVIYIDGEDI   41 (148)
T ss_pred             CCEEEEECCCCCcHHHHH-HHHHhccCCCC--CCEEEECCEEc
Confidence            567899999999999654 33333333211  24666666543

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.

>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=95.15  E-value=0.11  Score=41.49  Aligned_cols=59  Identities=15%  Similarity=0.099  Sum_probs=37.5

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhH-HHHhcCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECI-PQAVLGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i-~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ..+.++..++++.-+.   +.|  .+++.|..-+ -.+..+++++++++||||||. ++.+++..+
T Consensus       108 ~IRk~~~~~~t~~~l~---~~g--t~~~~~~ayL~~~ie~~~siii~G~t~sGKTt-~lnall~~I  167 (312)
T COG0630         108 TIRKFSDEPITPEDLI---EYG--TISPEQAAYLWLAIEARKSIIICGGTASGKTT-LLNALLDFI  167 (312)
T ss_pred             EEEcCCCCCCCHHHHh---hcC--CCCHHHHHHHHHHHHcCCcEEEECCCCCCHHH-HHHHHHHhC
Confidence            3444555555554433   333  4566666554 455578999999999999994 456665554

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.13  E-value=1.6  Score=38.29  Aligned_cols=80  Identities=18%  Similarity=0.257  Sum_probs=54.3

Q ss_pred             CCeEEEEEecCHHHH-----HHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhc-CCCeEEE--eecCccCCCC
Q psy1539          81 SNVYVLVMCHTRELA-----FQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKT-HNPQIVG--LVNYETNLSG  149 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~-----~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~-~~~iiv~--l~~~~~~~~~  149 (175)
                      ++.++++++|+.+-.     ....+.++.+.+.+++.++..++|+.+..+..   +.+++ ..+++|+  +....+++.+
T Consensus       447 ~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GvDiP~  526 (630)
T TIGR00643       447 KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN  526 (630)
T ss_pred             hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECceeecCcccCC
Confidence            456899999986421     12223333444444688999999998755443   34444 3578888  7777999999


Q ss_pred             ceEEEEeCCCC
Q psy1539         150 VVVNVMDVRSG  160 (175)
Q Consensus       150 ~~~lVlDEad~  160 (175)
                      ++++|+..++.
T Consensus       527 v~~VIi~~~~r  537 (630)
T TIGR00643       527 ATVMVIEDAER  537 (630)
T ss_pred             CcEEEEeCCCc
Confidence            99999988864

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=95.12  E-value=0.36  Score=40.12  Aligned_cols=82  Identities=15%  Similarity=0.099  Sum_probs=57.4

Q ss_pred             HHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCcc
Q psy1539          72 TLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYET  145 (175)
Q Consensus        72 ~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~  145 (175)
                      ++..+.......++||.|++++-+..+.+.++.    . ++.+..++|+.+..+..   +.+++| ..++|+  +....+
T Consensus       235 ~l~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~----~-~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~Gi  309 (434)
T PRK11192        235 LLCHLLKQPEVTRSIVFVRTRERVHELAGWLRK----A-GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGI  309 (434)
T ss_pred             HHHHHHhcCCCCeEEEEeCChHHHHHHHHHHHh----C-CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCc
Confidence            333443333456899999999999988877764    2 78899999998755443   344444 467777  666688


Q ss_pred             CCCCceEEEEeCC
Q psy1539         146 NLSGVVVNVMDVR  158 (175)
Q Consensus       146 ~~~~~~~lVlDEa  158 (175)
                      ++++++++|.=+.
T Consensus       310 Dip~v~~VI~~d~  322 (434)
T PRK11192        310 DIDDVSHVINFDM  322 (434)
T ss_pred             cCCCCCEEEEECC
Confidence            8899998885444

>PLN03025 replication factor C subunit; Provisional

Probab=95.10  E-value=0.42  Score=38.21  Aligned_cols=24  Identities=29%  Similarity=0.474  Sum_probs=17.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .+++++||+|+|||... ..+...+
T Consensus        35 ~~lll~Gp~G~GKTtla-~~la~~l   58 (319)
T PLN03025         35 PNLILSGPPGTGKTTSI-LALAHEL   58 (319)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999544 3334443

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.07  E-value=0.66  Score=36.39  Aligned_cols=19  Identities=26%  Similarity=0.368  Sum_probs=16.0

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      ..+.+.+++|+|||..+..
T Consensus        76 ~~i~~~G~~g~GKTtl~~~   94 (270)
T PRK06731         76 QTIALIGPTGVGKTTTLAK   94 (270)
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            6789999999999986654

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=95.07  E-value=0.23  Score=36.33  Aligned_cols=17  Identities=24%  Similarity=0.335  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ..+++.+|+|+|||...
T Consensus        15 ~~~L~~G~~G~gkt~~a   31 (188)
T TIGR00678        15 HAYLFAGPEGVGKELLA   31 (188)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            46899999999999543

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.

>PHA02535 P terminase ATPase subunit; Provisional

Probab=95.05  E-value=0.12  Score=44.58  Aligned_cols=89  Identities=8%  Similarity=0.038  Sum_probs=63.3

Q ss_pred             cCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          18 SRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        18 ~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      .-.++++..+.|.+.-...+.++|+..+..-...+.-++.-.-=.|||..|..-++.....  .|...++++|+++.+.+
T Consensus       120 kn~~s~~~~~~l~~~~~~~l~~YQ~~W~~~~~~~r~r~ilKSRQiG~T~~fA~EA~~dal~--~G~nqiflSas~~QA~~  197 (581)
T PHA02535        120 KNDISDEQTEKLIEAFLDSLFDYQKHWYRAGLHHRTRNILKSRQIGATYYFAREALEDALL--TGRNQIFLSASKAQAHV  197 (581)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHhCccccceeeEeeecccchHHHHHHHHHHHHHh--cCCceEEECCCHHHHHH
Confidence            3446777777777764568899999988553234555555556689999988776665554  23357899999999998


Q ss_pred             HHHHHHHHHhh
Q psy1539          98 ISKEYERFSKY  108 (175)
Q Consensus        98 ~~~~~~~~~~~  108 (175)
                      ..+.+..+.+.
T Consensus       198 f~~yi~~~a~~  208 (581)
T PHA02535        198 FKQYIIAFARE  208 (581)
T ss_pred             HHHHHHHHHHh
Confidence            77777777554

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.05  E-value=0.16  Score=41.48  Aligned_cols=17  Identities=29%  Similarity=0.411  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFV   69 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~   69 (175)
                      .+++.||.|+|||....
T Consensus        40 ~~L~~Gp~G~GKTtla~   56 (363)
T PRK14961         40 AWLLSGTRGVGKTTIAR   56 (363)
T ss_pred             EEEEecCCCCCHHHHHH
Confidence            46899999999996543

>KOG0344|consensus

Probab=95.02  E-value=0.88  Score=39.10  Aligned_cols=94  Identities=21%  Similarity=0.167  Sum_probs=70.4

Q ss_pred             CCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchH---HhHHHHhcC-CC
Q psy1539          60 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ---KDEEYLKTH-NP  135 (175)
Q Consensus        60 TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~---~~~~~l~~~-~~  135 (175)
                      .+.||+..-++++.+.+... -.|-++|.+-+.+-|.|++..+.    .++++.+.+++|+.+..   +..+.++.| ..
T Consensus       366 vF~gse~~K~lA~rq~v~~g-~~PP~lIfVQs~eRak~L~~~L~----~~~~i~v~vIh~e~~~~qrde~~~~FR~g~Iw  440 (593)
T KOG0344|consen  366 VFCGSEKGKLLALRQLVASG-FKPPVLIFVQSKERAKQLFEELE----IYDNINVDVIHGERSQKQRDETMERFRIGKIW  440 (593)
T ss_pred             eeeecchhHHHHHHHHHhcc-CCCCeEEEEecHHHHHHHHHHhh----hccCcceeeEecccchhHHHHHHHHHhccCee
Confidence            35666666667776666543 34578999999999999888887    23589999999996643   334456555 46


Q ss_pred             eEEE--eecCccCCCCceEEEEeCC
Q psy1539         136 QIVG--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       136 iiv~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      ++|+  ++.+.++|.++.++|.++.
T Consensus       441 vLicTdll~RGiDf~gvn~VInyD~  465 (593)
T KOG0344|consen  441 VLICTDLLARGIDFKGVNLVINYDF  465 (593)
T ss_pred             EEEehhhhhccccccCcceEEecCC
Confidence            6777  7778899999999999988

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

Probab=95.01  E-value=0.24  Score=42.33  Aligned_cols=73  Identities=16%  Similarity=0.242  Sum_probs=53.6

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.+.|+..+..+...++..     |+++..++|+.+..+..+   .+++ ...++|+  +..+.++++++.++|
T Consensus       272 ~~~~~IVF~~tk~~~~~l~~~l~~~-----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRGiDi~~v~~Vi  346 (513)
T COG0513         272 DEGRVIVFVRTKRLVEELAESLRKR-----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVI  346 (513)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHC-----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhccCCccccceeE
Confidence            3447999999999998866555544     789999999988655444   3333 4578888  666788888888886


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      -=+.
T Consensus       347 nyD~  350 (513)
T COG0513         347 NYDL  350 (513)
T ss_pred             EccC
Confidence            5443

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.99  E-value=0.26  Score=41.34  Aligned_cols=56  Identities=16%  Similarity=0.231  Sum_probs=31.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec-C-HHHHHHHHHHHHHHHhhCCCeEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-T-RELAFQISKEYERFSKYMSNIKV  114 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~i~v  114 (175)
                      ..+++++++|+|||.+..--+ ..+..  .+.+++++.. + |.-+   .++++.+.... ++.+
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA-~~L~~--~g~kV~lV~~D~~R~aa---~eQL~~la~~~-gvp~  153 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLA-RYFKK--KGLKVGLVAADTYRPAA---YDQLKQLAEKI-GVPF  153 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHH-HHHHH--cCCeEEEecCCCCCHHH---HHHHHHHHHHc-CCcE
Confidence            357899999999997654322 33332  2335555542 2 3322   34455555554 5554

>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=94.97  E-value=0.49  Score=37.72  Aligned_cols=43  Identities=21%  Similarity=0.147  Sum_probs=25.4

Q ss_pred             EEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          55 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        55 ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      ++.++.|+|||.....-++..+.....+.++++...+..+...
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~~~~~~~   43 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTYRQARDI   43 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESSHHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCHHHHHHH
Confidence            4678999999998887777776654444455555334555544

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.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.97  E-value=0.14  Score=43.77  Aligned_cols=24  Identities=17%  Similarity=-0.024  Sum_probs=17.5

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.+|+||+|+.-....+.+++
T Consensus       118 ~~~kV~iIDE~~~ls~~a~naLLk  141 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHSFNALLK  141 (509)
T ss_pred             CCcEEEEEEChHhcCHHHHHHHHH
Confidence            467899999998766666555543

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.93  E-value=0.021  Score=46.83  Aligned_cols=47  Identities=23%  Similarity=0.152  Sum_probs=34.9

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      ++++.||||||||.++++|-+-..     ...++|.=|.-|+........++
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~   47 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRA   47 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHH
Confidence            478999999999999988876542     12577778888888765554443

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.

>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=94.91  E-value=0.0083  Score=43.98  Aligned_cols=110  Identities=15%  Similarity=0.019  Sum_probs=43.8

Q ss_pred             EEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc-C
Q psy1539          55 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT-H  133 (175)
Q Consensus        55 ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~-~  133 (175)
                      ++.|+-|-|||.+.-+.+...+..  ...++++-+|+.+=++.+++.+..-.+.. +.+...    .........+.. +
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~--~~~~I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~~~----~~~~~~~~~~~~~~   73 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQK--GKIRILVTAPSPENVQTLFEFAEKGLKAL-GYKEEK----KKRIGQIIKLRFNK   73 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-------------------------------C
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHh--cCceEEEecCCHHHHHHHHHHHHhhcccc-cccccc----cccccccccccccc
Confidence            578999999997766555443332  23578899999988887777655444332 222200    000000000000 0


Q ss_pred             CCeEEEeecCccC-CCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         134 NPQIVGLVNYETN-LSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       134 ~~iiv~l~~~~~~-~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ..+-..-.+.... -...+++|+|||...-.+-++.++.
T Consensus        74 ~~i~f~~Pd~l~~~~~~~DlliVDEAAaIp~p~L~~ll~  112 (177)
T PF05127_consen   74 QRIEFVAPDELLAEKPQADLLIVDEAAAIPLPLLKQLLR  112 (177)
T ss_dssp             CC--B--HHHHCCT----SCEEECTGGGS-HHHHHHHHC
T ss_pred             ceEEEECCHHHHhCcCCCCEEEEechhcCCHHHHHHHHh
Confidence            0110000111111 1245899999998777777777763

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=94.90  E-value=0.18  Score=40.67  Aligned_cols=32  Identities=22%  Similarity=0.210  Sum_probs=25.5

Q ss_pred             CcHHHHHhHHHHhcC----CcEEEEcCCCChHHHHH
Q psy1539          37 QTSFQHECIPQAVLG----MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g----~~~ii~a~TGsGKT~~~   68 (175)
                      .+|+|...|..+...    +-+++++|.|.|||..+
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A   39 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALA   39 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHH
Confidence            478899999877743    46899999999999544

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=94.90  E-value=0.44  Score=39.84  Aligned_cols=80  Identities=16%  Similarity=0.122  Sum_probs=42.2

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCch-H---Hh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI-Q---KD  126 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~-~---~~  126 (175)
                      -+.+++++|+|||.+..--+ ..+..  .+.++++++  |.|.-+.   ++++.+.+.. ++.+.....+.+. .   +.
T Consensus       102 vi~lvG~~GvGKTTtaaKLA-~~l~~--~G~kV~lV~~D~~R~aA~---eQLk~~a~~~-~vp~~~~~~~~dp~~i~~~~  174 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLA-YYYQR--KGFKPCLVCADTFRAGAF---DQLKQNATKA-RIPFYGSYTESDPVKIASEG  174 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHH--CCCCEEEEcCcccchhHH---HHHHHHhhcc-CCeEEeecCCCCHHHHHHHH
Confidence            47899999999996543211 22222  234566555  3454443   3455555554 6665544443332 1   23


Q ss_pred             HHHHh-cCCCeEEE
Q psy1539         127 EEYLK-THNPQIVG  139 (175)
Q Consensus       127 ~~~l~-~~~~iiv~  139 (175)
                      .+.++ +++++|+.
T Consensus       175 l~~~~~~~~DvViI  188 (429)
T TIGR01425       175 VEKFKKENFDIIIV  188 (429)
T ss_pred             HHHHHhCCCCEEEE
Confidence            33333 36788776

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.85  E-value=0.35  Score=39.92  Aligned_cols=58  Identities=21%  Similarity=0.237  Sum_probs=31.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      ++.+.+.+|+|+|||....--.. .+..  .+.++.++.  |.|.=+   .++++.+.+.. ++.+.
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~-~l~~--~g~~V~lItaDtyR~gA---veQLk~yae~l-gvpv~  265 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGW-QLLK--QNRTVGFITTDTFRSGA---VEQFQGYADKL-DVELI  265 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH-HHHH--cCCeEEEEeCCccCccH---HHHHHHHhhcC-CCCEE
Confidence            56789999999999976543222 2222  233454444  334322   22455555554 55443

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.85  E-value=0.055  Score=40.24  Aligned_cols=23  Identities=22%  Similarity=0.492  Sum_probs=17.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +++++|||||||... ..++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            688999999999653 44555554

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=94.83  E-value=0.4  Score=40.45  Aligned_cols=73  Identities=15%  Similarity=0.265  Sum_probs=55.2

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+..+||.|+|+.-+.++.+.+++.     ++.+..++|+.+..+..+   .+.+ ..+++|+  .....+++++++++|
T Consensus       225 ~~~~~IIF~~s~~~~e~la~~L~~~-----g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI  299 (470)
T TIGR00614       225 KGKSGIIYCPSRKKSEQVTASLQNL-----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVI  299 (470)
T ss_pred             CCCceEEEECcHHHHHHHHHHHHhc-----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEE
Confidence            4456799999999999988777643     788999999987654433   3333 4577887  555689999999999


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-..
T Consensus       300 ~~~~  303 (470)
T TIGR00614       300 HYSL  303 (470)
T ss_pred             EeCC
Confidence            8776

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

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.82  E-value=0.24  Score=41.05  Aligned_cols=73  Identities=11%  Similarity=0.044  Sum_probs=53.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.|+++.-|..+.+.+...     +.++..++|+.+.++..+   .+++| .+++|+  +....+++++++++|
T Consensus       254 ~~~~~lVF~~t~~~~~~l~~~L~~~-----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~rGiDip~v~~VI  328 (423)
T PRK04837        254 WPDRAIIFANTKHRCEEIWGHLAAD-----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVF  328 (423)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhC-----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhcCCCccccCEEE
Confidence            3458999999999998877766532     788999999987554433   34443 577787  666688999999888


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       329 ~~d~  332 (423)
T PRK04837        329 NYDL  332 (423)
T ss_pred             EeCC
Confidence            6655

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=94.82  E-value=2.3  Score=37.79  Aligned_cols=80  Identities=15%  Similarity=0.300  Sum_probs=54.8

Q ss_pred             CCeEEEEEecCHHHH-----HHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCC
Q psy1539          81 SNVYVLVMCHTRELA-----FQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSG  149 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~-----~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~  149 (175)
                      ++.+++++||+.+-.     ....+..+.+.+.+++.++..++|+.+..+..   +.+++| .+++|+  +....+++++
T Consensus       470 ~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~vie~GiDip~  549 (681)
T PRK10917        470 KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPN  549 (681)
T ss_pred             cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECcceeeCcccCC
Confidence            456899999975421     12233344444445568899999998755443   344554 478888  7777999999


Q ss_pred             ceEEEEeCCCC
Q psy1539         150 VVVNVMDVRSG  160 (175)
Q Consensus       150 ~~~lVlDEad~  160 (175)
                      ++++|+..++.
T Consensus       550 v~~VIi~~~~r  560 (681)
T PRK10917        550 ATVMVIENAER  560 (681)
T ss_pred             CcEEEEeCCCC
Confidence            99999999864

>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=94.79  E-value=0.59  Score=33.56  Aligned_cols=102  Identities=15%  Similarity=0.036  Sum_probs=47.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH-hhCCCeEEEEEECC--CchHHhHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS-KYMSNIKVGVFFGG--LPIQKDEE  128 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~i~v~~~~g~--~~~~~~~~  128 (175)
                      +.+++.+|.|+||+... ..++..+.-......   -+....-+       +.+. ..+|++....-.+.  .-..++.+
T Consensus        20 ha~L~~G~~g~gk~~~a-~~~a~~ll~~~~~~~---~c~~c~~c-------~~~~~~~~~d~~~~~~~~~~~~i~i~~ir   88 (162)
T PF13177_consen   20 HALLFHGPSGSGKKTLA-LAFARALLCSNPNED---PCGECRSC-------RRIEEGNHPDFIIIKPDKKKKSIKIDQIR   88 (162)
T ss_dssp             SEEEEECSTTSSHHHHH-HHHHHHHC-TT-CTT-----SSSHHH-------HHHHTT-CTTEEEEETTTSSSSBSHHHHH
T ss_pred             eeEEEECCCCCCHHHHH-HHHHHHHcCCCCCCC---CCCCCHHH-------HHHHhccCcceEEEecccccchhhHHHHH
Confidence            46899999999998543 344444432211111   22222222       2222 22345554421111  11234444


Q ss_pred             HHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         129 YLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       129 ~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.       ....-.-...+.+|+||||..-.+--..+|+
T Consensus        89 ~i~~~-------~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK  124 (162)
T PF13177_consen   89 EIIEF-------LSLSPSEGKYKVIIIDEADKLTEEAQNALLK  124 (162)
T ss_dssp             HHHHH-------CTSS-TTSSSEEEEEETGGGS-HHHHHHHHH
T ss_pred             HHHHH-------HHHHHhcCCceEEEeehHhhhhHHHHHHHHH
Confidence            44331       1112222578899999997655555444443

...

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=94.76  E-value=0.22  Score=36.95  Aligned_cols=39  Identities=15%  Similarity=0.172  Sum_probs=26.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      .|.-+.+.+|+|+|||...+..+.+...   .+.+++++.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~---~g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAAR---QGKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEECC
Confidence            3577899999999999765544433332   24467777664

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=94.74  E-value=0.28  Score=43.32  Aligned_cols=19  Identities=26%  Similarity=0.410  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      +.++++||.|+|||....+
T Consensus        39 Ha~Lf~GP~GvGKTTlAri   57 (709)
T PRK08691         39 HAYLLTGTRGVGKTTIARI   57 (709)
T ss_pred             eEEEEECCCCCcHHHHHHH
Confidence            4689999999999976543

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.72  E-value=0.047  Score=45.85  Aligned_cols=49  Identities=22%  Similarity=0.274  Sum_probs=36.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .++++.||||||||..+++|.+-..    .+ -++|.=|--||.......+++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~----~~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNY----PG-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhc----cC-CEEEEECCCcHHHHHHHHHHHC
Confidence            4699999999999999999987431    22 4677778888876655544443

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

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.71  E-value=0.021  Score=45.67  Aligned_cols=18  Identities=33%  Similarity=0.399  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ..|+++.+|||||||+.+
T Consensus        97 KSNILLiGPTGsGKTlLA  114 (408)
T COG1219          97 KSNILLIGPTGSGKTLLA  114 (408)
T ss_pred             eccEEEECCCCCcHHHHH
Confidence            368999999999999743

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=94.68  E-value=0.19  Score=43.73  Aligned_cols=107  Identities=14%  Similarity=0.015  Sum_probs=50.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCC-chHHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~-~~~~~~~~l  130 (175)
                      +.+++++|.|+|||....+ +...+.-.......   -||..-|.+. ..|+.+.... ...+..+.... ..-++++.+
T Consensus        47 ha~L~~Gp~GvGKTt~Ar~-lAk~L~c~~~~~~~---~~~~~~cg~c-~~C~~i~~g~-h~Dv~e~~a~s~~gvd~IReI  120 (598)
T PRK09111         47 QAFMLTGVRGVGKTTTARI-LARALNYEGPDGDG---GPTIDLCGVG-EHCQAIMEGR-HVDVLEMDAASHTGVDDIREI  120 (598)
T ss_pred             ceEEEECCCCCCHHHHHHH-HHHhhCcCCccccC---CCccccCccc-HHHHHHhcCC-CCceEEecccccCCHHHHHHH
Confidence            4699999999999976543 33333311100000   1332333332 2344554432 22222222211 112333333


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ...       .+..-.+..-+.+|+||+|+.-....+.+++
T Consensus       121 ie~-------~~~~P~~a~~KVvIIDEad~Ls~~a~naLLK  154 (598)
T PRK09111        121 IES-------VRYRPVSARYKVYIIDEVHMLSTAAFNALLK  154 (598)
T ss_pred             HHH-------HHhchhcCCcEEEEEEChHhCCHHHHHHHHH
Confidence            221       1111224578899999997666555555553

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

Probab=94.65  E-value=1.5  Score=40.88  Aligned_cols=126  Identities=11%  Similarity=0.117  Sum_probs=92.4

Q ss_pred             HHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhh------------------------------cCCCCeEEEEEe
Q psy1539          40 FQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE------------------------------TTDSNVYVLVMC   89 (175)
Q Consensus        40 ~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~------------------------------~~~~~~~~lil~   89 (175)
                      -|++.+..+...-|++-.+.|--=+|+-..+.-+..+.                              .-..+.|+.||.
T Consensus       731 k~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~  810 (1139)
T COG1197         731 KHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLRGGQVFYVH  810 (1139)
T ss_pred             cHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHHhcCCEEEEEe
Confidence            47888888888888888888888888766554444331                              013466999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HH-hcCCCeEEE--eecCccCCCCceEEEEeCCCCCCH
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YL-KTHNPQIVG--LVNYETNLSGVVVNVMDVRSGGWW  163 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l-~~~~~iiv~--l~~~~~~~~~~~~lVlDEad~~f~  163 (175)
                      |..+-..++...++.+   .|..++++.+|..+..+-.+   .+ ....+++|+  ++...++.++...+|+|-||+.=.
T Consensus       811 NrV~~Ie~~~~~L~~L---VPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIEtGIDIPnANTiIIe~AD~fGL  887 (1139)
T COG1197         811 NRVESIEKKAERLREL---VPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGL  887 (1139)
T ss_pred             cchhhHHHHHHHHHHh---CCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeeecCcCCCCCceEEEeccccccH
Confidence            9988887777766655   57999999999987543332   22 335688998  888899999999999999985434


Q ss_pred             HHHHH
Q psy1539         164 LDLEA  168 (175)
Q Consensus       164 ~~v~~  168 (175)
                      .|+++
T Consensus       888 sQLyQ  892 (1139)
T COG1197         888 AQLYQ  892 (1139)
T ss_pred             HHHHH
Confidence            44443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.62  E-value=0.23  Score=44.82  Aligned_cols=102  Identities=14%  Similarity=0.063  Sum_probs=48.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC-CCeEEEEEECCCc-hHHhHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM-SNIKVGVFFGGLP-IQKDEEY  129 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~i~v~~~~g~~~-~~~~~~~  129 (175)
                      +-+++++|.|+|||.+..+-. ..++-. ++       ++-.-|..+ ..|+.+.... ....+..+.+... .-++++.
T Consensus        38 Ha~Lf~Gp~G~GKTt~A~~lA-r~L~C~-~~-------~~~~pCg~C-~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~  107 (824)
T PRK07764         38 HAYLFSGPRGCGKTSSARILA-RSLNCV-EG-------PTSTPCGEC-DSCVALAPGGPGSLDVTEIDAASHGGVDDARE  107 (824)
T ss_pred             ceEEEECCCCCCHHHHHHHHH-HHhCcc-cC-------CCCCCCccc-HHHHHHHcCCCCCCcEEEecccccCCHHHHHH
Confidence            447999999999997664433 333211 11       111111111 1134433221 1344545544332 1234444


Q ss_pred             HhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         130 LKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       130 l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      +...  ..     ..-...+.+.+||||+|+.-....+.+|
T Consensus       108 l~~~--~~-----~~p~~~~~KV~IIDEad~lt~~a~NaLL  141 (824)
T PRK07764        108 LRER--AF-----FAPAESRYKIFIIDEAHMVTPQGFNALL  141 (824)
T ss_pred             HHHH--HH-----hchhcCCceEEEEechhhcCHHHHHHHH
Confidence            4321  00     0111257789999999876665555544

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=94.60  E-value=0.52  Score=39.53  Aligned_cols=73  Identities=8%  Similarity=0.157  Sum_probs=54.3

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.|+|+.-+..+.+.+.+.     ++.+..++|+.+..+..+   .++++ ..++|+  +....+++++++++|
T Consensus       241 ~~~~~lVF~~t~~~~~~l~~~L~~~-----~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi~~v~~VI  315 (460)
T PRK11776        241 QPESCVVFCNTKKECQEVADALNAQ-----GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVI  315 (460)
T ss_pred             CCCceEEEECCHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccchhcCCeEE
Confidence            3447999999999999888777543     778999999987654433   34444 467777  666688899999988


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       316 ~~d~  319 (460)
T PRK11776        316 NYEL  319 (460)
T ss_pred             EecC
Confidence            7666

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=94.59  E-value=0.079  Score=42.23  Aligned_cols=28  Identities=18%  Similarity=0.343  Sum_probs=20.3

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +..|.++++.+|||||||.. +-.++..+
T Consensus       141 v~~~~~ili~G~tGsGKTTl-l~al~~~~  168 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF-LKSLVDEI  168 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH-HHHHHccC
Confidence            44689999999999999964 33344433

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=94.59  E-value=0.71  Score=40.81  Aligned_cols=71  Identities=8%  Similarity=0.094  Sum_probs=50.8

Q ss_pred             CCcHHHHHhHHHHh---cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          36 EQTSFQHECIPQAV---LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~---~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      -|+|.=.+=|..+.   +.+-.++.+|-|.|||++..+.+...+..  .+.++++.+|...-++++++.++...+.
T Consensus       169 ~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le~  242 (752)
T PHA03333        169 APSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVHA  242 (752)
T ss_pred             CCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHHH
Confidence            34554444444444   45677888999999998776555544332  3578999999999999999988887763

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.59  E-value=0.44  Score=44.65  Aligned_cols=80  Identities=8%  Similarity=0.083  Sum_probs=60.0

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.+++|++|+++-+..+.+.+++.   .|+.++..++|+.+..+..+   .+++ ..+++|+  +....+++.+++++|+
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~---~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierGIDIP~v~~VIi  885 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIII  885 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHh---CCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcccccccCCEEEE
Confidence            458999999998887776666654   45778999999987654333   3443 4678888  7778999999999999


Q ss_pred             eCCC-CCCHH
Q psy1539         156 DVRS-GGWWL  164 (175)
Q Consensus       156 DEad-~~f~~  164 (175)
                      +.+| ++..+
T Consensus       886 ~~ad~fglaq  895 (1147)
T PRK10689        886 ERADHFGLAQ  895 (1147)
T ss_pred             ecCCCCCHHH
Confidence            9996 45443

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=94.56  E-value=0.38  Score=37.72  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=17.6

Q ss_pred             HHHHhc-C--CcEEEEcCCCChHHHH
Q psy1539          45 IPQAVL-G--MDILCQAKSGMGKTAV   67 (175)
Q Consensus        45 i~~~~~-g--~~~ii~a~TGsGKT~~   67 (175)
                      ++.+.+ +  +++++.+|+|+|||..
T Consensus       102 l~~l~~~~~~~~~~i~g~~g~GKttl  127 (270)
T TIGR02858       102 LPYLVRNNRVLNTLIISPPQCGKTTL  127 (270)
T ss_pred             HHHHHhCCCeeEEEEEcCCCCCHHHH
Confidence            455543 3  6899999999999963

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

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

Probab=94.46  E-value=0.15  Score=45.70  Aligned_cols=121  Identities=19%  Similarity=0.172  Sum_probs=74.5

Q ss_pred             CCCcHHHHHhHHHHh-----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCC-CeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          35 REQTSFQHECIPQAV-----LGMDILCQAKSGMGKTAVFVLATLQQLETTDS-NVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~-----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~-~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      ..+.++|.+.+..+.     .+.+.++...-|.|||+-.+.-+......... .+.+++++|+. +..++.+.+.++.. 
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s-~~~nw~~e~~k~~~-  414 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPAS-LLSNWKREFEKFAP-  414 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHH-HHHHHHHHHhhhCc-
Confidence            467888999886644     26788888999999997654444432222222 34789999985 55566666766654 


Q ss_pred             CCCeE-EEEEECCCch----HHhHHHHhc-C----CCeEEE----eec---C--ccCCCCceEEEEeCCC
Q psy1539         109 MSNIK-VGVFFGGLPI----QKDEEYLKT-H----NPQIVG----LVN---Y--ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       109 ~~~i~-v~~~~g~~~~----~~~~~~l~~-~----~~iiv~----l~~---~--~~~~~~~~~lVlDEad  159 (175)
                        .++ +...+|....    .+....+.+ .    .+++++    +.+   .  .+.-.....+|+||+.
T Consensus       415 --~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~  482 (866)
T COG0553         415 --DLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAH  482 (866)
T ss_pred             --cccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHH
Confidence              455 6677776641    233333332 1    345555    222   1  2334467889999984

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.44  E-value=0.18  Score=45.74  Aligned_cols=24  Identities=17%  Similarity=0.007  Sum_probs=17.0

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.+||||+++.-....+.+|+
T Consensus       118 gk~KViIIDEAh~LT~eAqNALLK  141 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRSSFNALLK  141 (944)
T ss_pred             CCcEEEEEechHhcCHHHHHHHHH
Confidence            467899999998766555555443

>KOG0923|consensus

Probab=94.44  E-value=0.075  Score=46.32  Aligned_cols=60  Identities=15%  Similarity=0.171  Sum_probs=38.6

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEecCHHHHHHHHHH
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      .++-.+.+.++....-++|.+.||||||.-  +|  +.+...   +++.++-+--|.|--|.-+...
T Consensus       267 y~ykdell~av~e~QVLiI~GeTGSGKTTQ--iP--QyL~EaGytk~gk~IgcTQPRRVAAmSVAaR  329 (902)
T KOG0923|consen  267 YPYKDELLKAVKEHQVLIIVGETGSGKTTQ--IP--QYLYEAGYTKGGKKIGCTQPRRVAAMSVAAR  329 (902)
T ss_pred             hhhHHHHHHHHHhCcEEEEEcCCCCCcccc--cc--HHHHhcccccCCceEeecCcchHHHHHHHHH
Confidence            445555666777788899999999999963  23  223221   3343444555888777765554

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.38  E-value=0.19  Score=42.48  Aligned_cols=18  Identities=28%  Similarity=0.320  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      +.++++||+|+|||..+-
T Consensus        37 ~~~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         37 HAYIFAGPRGTGKTTVAR   54 (472)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347999999999996553

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=94.37  E-value=0.097  Score=42.38  Aligned_cols=27  Identities=19%  Similarity=0.282  Sum_probs=20.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+..+++++|||||||... ..++..+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~  147 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYIN  147 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhC
Confidence            3578999999999999654 45555554

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=94.36  E-value=0.33  Score=42.81  Aligned_cols=83  Identities=19%  Similarity=0.200  Sum_probs=58.9

Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEE
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVN  153 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~l  153 (175)
                      .++.+++|.++|+..+..+.+.+.+.     ++.+..++|+.+..+..   +.+++| .+++|+  ++...+++.+++++
T Consensus       440 ~~g~~vLIf~~tk~~ae~L~~~L~~~-----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t~~L~rGfDiP~v~lV  514 (655)
T TIGR00631       440 ARNERVLVTTLTKKMAEDLTDYLKEL-----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV  514 (655)
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHhhh-----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcChhcCCeeeCCCcEE
Confidence            35668999999999998877766654     77888888886644333   344443 456655  77779999999999


Q ss_pred             EEeCCC-CCCHHHHH
Q psy1539         154 VMDVRS-GGWWLDLE  167 (175)
Q Consensus       154 VlDEad-~~f~~~v~  167 (175)
                      |+-++| .||..+.+
T Consensus       515 vi~DadifG~p~~~~  529 (655)
T TIGR00631       515 AILDADKEGFLRSER  529 (655)
T ss_pred             EEeCcccccCCCCHH
Confidence            988875 45543433

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

>PF12846 AAA_10: AAA-like domain

Probab=94.34  E-value=0.09  Score=40.88  Aligned_cols=37  Identities=27%  Similarity=0.310  Sum_probs=23.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      .++++.|+||||||.... .++..+..  .+..++++=|.
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~--~g~~~~i~D~~   38 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR--RGPRVVIFDPK   38 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH--cCCCEEEEcCC
Confidence            578999999999997665 44444332  22344444443

>PRK06526 transposase; Provisional

Probab=94.33  E-value=0.13  Score=39.99  Aligned_cols=48  Identities=13%  Similarity=0.056  Sum_probs=28.1

Q ss_pred             HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      .+..+.++++.||+|+|||..... +...+..  .+.++++. ...++..++
T Consensus        94 fi~~~~nlll~Gp~GtGKThLa~a-l~~~a~~--~g~~v~f~-t~~~l~~~l  141 (254)
T PRK06526         94 FVTGKENVVFLGPPGTGKTHLAIG-LGIRACQ--AGHRVLFA-TAAQWVARL  141 (254)
T ss_pred             hhhcCceEEEEeCCCCchHHHHHH-HHHHHHH--CCCchhhh-hHHHHHHHH
Confidence            334578999999999999965433 2222222  23345443 334455554

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.31  E-value=0.038  Score=42.85  Aligned_cols=66  Identities=17%  Similarity=0.085  Sum_probs=36.3

Q ss_pred             HHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          23 EKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        23 ~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      ++++++|...|.....+.=-+.+.-+..|.-+++.|++|+|||.....-+.+....  .+..++++.-
T Consensus         2 ~~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--~g~~vl~iS~   67 (271)
T cd01122           2 EEIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQ--HGVRVGTISL   67 (271)
T ss_pred             chhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--cCceEEEEEc
Confidence            35666676444332222111222345567899999999999996443333322221  2456777763

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PTZ00110 helicase; Provisional

Probab=94.30  E-value=0.89  Score=39.23  Aligned_cols=84  Identities=14%  Similarity=0.094  Sum_probs=57.8

Q ss_pred             HHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--ee
Q psy1539          68 FVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LV  141 (175)
Q Consensus        68 ~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~  141 (175)
                      .+..++..+..  .+.++||.|+++.-|..+.+.++.    . ++.+..++|+.+..+..   +.++++ .+++|+  +.
T Consensus       365 ~L~~ll~~~~~--~~~k~LIF~~t~~~a~~l~~~L~~----~-g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~  437 (545)
T PTZ00110        365 KLKMLLQRIMR--DGDKILIFVETKKGADFLTKELRL----D-GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVA  437 (545)
T ss_pred             HHHHHHHHhcc--cCCeEEEEecChHHHHHHHHHHHH----c-CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchh
Confidence            34444444332  456899999999999887776653    2 67888899998755443   344444 467777  56


Q ss_pred             cCccCCCCceEEEEeCC
Q psy1539         142 NYETNLSGVVVNVMDVR  158 (175)
Q Consensus       142 ~~~~~~~~~~~lVlDEa  158 (175)
                      ...+++.+++++|.=+.
T Consensus       438 ~rGIDi~~v~~VI~~d~  454 (545)
T PTZ00110        438 SRGLDVKDVKYVINFDF  454 (545)
T ss_pred             hcCCCcccCCEEEEeCC
Confidence            66788888888886554

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=94.25  E-value=0.3  Score=41.71  Aligned_cols=19  Identities=26%  Similarity=0.268  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      +.++++||.|+|||.++-+
T Consensus        44 ~a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4799999999999976543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.25  E-value=0.22  Score=43.78  Aligned_cols=19  Identities=26%  Similarity=0.422  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      +-++++||.|+|||.++.+
T Consensus        38 HAyLF~GPpGvGKTTlAri   56 (702)
T PRK14960         38 HAYLFTGTRGVGKTTIARI   56 (702)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            4679999999999976543

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.25  E-value=0.31  Score=40.62  Aligned_cols=19  Identities=26%  Similarity=0.270  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~   69 (175)
                      |.-+.+.+|||+|||....
T Consensus       191 g~vi~lvGpnG~GKTTtla  209 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTA  209 (420)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5668999999999997654

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=94.18  E-value=0.091  Score=44.84  Aligned_cols=27  Identities=30%  Similarity=0.352  Sum_probs=19.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      .|+-+.+.+|+|||||.  ++-++..+..
T Consensus       360 ~G~~vaIvG~SGsGKST--Ll~lL~g~~~  386 (529)
T TIGR02868       360 PGERVAILGPSGSGKST--LLMLLTGLLD  386 (529)
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHhcCCC
Confidence            58899999999999996  3344444443

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.

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=94.18  E-value=0.079  Score=39.93  Aligned_cols=21  Identities=10%  Similarity=-0.385  Sum_probs=14.4

Q ss_pred             CCceEEEEeCCCCCCHHHHHH
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEA  168 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~  168 (175)
                      ...+.+++||+-+.....+..
T Consensus        61 ~~~~~liiDE~~~~~~g~l~~   81 (234)
T PF01443_consen   61 KSYDTLIIDEAQLLPPGYLLL   81 (234)
T ss_pred             CcCCEEEEeccccCChHHHHH
Confidence            458899999995555444444

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

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.16  E-value=0.058  Score=41.94  Aligned_cols=25  Identities=20%  Similarity=0.295  Sum_probs=20.1

Q ss_pred             hHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          44 CIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        44 ~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ++..+..|.++++.+|+|+|||...
T Consensus        14 ~l~~l~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        14 ALRYLKSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHhcCCeEEEEcCCCCCHHHHH
Confidence            3445557899999999999999754

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).

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=94.13  E-value=0.58  Score=39.31  Aligned_cols=74  Identities=14%  Similarity=0.096  Sum_probs=53.2

Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEE
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVN  153 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~l  153 (175)
                      ....++||.|++++-+..+.+.+...     ++.+..++|+.+..+..   +.++++ ..++|+  +....+++.+++++
T Consensus       243 ~~~~~~lVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDip~v~~V  317 (456)
T PRK10590        243 GNWQQVLVFTRTKHGANHLAEQLNKD-----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHV  317 (456)
T ss_pred             CCCCcEEEEcCcHHHHHHHHHHHHHC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCcccCCEE
Confidence            34458999999999998877766532     77889999998754443   344443 467777  55567888888888


Q ss_pred             EEeCC
Q psy1539         154 VMDVR  158 (175)
Q Consensus       154 VlDEa  158 (175)
                      |.=+.
T Consensus       318 I~~~~  322 (456)
T PRK10590        318 VNYEL  322 (456)
T ss_pred             EEeCC
Confidence            76554

>KOG1000|consensus

Probab=94.12  E-value=0.46  Score=40.33  Aligned_cols=115  Identities=21%  Similarity=0.198  Sum_probs=67.7

Q ss_pred             CCCcHHHHHhHHHHh-cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          35 REQTSFQHECIPQAV-LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~-~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      ..+-|+|.+-+...+ .|-.+++.-.-|-|||+-++ ++......  .+ -.||+||.. +-..+.+.+++|+...  ..
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAl-aIA~yyra--Ew-plliVcPAs-vrftWa~al~r~lps~--~p  269 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQAL-AIARYYRA--EW-PLLIVCPAS-VRFTWAKALNRFLPSI--HP  269 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHH-HHHHHHhh--cC-cEEEEecHH-HhHHHHHHHHHhcccc--cc
Confidence            356789999887655 57888899999999997653 33333332  23 368889964 3345666677776543  22


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEE---eecC---ccCCCCceEEEEeCCC
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVG---LVNY---ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~---l~~~---~~~~~~~~~lVlDEad  159 (175)
                      +.++.++.+.-..   +.....+.|.   +..+   .+.-...+.+|+||.+
T Consensus       270 i~vv~~~~D~~~~---~~t~~~v~ivSye~ls~l~~~l~~~~~~vvI~DEsH  318 (689)
T KOG1000|consen  270 IFVVDKSSDPLPD---VCTSNTVAIVSYEQLSLLHDILKKEKYRVVIFDESH  318 (689)
T ss_pred             eEEEecccCCccc---cccCCeEEEEEHHHHHHHHHHHhcccceEEEEechh
Confidence            4455555442211   1111223222   1111   3344568999999984

>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=94.11  E-value=0.087  Score=43.36  Aligned_cols=49  Identities=20%  Similarity=0.245  Sum_probs=32.2

Q ss_pred             HHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          46 PQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        46 ~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      |.-...+++++.+.||||||. ++..++..+..  .+-+++|.=|.-+....
T Consensus        10 ~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~--~g~~~iI~D~kg~~~~~   58 (386)
T PF10412_consen   10 PKDSENRHILIIGATGSGKTQ-AIRHLLDQIRA--RGDRAIIYDPKGEFTER   58 (386)
T ss_dssp             -GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHH--TT-EEEEEEETTHHHHH
T ss_pred             ccchhhCcEEEECCCCCCHHH-HHHHHHHHHHH--cCCEEEEEECCchHHHH
Confidence            344566899999999999996 45667766654  24477887788766543

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.07  E-value=0.2  Score=41.35  Aligned_cols=19  Identities=21%  Similarity=0.303  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      +.+++++|.|+|||.++..
T Consensus        39 ha~lf~Gp~G~GKtt~A~~   57 (397)
T PRK14955         39 HGYIFSGLRGVGKTTAARV   57 (397)
T ss_pred             eeEEEECCCCCCHHHHHHH
Confidence            3488999999999976543

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=94.03  E-value=0.63  Score=37.40  Aligned_cols=42  Identities=29%  Similarity=0.392  Sum_probs=29.7

Q ss_pred             CCCCcHHHHHhHHHHh----cC---CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          34 FREQTSFQHECIPQAV----LG---MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~----~g---~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +..++|+|..+|..+.    +|   +-+++.+|.|.||+..+ ..+.+.+
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA-~~lA~~L   50 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVA-LALAEHV   50 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH-HHHHHHH
Confidence            3467899999987665    34   35899999999998543 3344444

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.03  E-value=0.42  Score=42.70  Aligned_cols=82  Identities=10%  Similarity=0.086  Sum_probs=40.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec-C-HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-T-RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  129 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~  129 (175)
                      +-+.+.+|||+|||.+...-....... .++.++.++.- + |.=+   .++++.+.+.. ++.+..........+.++.
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~-~G~kkV~lit~Dt~RigA---~eQL~~~a~~~-gvpv~~~~~~~~l~~al~~  260 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVAR-EGADQLALLTTDSFRIGA---LEQLRIYGRIL-GVPVHAVKDAADLRFALAA  260 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHH-cCCCeEEEecCcccchHH---HHHHHHHHHhC-CCCccccCCHHHHHHHHHH
Confidence            457899999999997654322222112 12224444443 2 2112   34566666665 6655433322222233333


Q ss_pred             HhcCCCeEEE
Q psy1539         130 LKTHNPQIVG  139 (175)
Q Consensus       130 l~~~~~iiv~  139 (175)
                      +. +.++|+.
T Consensus       261 ~~-~~D~VLI  269 (767)
T PRK14723        261 LG-DKHLVLI  269 (767)
T ss_pred             hc-CCCEEEE
Confidence            43 4566665

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.02  E-value=0.074  Score=46.29  Aligned_cols=49  Identities=29%  Similarity=0.106  Sum_probs=37.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .++++.||||||||..+++|-+-.+.     .-++|+=|--|+........++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~~-----~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFWE-----DSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhCC-----CCEEEEeCcHHHHHHHHHHHHHC
Confidence            57999999999999999999987642     13677778888887766555443

>KOG0058|consensus

Probab=94.02  E-value=0.072  Score=46.67  Aligned_cols=29  Identities=21%  Similarity=0.260  Sum_probs=23.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCC
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTD   80 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~   80 (175)
                      .|+.+-+.+|.|+|||.+  ..++.+++...
T Consensus       493 pGe~vALVGPSGsGKSTi--asLL~rfY~Pt  521 (716)
T KOG0058|consen  493 PGEVVALVGPSGSGKSTI--ASLLLRFYDPT  521 (716)
T ss_pred             CCCEEEEECCCCCCHHHH--HHHHHHhcCCC
Confidence            589999999999999985  46677776543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.02  E-value=0.37  Score=41.90  Aligned_cols=102  Identities=16%  Similarity=0.054  Sum_probs=49.1

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC-CCeEEEEEECCCc-hHHhHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM-SNIKVGVFFGGLP-IQKDEEYL  130 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~i~v~~~~g~~~-~~~~~~~l  130 (175)
                      -+++++|.|+|||.+..+ +...+.-. ++       |+-+-|.+.. .|+.+.... ....+..+.+..+ .-++.+.+
T Consensus        37 a~Lf~Gp~G~GKTt~A~~-lAk~l~c~-~~-------~~~~pCg~C~-~C~~i~~~~~~~~dvieidaas~~gvd~iRel  106 (584)
T PRK14952         37 AYLFSGPRGCGKTSSARI-LARSLNCA-QG-------PTATPCGVCE-SCVALAPNGPGSIDVVELDAASHGGVDDTREL  106 (584)
T ss_pred             EEEEECCCCCCHHHHHHH-HHHHhccc-cC-------CCCCcccccH-HHHHhhcccCCCceEEEeccccccCHHHHHHH
Confidence            368999999999976544 33333211 11       1111122211 244443211 1234444444322 12333333


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.       ....-...+-+.+|+||+|+.-....+.+++
T Consensus       107 ~~~-------~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK  140 (584)
T PRK14952        107 RDR-------AFYAPAQSRYRIFIVDEAHMVTTAGFNALLK  140 (584)
T ss_pred             HHH-------HHhhhhcCCceEEEEECCCcCCHHHHHHHHH
Confidence            321       0111123578999999998776666555543

>PRK04328 hypothetical protein; Provisional

Probab=93.97  E-value=0.14  Score=39.47  Aligned_cols=53  Identities=15%  Similarity=0.142  Sum_probs=33.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|..+++.+++|+|||....--+.+.+..   +-.+++++ +.+-..++.+.++.+.
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~---ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            46789999999999996544444444432   33567766 4445555666665553

>KOG0335|consensus

Probab=93.95  E-value=1.3  Score=37.35  Aligned_cols=151  Identities=12%  Similarity=0.031  Sum_probs=93.4

Q ss_pred             cccccCCCCHHHHHHHhhCCC-------------CCCcHHHHHhHHHHhcCCcEEEEcCCCChHH--------------H
Q psy1539          14 KVLSSRNRREKEDRIGESQPF-------------REQTSFQHECIPQAVLGMDILCQAKSGMGKT--------------A   66 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~-------------~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT--------------~   66 (175)
                      +-.+++++-|++.+.+...+-             +.|..+|..+...+.+++..+-.+.-|+.--              .
T Consensus       237 rMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr  316 (482)
T KOG0335|consen  237 RMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKR  316 (482)
T ss_pred             HhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchhhH
Confidence            345568888888887766654             2578899966666666676666666654311              1


Q ss_pred             HHHHHHHHhhhcC-----CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH---hc-CCCeE
Q psy1539          67 VFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL---KT-HNPQI  137 (175)
Q Consensus        67 ~~~~~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l---~~-~~~ii  137 (175)
                      ..++-++......     ...-+.++.|-|+.-+.++...+...     +.....++|+....+..+.+   ++ .+|++
T Consensus       317 ~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~-----~~~~~sIhg~~tq~er~~al~~Fr~g~~pvl  391 (482)
T KOG0335|consen  317 SKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSN-----GYPAKSIHGDRTQIEREQALNDFRNGKAPVL  391 (482)
T ss_pred             HHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcC-----CCCceeecchhhhhHHHHHHHHhhcCCcceE
Confidence            2233333322211     01126889999998888866655432     77788888887655554444   33 36888


Q ss_pred             EE--eecCccCCCCceEEEEeCCCCCCHHHHHHH
Q psy1539         138 VG--LVNYETNLSGVVVNVMDVRSGGWWLDLEAL  169 (175)
Q Consensus       138 v~--l~~~~~~~~~~~~lVlDEad~~f~~~v~~i  169 (175)
                      |+  +..+.+++++++++|.=+.-..+-+++..|
T Consensus       392 VaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRI  425 (482)
T KOG0335|consen  392 VATNVAARGLDIPNVKHVINYDMPADIDDYVHRI  425 (482)
T ss_pred             EEehhhhcCCCCCCCceeEEeecCcchhhHHHhc
Confidence            88  666788899999988766522244444443

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

Probab=93.95  E-value=3.3  Score=36.45  Aligned_cols=122  Identities=15%  Similarity=0.233  Sum_probs=81.4

Q ss_pred             cHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHH------HHHHhh------------------------h-cCCCCeEE
Q psy1539          38 TSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVL------ATLQQL------------------------E-TTDSNVYV   85 (175)
Q Consensus        38 t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~------~~l~~l------------------------~-~~~~~~~~   85 (175)
                      =-.|+..+..--. ..++++.+.|--=+|+|...      .++..+                        . .-.+|.|+
T Consensus       397 GV~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei~~GrQa  476 (677)
T COG1200         397 GVHQRLALREKGEQNPHVLVMTATPIPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREEIAKGRQA  476 (677)
T ss_pred             cHHHHHHHHHhCCCCCcEEEEeCCCchHHHHHHHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHHHHcCCEE
Confidence            3456665543323 45888888888888876432      111111                        0 01356799


Q ss_pred             EEEecCHHHHH-----HHHHHHHHHHhhCCCeEEEEEECCCchH---HhHHHHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          86 LVMCHTRELAF-----QISKEYERFSKYMSNIKVGVFFGGLPIQ---KDEEYLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        86 lil~Pt~~L~~-----q~~~~~~~~~~~~~~i~v~~~~g~~~~~---~~~~~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+|||..+-.+     -..+.+..+...+|+.++++++|..+.+   +-++.+++ ..+|+|+  ++.-.++.++-.+.|
T Consensus       477 Y~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTVIEVGVdVPnATvMV  556 (677)
T COG1200         477 YVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMV  556 (677)
T ss_pred             EEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeEEEecccCCCCeEEE
Confidence            99999766543     3334455555566789999999998743   33456666 5688888  666789999999999


Q ss_pred             EeCCC
Q psy1539         155 MDVRS  159 (175)
Q Consensus       155 lDEad  159 (175)
                      +..|+
T Consensus       557 Ie~AE  561 (677)
T COG1200         557 IENAE  561 (677)
T ss_pred             Eechh
Confidence            99995

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=93.93  E-value=1.1  Score=37.85  Aligned_cols=73  Identities=14%  Similarity=0.160  Sum_probs=52.6

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.|++++-+..+.+.+.+.     ++.+..++|+.+..+..   +.+++| ..++|+  +....+++.+++++|
T Consensus       334 ~~~~~IVF~~s~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI  408 (475)
T PRK01297        334 PWERVMVFANRKDEVRRIEERLVKD-----GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVI  408 (475)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEE
Confidence            4458999999999988877666432     67788889988765443   344444 466777  666688888888888


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-..
T Consensus       409 ~~~~  412 (475)
T PRK01297        409 NFTL  412 (475)
T ss_pred             EeCC
Confidence            7655

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.93  E-value=0.33  Score=42.47  Aligned_cols=109  Identities=13%  Similarity=0.087  Sum_probs=50.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCch-HHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI-QKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~-~~~~~~l  130 (175)
                      +.++++||.|.|||.++.+ +...+.-.......-+.-++.+-|.+ ...|+.+.... ...+..+.|+... -++++.+
T Consensus        39 ha~Lf~Gp~GvGKttlA~~-lAk~L~c~~~~~~~~~~~~~~~~Cg~-C~sC~~~~~g~-~~n~~~~d~~s~~~vd~Ir~l  115 (620)
T PRK14954         39 HGYIFSGLRGVGKTTAARV-FAKAVNCQRMIDDPVYLQEVTEPCGE-CESCRDFDAGT-SLNISEFDAASNNSVDDIRQL  115 (620)
T ss_pred             eeEEEECCCCCCHHHHHHH-HHHHhCCCCcCCccccccccCCCCcc-CHHHHHHhccC-CCCeEEecccccCCHHHHHHH
Confidence            4588999999999976543 22333211100000000011122222 12345554433 3444445553322 2444443


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      ...       ....-.+.+-+.+|+||+|..-....+.++
T Consensus       116 ~e~-------~~~~P~~~~~KVvIIdEad~Lt~~a~naLL  148 (620)
T PRK14954        116 REN-------VRYGPQKGRYRVYIIDEVHMLSTAAFNAFL  148 (620)
T ss_pred             HHH-------HHhhhhcCCCEEEEEeChhhcCHHHHHHHH
Confidence            321       111123457789999999755444444443

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.92  E-value=0.43  Score=40.50  Aligned_cols=19  Identities=26%  Similarity=0.315  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~   69 (175)
                      |.-+.+.+|||+|||.+..
T Consensus       256 g~Vi~LvGpnGvGKTTTia  274 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTA  274 (484)
T ss_pred             CcEEEEECCCCccHHHHHH
Confidence            4558899999999998654

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=93.86  E-value=0.25  Score=46.29  Aligned_cols=57  Identities=18%  Similarity=0.141  Sum_probs=44.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .++++|.|+-|||||....--++..+......-+.++|+-|+.=+.++.+.+.+...
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            578999999999999887766666665443345799999999999998888766554

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.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=93.85  E-value=0.12  Score=39.84  Aligned_cols=25  Identities=32%  Similarity=0.452  Sum_probs=18.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      -++++.|++||||| .++.-++..+.
T Consensus        14 fr~viIG~sGSGKT-~li~~lL~~~~   38 (241)
T PF04665_consen   14 FRMVIIGKSGSGKT-TLIKSLLYYLR   38 (241)
T ss_pred             ceEEEECCCCCCHH-HHHHHHHHhhc
Confidence            37899999999999 45566665543

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.84  E-value=0.29  Score=42.80  Aligned_cols=24  Identities=13%  Similarity=-0.067  Sum_probs=18.8

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.+||||+|+.-....+.+++
T Consensus       123 g~~KV~IIDEvh~Ls~~a~NaLLK  146 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAFNAMLK  146 (618)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHH
Confidence            468999999998877777666654

>PRK08727 hypothetical protein; Validated

Probab=93.83  E-value=0.22  Score=38.02  Aligned_cols=51  Identities=18%  Similarity=0.141  Sum_probs=31.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      ..+++.||+|+|||-. +.++...+..  .+.+++++ |..++.....+.++.+.
T Consensus        42 ~~l~l~G~~G~GKThL-~~a~~~~~~~--~~~~~~y~-~~~~~~~~~~~~~~~l~   92 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL-ALALCAAAEQ--AGRSSAYL-PLQAAAGRLRDALEALE   92 (233)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHH--cCCcEEEE-eHHHhhhhHHHHHHHHh
Confidence            4599999999999943 3344444433  34466665 45555555555555443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.79  E-value=0.19  Score=39.03  Aligned_cols=38  Identities=18%  Similarity=0.024  Sum_probs=25.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-++|.+++|+|||...+.-+.+.+.   ++-+++|++-
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~---~Ge~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQAS---RGNPVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh---CCCcEEEEEe
Confidence            4678999999999999755443333332   3446788773

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.75  E-value=0.43  Score=41.52  Aligned_cols=18  Identities=28%  Similarity=0.333  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      +.++++||.|+|||....
T Consensus        39 ~a~Lf~Gp~G~GKTtlA~   56 (585)
T PRK14950         39 HAYLFTGPRGVGKTSTAR   56 (585)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            456899999999996543

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.68  E-value=0.19  Score=38.29  Aligned_cols=53  Identities=15%  Similarity=0.095  Sum_probs=32.3

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      ..|.-+++.+++|+|||....--+...+.   ++.++++++.. +-..+..+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~---~g~~~~yi~~e-~~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQ---NGYSVSYVSTQ-LTTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHh---CCCcEEEEeCC-CCHHHHHHHHHHh
Confidence            45788999999999999754333333222   34467888743 3334444444443

>TIGR00416 sms DNA repair protein RadA

Probab=93.67  E-value=0.45  Score=40.09  Aligned_cols=52  Identities=27%  Similarity=0.323  Sum_probs=33.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      |.-+++.+++|+|||...+.- +..+..  ++.+++|+... +-..|+....+++.
T Consensus        94 GsvilI~G~pGsGKTTL~lq~-a~~~a~--~g~kvlYvs~E-Es~~qi~~ra~rlg  145 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQV-ACQLAK--NQMKVLYVSGE-ESLQQIKMRAIRLG  145 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHH-HHHHHh--cCCcEEEEECc-CCHHHHHHHHHHcC
Confidence            467899999999999655443 333322  23368888754 44566666555553

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)).

>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=93.66  E-value=0.11  Score=39.23  Aligned_cols=43  Identities=19%  Similarity=0.287  Sum_probs=29.0

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      .+++.||+|+|||- .+.++.+.+.....+.+++++... +....
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~~~~~~~v~y~~~~-~f~~~   78 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQKQHPGKRVVYLSAE-EFIRE   78 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHHCTTS-EEEEEHH-HHHHH
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHhccccccceeecHH-HHHHH
Confidence            58999999999995 566777666554456677777543 44433

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.

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=93.65  E-value=0.13  Score=39.77  Aligned_cols=77  Identities=23%  Similarity=0.246  Sum_probs=57.9

Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCC-chHHhHHHHhc-CCCeEEE--------eecCccCCCC
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYLKT-HNPQIVG--------LVNYETNLSG  149 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~-~~~~~~~~l~~-~~~iiv~--------l~~~~~~~~~  149 (175)
                      .+.|.+|||+.+---|..+.+.++.+...  +..|+-+++.. ...++...+++ ..++.||        +.+..+.+++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~  201 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSN  201 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCccc
Confidence            46789999999988888888888777422  35666667665 77899999986 4567777        3333788899


Q ss_pred             ceEEEEeCC
Q psy1539         150 VVVNVMDVR  158 (175)
Q Consensus       150 ~~~lVlDEa  158 (175)
                      ++++|+|--
T Consensus       202 l~~ivlD~s  210 (252)
T PF14617_consen  202 LKRIVLDWS  210 (252)
T ss_pred             CeEEEEcCC
Confidence            999999963

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.62  E-value=1.5  Score=34.35  Aligned_cols=56  Identities=25%  Similarity=0.342  Sum_probs=31.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKV  114 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v  114 (175)
                      +-+.+.+|+|+|||.+..--+. .+..  .+.+++++.  +.|.-+.   ++++.+.... ++.+
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~-~l~~--~g~~V~li~~D~~r~~a~---~ql~~~~~~~-~i~~  130 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLAN-KLKK--QGKSVLLAAGDTFRAAAI---EQLEEWAKRL-GVDV  130 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH-HHHh--cCCEEEEEeCCCCCHHHH---HHHHHHHHhC-CeEE
Confidence            4577889999999976543332 2222  344566665  3344433   2455555544 5443

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=93.61  E-value=0.071  Score=32.10  Aligned_cols=19  Identities=26%  Similarity=0.396  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|...++.+++|||||..+
T Consensus        22 ~g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4567999999999999743

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=93.55  E-value=0.42  Score=41.36  Aligned_cols=102  Identities=13%  Similarity=0.032  Sum_probs=49.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCc-hHHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP-IQKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~-~~~~~~~l  130 (175)
                      +-++++||.|+|||.+.-.-. ..+.-. +.       +..+-|.+. +.|+.+.... ...+..+.+... .-++++.+
T Consensus        39 hayLf~Gp~GtGKTt~Ak~lA-kal~c~-~~-------~~~~pC~~C-~~C~~i~~g~-~~dv~eidaas~~~vd~ir~i  107 (559)
T PRK05563         39 HAYLFSGPRGTGKTSAAKIFA-KAVNCL-NP-------PDGEPCNEC-EICKAITNGS-LMDVIEIDAASNNGVDEIRDI  107 (559)
T ss_pred             eEEEEECCCCCCHHHHHHHHH-HHhcCC-CC-------CCCCCCCcc-HHHHHHhcCC-CCCeEEeeccccCCHHHHHHH
Confidence            457889999999997654322 222211 10       000111111 1344444332 333444433221 12233333


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ...       ....-...+-+.+|+||+|+.-......+++
T Consensus       108 ~~~-------v~~~p~~~~~kViIIDE~~~Lt~~a~naLLK  141 (559)
T PRK05563        108 RDK-------VKYAPSEAKYKVYIIDEVHMLSTGAFNALLK  141 (559)
T ss_pred             HHH-------HhhCcccCCeEEEEEECcccCCHHHHHHHHH
Confidence            321       0111123578899999998776666666654

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=93.55  E-value=0.58  Score=37.09  Aligned_cols=15  Identities=40%  Similarity=0.678  Sum_probs=11.8

Q ss_pred             cEEE-EcCCCChHHHH
Q psy1539          53 DILC-QAKSGMGKTAV   67 (175)
Q Consensus        53 ~~ii-~a~TGsGKT~~   67 (175)
                      +.++ .||+|+|||..
T Consensus        44 ~~lll~G~~G~GKT~l   59 (316)
T PHA02544         44 NMLLHSPSPGTGKTTV   59 (316)
T ss_pred             eEEEeeCcCCCCHHHH
Confidence            4555 89999999954

>PRK09183 transposase/IS protein; Provisional

Probab=93.51  E-value=0.23  Score=38.60  Aligned_cols=47  Identities=19%  Similarity=0.204  Sum_probs=28.7

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      +.+|.++++.+|+|+|||..... +......  .+..++++ +..++..++
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~a-l~~~a~~--~G~~v~~~-~~~~l~~~l  145 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIA-LGYEAVR--AGIKVRFT-TAADLLLQL  145 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHH-HHHHHHH--cCCeEEEE-eHHHHHHHH
Confidence            45689999999999999954432 2222222  34355554 445666443

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=93.51  E-value=0.57  Score=35.13  Aligned_cols=42  Identities=14%  Similarity=0.036  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEecCH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTR   92 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~Pt~   92 (175)
                      |.-+.+.+++|+|||...+.-+.......   ....+++++....
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            57789999999999975554333332221   0124677877643

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.

>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=93.50  E-value=0.25  Score=34.70  Aligned_cols=19  Identities=26%  Similarity=0.336  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|+-+.+.+++|+|||..
T Consensus        24 ~~Ge~~~i~G~nGsGKStL   42 (144)
T cd03221          24 NPGDRIGLVGRNGAGKSTL   42 (144)
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4678899999999999963

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.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=93.47  E-value=0.85  Score=35.98  Aligned_cols=27  Identities=30%  Similarity=0.288  Sum_probs=19.0

Q ss_pred             cCCc-EEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMD-ILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~-~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      ++.. +++.+|+|+|||.++ ..+.+.+.
T Consensus        22 ~~~halL~~Gp~G~Gktt~a-~~lA~~l~   49 (325)
T COG0470          22 RLPHALLFYGPPGVGKTTAA-LALAKELL   49 (325)
T ss_pred             CCCceeeeeCCCCCCHHHHH-HHHHHHHh
Confidence            3455 999999999999664 44444443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.47  E-value=0.46  Score=41.84  Aligned_cols=24  Identities=13%  Similarity=-0.051  Sum_probs=18.6

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.+||||+|+.-....+.+|+
T Consensus       123 gr~KViIIDEah~Ls~~AaNALLK  146 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAFNAMLK  146 (700)
T ss_pred             CCceEEEEEChHhcCHHHHHHHHH
Confidence            468899999998776666666665

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.46  E-value=0.4  Score=41.91  Aligned_cols=19  Identities=26%  Similarity=0.406  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      ..+++++|.|+|||.+..+
T Consensus        39 ha~Lf~GPpG~GKTtiAri   57 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARI   57 (624)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4688999999999976543

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.45  E-value=0.25  Score=37.32  Aligned_cols=51  Identities=18%  Similarity=0.196  Sum_probs=29.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      .|..+++.+++|+|||.....-+.+.+.   ++..++++.. .+...++.+..+.
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~---~g~~~~~is~-e~~~~~i~~~~~~   69 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLR---DGDPVIYVTT-EESRESIIRQAAQ   69 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHh---cCCeEEEEEc-cCCHHHHHHHHHH
Confidence            4689999999999999654433333332   2335666664 3333444444333

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=93.42  E-value=0.26  Score=39.61  Aligned_cols=43  Identities=16%  Similarity=0.055  Sum_probs=27.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF   96 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~   96 (175)
                      |+-+.+.+|+|||||...+..+.+...   .+..++++.....+-.
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~---~g~~v~yId~E~~~~~   97 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQK---AGGTAAFIDAEHALDP   97 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEcccchhHH
Confidence            467889999999999765544444332   2446777765554443

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.

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.42  E-value=0.11  Score=45.67  Aligned_cols=47  Identities=23%  Similarity=0.183  Sum_probs=35.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .++++.||||||||..+++|-+-.+.    + .++|+=|--|+........+
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~~----g-S~VV~DpKGE~~~~Ta~~R~  186 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTFK----G-SVIALDVKGELFELTSRARK  186 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcCC----C-CEEEEeCCchHHHHHHHHHH
Confidence            58999999999999999999876532    1 47777788888766544443

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=93.41  E-value=0.44  Score=37.09  Aligned_cols=28  Identities=7%  Similarity=0.008  Sum_probs=21.2

Q ss_pred             CCCCceEEEEeCC----CCCCHHHHHHHHhhh
Q psy1539         146 NLSGVVVNVMDVR----SGGWWLDLEALILSK  173 (175)
Q Consensus       146 ~~~~~~~lVlDEa----d~~f~~~v~~il~~~  173 (175)
                      ..++-+.+.+||-    |..+.-++-+++.+.
T Consensus       153 LaQ~~~iLLLDEPTs~LDi~~Q~evl~ll~~l  184 (258)
T COG1120         153 LAQETPILLLDEPTSHLDIAHQIEVLELLRDL  184 (258)
T ss_pred             HhcCCCEEEeCCCccccCHHHHHHHHHHHHHH
Confidence            3467889999998    777777777777653

>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=93.34  E-value=2.8  Score=34.37  Aligned_cols=50  Identities=12%  Similarity=0.179  Sum_probs=28.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .+.+.+.|+.|.|||+.  +-+.-...+.+.+.+    ++-.+...++.+.+.++.
T Consensus        62 ~~GlYl~G~vG~GKT~L--md~f~~~lp~~~k~R----~HFh~Fm~~vh~~l~~~~  111 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTML--MDLFYDSLPIKRKRR----VHFHEFMLDVHSRLHQLR  111 (362)
T ss_pred             CceEEEECCCCCchhHH--HHHHHHhCCcccccc----ccccHHHHHHHHHHHHHh
Confidence            47899999999999973  333322222111111    144466666666666554

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

>KOG0333|consensus

Probab=93.30  E-value=0.66  Score=39.63  Aligned_cols=70  Identities=16%  Similarity=0.251  Sum_probs=52.9

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ..+.++|.+.++.=|.-+.+.+.+.     ++++..++||.+..+...   .+++ ..+|+|+  ...+.++..++.++|
T Consensus       516 ~~ppiIIFvN~kk~~d~lAk~LeK~-----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVi  590 (673)
T KOG0333|consen  516 FDPPIIIFVNTKKGADALAKILEKA-----GYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVI  590 (673)
T ss_pred             CCCCEEEEEechhhHHHHHHHHhhc-----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceee
Confidence            4578999999998887766666655     789999999988654443   3444 4688888  666688999999887


Q ss_pred             E
Q psy1539         155 M  155 (175)
Q Consensus       155 l  155 (175)
                      -
T Consensus       591 n  591 (673)
T KOG0333|consen  591 N  591 (673)
T ss_pred             e
Confidence            4

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=93.25  E-value=0.066  Score=41.98  Aligned_cols=21  Identities=33%  Similarity=0.395  Sum_probs=17.7

Q ss_pred             HHhcCCcEEEEcCCCChHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~   67 (175)
                      .+.+++.++++||+|+|||..
T Consensus        29 l~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   29 LLSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HHHCTEEEEEESSTTSSHHHH
T ss_pred             HHHcCCcEEEECCCCCchhHH
Confidence            344689999999999999964

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=93.23  E-value=0.27  Score=42.62  Aligned_cols=31  Identities=13%  Similarity=-0.125  Sum_probs=23.8

Q ss_pred             ccCCCCceEEEEeCC----CCCCHHHHHHHHhhhc
Q psy1539         144 ETNLSGVVVNVMDVR----SGGWWLDLEALILSKC  174 (175)
Q Consensus       144 ~~~~~~~~~lVlDEa----d~~f~~~v~~il~~~~  174 (175)
                      ++.+.+-+++|+|||    |..-+..+.+.++.+|
T Consensus       528 RilL~kP~~v~LDEATsALDe~~e~~l~q~l~~~l  562 (604)
T COG4178         528 RLLLHKPKWVFLDEATSALDEETEDRLYQLLKEEL  562 (604)
T ss_pred             HHHHcCCCEEEEecchhccChHHHHHHHHHHHhhC
Confidence            345678999999999    6677777777777655

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=93.12  E-value=0.49  Score=41.62  Aligned_cols=24  Identities=17%  Similarity=0.009  Sum_probs=18.0

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+.+||||+|+.-....+.+|+
T Consensus       118 g~~KV~IIDEah~Ls~~a~NALLK  141 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRHSFNALLK  141 (647)
T ss_pred             CCCEEEEEechHhCCHHHHHHHHH
Confidence            478899999998776666666554

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=93.11  E-value=1.4  Score=38.54  Aligned_cols=73  Identities=12%  Similarity=0.122  Sum_probs=54.3

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.|+|+.-+.++.+.+++.     ++.+..++|+.+..+..+   .+.+ ..+++|+  .....+++++++++|
T Consensus       235 ~~~~~IIFc~tr~~~e~la~~L~~~-----g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI  309 (607)
T PRK11057        235 RGKSGIIYCNSRAKVEDTAARLQSR-----GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV  309 (607)
T ss_pred             CCCCEEEEECcHHHHHHHHHHHHhC-----CCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccCCCCCcCEEE
Confidence            3457899999999999887777643     788999999987554433   3333 3577887  556689999999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-..
T Consensus       310 ~~d~  313 (607)
T PRK11057        310 HFDI  313 (607)
T ss_pred             EeCC
Confidence            6655

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=93.10  E-value=0.095  Score=43.47  Aligned_cols=48  Identities=13%  Similarity=0.209  Sum_probs=29.9

Q ss_pred             HHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          45 IPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        45 i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      +|.-...+++++.|+||||||.. +..++..+..  .+.+++|+=|..++.
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~--~~~~~vi~D~kg~~~   83 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRA--RGDRAIIYDPNGGFV   83 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHh--cCCCEEEEeCCcchh
Confidence            44444568999999999999975 4444444332  122455555655544

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.10  E-value=0.53  Score=34.29  Aligned_cols=57  Identities=18%  Similarity=0.130  Sum_probs=32.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhc-------CCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLET-------TDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|.=.++.|++|+|||...+--+......       .....+++++..--. ..++.+.+..+..
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            56779999999999996544333333321       013457788766544 4566666666554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=93.06  E-value=2  Score=35.01  Aligned_cols=24  Identities=17%  Similarity=0.386  Sum_probs=17.2

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      -+++.+|.|+|||... ..+...+.
T Consensus        47 a~L~~G~~G~GKttlA-~~lA~~Ll   70 (351)
T PRK09112         47 ALLFEGPEGIGKATLA-FHLANHIL   70 (351)
T ss_pred             eEeeECCCCCCHHHHH-HHHHHHHc
Confidence            5999999999999544 33444443

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=93.06  E-value=0.38  Score=42.22  Aligned_cols=70  Identities=17%  Similarity=0.170  Sum_probs=52.4

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .+++-|++|+...  ...++|.|+.|||||.+-..-+...+... -...+.+.++=|+.-|.++.+.+.++..
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            5789999988655  56778889999999987665555554432 1222588888899999998888888875

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=93.01  E-value=0.23  Score=38.39  Aligned_cols=53  Identities=21%  Similarity=0.202  Sum_probs=34.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|+.++|.+++|||||....--+.+.+..   +-.++++ .+.+...++.+.+..+.
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~---ge~vlyv-s~~e~~~~l~~~~~~~g   74 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGARE---GEPVLYV-STEESPEELLENARSFG   74 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhc---CCcEEEE-EecCCHHHHHHHHHHcC
Confidence            46899999999999996554444444332   3355655 45566666666666543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=92.98  E-value=0.94  Score=36.49  Aligned_cols=31  Identities=23%  Similarity=0.392  Sum_probs=22.7

Q ss_pred             cHHHHHhHHHHh----cC---CcEEEEcCCCChHHHHH
Q psy1539          38 TSFQHECIPQAV----LG---MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        38 t~~Q~~~i~~~~----~g---~~~ii~a~TGsGKT~~~   68 (175)
                      +|+|+..|..+.    +|   +-.++.||.|.||+..+
T Consensus         4 yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA   41 (325)
T PRK06871          4 YPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLI   41 (325)
T ss_pred             CcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHH
Confidence            567777776554    34   56889999999999544

>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=92.96  E-value=1.8  Score=31.02  Aligned_cols=15  Identities=40%  Similarity=0.499  Sum_probs=12.7

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      +++.+++|+|||...
T Consensus         3 ~~~~G~~G~GKTt~~   17 (173)
T cd03115           3 ILLVGLQGVGKTTTA   17 (173)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999764

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.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=92.92  E-value=0.25  Score=35.53  Aligned_cols=27  Identities=33%  Similarity=0.489  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      ++.+++.|+.|+|||.. +-.++.++..
T Consensus        24 ~~~~ll~G~~G~GKT~l-l~~~~~~~~~   50 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSL-LRALLDRLAE   50 (185)
T ss_dssp             ---EEE-B-TTSSHHHH-HHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            47899999999999953 3445555544

>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=92.91  E-value=0.26  Score=36.53  Aligned_cols=24  Identities=21%  Similarity=0.346  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      ..+++|.+.||||||.+...-+..
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~   61 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLS   61 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHH
T ss_pred             CceEEEEcCCCCCccHHHHHHHHH
Confidence            458999999999999665433333

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.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=92.91  E-value=0.67  Score=40.15  Aligned_cols=102  Identities=16%  Similarity=0.063  Sum_probs=49.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCC-chHHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~-~~~~~~~~l  130 (175)
                      +-+++.||.|.|||.+... +...+... .+       ++.+-|.+.. .++.+.... ...+..+.|.. ..-++++.+
T Consensus        39 hayLf~Gp~G~GKTt~Ar~-lAk~L~c~-~~-------~~~~pC~~C~-~C~~i~~~~-~~dv~~idgas~~~vddIr~l  107 (563)
T PRK06647         39 NAYIFSGPRGVGKTSSARA-FARCLNCV-NG-------PTPMPCGECS-SCKSIDNDN-SLDVIEIDGASNTSVQDVRQI  107 (563)
T ss_pred             eEEEEECCCCCCHHHHHHH-HHHhhccc-cC-------CCCCCCccch-HHHHHHcCC-CCCeEEecCcccCCHHHHHHH
Confidence            4578999999999976533 33433321 11       1111121111 234443332 34444444443 212333333


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ...       ........+-+.+|+||+++.-....+.+++
T Consensus       108 ~e~-------~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK  141 (563)
T PRK06647        108 KEE-------IMFPPASSRYRVYIIDEVHMLSNSAFNALLK  141 (563)
T ss_pred             HHH-------HHhchhcCCCEEEEEEChhhcCHHHHHHHHH
Confidence            211       0111124678899999998665555555543

>PRK05642 DNA replication initiation factor; Validated

Probab=92.88  E-value=0.42  Score=36.52  Aligned_cols=43  Identities=19%  Similarity=0.145  Sum_probs=27.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ..++++||+|+|||-. +.++.+.+..  .+.+++++. ..++....
T Consensus        46 ~~l~l~G~~G~GKTHL-l~a~~~~~~~--~~~~v~y~~-~~~~~~~~   88 (234)
T PRK05642         46 SLIYLWGKDGVGRSHL-LQAACLRFEQ--RGEPAVYLP-LAELLDRG   88 (234)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHh--CCCcEEEee-HHHHHhhh
Confidence            5789999999999953 4455554433  244666654 45666543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=92.87  E-value=0.74  Score=37.00  Aligned_cols=25  Identities=24%  Similarity=0.279  Sum_probs=17.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +.+++.||+|+|||... ..+...+.
T Consensus        37 ~~~Ll~G~~G~GKt~~a-~~la~~l~   61 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIA-RIFAKALN   61 (355)
T ss_pred             eEEEEECCCCCCHHHHH-HHHHHHhc
Confidence            45789999999999543 44444443

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.

>PRK09354 recA recombinase A; Provisional

Probab=92.85  E-value=0.35  Score=39.27  Aligned_cols=43  Identities=14%  Similarity=0.048  Sum_probs=30.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF   96 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~   96 (175)
                      |+-+.+.+|+|||||...+..+.+...   .+..++++..-..+-.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~---~G~~~~yId~E~s~~~  102 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQK---AGGTAAFIDAEHALDP  102 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEECCccchHH
Confidence            467889999999999766555544433   3457888887665553

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=92.84  E-value=0.33  Score=40.71  Aligned_cols=46  Identities=15%  Similarity=0.218  Sum_probs=28.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      ..+++.||+|+|||.. +.++.+.+.....+.+++++ +..++..+..
T Consensus       149 ~~l~l~G~~G~GKThL-~~ai~~~~~~~~~~~~v~yi-~~~~~~~~~~  194 (450)
T PRK00149        149 NPLFIYGGVGLGKTHL-LHAIGNYILEKNPNAKVVYV-TSEKFTNDFV  194 (450)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHHhCCCCeEEEE-EHHHHHHHHH
Confidence            4699999999999953 45555555543334566666 4445544433

>PTZ00424 helicase 45; Provisional

Probab=92.83  E-value=1.5  Score=35.91  Aligned_cols=73  Identities=11%  Similarity=0.201  Sum_probs=52.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++++.|+|++-+..+.+.++..     ++.+..++|+.+..+...   .+++| .+++|+  +....+++++++++|
T Consensus       266 ~~~~~ivF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~GiDip~v~~VI  340 (401)
T PTZ00424        266 TITQAIIYCNTRRKVDYLTKKMHER-----DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI  340 (401)
T ss_pred             CCCeEEEEecCcHHHHHHHHHHHHC-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCCcCcccCCEEE
Confidence            3457999999999888776665432     678899999987554433   34443 567777  666788999999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-..
T Consensus       341 ~~~~  344 (401)
T PTZ00424        341 NYDL  344 (401)
T ss_pred             EECC
Confidence            6554

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=92.82  E-value=0.26  Score=39.68  Aligned_cols=43  Identities=19%  Similarity=0.056  Sum_probs=28.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF   96 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~   96 (175)
                      |+-+.+.+|+|+|||...+..+.+...   .+..++++.+...+-.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~---~g~~~vyId~E~~~~~   97 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQK---LGGTVAFIDAEHALDP   97 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCCEEEECccccHHH
Confidence            467889999999999655544444332   3447888887655543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=92.81  E-value=0.93  Score=39.03  Aligned_cols=24  Identities=13%  Similarity=0.025  Sum_probs=16.8

Q ss_pred             CCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         147 LSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       147 ~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      ....+.+|+||||+.-.+..+.++
T Consensus       115 ~~~~KVvIIDEad~Lt~~A~NALL  138 (535)
T PRK08451        115 MARFKIFIIDEVHMLTKEAFNALL  138 (535)
T ss_pred             cCCeEEEEEECcccCCHHHHHHHH
Confidence            357899999999866555544443

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=92.80  E-value=0.16  Score=38.68  Aligned_cols=29  Identities=28%  Similarity=0.320  Sum_probs=21.7

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      +..|.-+.|.+|+|||||.  ++-++.-+..
T Consensus        28 i~~Ge~vaI~GpSGSGKST--LLniig~ld~   56 (226)
T COG1136          28 IEAGEFVAIVGPSGSGKST--LLNLLGGLDK   56 (226)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHhcccC
Confidence            3468899999999999997  4555555543

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=92.80  E-value=0.26  Score=46.17  Aligned_cols=58  Identities=26%  Similarity=0.264  Sum_probs=44.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcC--CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETT--DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~--~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .+.+++|.|..|||||.+..--+++.+...  -.-.+.|+++-|+.=+.+....+.+-..
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L~   74 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLK   74 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHHH
Confidence            468999999999999988777777777653  2334689999998888887777655433

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=92.73  E-value=0.59  Score=35.29  Aligned_cols=41  Identities=12%  Similarity=-0.040  Sum_probs=25.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~P   90 (175)
                      .|.-+.+.+++|+|||.....-++......   ..+..++++..
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~   61 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDT   61 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeC
Confidence            357789999999999966544433322221   01246788774

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 .

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=92.73  E-value=0.37  Score=39.82  Aligned_cols=45  Identities=16%  Similarity=0.248  Sum_probs=28.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ..+++.||+|+|||.. +.++.+.+.....+..++++.. .++..+.
T Consensus       137 n~l~l~G~~G~GKThL-~~ai~~~l~~~~~~~~v~yi~~-~~~~~~~  181 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHL-LHAIGNEILENNPNAKVVYVSS-EKFTNDF  181 (405)
T ss_pred             CeEEEECCCCCcHHHH-HHHHHHHHHHhCCCCcEEEEEH-HHHHHHH
Confidence            4589999999999954 3555555554333456777643 4444443

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).

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=92.69  E-value=0.37  Score=42.32  Aligned_cols=54  Identities=22%  Similarity=0.251  Sum_probs=36.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH--HHHHHHHHHHHHHh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE--LAFQISKEYERFSK  107 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~--L~~q~~~~~~~~~~  107 (175)
                      ..+++|.++||+|||..+..-+.+.+..   +..++++=|-.+  |...+...+++.+.
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~---g~~viv~DpKgD~~l~~~~~~~~~~~G~  231 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRR---GDVVIVIDPKGDADLKRRMRAEAKRAGR  231 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCchHHHHHHHHHHHHhCC
Confidence            3689999999999997764444444432   345677777654  76666666666643

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.

>PF05729 NACHT: NACHT domain

Probab=92.68  E-value=0.27  Score=34.56  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=17.4

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      -++|.|+.|+|||.. +--++..+..
T Consensus         2 ~l~I~G~~G~GKStl-l~~~~~~~~~   26 (166)
T PF05729_consen    2 VLWISGEPGSGKSTL-LRKLAQQLAE   26 (166)
T ss_pred             EEEEECCCCCChHHH-HHHHHHHHHh
Confidence            378999999999964 3444444443

>KOG1131|consensus

Probab=92.66  E-value=1.1  Score=38.30  Aligned_cols=74  Identities=16%  Similarity=0.087  Sum_probs=44.8

Q ss_pred             CCCCCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCC-CCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          33 PFREQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTD-SNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~-~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|...+|-|.+-.-.+.    .+-+.++..|+|+|||.+.+--++.+-..-+ ...+.++-+-|..-.+.....++++.
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l~   91 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRLM   91 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHHH
Confidence            35667888877665443    3467889999999999876654444432222 33355555555544444445555543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=92.66  E-value=0.74  Score=41.28  Aligned_cols=24  Identities=13%  Similarity=-0.042  Sum_probs=17.0

Q ss_pred             CCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         148 SGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       148 ~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+++||||+|+.-....+.+|+
T Consensus       118 gr~KVIIIDEah~LT~~A~NALLK  141 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAFNAMLK  141 (830)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHH
Confidence            467999999998765555555544

>KOG0744|consensus

Probab=92.62  E-value=0.79  Score=37.03  Aligned_cols=25  Identities=36%  Similarity=0.372  Sum_probs=18.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +=+++.+|+|+||| ...=++.+++.
T Consensus       178 RliLlhGPPGTGKT-SLCKaLaQkLS  202 (423)
T KOG0744|consen  178 RLILLHGPPGTGKT-SLCKALAQKLS  202 (423)
T ss_pred             eEEEEeCCCCCChh-HHHHHHHHhhe
Confidence            45789999999999 34455566653

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=92.61  E-value=0.092  Score=35.31  Aligned_cols=15  Identities=27%  Similarity=0.508  Sum_probs=12.7

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      ++|.+++|||||...
T Consensus         2 I~I~G~~gsGKST~a   16 (121)
T PF13207_consen    2 IIISGPPGSGKSTLA   16 (121)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999643

...

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.61  E-value=0.74  Score=39.57  Aligned_cols=19  Identities=26%  Similarity=0.399  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      +-+++.||.|+|||.....
T Consensus        39 ha~Lf~Gp~G~GKTt~A~~   57 (527)
T PRK14969         39 HAYLFTGTRGVGKTTLARI   57 (527)
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            3468999999999976543

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=92.55  E-value=0.2  Score=40.94  Aligned_cols=37  Identities=27%  Similarity=0.390  Sum_probs=23.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      .|+.+++.+|+|+||| |..+++.+.+..  +-|.+-+..
T Consensus        49 aGr~iLiaGppGtGKT-AlA~~ia~eLG~--~~PF~~isg   85 (398)
T PF06068_consen   49 AGRAILIAGPPGTGKT-ALAMAIAKELGE--DVPFVSISG   85 (398)
T ss_dssp             TT-EEEEEE-TTSSHH-HHHHHHHHHCTT--TS-EEEEEG
T ss_pred             cCcEEEEeCCCCCCch-HHHHHHHHHhCC--CCCeeEccc
Confidence            3789999999999999 455667666653  445554443

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>KOG0926|consensus

Probab=92.51  E-value=0.85  Score=41.00  Aligned_cols=106  Identities=14%  Similarity=0.107  Sum_probs=52.1

Q ss_pred             hHHHHhcCCcEEEEcCCCChHHHHHHHHHHH--hhhcC--CCCeEEEEEe-cCHHHHHHHHHHH-HHHHhhCCCeEEEEE
Q psy1539          44 CIPQAVLGMDILCQAKSGMGKTAVFVLATLQ--QLETT--DSNVYVLVMC-HTRELAFQISKEY-ERFSKYMSNIKVGVF  117 (175)
Q Consensus        44 ~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~--~l~~~--~~~~~~lil~-Pt~~L~~q~~~~~-~~~~~~~~~i~v~~~  117 (175)
                      ....|..+.-++||+.||||||.-  +|-+-  .=...  ...+..|=|+ |.|--|.-..+.. ..+...-..+.....
T Consensus       264 IMEaIn~n~vvIIcGeTGsGKTTQ--vPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqIR  341 (1172)
T KOG0926|consen  264 IMEAINENPVVIICGETGSGKTTQ--VPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQIR  341 (1172)
T ss_pred             HHHHhhcCCeEEEecCCCCCcccc--chHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEEE
Confidence            344555667799999999999963  22211  10111  1122233343 6665554443332 233321113333333


Q ss_pred             ECCCchHHhHHHHhcCCCeEEE----eec---CccCCCCceEEEEeCCC
Q psy1539         118 FGGLPIQKDEEYLKTHNPQIVG----LVN---YETNLSGVVVNVMDVRS  159 (175)
Q Consensus       118 ~g~~~~~~~~~~l~~~~~iiv~----l~~---~~~~~~~~~~lVlDEad  159 (175)
                      +.|+- .+       ...|-..    |++   +.+.+..-..+|+|||+
T Consensus       342 fd~ti-~e-------~T~IkFMTDGVLLrEi~~DflL~kYSvIIlDEAH  382 (1172)
T KOG0926|consen  342 FDGTI-GE-------DTSIKFMTDGVLLREIENDFLLTKYSVIILDEAH  382 (1172)
T ss_pred             ecccc-CC-------CceeEEecchHHHHHHHHhHhhhhceeEEechhh
Confidence            43332 11       1122222    222   25667889999999993

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=92.42  E-value=0.44  Score=37.87  Aligned_cols=16  Identities=31%  Similarity=0.420  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      .++++.|+|+.|||..
T Consensus        62 p~lLivG~snnGKT~I   77 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMI   77 (302)
T ss_pred             CceEEecCCCCcHHHH
Confidence            6999999999999973

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK13342 recombination factor protein RarA; Reviewed

Probab=92.39  E-value=1.1  Score=37.30  Aligned_cols=17  Identities=24%  Similarity=0.372  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.||+|+|||...
T Consensus        37 ~~ilL~GppGtGKTtLA   53 (413)
T PRK13342         37 SSMILWGPPGTGKTTLA   53 (413)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            47999999999999654

>PRK08084 DNA replication initiation factor; Provisional

Probab=92.38  E-value=0.33  Score=37.08  Aligned_cols=37  Identities=16%  Similarity=0.121  Sum_probs=23.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      +..+++.||+|+|||-. +..+.+.+..  .+.++.++.-
T Consensus        45 ~~~l~l~Gp~G~GKThL-l~a~~~~~~~--~~~~v~y~~~   81 (235)
T PRK08084         45 SGYIYLWSREGAGRSHL-LHAACAELSQ--RGRAVGYVPL   81 (235)
T ss_pred             CCeEEEECCCCCCHHHH-HHHHHHHHHh--CCCeEEEEEH
Confidence            46899999999999953 2344444433  2445666543

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=92.38  E-value=0.33  Score=41.80  Aligned_cols=18  Identities=28%  Similarity=0.405  Sum_probs=16.0

Q ss_pred             hcCCcEEEEcCCCChHHH
Q psy1539          49 VLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~   66 (175)
                      ..|+-+.+.+++|+|||.
T Consensus       356 ~~G~~v~IvG~sGsGKST  373 (571)
T TIGR02203       356 EPGETVALVGRSGSGKST  373 (571)
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            358899999999999996

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.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=92.34  E-value=0.2  Score=38.00  Aligned_cols=30  Identities=30%  Similarity=0.389  Sum_probs=22.9

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQLETT   79 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~   79 (175)
                      +..|.-+.+++|+|||||.  ++-.++.+..-
T Consensus        25 v~~Gevv~iiGpSGSGKST--lLRclN~LE~~   54 (240)
T COG1126          25 VEKGEVVVIIGPSGSGKST--LLRCLNGLEEP   54 (240)
T ss_pred             EcCCCEEEEECCCCCCHHH--HHHHHHCCcCC
Confidence            3467889999999999996  55666666543

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=92.34  E-value=0.097  Score=35.59  Aligned_cols=19  Identities=21%  Similarity=0.288  Sum_probs=12.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      +++.+++.|++|+|||...
T Consensus         3 ~~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ----EEEEE-TTSSHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHH
Confidence            3567899999999999654

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=92.26  E-value=0.2  Score=37.58  Aligned_cols=27  Identities=26%  Similarity=0.329  Sum_probs=17.1

Q ss_pred             HHhHHHHh-cCCcEEEEcCCCChHHHHH
Q psy1539          42 HECIPQAV-LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        42 ~~~i~~~~-~g~~~ii~a~TGsGKT~~~   68 (175)
                      ++|+.... .++++++.+|.|+|||+..
T Consensus        12 KrAL~iAAaG~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   12 KRALEIAAAGGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             HHHHHHHHHCC--EEEES-CCCTHHHHH
T ss_pred             HHHHHHHHcCCCCeEEECCCCCCHHHHH
Confidence            44444333 5699999999999999754

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.25  E-value=2.6  Score=33.90  Aligned_cols=18  Identities=33%  Similarity=0.471  Sum_probs=14.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.-+.+.+|+|+|||...
T Consensus       114 ~~vi~lvGpnGsGKTTt~  131 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTI  131 (318)
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            345788999999999754

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.24  E-value=0.76  Score=39.94  Aligned_cols=101  Identities=17%  Similarity=0.093  Sum_probs=48.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCc-hHHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP-IQKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~-~~~~~~~l  130 (175)
                      +-++++||.|+|||.+... +...+.... +.       +.+-|.+ ...|+.+.... ...+..+.|... .-++++.+
T Consensus        39 hayLf~Gp~G~GKtt~A~~-lak~l~c~~-~~-------~~~~c~~-c~~c~~i~~g~-~~d~~eid~~s~~~v~~ir~l  107 (576)
T PRK14965         39 HAFLFTGARGVGKTSTARI-LAKALNCEQ-GL-------TAEPCNV-CPPCVEITEGR-SVDVFEIDGASNTGVDDIREL  107 (576)
T ss_pred             eEEEEECCCCCCHHHHHHH-HHHhhcCCC-CC-------CCCCCCc-cHHHHHHhcCC-CCCeeeeeccCccCHHHHHHH
Confidence            3468999999999976543 333333211 10       0000111 12233443332 333444444321 12334444


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      ....       ...-...+.+.+|+||+|+.-....+.++
T Consensus       108 ~~~~-------~~~p~~~~~KVvIIdev~~Lt~~a~naLL  140 (576)
T PRK14965        108 RENV-------KYLPSRSRYKIFIIDEVHMLSTNAFNALL  140 (576)
T ss_pred             HHHH-------HhccccCCceEEEEEChhhCCHHHHHHHH
Confidence            3221       11112357899999999866555554444

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.22  E-value=2  Score=37.82  Aligned_cols=72  Identities=13%  Similarity=0.144  Sum_probs=52.6

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      ..++||.|+|+.-+.++.+.+...     ++.+..++|+.+..+..   +.++++ .+++|+  +....++++++.++|.
T Consensus       245 ~~~~IVF~~tk~~a~~l~~~L~~~-----g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~  319 (629)
T PRK11634        245 FDAAIIFVRTKNATLEVAEALERN-----GYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVN  319 (629)
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhC-----CCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCcccCCEEEE
Confidence            347999999999999887777643     67888899998755443   334443 567777  6666888999999876


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      -+.
T Consensus       320 ~d~  322 (629)
T PRK11634        320 YDI  322 (629)
T ss_pred             eCC
Confidence            444

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

Probab=92.20  E-value=1.1  Score=38.36  Aligned_cols=85  Identities=22%  Similarity=0.239  Sum_probs=64.5

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+-++||.+-|+-.|+++.+-+    ... |+++..++++.+.-+..   +.|+.| .+++||  |++..+++..+.++.
T Consensus       445 ~~eRvLVTtLTKkmAEdLT~Yl----~e~-gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVA  519 (663)
T COG0556         445 KNERVLVTTLTKKMAEDLTEYL----KEL-GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVA  519 (663)
T ss_pred             cCCeEEEEeehHHHHHHHHHHH----Hhc-CceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEE
Confidence            4468999999999988755544    444 99999999998755444   445555 588888  888899999999998


Q ss_pred             EeCCC-CCCHHHHHHHH
Q psy1539         155 MDVRS-GGWWLDLEALI  170 (175)
Q Consensus       155 lDEad-~~f~~~v~~il  170 (175)
                      +=+|| .||...-++++
T Consensus       520 IlDADKeGFLRse~SLI  536 (663)
T COG0556         520 ILDADKEGFLRSERSLI  536 (663)
T ss_pred             EeecCccccccccchHH
Confidence            88886 58876655554

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.16  E-value=0.89  Score=39.24  Aligned_cols=17  Identities=29%  Similarity=0.360  Sum_probs=14.1

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFV   69 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~   69 (175)
                      .++++||.|+|||....
T Consensus        40 a~Lf~Gp~GvGKTTlAr   56 (546)
T PRK14957         40 AYLFTGTRGVGKTTLGR   56 (546)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999996543

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.16  E-value=0.34  Score=41.13  Aligned_cols=52  Identities=15%  Similarity=0.139  Sum_probs=34.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      |.-+++.+|+|+|||...+.-+.+.+.   ++-+++|++ .-|-..|+...++.+.
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~---~ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACA---NKERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            478999999999999755443333332   344677776 5555667777776664

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=92.13  E-value=0.51  Score=39.59  Aligned_cols=45  Identities=11%  Similarity=0.232  Sum_probs=29.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      ..+++.||+|+|||.. +.++.+.+.....+.+++++.. .++..+.
T Consensus       131 n~l~lyG~~G~GKTHL-l~ai~~~l~~~~~~~~v~yi~~-~~f~~~~  175 (440)
T PRK14088        131 NPLFIYGGVGLGKTHL-LQSIGNYVVQNEPDLRVMYITS-EKFLNDL  175 (440)
T ss_pred             CeEEEEcCCCCcHHHH-HHHHHHHHHHhCCCCeEEEEEH-HHHHHHH
Confidence            4699999999999953 4555565554333456777654 3444443

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=92.08  E-value=0.56  Score=38.79  Aligned_cols=17  Identities=18%  Similarity=0.276  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.+|.|+|||...
T Consensus        37 ha~Lf~Gp~G~GKt~lA   53 (394)
T PRK07940         37 HAWLFTGPPGSGRSVAA   53 (394)
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            56899999999999654

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=92.05  E-value=0.41  Score=39.08  Aligned_cols=28  Identities=29%  Similarity=0.451  Sum_probs=22.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      .|+.+++.+|+||||| |..+.+.+.+..
T Consensus        64 aGrgiLi~GppgTGKT-AlA~gIa~eLG~   91 (450)
T COG1224          64 AGRGILIVGPPGTGKT-ALAMGIARELGE   91 (450)
T ss_pred             cccEEEEECCCCCcHH-HHHHHHHHHhCC
Confidence            4689999999999999 455667666653

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

Probab=92.03  E-value=1.2  Score=38.24  Aligned_cols=73  Identities=15%  Similarity=0.100  Sum_probs=52.8

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      .+++||.++++.-+..+.+.+...   . ++++..++|+.+..+..+   .+++| .+++|+  +....+++.+++++|.
T Consensus       367 ~~~~iVFv~s~~~a~~l~~~L~~~---~-g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~  442 (518)
T PLN00206        367 KPPAVVFVSSRLGADLLANAITVV---T-GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVII  442 (518)
T ss_pred             CCCEEEEcCCchhHHHHHHHHhhc---c-CcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEE
Confidence            357999999999888776655532   2 778889999987654443   34443 577887  6666888889988887


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      =+.
T Consensus       443 ~d~  445 (518)
T PLN00206        443 FDM  445 (518)
T ss_pred             eCC
Confidence            655

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.02  E-value=0.32  Score=41.29  Aligned_cols=54  Identities=20%  Similarity=0.203  Sum_probs=34.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|+.++|.+++|+|||+..+.-+.+.+..  .+-++++++- .|-..++.+.+..+.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~--~ge~~lyvs~-eE~~~~l~~~~~~~G   73 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIH--FDEPGVFVTF-EESPQDIIKNARSFG   73 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEEEE-ecCHHHHHHHHHHcC
Confidence            46889999999999997655444443332  1335777764 355556666665553

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.

>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=92.00  E-value=0.078  Score=39.81  Aligned_cols=46  Identities=26%  Similarity=0.286  Sum_probs=32.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCe-----EEEEEecCHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----YVLVMCHTRELAFQ   97 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~-----~~lil~Pt~~L~~q   97 (175)
                      .|+=.-+.+|+|.||+.  ++.+..++.+...|.     +-+-=+|+.+||..
T Consensus        26 ~g~iTs~IGPNGAGKST--LLS~~sRL~~~d~G~i~i~g~~~~~~~s~~LAk~   76 (252)
T COG4604          26 KGGITSIIGPNGAGKST--LLSMMSRLLKKDSGEITIDGLELTSTPSKELAKK   76 (252)
T ss_pred             CCceeEEECCCCccHHH--HHHHHHHhccccCceEEEeeeecccCChHHHHHH
Confidence            46666788999999987  677788887654431     22344588999865

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=91.98  E-value=0.27  Score=37.30  Aligned_cols=39  Identities=26%  Similarity=0.204  Sum_probs=25.7

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      ..|.-+++.|++|+|||...+--+.+....  .+..+++++
T Consensus        11 ~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~--~g~~vly~s   49 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAFALNIAENIAKK--QGKPVLFFS   49 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCceEEEe
Confidence            356789999999999996544333333332  144678877

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.

>KOG1564|consensus

Probab=91.97  E-value=0.48  Score=37.41  Aligned_cols=39  Identities=31%  Similarity=0.388  Sum_probs=24.8

Q ss_pred             EEcCCCChHHHH-HHHHHHHhhhcC--CCCeEEEEEe-----cCHHH
Q psy1539          56 CQAKSGMGKTAV-FVLATLQQLETT--DSNVYVLVMC-----HTREL   94 (175)
Q Consensus        56 i~a~TGsGKT~~-~~~~~l~~l~~~--~~~~~~lil~-----Pt~~L   94 (175)
                      +++..|+|||-. .-+.++-.+-..  .-+..++||+     |+|-|
T Consensus       107 i~GeSg~GKtQL~lQL~L~VQLp~~~GGL~~~~vYI~TE~~fP~rRL  153 (351)
T KOG1564|consen  107 ICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAVYICTESPFPTRRL  153 (351)
T ss_pred             HhhccCCcHHHHHHHHHHHhhCchhhCCCCCceEEEEcCCCCcHHHH
Confidence            678999999943 334555444332  2234689998     66665

>TIGR00959 ffh signal recognition particle protein

Probab=91.93  E-value=2.2  Score=35.74  Aligned_cols=81  Identities=19%  Similarity=0.154  Sum_probs=39.9

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHH----h
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQK----D  126 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~----~  126 (175)
                      -+++++++|+|||.+..--+. .+... .+.+++++.  +.|.-+.+   +++.+.... ++.+.....+.+..+    .
T Consensus       101 vi~~vG~~GsGKTTtaakLA~-~l~~~-~g~kV~lV~~D~~R~~a~~---QL~~~a~~~-gvp~~~~~~~~~P~~i~~~a  174 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAY-YLKKK-QGKKVLLVACDLYRPAAIE---QLKVLGQQV-GVPVFALGKGQSPVEIARRA  174 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHH-HHHHh-CCCeEEEEeccccchHHHH---HHHHHHHhc-CCceEecCCCCCHHHHHHHH
Confidence            478999999999976533222 22211 233555554  33444322   344454444 555444333233211    1


Q ss_pred             HHH-HhcCCCeEEE
Q psy1539         127 EEY-LKTHNPQIVG  139 (175)
Q Consensus       127 ~~~-l~~~~~iiv~  139 (175)
                      .+. ..++.++||.
T Consensus       175 l~~~~~~~~DvVII  188 (428)
T TIGR00959       175 LEYAKENGFDVVIV  188 (428)
T ss_pred             HHHHHhcCCCEEEE
Confidence            222 2345676665

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.

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=91.89  E-value=0.87  Score=39.72  Aligned_cols=18  Identities=22%  Similarity=0.394  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      +.++++||.|+|||..+.
T Consensus        39 hA~Lf~GP~GvGKTTlA~   56 (605)
T PRK05896         39 HAYIFSGPRGIGKTSIAK   56 (605)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            468899999999996543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.89  E-value=1.2  Score=39.08  Aligned_cols=18  Identities=28%  Similarity=0.253  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      ..+++.||.|+|||....
T Consensus        39 ~a~Lf~Gp~G~GKttlA~   56 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSAR   56 (620)
T ss_pred             ceEEEECCCCCChHHHHH
Confidence            567999999999996543

>PTZ00301 uridine kinase; Provisional

Probab=91.88  E-value=0.33  Score=36.56  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=14.9

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhh
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +-|.|++|||||... -.+.+.+
T Consensus         6 IgIaG~SgSGKTTla-~~l~~~l   27 (210)
T PTZ00301          6 IGISGASGSGKSSLS-TNIVSEL   27 (210)
T ss_pred             EEEECCCcCCHHHHH-HHHHHHH
Confidence            568899999999643 3333333

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=91.86  E-value=0.13  Score=34.69  Aligned_cols=15  Identities=33%  Similarity=0.366  Sum_probs=12.8

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      +++.|++|||||...
T Consensus         1 I~i~G~~GsGKtTia   15 (129)
T PF13238_consen    1 IGISGIPGSGKTTIA   15 (129)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             CEEECCCCCCHHHHH
Confidence            578999999999754

...

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=91.85  E-value=0.4  Score=40.31  Aligned_cols=47  Identities=21%  Similarity=0.172  Sum_probs=34.2

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      ..++++.+|++.+.+.|.+                  ..+.+++.+|+|+||| +|..++...+..
T Consensus       243 k~~ledY~L~dkl~eRL~e------------------raeGILIAG~PGaGKs-TFaqAlAefy~~  289 (604)
T COG1855         243 KLSLEDYGLSDKLKERLEE------------------RAEGILIAGAPGAGKS-TFAQALAEFYAS  289 (604)
T ss_pred             EechhhcCCCHHHHHHHHh------------------hhcceEEecCCCCChh-HHHHHHHHHHHh
Confidence            3446777777777777654                  2478999999999999 566777666543

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=91.80  E-value=0.17  Score=42.50  Aligned_cols=27  Identities=26%  Similarity=0.356  Sum_probs=19.9

Q ss_pred             HHhHHHHh-cCCcEEEEcCCCChHHHHH
Q psy1539          42 HECIPQAV-LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        42 ~~~i~~~~-~g~~~ii~a~TGsGKT~~~   68 (175)
                      ++|+.... .|+|+++.+|+|||||+..
T Consensus       188 KrAleiAAAGgHnLl~~GpPGtGKTmla  215 (490)
T COG0606         188 KRALEIAAAGGHNLLLVGPPGTGKTMLA  215 (490)
T ss_pred             HHHHHHHHhcCCcEEEecCCCCchHHhh
Confidence            34444333 4699999999999999743

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=91.77  E-value=0.31  Score=36.77  Aligned_cols=26  Identities=23%  Similarity=0.283  Sum_probs=18.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      ++.+.|.|.||||||... --++..+.
T Consensus        23 ~~H~~I~G~TGsGKS~~~-~~ll~~l~   48 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTV-KVLLEELL   48 (229)
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            478899999999999654 33444443

It contains several conserved aspartates and histidines that could be metal ligands.

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 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=91.74  E-value=0.14  Score=37.74  Aligned_cols=20  Identities=40%  Similarity=0.483  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCChHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~   70 (175)
                      ...+++.+|.|||||..|..
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~   22 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQ   22 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            46799999999999976654

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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=91.68  E-value=4.2  Score=33.08  Aligned_cols=70  Identities=10%  Similarity=0.126  Sum_probs=50.2

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--eecCccCCCCceEEEEe
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--LVNYETNLSGVVVNVMD  156 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--l~~~~~~~~~~~~lVlD  156 (175)
                      .+.++||+++|+.-++.+++.+++..  . +..+..++|..+..+..+..  ..+++|+  +....++++.. .+|.|
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~--~-~~~~~~l~g~~~~~~R~~~~--~~~iLVaTdv~~rGiDi~~~-~vi~~  342 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQG--L-GDDIGRITGFAPKKDRERAM--QFDILLGTSTVDVGVDFKRD-WLIFS  342 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhC--C-CceEEeeecCCCHHHHHHhc--cCCEEEEecHHhcccCCCCc-eEEEC
Confidence            45589999999999999888887642  1 45677788887755443333  3578888  66678888776 56665

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=91.65  E-value=0.4  Score=37.76  Aligned_cols=18  Identities=28%  Similarity=0.434  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.++++.+|+|+|||..+
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999765

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.

>KOG1806|consensus

Probab=91.65  E-value=0.39  Score=43.90  Aligned_cols=71  Identities=23%  Similarity=0.176  Sum_probs=52.7

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      +-..||-|.++|..-.+--++.+.+|+|+|||-... -++..+......++++|++.+..--+|.++.+.+.
T Consensus       736 ~v~ft~~qveai~sg~qpgltmvvgppgtgktd~av-qil~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  736 QVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAV-QILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             hhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhh-hhhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            445689999998877777899999999999996653 33444444445678999999887777777665443

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=91.60  E-value=0.26  Score=41.42  Aligned_cols=31  Identities=23%  Similarity=0.314  Sum_probs=24.4

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      -......+..+..++++++.+|+|+|||..+
T Consensus       181 e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        181 ETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            3444555667778999999999999999655

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=91.59  E-value=0.13  Score=35.52  Aligned_cols=16  Identities=31%  Similarity=0.461  Sum_probs=13.6

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      ++++.+|+|+|||...
T Consensus         1 ~vlL~G~~G~GKt~l~   16 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLA   16 (139)
T ss_dssp             EEEEEESSSSSHHHHH
T ss_pred             CEEEECCCCCCHHHHH
Confidence            5899999999999643

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PLN03130 ABC transporter C family member; Provisional

Probab=91.54  E-value=0.46  Score=46.15  Aligned_cols=27  Identities=19%  Similarity=0.314  Sum_probs=20.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      .|+-+-++++||||||.  ++-++.++..
T Consensus      1264 ~GekVaIVGrSGSGKST--Ll~lL~rl~~ 1290 (1622)
T PLN03130       1264 PSEKVGIVGRTGAGKSS--MLNALFRIVE 1290 (1622)
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHhCcCC
Confidence            57889999999999996  3444555543

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=91.54  E-value=2.3  Score=38.67  Aligned_cols=70  Identities=11%  Similarity=0.248  Sum_probs=53.4

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc---C-CCeEEE--eecCccCCCCceEEE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT---H-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~---~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ..+||.+|+++-+..+.+.+++...  +++.+..++|+.+..++.+.+..   | ..+||+  +....+.+.++++||
T Consensus       210 g~iLVFlpg~~eI~~l~~~L~~~~~--~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VI  285 (819)
T TIGR01970       210 GSILVFLPGQAEIRRVQEQLAERLD--SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVI  285 (819)
T ss_pred             CcEEEEECCHHHHHHHHHHHHhhcC--CCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEE
Confidence            4799999999999888887775332  37889999999998777777653   2 357777  666688888988665

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=91.49  E-value=4.4  Score=33.19  Aligned_cols=25  Identities=20%  Similarity=0.214  Sum_probs=17.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +-.++.+|.|+||+... ..+...+.
T Consensus        42 HA~Lf~Gp~G~GK~~lA-~~~A~~Ll   66 (365)
T PRK07471         42 HAWLIGGPQGIGKATLA-YRMARFLL   66 (365)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHh
Confidence            36899999999999543 34444443

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=91.47  E-value=0.68  Score=40.64  Aligned_cols=53  Identities=21%  Similarity=0.207  Sum_probs=38.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH--HHHHHHHHHHHHHHh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR--ELAFQISKEYERFSK  107 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~  107 (175)
                      .+.+|.++||+|||..+.+-+.+.+..   +..++++=|-.  ++...++..++++.+
T Consensus       181 gHtlV~GtTGsGKT~l~~~li~q~i~~---g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       181 GHTLVLGTTRVGKTRLAELLITQDIRR---GDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            578999999999998877666665543   34677777865  567777777777665

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>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=91.47  E-value=0.15  Score=34.41  Aligned_cols=14  Identities=43%  Similarity=0.683  Sum_probs=12.2

Q ss_pred             EEEEcCCCChHHHH
Q psy1539          54 ILCQAKSGMGKTAV   67 (175)
Q Consensus        54 ~ii~a~TGsGKT~~   67 (175)
                      +++.+|+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            58999999999964

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 ....

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=91.45  E-value=0.52  Score=35.50  Aligned_cols=52  Identities=19%  Similarity=0.100  Sum_probs=30.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .|.-+++.+++|+|||...+--+...+.   ++-.++++... +-..|+.+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~---~g~~~~y~s~e-~~~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLK---NGEKAMYISLE-EREERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEECC-CCHHHHHHHHHHc
Confidence            3578899999999999654333333333   23356666543 3445555555444

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=91.43  E-value=0.16  Score=44.68  Aligned_cols=44  Identities=23%  Similarity=0.136  Sum_probs=33.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      .++++.||||||||..+++|-+-.+.     .-++|.=|--|+......
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~~-----~S~VV~D~KGEl~~~Ta~  188 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTWP-----GSAIVHDIKGENWQLTAG  188 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhCC-----CCEEEEeCcchHHHHHHH
Confidence            68999999999999999999876542     136666677777655443

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=91.42  E-value=0.19  Score=44.07  Aligned_cols=44  Identities=20%  Similarity=0.115  Sum_probs=33.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      .++++.||||||||..+++|-+-..     +..++|+=|--|+......
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~~-----~~S~VV~D~KGE~~~~Tag  219 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLSW-----GHSSVITDLKGELWALTAG  219 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhhC-----CCCEEEEeCcHHHHHHHHH
Confidence            6799999999999999999887643     1247777788888654433

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=91.41  E-value=2.5  Score=36.81  Aligned_cols=72  Identities=11%  Similarity=0.078  Sum_probs=52.4

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.++||.|+|+..+.++.+.+...     ++.+..++|+.+..+..+   .+.+ ..+++|+  .....++.++++++|.
T Consensus       224 ~~~~IIf~~sr~~~e~la~~L~~~-----g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~  298 (591)
T TIGR01389       224 GQSGIIYASSRKKVEELAERLESQ-----GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIH  298 (591)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHhC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEE
Confidence            457899999999999988776542     788899999987554433   2333 4577777  5555888999998886


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      =..
T Consensus       299 ~~~  301 (591)
T TIGR01389       299 YDM  301 (591)
T ss_pred             cCC
Confidence            544

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=91.40  E-value=1  Score=36.34  Aligned_cols=32  Identities=31%  Similarity=0.361  Sum_probs=23.8

Q ss_pred             CcHHHHHhHHHHh----cC---CcEEEEcCCCChHHHHH
Q psy1539          37 QTSFQHECIPQAV----LG---MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~g---~~~ii~a~TGsGKT~~~   68 (175)
                      .+|+|...|..+.    +|   +-.++.||.|.||+..+
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA   41 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHH
Confidence            4677777776654    33   47889999999999543

>KOG0745|consensus

Probab=91.37  E-value=0.13  Score=42.82  Aligned_cols=17  Identities=29%  Similarity=0.456  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      ..|+++.+|||||||+.
T Consensus       226 KSNvLllGPtGsGKTll  242 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLL  242 (564)
T ss_pred             cccEEEECCCCCchhHH
Confidence            35899999999999974

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=91.30  E-value=3.6  Score=36.36  Aligned_cols=81  Identities=17%  Similarity=0.191  Sum_probs=56.7

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.+++|.|+|+.-+..+.+.+..    . ++++..++|+.+..+..   +.+++| ..++|+  .....+++.+++++|
T Consensus       445 ~g~~viIf~~t~~~ae~L~~~L~~----~-gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGfdlp~v~lVi  519 (652)
T PRK05298        445 KGERVLVTTLTKRMAEDLTDYLKE----L-GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLVA  519 (652)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHhh----c-ceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCccccCCcEEE
Confidence            566899999999988886666654    3 78888888887644333   334443 456655  667789999999998


Q ss_pred             EeCCC-CCCHHHH
Q psy1539         155 MDVRS-GGWWLDL  166 (175)
Q Consensus       155 lDEad-~~f~~~v  166 (175)
                      +=|++ .||..+.
T Consensus       520 i~d~eifG~~~~~  532 (652)
T PRK05298        520 ILDADKEGFLRSE  532 (652)
T ss_pred             EeCCcccccCCCH
Confidence            87774 4554333

>PRK06893 DNA replication initiation factor; Validated

Probab=91.29  E-value=0.32  Score=36.99  Aligned_cols=36  Identities=8%  Similarity=-0.037  Sum_probs=22.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      ..+++.||+|+|||- .+.++.+.+...  +..+.++..
T Consensus        40 ~~l~l~G~~G~GKTh-L~~ai~~~~~~~--~~~~~y~~~   75 (229)
T PRK06893         40 PFFYIWGGKSSGKSH-LLKAVSNHYLLN--QRTAIYIPL   75 (229)
T ss_pred             CeEEEECCCCCCHHH-HHHHHHHHHHHc--CCCeEEeeH
Confidence            457999999999994 344455544432  335666544

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=91.19  E-value=0.41  Score=37.15  Aligned_cols=50  Identities=14%  Similarity=0.063  Sum_probs=29.9

Q ss_pred             HhHHHHhcC-----CcEEEEcCCCChHHHHHHHHHHHhhhc---CCCCeEEEEEecCH
Q psy1539          43 ECIPQAVLG-----MDILCQAKSGMGKTAVFVLATLQQLET---TDSNVYVLVMCHTR   92 (175)
Q Consensus        43 ~~i~~~~~g-----~~~ii~a~TGsGKT~~~~~~~l~~l~~---~~~~~~~lil~Pt~   92 (175)
                      ..+..++.|     .=.=++++.|+|||-..+--.+....+   ...+.+++||--..
T Consensus        25 ~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~   82 (256)
T PF08423_consen   25 KSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEG   82 (256)
T ss_dssp             HHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSS
T ss_pred             HHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCC
Confidence            356666654     345589999999995544333333222   12345799997544

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK10867 signal recognition particle protein; Provisional

Probab=91.18  E-value=3.6  Score=34.54  Aligned_cols=58  Identities=19%  Similarity=0.201  Sum_probs=31.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEE
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGV  116 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~  116 (175)
                      -+++++++|+|||.+..--+ .++.. ..+.+++++.  +.|.-+.   ++++.+.+.. ++.+..
T Consensus       102 vI~~vG~~GsGKTTtaakLA-~~l~~-~~G~kV~lV~~D~~R~aa~---eQL~~~a~~~-gv~v~~  161 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLA-KYLKK-KKKKKVLLVAADVYRPAAI---EQLKTLGEQI-GVPVFP  161 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHH-HHHHH-hcCCcEEEEEccccchHHH---HHHHHHHhhc-CCeEEe
Confidence            47889999999997643322 22322 1244555555  3454443   2344555554 665543

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

Probab=91.18  E-value=3.1  Score=27.69  Aligned_cols=75  Identities=15%  Similarity=0.220  Sum_probs=51.6

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhcCC-CeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHN-PQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~~~-~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.+.|+.++++.-+.++.+.+++     ++..+..++|+.+..+.   ...+.++. .++++  .....+++...+.+|
T Consensus        27 ~~~~~lvf~~~~~~~~~~~~~l~~-----~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi  101 (131)
T cd00079          27 KGGKVLIFCPSKKMLDELAELLRK-----PGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVI  101 (131)
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHh-----cCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEE
Confidence            345799999999998888877776     26778888888764332   23444544 34554  334477888899888


Q ss_pred             EeCCCC
Q psy1539         155 MDVRSG  160 (175)
Q Consensus       155 lDEad~  160 (175)
                      +.+...
T Consensus       102 ~~~~~~  107 (131)
T cd00079         102 NYDLPW  107 (131)
T ss_pred             EeCCCC
Confidence            887743

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=91.13  E-value=0.17  Score=35.02  Aligned_cols=14  Identities=29%  Similarity=0.527  Sum_probs=12.3

Q ss_pred             EEEEcCCCChHHHH
Q psy1539          54 ILCQAKSGMGKTAV   67 (175)
Q Consensus        54 ~ii~a~TGsGKT~~   67 (175)
                      ++++|++|||||..
T Consensus         2 ii~~G~pgsGKSt~   15 (143)
T PF13671_consen    2 IILCGPPGSGKSTL   15 (143)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            68999999999964

...

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=91.09  E-value=0.32  Score=42.78  Aligned_cols=47  Identities=26%  Similarity=0.162  Sum_probs=34.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .++++.||||+|||..+++|-+-.+    .+ -++++=|..|+...+....+
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnLL~~----~g-S~VV~DpKgEl~~~Ta~~R~  271 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTALKW----GG-PLVVLDPSTEVAPMVSEHRR  271 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhhhcC----CC-CEEEEeCcHHHHHHHHHHHH
Confidence            6889999999999999999976432    11 36666688888766555443

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=91.05  E-value=1.2  Score=32.38  Aligned_cols=46  Identities=13%  Similarity=0.104  Sum_probs=30.3

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      ++|.+++|||||....- .+..     .+.+++++...+..-....+.+.+.
T Consensus         2 ~li~G~~~sGKS~~a~~-~~~~-----~~~~~~y~at~~~~d~em~~rI~~H   47 (169)
T cd00544           2 ILVTGGARSGKSRFAER-LAAE-----LGGPVTYIATAEAFDDEMAERIARH   47 (169)
T ss_pred             EEEECCCCCCHHHHHHH-HHHh-----cCCCeEEEEccCcCCHHHHHHHHHH
Confidence            57899999999954432 2222     2347888888777766666655543

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.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=91.04  E-value=0.27  Score=43.54  Aligned_cols=68  Identities=12%  Similarity=0.121  Sum_probs=39.4

Q ss_pred             HHHHHHHhhCCCCCCcHHHHHhHH--HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          23 EKEDRIGESQPFREQTSFQHECIP--QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        23 ~~l~~~l~~~g~~~~t~~Q~~~i~--~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      .++.+.+++.|-.  +++.-.-+|  .-.+.+++++.+.||||||.+. .-++..+..  ++-++||.=|+-+.+
T Consensus       157 ~~l~k~lk~~~~~--s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~--RGdrAIIyD~~GeFv  226 (732)
T PRK13700        157 KDVARMLKKDGKD--SDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQ--RGDMVVIYDRSGEFV  226 (732)
T ss_pred             HHHHHHHHhcCCC--CCeeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHH--cCCeEEEEeCCCchH
Confidence            4555667766533  333333333  3445699999999999999754 555555433  222444444444443

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=91.03  E-value=1.2  Score=35.72  Aligned_cols=54  Identities=17%  Similarity=-0.004  Sum_probs=30.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhc---CCCCeEEEEEecCHHH-HHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLET---TDSNVYVLVMCHTREL-AFQISKEYERF  105 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~---~~~~~~~lil~Pt~~L-~~q~~~~~~~~  105 (175)
                      .-+.+.+++|+|||...+..++....+   ...+.+++|+.-...+ ..++.+..+.+
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            456799999999996554333332221   1224478888754332 34444444443

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.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=90.81  E-value=1.1  Score=36.37  Aligned_cols=25  Identities=8%  Similarity=0.005  Sum_probs=18.4

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCC
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFR   35 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~   35 (175)
                      .+...+...|+++...+.|++.||.
T Consensus        29 ~~~~~l~~~g~~~~~~~kL~~~g~~   53 (344)
T PLN03187         29 ESIDKLISQGINAGDVKKLQDAGIY   53 (344)
T ss_pred             cCHHHHhhCCCCHHHHHHHHHcCCC
Confidence            3455566678888888888888875

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=90.79  E-value=0.48  Score=35.70  Aligned_cols=17  Identities=12%  Similarity=0.208  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      +..+++.+++|+|||..
T Consensus        42 ~~~~~l~G~~G~GKT~L   58 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHL   58 (227)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            46899999999999953

>KOG2340|consensus

Probab=90.75  E-value=1.6  Score=37.43  Aligned_cols=73  Identities=22%  Similarity=0.252  Sum_probs=53.9

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCC-CChH--HHHHHHHHHHhhhcC----------------------------CCCe
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKS-GMGK--TAVFVLATLQQLETT----------------------------DSNV   83 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~T-GsGK--T~~~~~~~l~~l~~~----------------------------~~~~   83 (175)
                      ..+|+.|.+.+....+-+|++.-..| +.|+  +-.|++-+++++.+.                            -..|
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            36799999999888888998754433 2454  345777777776311                            1248


Q ss_pred             EEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          84 YVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        84 ~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ++||+||+|+-|-.+.+.+..++.
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~  318 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLS  318 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhc
Confidence            999999999999999888887743

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=90.73  E-value=0.66  Score=37.49  Aligned_cols=24  Identities=33%  Similarity=0.499  Sum_probs=17.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .++++.||+|+|||... -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            68999999999999653 4444444

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.

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=90.69  E-value=0.49  Score=35.85  Aligned_cols=22  Identities=18%  Similarity=0.105  Sum_probs=14.6

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhh
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +-+.+++|||||... -.+...+
T Consensus         2 igI~G~sGSGKTTla-~~L~~~l   23 (220)
T cd02025           2 IGIAGSVAVGKSTTA-RVLQALL   23 (220)
T ss_pred             EEeeCCCCCCHHHHH-HHHHHHH
Confidence            357899999999654 3333333

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=90.67  E-value=1  Score=34.09  Aligned_cols=51  Identities=20%  Similarity=0.173  Sum_probs=31.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      |.-+++.+++|+|||.....-+...+.   ++.+++++.-... ..++.+.+..+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~---~g~~~~y~~~e~~-~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALK---QGKKVYVITTENT-SKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHh---CCCEEEEEEcCCC-HHHHHHHHHHC
Confidence            578899999999999654433333333   3446777765433 34555555554

>PRK09694 helicase Cas3; Provisional

Probab=90.65  E-value=1.8  Score=39.53  Aligned_cols=75  Identities=12%  Similarity=0.265  Sum_probs=51.3

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh-------HHHH-hcCC----CeEEE--eecCccC
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD-------EEYL-KTHN----PQIVG--LVNYETN  146 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~-------~~~l-~~~~----~iiv~--l~~~~~~  146 (175)
                      ++.+++|+++|++-++++++.+++...  ++..+.+++|.....+.       .+.+ +++.    .++|+  ++...++
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~--~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLD  636 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNN--TQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLD  636 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCC--CCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheee
Confidence            455899999999999999998886431  24678899998664333       2223 3332    47777  5666666


Q ss_pred             CCCceEEEEeCC
Q psy1539         147 LSGVVVNVMDVR  158 (175)
Q Consensus       147 ~~~~~~lVlDEa  158 (175)
                      + +++++|-|-+
T Consensus       637 I-d~DvlItdla  647 (878)
T PRK09694        637 L-DFDWLITQLC  647 (878)
T ss_pred             c-CCCeEEECCC
Confidence            6 4678888765

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

Probab=90.64  E-value=0.25  Score=38.79  Aligned_cols=22  Identities=18%  Similarity=0.309  Sum_probs=15.9

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      =+++.++|||||+... .+++.+
T Consensus       129 LviiVGaTGSGKSTtm-AaMi~y  150 (375)
T COG5008         129 LVIIVGATGSGKSTTM-AAMIGY  150 (375)
T ss_pred             eEEEECCCCCCchhhH-HHHhcc
Confidence            3688999999999653 444444

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=90.63  E-value=2.7  Score=38.12  Aligned_cols=70  Identities=9%  Similarity=0.190  Sum_probs=53.4

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhc---C-CCeEEE--eecCccCCCCceEEE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT---H-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~---~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ..+||.+|++.-++++.+.+++...  .++.+..++|+.+..++.+.+..   | ..+||+  +....+.+.++++||
T Consensus       213 g~iLVFlpg~~ei~~l~~~L~~~~~--~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VI  288 (812)
T PRK11664        213 GSLLLFLPGVGEIQRVQEQLASRVA--SDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVV  288 (812)
T ss_pred             CCEEEEcCCHHHHHHHHHHHHHhcc--CCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEE
Confidence            4799999999999998888875321  27889999999998777766653   2 356777  666688889999666

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=90.58  E-value=0.21  Score=36.59  Aligned_cols=18  Identities=33%  Similarity=0.445  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |..+++.+|+|+|||...
T Consensus         2 g~~i~l~G~sGsGKsTl~   19 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLL   19 (186)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            567899999999999753

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=90.53  E-value=0.26  Score=43.12  Aligned_cols=49  Identities=18%  Similarity=0.143  Sum_probs=35.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .++++.||||||||..+++|-+-.+.    + -++++=|.-|+.......-++.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~~~----g-S~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALKYG----G-PLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhcCC----C-CEEEEEChHHHHHHHHHHHHHc
Confidence            68999999999999999999754321    1 3677778888876655433333

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=90.52  E-value=0.17  Score=44.75  Aligned_cols=27  Identities=26%  Similarity=0.335  Sum_probs=19.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      .|+.+.+.+++|||||.  ++-++..+..
T Consensus       490 ~G~~iaIvG~sGsGKST--LlklL~gl~~  516 (694)
T TIGR03375       490 PGEKVAIIGRIGSGKST--LLKLLLGLYQ  516 (694)
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHhcCCC
Confidence            58899999999999996  3344444443

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.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=90.51  E-value=0.39  Score=41.63  Aligned_cols=26  Identities=23%  Similarity=0.319  Sum_probs=19.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +.+++++.|+||||||. ++..++..+
T Consensus       175 e~~h~li~G~tGsGKs~-~i~~ll~~~  200 (566)
T TIGR02759       175 ETQHILIHGTTGSGKSV-AIRKLLRWI  200 (566)
T ss_pred             cccceEEEcCCCCCHHH-HHHHHHHHH
Confidence            45799999999999995 344455554

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>KOG0060|consensus

Probab=90.50  E-value=0.32  Score=41.89  Aligned_cols=20  Identities=35%  Similarity=0.544  Sum_probs=17.5

Q ss_pred             HHhcCCcEEEEcCCCChHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~   66 (175)
                      .+.+|++++|++|+|+|||-
T Consensus       457 ~V~~g~~LLItG~sG~GKtS  476 (659)
T KOG0060|consen  457 EVPSGQNLLITGPSGCGKTS  476 (659)
T ss_pred             EecCCCeEEEECCCCCchhH
Confidence            34579999999999999995

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=90.47  E-value=2.1  Score=34.73  Aligned_cols=31  Identities=16%  Similarity=0.244  Sum_probs=23.7

Q ss_pred             cHHHHHhHHHHhc--C---CcEEEEcCCCChHHHHH
Q psy1539          38 TSFQHECIPQAVL--G---MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        38 t~~Q~~~i~~~~~--g---~~~ii~a~TGsGKT~~~   68 (175)
                      +|+|...|..+..  |   +-+++.+|.|.||+..+
T Consensus         3 yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA   38 (342)
T PRK06964          3 YPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFA   38 (342)
T ss_pred             CcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHH
Confidence            6777777776653  3   57889999999999654

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.36  E-value=1.4  Score=36.83  Aligned_cols=19  Identities=21%  Similarity=0.282  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~   70 (175)
                      .-+++.+|+|+|||....-
T Consensus       224 ~vi~lvGptGvGKTTtaaK  242 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAK  242 (432)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3478999999999976543

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=90.35  E-value=2.4  Score=36.46  Aligned_cols=74  Identities=12%  Similarity=0.042  Sum_probs=54.2

Q ss_pred             CCcHHHHHhHHHHhc------C----CcEEEEcCCCChHHHHHH-HHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVL------G----MDILCQAKSGMGKTAVFV-LATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~------g----~~~ii~a~TGsGKT~~~~-~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      .+-|+|+-.+-.++.      |    +-.+|.-|-+.|||.... +.....+.....+.+..|++|+.+-+.+.+..++.
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            568899999877762      2    457888999999996543 33333333335666889999999999999998888


Q ss_pred             HHhhC
Q psy1539         105 FSKYM  109 (175)
Q Consensus       105 ~~~~~  109 (175)
                      .....
T Consensus       141 mv~~~  145 (546)
T COG4626         141 MVKRD  145 (546)
T ss_pred             HHHhC
Confidence            77665

>PRK13531 regulatory ATPase RavA; Provisional

Probab=90.34  E-value=0.64  Score=39.50  Aligned_cols=27  Identities=19%  Similarity=0.409  Sum_probs=21.6

Q ss_pred             HHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          42 HECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        42 ~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..++-.++.|.++++.+|+|+|||...
T Consensus        30 ~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         30 RLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHHHccCCCEEEECCCChhHHHHH
Confidence            334456678999999999999999754

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=90.23  E-value=1.2  Score=36.99  Aligned_cols=41  Identities=17%  Similarity=0.180  Sum_probs=29.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      ..-+++.||+|+|||- .+.++.+.........+++++....
T Consensus       113 ~nplfi~G~~GlGKTH-Ll~Aign~~~~~~~~a~v~y~~se~  153 (408)
T COG0593         113 YNPLFIYGGVGLGKTH-LLQAIGNEALANGPNARVVYLTSED  153 (408)
T ss_pred             CCcEEEECCCCCCHHH-HHHHHHHHHHhhCCCceEEeccHHH
Confidence            3679999999999994 4556666665545555777777643

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=90.20  E-value=0.22  Score=39.68  Aligned_cols=17  Identities=12%  Similarity=0.311  Sum_probs=13.8

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +=++|.+|||||||-..
T Consensus         5 ~ii~I~GpTasGKS~LA   21 (300)
T PRK14729          5 KIVFIFGPTAVGKSNIL   21 (300)
T ss_pred             cEEEEECCCccCHHHHH
Confidence            45889999999999543

>PHA02244 ATPase-like protein

Probab=90.19  E-value=0.44  Score=39.08  Aligned_cols=22  Identities=14%  Similarity=0.302  Sum_probs=18.1

Q ss_pred             HHHhcCCcEEEEcCCCChHHHH
Q psy1539          46 PQAVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        46 ~~~~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..+..+.++++.+|||+|||..
T Consensus       114 r~l~~~~PVLL~GppGtGKTtL  135 (383)
T PHA02244        114 KIVNANIPVFLKGGAGSGKNHI  135 (383)
T ss_pred             HHHhcCCCEEEECCCCCCHHHH
Confidence            3445689999999999999954

>CHL00181 cbbX CbbX; Provisional

Probab=90.18  E-value=0.85  Score=36.03  Aligned_cols=19  Identities=32%  Similarity=0.566  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~   69 (175)
                      |.++++.+|+|+|||..+-
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5679999999999997654

>PHA00729 NTP-binding motif containing protein

Probab=90.17  E-value=1  Score=34.34  Aligned_cols=16  Identities=31%  Similarity=0.424  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      .++++.|++|+|||..
T Consensus        18 ~nIlItG~pGvGKT~L   33 (226)
T PHA00729         18 VSAVIFGKQGSGKTTY   33 (226)
T ss_pred             EEEEEECCCCCCHHHH
Confidence            4899999999999953

>PLN03232 ABC transporter C family member; Provisional

Probab=90.05  E-value=0.56  Score=45.26  Aligned_cols=27  Identities=19%  Similarity=0.327  Sum_probs=19.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      .|+.+-++++||||||.  ++-++.++..
T Consensus      1261 ~GekvaIVG~SGSGKST--L~~lL~rl~~ 1287 (1495)
T PLN03232       1261 PSEKVGVVGRTGAGKSS--MLNALFRIVE 1287 (1495)
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHhCCCc
Confidence            57889999999999996  3344444443

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=89.95  E-value=5.2  Score=35.07  Aligned_cols=114  Identities=10%  Similarity=0.012  Sum_probs=67.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh-CCCeEEEEEECCC-chHHhHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY-MSNIKVGVFFGGL-PIQKDEEY  129 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~-~~~i~v~~~~g~~-~~~~~~~~  129 (175)
                      +-.+.--|---|||| |+.|++..+...-.+.++.|++.-|.-++-+++++..-+.+ +|.-.+...-++. ..+..  .
T Consensus       203 kaTVFLVPRRHGKTW-f~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~k~~tI~~s~p--g  279 (668)
T PHA03372        203 KATVFLVPRRHGKTW-FIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIENKDNVISIDHR--G  279 (668)
T ss_pred             cceEEEecccCCcee-hHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeeecCcEEEEecC--C
Confidence            344555688999995 68888888887778899999999998888877776543332 3322221111110 00000  0


Q ss_pred             HhcCCCeEEE--eecCccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         130 LKTHNPQIVG--LVNYETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       130 l~~~~~iiv~--l~~~~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      . + ...+.+  -..+.+.=++..++++|||...-.+-+..||
T Consensus       280 ~-K-st~~fasc~n~NsiRGQ~fnll~VDEA~FI~~~a~~til  320 (668)
T PHA03372        280 A-K-STALFASCYNTNSIRGQNFHLLLVDEAHFIKKDAFNTIL  320 (668)
T ss_pred             C-c-ceeeehhhccCccccCCCCCEEEEehhhccCHHHHHHhh
Confidence            0 0 011112  1111445568999999999766556555554

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=89.90  E-value=2.2  Score=34.29  Aligned_cols=32  Identities=16%  Similarity=0.220  Sum_probs=23.7

Q ss_pred             CcHHHHHhHHHHh----cC---CcEEEEcCCCChHHHHH
Q psy1539          37 QTSFQHECIPQAV----LG---MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~g---~~~ii~a~TGsGKT~~~   68 (175)
                      ++|+|...+..+.    +|   +-.++.+|.|.||+..+
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA   42 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLV   42 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH
Confidence            5677777776554    34   47999999999998543

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=89.87  E-value=1.2  Score=34.56  Aligned_cols=27  Identities=7%  Similarity=-0.080  Sum_probs=20.2

Q ss_pred             CCCCceEEEEeCC----CCCCHHHHHHHHhh
Q psy1539         146 NLSGVVVNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       146 ~~~~~~~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      ..++-+++++||-    |..-..++.++|..
T Consensus       154 L~~~p~lllLDEP~~gvD~~~~~~i~~lL~~  184 (254)
T COG1121         154 LAQNPDLLLLDEPFTGVDVAGQKEIYDLLKE  184 (254)
T ss_pred             hccCCCEEEecCCcccCCHHHHHHHHHHHHH
Confidence            3468889999998    76667777777654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=89.81  E-value=1.1  Score=35.70  Aligned_cols=16  Identities=44%  Similarity=0.632  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.||+|+|||...
T Consensus        38 ~lll~Gp~GtGKT~la   53 (337)
T PRK12402         38 HLLVQGPPGSGKTAAV   53 (337)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999654

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=89.80  E-value=2.2  Score=29.51  Aligned_cols=55  Identities=11%  Similarity=0.102  Sum_probs=29.6

Q ss_pred             CcEE--EEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe-----cCHHHHHHHHHHHHHHH
Q psy1539          52 MDIL--CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC-----HTRELAFQISKEYERFS  106 (175)
Q Consensus        52 ~~~i--i~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~-----Pt~~L~~q~~~~~~~~~  106 (175)
                      +.++  ..++||+|||.+.-+-+-+......++..+....     |....+.+-.++++++.
T Consensus        52 KpLVlSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~I  113 (127)
T PF06309_consen   52 KPLVLSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSWI  113 (127)
T ss_pred             CCEEEEeecCCCCcHHHHHHHHHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHHH
Confidence            4555  7899999999776553333222222333343333     45555555455555443

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=89.72  E-value=0.24  Score=38.40  Aligned_cols=17  Identities=29%  Similarity=0.606  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.+|+|+|||...
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            57999999999999654

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.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=89.71  E-value=0.58  Score=33.78  Aligned_cols=44  Identities=20%  Similarity=0.172  Sum_probs=33.3

Q ss_pred             HHHHHHHhhCCCCC-----CcHHHHHhHHHHhcCCcEEEEcCCCChHHH
Q psy1539          23 EKEDRIGESQPFRE-----QTSFQHECIPQAVLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        23 ~~l~~~l~~~g~~~-----~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~   66 (175)
                      +++++..++.||+.     -+....+.+...+.++-+++.+++|.||+.
T Consensus         2 ~~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k~~vl~G~SGvGKSS   50 (161)
T PF03193_consen    2 EELLEQYEKLGYPVFFISAKTGEGIEELKELLKGKTSVLLGQSGVGKSS   50 (161)
T ss_dssp             HHHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTSEEEEECSTTSSHHH
T ss_pred             HHHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCCEEEEECCCCCCHHH
Confidence            35667777888762     244556667777888999999999999994

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=89.67  E-value=0.26  Score=35.17  Aligned_cols=20  Identities=25%  Similarity=0.335  Sum_probs=16.7

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+..+++.+++|||||...
T Consensus         2 ~~~~~i~l~G~~GsGKstla   21 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIG   21 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHH
Confidence            35678999999999999754

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=89.66  E-value=2.6  Score=33.90  Aligned_cols=17  Identities=29%  Similarity=0.370  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +-.++.||.|.||+...
T Consensus        29 ha~Lf~G~~G~gk~~~a   45 (329)
T PRK08058         29 HAYLFEGAKGTGKKATA   45 (329)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            35699999999998543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.66  E-value=2.3  Score=36.20  Aligned_cols=24  Identities=17%  Similarity=-0.024  Sum_probs=16.6

Q ss_pred             CCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         147 LSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       147 ~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      ..+-+.+|+||+|+.-.+..+.++
T Consensus       117 ~~~~KVvIIDEad~Lt~~a~naLL  140 (486)
T PRK14953        117 KGKYKVYIIDEAHMLTKEAFNALL  140 (486)
T ss_pred             cCCeeEEEEEChhhcCHHHHHHHH
Confidence            357789999999866555555444

>cd01394 radB RadB

Probab=89.65  E-value=0.69  Score=34.60  Aligned_cols=36  Identities=17%  Similarity=0.168  Sum_probs=23.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      |.-+.+.+++|+|||...+.-+.+...   .+.+++++.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~~~~---~g~~v~yi~   54 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAG---QGKKVAYID   54 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEE
Confidence            466899999999999654433333222   244677774

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=89.63  E-value=0.44  Score=33.29  Aligned_cols=43  Identities=30%  Similarity=0.274  Sum_probs=28.9

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      ..|.-+++.++.|+||| ++.-.++..+...     .-+-+||-.|++.
T Consensus        20 ~~~~~i~l~G~lGaGKT-tl~~~l~~~lg~~-----~~v~SPTf~lv~~   62 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKT-TLVQGLLQGLGIQ-----GNVTSPTFTLVNE   62 (133)
T ss_pred             CCCCEEEEEcCCCCCHH-HHHHHHHHHcCCC-----CcccCCCeeeeee
Confidence            35678899999999999 4555555554321     2366788766644

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PLN02165 adenylate isopentenyltransferase

Probab=89.62  E-value=0.3  Score=39.42  Aligned_cols=20  Identities=20%  Similarity=0.275  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~   69 (175)
                      .|+.+++.+|||||||....
T Consensus        42 ~g~iivIiGPTGSGKStLA~   61 (334)
T PLN02165         42 KDKVVVIMGATGSGKSRLSV   61 (334)
T ss_pred             CCCEEEEECCCCCcHHHHHH
Confidence            35789999999999996553

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=89.62  E-value=0.62  Score=42.59  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=17.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      ..|.+|.|+||||||...-.-+.+
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q  498 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQ  498 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999765433333

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=89.56  E-value=1.2  Score=36.20  Aligned_cols=24  Identities=4%  Similarity=0.001  Sum_probs=18.4

Q ss_pred             cccccccCCCCHHHHHHHhhCCCC
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFR   35 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~   35 (175)
                      ..+.+...|+++..++.|++.||.
T Consensus        27 ~~~~l~~~gi~~~~i~kL~~~g~~   50 (342)
T PLN03186         27 PIEQLQASGIAALDIKKLKDAGIH   50 (342)
T ss_pred             cHHHHHhCCCCHHHHHHHHHcCCC
Confidence            455666778888888888888876

>KOG2228|consensus

Probab=89.54  E-value=1.9  Score=35.08  Aligned_cols=17  Identities=24%  Similarity=0.390  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      +..+++.+|-|||||.-
T Consensus        49 snsviiigprgsgkT~l   65 (408)
T KOG2228|consen   49 SNSVIIIGPRGSGKTIL   65 (408)
T ss_pred             CCceEEEccCCCCceEe
Confidence            48999999999999954

>KOG1533|consensus

Probab=89.44  E-value=0.36  Score=37.11  Aligned_cols=23  Identities=22%  Similarity=0.277  Sum_probs=17.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+|.+|+||||| +|...+.+.+.
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls   27 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLS   27 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHH
Confidence            478999999999 56665555443

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=89.39  E-value=0.37  Score=38.43  Aligned_cols=22  Identities=32%  Similarity=0.478  Sum_probs=16.3

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhh
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ++|.+||+||||- ..+.+.+++
T Consensus         6 i~I~GPTAsGKT~-lai~LAk~~   27 (308)
T COG0324           6 IVIAGPTASGKTA-LAIALAKRL   27 (308)
T ss_pred             EEEECCCCcCHHH-HHHHHHHHc
Confidence            7899999999994 445555544

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=89.39  E-value=2.7  Score=30.52  Aligned_cols=17  Identities=29%  Similarity=0.294  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.++|.+++|||||...
T Consensus         2 ~~ili~G~~~sGKS~~a   18 (170)
T PRK05800          2 MLILVTGGARSGKSRFA   18 (170)
T ss_pred             CEEEEECCCCccHHHHH
Confidence            45899999999999543

>PRK14530 adenylate kinase; Provisional

Probab=89.38  E-value=0.3  Score=36.64  Aligned_cols=19  Identities=26%  Similarity=0.186  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .++.+++.+++|||||...
T Consensus         2 ~~~~I~i~G~pGsGKsT~~   20 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQS   20 (215)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999643

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=89.30  E-value=0.7  Score=39.30  Aligned_cols=80  Identities=18%  Similarity=0.142  Sum_probs=54.6

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .+++.+++. ...+..-|..+.-..-.|+- .|.+-.|||||...++-+.+ +..+...-+.++-+=|+.|+.+..+...
T Consensus       151 a~l~~iesk-IanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~-lh~knPd~~I~~Tfftk~L~s~~r~lv~  227 (660)
T COG3972         151 ALLDTIESK-IANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAE-LHSKNPDSRIAFTFFTKILASTMRTLVP  227 (660)
T ss_pred             HHHHHHHHH-HhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHH-HhcCCCCceEEEEeehHHHHHHHHHHHH
Confidence            444444443 44556677776555555655 57888999999876554443 3333344588899999999999999888


Q ss_pred             HHH
Q psy1539         104 RFS  106 (175)
Q Consensus       104 ~~~  106 (175)
                      +|.
T Consensus       228 ~F~  230 (660)
T COG3972         228 EFF  230 (660)
T ss_pred             HHH
Confidence            876

>PTZ00243 ABC transporter; Provisional

Probab=89.29  E-value=0.36  Score=46.67  Aligned_cols=18  Identities=17%  Similarity=0.278  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|+-+-|+++||||||..
T Consensus      1335 ~GekVaIVGrTGSGKSTL 1352 (1560)
T PTZ00243       1335 PREKVGIVGRTGSGKSTL 1352 (1560)
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            578899999999999963

>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP)

Probab=89.28  E-value=0.49  Score=45.69  Aligned_cols=26  Identities=19%  Similarity=0.317  Sum_probs=19.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .|+-+-++++||||||.  ++-++.++.
T Consensus      1311 ~GekiaIVGrTGsGKST--L~~lL~rl~ 1336 (1522)
T TIGR00957      1311 GGEKVGIVGRTGAGKSS--LTLGLFRIN 1336 (1522)
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHhcCc
Confidence            57889999999999996  333444443

This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=89.22  E-value=4.7  Score=31.23  Aligned_cols=71  Identities=20%  Similarity=0.323  Sum_probs=43.9

Q ss_pred             HHhcC---CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCch
Q psy1539          47 QAVLG---MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  123 (175)
Q Consensus        47 ~~~~g---~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~  123 (175)
                      .+++|   .|+++.++.|+|||. .+-+++.....  .+.+ +|=++...|. ++.+.+..+...  ..+.++++.+.+.
T Consensus        45 ~Fl~G~pannvLL~G~rGtGKSS-lVkall~~y~~--~GLR-lIev~k~~L~-~l~~l~~~l~~~--~~kFIlf~DDLsF  117 (249)
T PF05673_consen   45 QFLQGLPANNVLLWGARGTGKSS-LVKALLNEYAD--QGLR-LIEVSKEDLG-DLPELLDLLRDR--PYKFILFCDDLSF  117 (249)
T ss_pred             HHHcCCCCcceEEecCCCCCHHH-HHHHHHHHHhh--cCce-EEEECHHHhc-cHHHHHHHHhcC--CCCEEEEecCCCC
Confidence            44555   799999999999984 34455555443  3444 5555655553 444545554432  4577778777665


Q ss_pred             H
Q psy1539         124 Q  124 (175)
Q Consensus       124 ~  124 (175)
                      .
T Consensus       118 e  118 (249)
T PF05673_consen  118 E  118 (249)
T ss_pred             C
Confidence            4

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=89.17  E-value=5  Score=32.43  Aligned_cols=80  Identities=21%  Similarity=0.185  Sum_probs=45.7

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec-C-HHHHHHHHHHHHHHHhhCCCeEEEEE-ECCCch----HH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-T-RELAFQISKEYERFSKYMSNIKVGVF-FGGLPI----QK  125 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~i~v~~~-~g~~~~----~~  125 (175)
                      -+++.+-+|+|||.+-  .=+.+++.+ ++.++++.+- | |+=|.+   +++.+.++. ++.++.- .|+.+.    +.
T Consensus       141 Vil~vGVNG~GKTTTI--aKLA~~l~~-~g~~VllaA~DTFRAaAiE---QL~~w~er~-gv~vI~~~~G~DpAaVafDA  213 (340)
T COG0552         141 VILFVGVNGVGKTTTI--AKLAKYLKQ-QGKSVLLAAGDTFRAAAIE---QLEVWGERL-GVPVISGKEGADPAAVAFDA  213 (340)
T ss_pred             EEEEEecCCCchHhHH--HHHHHHHHH-CCCeEEEEecchHHHHHHH---HHHHHHHHh-CCeEEccCCCCCcHHHHHHH
Confidence            3788999999999753  333333332 3445555442 3 666644   455666665 7777653 344332    22


Q ss_pred             hHHHHhcCCCeEEE
Q psy1539         126 DEEYLKTHNPQIVG  139 (175)
Q Consensus       126 ~~~~l~~~~~iiv~  139 (175)
                      -.....++.+++++
T Consensus       214 i~~Akar~~Dvvli  227 (340)
T COG0552         214 IQAAKARGIDVVLI  227 (340)
T ss_pred             HHHHHHcCCCEEEE
Confidence            23344566777776

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=89.16  E-value=0.96  Score=32.30  Aligned_cols=34  Identities=18%  Similarity=0.245  Sum_probs=20.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      +.+.+++|||||.. +-.++..+..  .+.++-++-+
T Consensus         2 i~i~G~~gsGKTtl-~~~l~~~l~~--~G~~V~viK~   35 (155)
T TIGR00176         2 LQIVGPKNSGKTTL-IERLVKALKA--RGYRVATIKH   35 (155)
T ss_pred             EEEECCCCCCHHHH-HHHHHHHHHh--cCCeEEEEec
Confidence            46789999999953 3444444432  3445555544

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>KOG1015|consensus

Probab=89.09  E-value=2  Score=39.50  Aligned_cols=55  Identities=22%  Similarity=0.287  Sum_probs=36.3

Q ss_pred             CCcEEEEcCCCChHHH---HHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTA---VFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~---~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      |...|+.---|-|||+   +|+..++..-.  .+-.++||++|...+ .-+...|.++...
T Consensus       696 GsGcILAHcMGLGKTlQVvtflhTvL~c~k--lg~ktaLvV~PlNt~-~NW~~EFekWm~~  753 (1567)
T KOG1015|consen  696 GSGCILAHCMGLGKTLQVVTFLHTVLLCDK--LGFKTALVVCPLNTA-LNWMNEFEKWMEG  753 (1567)
T ss_pred             CcchHHHHhhcccceehhhHHHHHHHHhhc--cCCceEEEEcchHHH-HHHHHHHHHhccc
Confidence            5667777778999995   34444433322  344579999998655 4567778777664

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=89.03  E-value=0.35  Score=35.03  Aligned_cols=18  Identities=28%  Similarity=0.401  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |+-+++++++|||||...
T Consensus         2 ~~~i~l~G~~gsGKst~a   19 (175)
T cd00227           2 GRIIILNGGSSAGKSSIA   19 (175)
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            677899999999999754

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=89.00  E-value=0.65  Score=32.21  Aligned_cols=22  Identities=23%  Similarity=0.290  Sum_probs=16.9

Q ss_pred             HHhcCCcEEEEcCCCChHHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ....+..+++.+++||||+.++
T Consensus        17 ~a~~~~pvli~GE~GtGK~~~A   38 (138)
T PF14532_consen   17 LAKSSSPVLITGEPGTGKSLLA   38 (138)
T ss_dssp             HHCSSS-EEEECCTTSSHHHHH
T ss_pred             HhCCCCcEEEEcCCCCCHHHHH
Confidence            3345689999999999999753

>PRK08118 topology modulation protein; Reviewed

Probab=88.98  E-value=0.32  Score=35.15  Aligned_cols=16  Identities=25%  Similarity=0.468  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      +.++|.+++|||||..
T Consensus         2 ~rI~I~G~~GsGKSTl   17 (167)
T PRK08118          2 KKIILIGSGGSGKSTL   17 (167)
T ss_pred             cEEEEECCCCCCHHHH
Confidence            3589999999999963

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=88.96  E-value=0.26  Score=41.36  Aligned_cols=19  Identities=21%  Similarity=0.254  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+.+++.+|+|+|||+..
T Consensus       216 ~p~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLA  234 (438)
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3578999999999999754

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=88.96  E-value=0.59  Score=34.05  Aligned_cols=17  Identities=29%  Similarity=0.401  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      ++-++++||+|+|||..
T Consensus         2 ~r~ivl~Gpsg~GK~~l   18 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTL   18 (183)
T ss_dssp             SSEEEEESSTTSSHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            57789999999999964

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>KOG0055|consensus

Probab=88.94  E-value=0.3  Score=45.52  Aligned_cols=52  Identities=19%  Similarity=0.236  Sum_probs=35.9

Q ss_pred             HhhCCCCCCcHHHHHhHHH----HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCC
Q psy1539          29 GESQPFREQTSFQHECIPQ----AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN   82 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~----~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~   82 (175)
                      +++..|..|+.--..++.-    +..|+.+-+.+|.||||+.  ++.++++.+....|
T Consensus       990 ~~~V~F~YPsRP~~~Il~~l~l~i~~GqTvALVG~SGsGKST--vI~LLeRfYdp~~G 1045 (1228)
T KOG0055|consen  990 FRNVSFAYPTRPDVPVLNNLSLSIRAGQTVALVGPSGSGKST--VISLLERFYDPDAG 1045 (1228)
T ss_pred             EeeeEeeCCCCCCchhhcCCcEEecCCCEEEEECCCCCCHHH--HHHHHHHhcCCCCC
Confidence            4445566775544444432    3468999999999999997  57888888754443

>PRK14737 gmk guanylate kinase; Provisional

Probab=88.92  E-value=1.1  Score=33.10  Aligned_cols=17  Identities=18%  Similarity=0.286  Sum_probs=14.4

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      ++=+++++|+|+|||..
T Consensus         4 ~~~ivl~GpsG~GK~tl   20 (186)
T PRK14737          4 PKLFIISSVAGGGKSTI   20 (186)
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45689999999999964

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=88.90  E-value=0.49  Score=39.52  Aligned_cols=24  Identities=17%  Similarity=0.368  Sum_probs=20.1

Q ss_pred             HHHhcCCcEEEEcCCCChHHHHHH
Q psy1539          46 PQAVLGMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        46 ~~~~~g~~~ii~a~TGsGKT~~~~   69 (175)
                      |.+-++.|++..+|+|+|||-.|.
T Consensus       204 ~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       204 PLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHH
Confidence            556678999999999999996554

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	175
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		2e-43
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		2e-43
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-43
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-43
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		6e-12
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		6e-12
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		8e-12
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		2e-11
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		3e-11
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		3e-11
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		4e-11
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		5e-11
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		6e-11
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		3e-10
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		3e-10
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		7e-10
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		7e-10
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		7e-10
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		8e-10
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-09
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		2e-09
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		4e-09
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		7e-08
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		8e-08
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-07
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		2e-07
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-07
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-07
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		5e-07
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		6e-07
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		7e-07
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		7e-07
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		8e-07
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-06
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-06
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		3e-06
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		5e-06
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		7e-06
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		5e-05
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		6e-05
3ly5_A	262	Ddx18 Dead-Domain Length = 262		2e-04
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		3e-04
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		3e-04
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		4e-04

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  171 bits (433), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 34  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 93
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 94  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 138

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  171 bits (433), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 27  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 86
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 87  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 131

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  171 bits (432), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 28  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 87
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 88  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 132

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  171 bits (432), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 81/105 (77%), Positives = 87/105 (82%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 28  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 87
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 88  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 132

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 67.0 bits (162), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 33/93 (35%), Positives = 55/93 (59%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           + + +  Q E IP A+ G DIL +AK+G GK+  +++  L++L+    N+  +V+  TRE
Sbjct: 23  WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE 82
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA Q+S+   + SK+M   KV    GG  ++ D
Sbjct: 83  LALQVSQICIQVSKHMGGAKVMATTGGTNLRDD 115

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 67.0 bits (162), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 55/96 (57%), Gaps = 5/96 (5%)
Query: 26  DRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYV 85
           D++G ++P    T  Q E IP A+ G DI+  A++G GKT  F L  L  L  T   ++ 
Sbjct: 59  DQLGWTKP----TKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFA 114
Query: 86  LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL 121
           LV+  TRELAFQIS+++E     +  ++  V  GG+
Sbjct: 115 LVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGI 149

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 66.2 bits (160), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 36/93 (38%), Positives = 53/93 (56%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + +  Q E IP A+ G DIL +AK+G GKTA FV+ TL++++   + +  L+M  TRE
Sbjct: 41  FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE 100
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA Q S+      K+   I   V  GG  ++ D
Sbjct: 101 LALQTSQVVRTLGKH-CGISCMVTTGGTNLRDD 132

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/98 (34%), Positives = 50/98 (51%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  Q + IP    G+D++ QAKSG GKT VF    L  L   + +  +L++  TRE
Sbjct: 44  FERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTRE 103
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
           +A QI          M  ++  VF GG P+ +D+  LK
Sbjct: 104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK 141

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F E ++ Q   I   + G D+L QA+SG GKT  F +A LQ+++T+      L++  TRE
Sbjct: 41  FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 100
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K     + +M +IKV    GG    +D E L+  + QIV
Sbjct: 101 LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 142

>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 = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F E ++ Q   I   + G D+L QA+SG GKT  F +A LQ+++T+      L++  TRE
Sbjct: 34  FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 93
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K     + +M +IKV    GG    +D E L+  + QIV
Sbjct: 94  LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 135

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 63.9 bits (154), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F E ++ Q   I   + G D+L QA+SG GKT  F +A LQ+++T+      L++  TRE
Sbjct: 42  FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 101
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K     + +M +IKV    GG    +D E L+  + QIV
Sbjct: 102 LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 143

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 63.5 bits (153), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 39/105 (37%), Positives = 56/105 (53%), Gaps = 3/105 (2%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F E ++ Q   I   + G D+L QA+SG GKT  F +A LQ+++T+      L +  TRE
Sbjct: 41  FEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALXLAPTRE 100
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K     + +  +IKV    GG    +D E L+  + QIV
Sbjct: 101 LALQIQKVVXALA-FHXDIKVHACIGGTSFVEDAEGLR--DAQIV 142

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 63.5 bits (153), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I   + G D++ QA+SG GKTA F ++ LQQLE        LV+  TRE
Sbjct: 50  FEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRE 109
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K       YM         GG  ++ + + L+   P IV
Sbjct: 110 LAQQIQKVILALGDYMGA-TCHACIGGTNVRNEMQKLQAEAPHIV 153

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I   + G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRE
Sbjct: 60  FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRE 119
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K       YM         GG  ++ + + L+   P I+
Sbjct: 120 LAQQIQKVVMALGDYMG-ASCHACIGGTNVRAEVQKLQMEAPHII 163

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 61.2 bits (147), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 1/105 (0%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I   + G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRE
Sbjct: 34  FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRE 93
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K       YM         GG  ++ + + L+   P I+
Sbjct: 94  LAQQIQKVVMALGDYMGA-SCHACIGGTNVRAEVQKLQMEAPHII 137

>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 = 59.7 bits (143), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 58  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE 117
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA QI K       YM N++     GG  + +D
Sbjct: 118 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGED 149

>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 = 59.7 bits (143), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 58  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE 117
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA QI K       YM N++     GG  + +D
Sbjct: 118 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGED 149

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 59.7 bits (143), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 57  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE 116
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA QI K       YM N++     GG  + +D
Sbjct: 117 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGED 148

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 59.7 bits (143), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 36  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE 95
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA QI K       YM N++     GG  + +D
Sbjct: 96  LAVQIQKGLLALGDYM-NVQCHACIGGTNVGED 127

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 21  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRE 80
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA Q+ K       YM N++     GG  + +D
Sbjct: 81  LAVQVQKGLLALGDYM-NVQCHACIGGTNVGED 112

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 49/93 (52%), Gaps = 1/93 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 21  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRE 80
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           LA Q+ K       YM N++     GG  + +D
Sbjct: 81  LAVQVQKGLLALGDYM-NVQSHACIGGTNVGED 112

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 1/105 (0%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   ++ Q   I   + G D++ QA+SG G TA F ++ LQQ+E        LV+  TRE
Sbjct: 35  FEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQIELDLXATQALVLAPTRE 94
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI         YM         GG  ++ + + L+   P I+
Sbjct: 95  LAQQIQXVVMALGDYMGA-SCHACIGGTNVRAEVQXLQMEAPHII 138

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 53.5 bits (127), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 6/96 (6%)
Query: 38  TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTREL 94
           T  Q   +P A+ G D++ QA++G GKT  F L   ++L  +         LV+  TREL
Sbjct: 25  TPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTREL 84
Query: 95  AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL 130
           A Q++ E    +    ++KV   +GG    K +E L
Sbjct: 85  ALQVASE---LTAVAPHLKVVAVYGGTGYGKQKEAL 117

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 53.1 bits (126), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 33/100 (33%), Positives = 52/100 (52%), Gaps = 6/100 (6%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQL-----ETTDSNVYVLVM 88
           ++  T  Q   IP    G D++  A++G GKTA F+L  L +L     E       V+++
Sbjct: 76  YKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIV 135
Query: 89  CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE 128
             TRELA QI  E  +F+ + S +K+G+ +GG   +   E
Sbjct: 136 SPTRELAIQIFNEARKFA-FESYLKIGIVYGGTSFRHQNE 174

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 79/156 (50%), Gaps = 15/156 (9%)
Query: 31  SQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC 89
           ++ F + T  Q + IP  +    +I+ QA++G GKTA F +  L +L   ++ +  +++ 
Sbjct: 23  NKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIP-LIELVNENNGIEAIILT 81
Query: 90  HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN-----P-QIVGLVNY 143
            TRELA Q++ E E   K   N+K+   +GG  I    + LK  N     P +I+  +N 
Sbjct: 82  PTRELAIQVADEIESL-KGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINR 140
Query: 144 ET-NLSGVVVNVMD----VRSGGWWLDLEALILSKC 174
            T NL  V   ++D      + G+  D+E  IL+ C
Sbjct: 141 GTLNLKNVKYFILDEADEXLNXGFIKDVEK-ILNAC 175

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 48/96 (50%), Gaps = 6/96 (6%)
Query: 38  TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTREL 94
           T  +   +P A+ G D++ QA++G GKT  F L   ++L  +         LV+  TREL
Sbjct: 25  TPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTREL 84
Query: 95  AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL 130
           A Q++ E    +    ++KV   +GG    K +E L
Sbjct: 85  ALQVASE---LTAVAPHLKVVAVYGGTGYGKQKEAL 117

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 47/89 (52%), Gaps = 7/89 (7%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F+  T  Q + IP  + G +++ +AK+G GKTA + +  L+        +  LV+  TRE
Sbjct: 14  FKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRE 67
Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLP 122
           L  Q++       +YM + KV   +GG+P
Sbjct: 68  LTRQVASHIRDIGRYM-DTKVAEVYGGMP 95

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 2/89 (2%)
Query: 34  FREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P   A    +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 171
Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGG 120
            ELA Q  K  E+  K+   +K+     G
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRG 200

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 2/89 (2%)
Query: 34  FREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P   A    +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 45  FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 104
Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGG 120
            ELA Q  K  E+  K+   +K+     G
Sbjct: 105 YELALQTGKVIEQMGKFYPELKLAYAVRG 133

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 46/94 (48%), Gaps = 2/94 (2%)
Query: 34  FREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P   A    +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 171
Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQK 125
            ELA Q  K  E+  K+   +K+     G  +++
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 205

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 48/97 (49%), Gaps = 2/97 (2%)
Query: 34  FREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P   A    +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 82  FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 141
Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE 128
            ELA Q  K  E+  K+   +K+     G  +++ ++
Sbjct: 142 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 178

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 50.1 bits (118), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 48/97 (49%), Gaps = 2/97 (2%)
Query: 34  FREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P   A    +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 61  FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 120
Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE 128
            ELA Q  K  E+  K+   +K+     G  +++ ++
Sbjct: 121 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 157

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 49.7 bits (117), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 48/97 (49%), Gaps = 2/97 (2%)
Query: 34  FREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P   A    +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 45  FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 104
Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE 128
            ELA Q  K  E+  K+   +K+     G  +++ ++
Sbjct: 105 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK 141

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 53/105 (50%), Gaps = 5/105 (4%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE----TTDSNVYVLVMC 89
           +R  T  Q + I  A+ G D+L  AK+G GKT  F++  L+ L     T+   + VL++ 
Sbjct: 45  YRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIIS 104
Query: 90  HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN 134
            TRELA+Q  +   +  K   +   G+  GG  ++ + E +   N
Sbjct: 105 PTRELAYQTFEVLRKVGKN-HDFSAGLIIGGKDLKHEAERINNIN 148

>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 = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/96 (31%), Positives = 47/96 (48%), Gaps = 10/96 (10%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---------VY 84
           ++  T  Q   IP  +   DI+  A++G GKTA F++  +  L   D N           
Sbjct: 43  YQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK 102
Query: 85  VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGG 120
            L++  TRELA QI  E ++FS   + ++  V +GG
Sbjct: 103 CLILAPTRELAIQILSESQKFS-LNTPLRSCVVYGG 137

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 52/108 (48%), Gaps = 4/108 (3%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + T  Q   IP A+ G   + Q+++G GKT  ++L   ++++   + V  ++   TRE
Sbjct: 24  FYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQAVITAPTRE 83
Query: 94  LAFQISKEYERFSKYMSNIKVGV---FFGGLPIQKDEEYLKTHNPQIV 138
           LA QI  E  + +K+    +  V     GG   QK  E L    P IV
Sbjct: 84  LATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNV-QPHIV 130

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTR 92
           F+  T  Q + IP  + G ++L  A +G GKT  F +  L QL +  +     L++  TR
Sbjct: 49  FQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTR 108
Query: 93  ELAFQISKEYERFSK 107
           ELA QI +E  + S+
Sbjct: 109 ELASQIHRELIKISE 123

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 48/108 (44%), Gaps = 19/108 (17%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYV-------- 85
           +   T  Q   IP      D++  A++G GKTA F+L  L Q+ +      +        
Sbjct: 35  YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94
Query: 86  ----------LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
                     LV+  TRELA QI +E  +FS Y S ++  V +GG  I
Sbjct: 95  YGRRKQYPISLVLAPTRELAVQIYEEARKFS-YRSRVRPCVVYGGADI 141

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 49/97 (50%), Gaps = 8/97 (8%)
Query: 32  QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQ------LETTDSNVYV 85
           Q F E T+ Q +  P A+ G+D++  A++G GKT  ++L  +        LE  D  +  
Sbjct: 47  QNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI-C 105
Query: 86  LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP 122
           LV+  TRELA Q+ +    + +    +K    +GG P
Sbjct: 106 LVLAPTRELAQQVQQVAAEYCR-ACRLKSTCIYGGAP 141

>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 = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 49/97 (50%), Gaps = 8/97 (8%)
Query: 32  QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQ------LETTDSNVYV 85
           Q F E T+ Q +  P A+ G+D++  A++G GKT  ++L  +        LE  D  +  
Sbjct: 61  QNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI-C 119
Query: 86  LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP 122
           LV+  TRELA Q+ +    + +    +K    +GG P
Sbjct: 120 LVLAPTRELAQQVQQVAAEYCR-ACRLKSTCIYGGAP 155

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQ---QLETTDSN-VYVLVMC 89
           F   T  QH+ I   + G D+L  AK+G GKT  F++  ++   +L     N   VL++ 
Sbjct: 74  FTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILS 133
Query: 90  HTRELAFQ 97
            TRELA Q
Sbjct: 134 PTRELAMQ 141

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 34  FREQTSFQHECIPQAV--LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F++ +  Q   +P  +     +++ Q++SG GKTA F L  L ++   D++   + +  +
Sbjct: 42  FQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS 101
Query: 92  RELAFQ---ISKEYERFSKYMSNIKVGVFF 118
           RELA Q   + +E  +F+K  S + V   F
Sbjct: 102 RELARQTLEVVQEMGKFTKITSQLIVPDSF 131

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 34  FREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F++ +  Q   +P  +     +++ Q++SG GKTA F L  L ++   D++   + +  +
Sbjct: 25  FQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS 84
Query: 92  RELAFQ---ISKEYERFSKYMSNIKVGVFF 118
           RELA Q   + +E  +F+K  S + V   F
Sbjct: 85  RELARQTLEVVQEMGKFTKITSQLIVPDSF 114

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 34  FREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F++ +  Q   +P  +     +++ Q++SG GKTA F L  L ++   D++   + +  +
Sbjct: 25  FQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS 84
Query: 92  RELAFQ---ISKEYERFSKYMSNIKVGVFF 118
           RELA Q   + +E  +F+K  S + V   F
Sbjct: 85  RELARQTLEVVQEMGKFTKITSQLIVPDSF 114

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	175
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	3e-53
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-50
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	3e-42
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	7e-40
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-31
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-30
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	3e-30
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	2e-29
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-29
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-28
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	4e-27
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-25
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	2e-24
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-24
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-24
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-22
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	4e-22
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-21
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-21
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-21
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	4e-21
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-20
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-19
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-19
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	6e-19
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-18
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-15
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	9e-15
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	3e-14
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	6e-14
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	3e-05
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-04
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-04
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	3e-04

>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 =  167 bits (426), Expect = 3e-53
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 34  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 93

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 94  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 138

>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 =  166 bits (422), Expect = 1e-50
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 28  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 87

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 88  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 132

>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 =  140 bits (354), Expect = 3e-42
 Identities = 35/105 (33%), Positives = 51/105 (48%), Gaps = 2/105 (1%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  Q + IP    G+D++ QAKSG GKT VF    L  L   + +  +L++  TRE
Sbjct: 44  FERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTRE 103

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           +A QI          M  ++  VF GG P+ +D+  LK     I 
Sbjct: 104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KCHIA 146

>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 =  138 bits (349), Expect = 7e-40
 Identities = 38/105 (36%), Positives = 56/105 (53%), Gaps = 2/105 (1%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + +  Q E IP A+ G DIL +AK+G GKTA FV+ TL++++   + +  L+M  TRE
Sbjct: 41  FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE 100

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA Q S+      K+   I   V  GG  ++ D   L      I+
Sbjct: 101 LALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLN-ETVHIL 143

>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 =  112 bits (282), Expect = 2e-31
 Identities = 37/105 (35%), Positives = 52/105 (49%), Gaps = 1/105 (0%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I   + G D++ QA+SG GKTA F ++ LQQLE        LV+  TRE
Sbjct: 50  FEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRE 109

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K       YM         GG  ++ + + L+   P IV
Sbjct: 110 LAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIV 153

>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 =  113 bits (286), Expect = 1e-30
 Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 1/105 (0%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I   + G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRE
Sbjct: 60  FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRE 119

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K       YM         GG  ++ + + L+   P I+
Sbjct: 120 LAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHII 163

>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 =  108 bits (272), Expect = 3e-30
 Identities = 35/105 (33%), Positives = 58/105 (55%), Gaps = 1/105 (0%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           + + +  Q E IP A+ G DIL +AK+G GK+  +++  L++L+    N+  +V+  TRE
Sbjct: 23  WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE 82

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA Q+S+   + SK+M   KV    GG  ++ D   L      +V
Sbjct: 83  LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-DTVHVV 126

>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 =  106 bits (268), Expect = 2e-29
 Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F E ++ Q   I   + G D+L QA+SG GKT  F +A LQ+++T+      L++  TRE
Sbjct: 34  FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 93

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K     + +M +IKV    GG    +D E L+  + QIV
Sbjct: 94  LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 135

>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 =  109 bits (276), Expect = 3e-29
 Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 3/105 (2%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F E ++ Q   I   + G D+L QA+SG GKT  F +A LQ+++T+      L++  TRE
Sbjct: 41  FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE 100

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K     + +M +IKV    GG    +D E L+  + QIV
Sbjct: 101 LALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIV 142

>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 =  108 bits (271), Expect = 2e-28
 Identities = 34/105 (32%), Positives = 53/105 (50%), Gaps = 2/105 (1%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + ++ Q   I Q + G D++ Q++SG GKTA F ++ LQ L+        L++  TRE
Sbjct: 57  FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE 116

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI K       YM N++     GG  + +D   L  +   +V
Sbjct: 117 LAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLD-YGQHVV 159

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  100 bits (252), Expect = 4e-27
 Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 4/108 (3%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F + T  Q   IP A+ G  ++ Q+++G GKT  ++L  +++++   + V  ++   TRE
Sbjct: 24  FYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE 83

Query: 94  LAFQISKEYERFSKYMSN---IKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LA QI  E  + +K+      I      GG   QK  E L    P IV
Sbjct: 84  LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN-VQPHIV 130

>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 = 99.0 bits (247), Expect = 1e-25
 Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 6/107 (5%)

Query: 34  FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P  +     +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 171

Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
            ELA Q  K  E+  K+   +K+     G  +++ ++     + QIV
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK----ISEQIV 214

>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 = 97.2 bits (243), Expect = 2e-24
 Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 6/107 (5%)

Query: 34  FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P  +     +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 45  FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 104

Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
            ELA Q  K  E+  K+   +K+     G  +++ ++     + QIV
Sbjct: 105 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK----ISEQIV 147

>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 = 97.4 bits (243), Expect = 2e-24
 Identities = 31/107 (28%), Positives = 52/107 (48%), Gaps = 6/107 (5%)

Query: 34  FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F   +  Q   +P  +     +++ Q++SG GKTA FVLA L Q+E  +     L +  T
Sbjct: 112 FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPT 171

Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
            ELA Q  K  E+  K+   +K+     G  +++ ++     + QIV
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQK----ISEQIV 214

>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 = 93.9 bits (234), Expect = 3e-24
 Identities = 37/109 (33%), Positives = 55/109 (50%), Gaps = 2/109 (1%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC 89
           +   + + T  Q E IP A+ G DI+  A++G GKT  F L  L  L  T   ++ LV+ 
Sbjct: 59  DQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLT 118

Query: 90  HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
            TRELAFQIS+++E     +  ++  V  GG+        L    P I+
Sbjct: 119 PTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKK-PHII 165

>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 = 88.1 bits (219), Expect = 4e-22
 Identities = 33/109 (30%), Positives = 54/109 (49%), Gaps = 7/109 (6%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE----TTDSNVYVLVMC 89
           +R  T  Q + I  A+ G D+L  AK+G GKT  F++  L+ L     T+   + VL++ 
Sbjct: 45  YRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIIS 104

Query: 90  HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
            TRELA+Q  +   +  K       G+  GG  ++ + E +   N  I+
Sbjct: 105 PTRELAYQTFEVLRKVGKNHD-FSAGLIIGGKDLKHEAERIN--NINIL 150

>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 = 86.1 bits (214), Expect = 1e-21
 Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 7/108 (6%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---VYVLVMCH 90
               T  Q   +P A+ G D++ QA++G GKT  F L   ++L  +         LV+  
Sbjct: 21  LTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTP 80

Query: 91  TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           TRELA Q++ E    + ++   KV   +GG    K +E L       V
Sbjct: 81  TRELALQVASELTAVAPHL---KVVAVYGGTGYGKQKEALL-RGADAV 124

>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 = 88.7 bits (220), Expect = 3e-21
 Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 9/114 (7%)

Query: 34  FREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLV 87
           F   T  Q + I   +     D++ +AK+G GKT  F++   Q L  T       V  ++
Sbjct: 41  FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVI 100

Query: 88  MCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           +  TR+LA QI  E ++       +         GG   +     +    P IV
Sbjct: 101 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 154

>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 = 88.7 bits (220), Expect = 3e-21
 Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 9/114 (7%)

Query: 34  FREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLV 87
           F   T  Q + I   +     D++ +AK+G GKT  F++   Q L  T       V  ++
Sbjct: 92  FPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVI 151

Query: 88  MCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           +  TR+LA QI  E ++       +         GG   +     +    P IV
Sbjct: 152 VAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 205

>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 = 87.6 bits (218), Expect = 4e-21
 Identities = 23/107 (21%), Positives = 46/107 (42%), Gaps = 8/107 (7%)

Query: 34  FREQTSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT 91
           F++ +  Q   +P  +     +++ Q++SG GKTA F L  L ++   D++   + +  +
Sbjct: 25  FQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPS 84

Query: 92  RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           RELA Q  +  +   K+       +        K        N Q++
Sbjct: 85  RELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQ------INAQVI 125

>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 = 84.9 bits (211), Expect = 2e-20
 Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 9/105 (8%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F+  T  Q + IP  + G +++ +AK+G GKTA + +  L+        +  LV+  TRE
Sbjct: 14  FKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRE 67

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           L  Q++       +YM + KV   +GG+P +     ++  N  IV
Sbjct: 68  LTRQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVR--NADIV 109

>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 = 83.3 bits (207), Expect = 1e-19
 Identities = 32/106 (30%), Positives = 55/106 (51%), Gaps = 5/106 (4%)

Query: 34  FREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR 92
           F + T  Q + IP  +    +I+ QA++G GKTA F +  ++ +   ++ +  +++  TR
Sbjct: 26  FEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-NNGIEAIILTPTR 84

Query: 93  ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           ELA Q++ E E       N+K+   +GG  I    + LK  N  IV
Sbjct: 85  ELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK--NANIV 127

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score = 80.8 bits (200), Expect = 3e-19
 Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 6/113 (5%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN----VYV 85
           +   F   T  QH+ I   + G D+L  AK+G GKT  F++  ++ +            V
Sbjct: 70  KEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGV 129

Query: 86  LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           L++  TRELA Q     +    +      G+  GG     + + L  +   I+
Sbjct: 130 LILSPTRELAMQTFGVLKELMTHHV-HTYGLIMGGSNRSAEAQKLG-NGINII 180

>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 = 79.9 bits (198), Expect = 6e-19
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 2/94 (2%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN-VYVLVMCHTR 92
           F+  T  Q + IP  + G ++L  A +G GKT  F +  L QL+   +     L++  TR
Sbjct: 49  FQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTR 108

Query: 93  ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD 126
           ELA QI +E  + S+  +  ++ +        K 
Sbjct: 109 ELASQIHRELIKISEG-TGFRIHMIHKAAVAAKK 141

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 80.5 bits (199), Expect = 2e-18
 Identities = 17/98 (17%), Positives = 39/98 (39%), Gaps = 5/98 (5%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
            ++ T +Q     + V G      A +G+GKT   ++  L             ++  T  
Sbjct: 19  GKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVT 75

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
           L  Q  +  ++ +     +K+  F+  +  ++ E++ K
Sbjct: 76  LVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEK 111

>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 = 71.0 bits (175), Expect = 1e-15
 Identities = 31/138 (22%), Positives = 56/138 (40%), Gaps = 18/138 (13%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE------TTDSNVYVLV 87
             + T  Q +  P  + G+D++  A++G GKT  +++     L+         +   +LV
Sbjct: 40  ILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLV 99

Query: 88  MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV----G---- 139
           +  TRELA  +  E  ++S     +K    +GG       E +      I+    G    
Sbjct: 100 LTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDIS-KGVDIIIATPGRLND 156

Query: 140 -LVNYETNLSGVVVNVMD 156
             +N   NL  +   V+D
Sbjct: 157 LQMNNSVNLRSITYLVID 174

>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 = 68.7 bits (169), Expect = 9e-15
 Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 10/99 (10%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV---------Y 84
           ++  T  Q   IP  +   DI+  A++G GKTA F++  +  L   D N           
Sbjct: 43  YQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK 102

Query: 85  VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
            L++  TRELA QI  E ++FS   + ++  V +GG   
Sbjct: 103 CLILAPTRELAIQILSESQKFSLN-TPLRSCVVYGGADT 140

>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 = 67.2 bits (165), Expect = 3e-14
 Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 6/99 (6%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----Y 84
             Q F E T+ Q +  P A+ G+D++  A++G GKT  ++L  +  +             
Sbjct: 45  ARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI 104

Query: 85  VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
            LV+  TRELA Q+ +    +      +K    +GG P 
Sbjct: 105 CLVLAPTRELAQQVQQVAAEYC-RACRLKSTCIYGGAPK 142

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score = 67.6 bits (166), Expect = 6e-14
 Identities = 31/95 (32%), Positives = 50/95 (52%), Gaps = 6/95 (6%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----YVLVM 88
           ++  T  Q   IP    G D++  A++G GKTA F+L  L +L      +      V+++
Sbjct: 76  YKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIV 135

Query: 89  CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
             TRELA QI  E  +F+ + S +K+G+ +GG   
Sbjct: 136 SPTRELAIQIFNEARKFA-FESYLKIGIVYGGTSF 169

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 61.4 bits (150), Expect = 7e-12
 Identities = 33/108 (30%), Positives = 46/108 (42%), Gaps = 19/108 (17%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVL---------ATLQQLETTDSNV- 83
           +   T  Q   IP      D++  A++G GKTA F+L            + L     N  
Sbjct: 35  YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94

Query: 84  --------YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI 123
                     LV+  TRELA QI +E  +FS Y S ++  V +GG  I
Sbjct: 95  YGRRKQYPISLVLAPTRELAVQIYEEARKFS-YRSRVRPCVVYGGADI 141

>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 = 47.2 bits (111), Expect = 8e-07
 Identities = 37/191 (19%), Positives = 67/191 (35%), Gaps = 57/191 (29%)

Query: 10  GVTVKVLSSRNRREKEDRIGESQPF------REQTSFQ-HECIPQ-------AVLGMDIL 55
            +T   +  R+R        ++Q F      R Q   +  + + +        + G+   
Sbjct: 107 MMTRMYIEQRDRLY-----NDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGV--- 158

Query: 56  CQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVM--CHTRE--------LAFQISKEY 102
                G GKT    L      +     D  ++ L +  C++ E        L +QI   +
Sbjct: 159 ----LGSGKT-WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW 213

Query: 103 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGW 162
              S + SNIK       L I   +  L+     ++    YE  L  +V+   +V++   
Sbjct: 214 TSRSDHSSNIK-------LRIHSIQAELRR----LLKSKPYENCL--LVLL--NVQNAKA 258

Query: 163 W--LDLEALIL 171
           W   +L   IL
Sbjct: 259 WNAFNLSCKIL 269

>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 = 42.5 bits (100), Expect = 3e-05
 Identities = 17/91 (18%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC 89
           + +   E    Q E + +   G ++L    +  GKT +  +A +++      ++YV+ + 
Sbjct: 19  KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPL- 77

Query: 90  HTRELAFQISKEYERFSKYMSNIKVGVFFGG 120
             R LA +  + ++++ K    +++G+  G 
Sbjct: 78  --RALAGEKYESFKKWEKI--GLRIGISTGD 104

>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 = 39.4 bits (92), Expect = 2e-04
 Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 12/110 (10%)

Query: 39  SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY---VLVMCHTRELA 95
            +Q E    A+ G +I+    +G GKT V V      L+          V+V+ +   L 
Sbjct: 36  PYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLV 95

Query: 96  FQ-ISKEYERFSKYMSNIKVGVFFGGLPIQKD-EEYLKTHN-----PQIV 138
            Q   KE++ F K     +V    G   ++    E +K+ +      QI+
Sbjct: 96  EQLFRKEFQPFLKKW--YRVIGLSGDTQLKISFPEVVKSCDIIISTAQIL 143

>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 = 39.8 bits (92), Expect = 2e-04
 Identities = 18/108 (16%), Positives = 38/108 (35%), Gaps = 9/108 (8%)

Query: 36  EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA 95
           +   +Q   I       + L    +G+GKT + ++    +L        VL++  T+ L 
Sbjct: 9   QPRIYQEV-IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGK--VLMLAPTKPLV 65

Query: 96  FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-----NPQIV 138
            Q ++ + R        K+    G    ++  +           PQ +
Sbjct: 66  LQHAESFRRLFNL-PPEKIVALTGEKSPEERSKAWARAKVIVATPQTI 112

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 39.1 bits (90), Expect = 3e-04
 Identities = 19/108 (17%), Positives = 41/108 (37%), Gaps = 9/108 (8%)

Query: 39  SFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY--VLVMCHTRELAF 96
           ++Q E    A  G + +  A +G GKT V +L     L+         V+   +   +  
Sbjct: 7   NYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYE 66

Query: 97  QISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYLKTHN-----PQIV 138
           Q +  + R+ + +    +    G        +  ++ ++     PQI+
Sbjct: 67  QQATVFSRYFERLG-YNIASISGATSDSVSVQHIIEDNDIIILTPQIL 113

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	175
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	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
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.98
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.97
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.97
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.97
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.97
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.97
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.97
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.97
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.96
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.96
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.96
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.96
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.95
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.95
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.95
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.95
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.95
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.95
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.94
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.93
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.9
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.9
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.9
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.9
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.89
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.89
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.89
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.89
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.89
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.88
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.88
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.87
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.87
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.87
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.85
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.85
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.85
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.84
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.84
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.83
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.82
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.82
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.81
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.81
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.81
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.8
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.78
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.78
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.76
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.73
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.73
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.71
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.7
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.67
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.67
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.67
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.6
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.58
3h1t_A	590	Type I site-specific restriction-modification syst	99.57
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.56
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.56
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.55
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.55
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.53
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.41
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.38
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.26
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.26
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.19
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.17
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.15
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.55
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.47
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.41
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.39
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.31
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.19
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.75
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.61
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.6
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.46
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.39
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.02
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.82
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.8
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.72
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	96.39
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	96.31
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	96.22
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.19
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	95.99
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	95.94
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	95.88
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	95.79
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	95.57
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	95.4
2chg_A	226	Replication factor C small subunit; DNA-binding pr	95.37
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.28
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	95.21
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	95.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.67
3co5_A	143	Putative two-component system transcriptional RES	94.63
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.56
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.5
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	94.49
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.44
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	94.31
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	94.22
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	94.09
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.05
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	93.91
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	93.87
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	93.73
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	93.67
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	93.63
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	93.61
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	93.6
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	93.47
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	93.44
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.42
1p9r_A	418	General secretion pathway protein E; bacterial typ	93.36
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	93.35
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	93.2
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	93.07
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	93.05
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.03
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	92.88
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	92.87
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	92.84
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.77
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.74
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	92.6
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	92.58
2qgz_A	308	Helicase loader, putative primosome component; str	92.57
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	92.39
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	91.51
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.24
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	92.14
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	92.1
3io5_A	333	Recombination and repair protein; storage dimer, i	92.01
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	91.99
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	91.98
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	91.72
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	91.72
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	91.6
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	91.48
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	91.4
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	91.39
3bos_A	242	Putative DNA replication factor; P-loop containing	91.26
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	91.07
2r44_A	331	Uncharacterized protein; putative ATPase, structur	91.0
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	90.98
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	90.96
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	90.91
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	90.89
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	90.87
1tue_A	212	Replication protein E1; helicase, replication, E1E	90.85
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	90.77
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	90.69
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	90.63
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	90.56
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	90.52
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	90.47
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	90.46
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	90.44
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	90.42
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	90.42
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	90.38
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	90.34
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	90.24
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	90.21
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	90.19
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	90.04
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	90.01
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	89.89
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	89.75
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	89.75
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	89.71
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	89.68
3h1t_A	590	Type I site-specific restriction-modification syst	89.63
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	89.51
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	89.46
1yks_A	440	Genome polyprotein [contains: flavivirin protease	89.42
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	89.36
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.26
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	89.2
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	89.2
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	89.17
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	89.04
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	88.99
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	88.98
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	88.96
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	88.95
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	88.95
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	88.88
2ewv_A	372	Twitching motility protein PILT; pilus retraction	88.85
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	88.85
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	88.72
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	88.71
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	88.71
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	88.7
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	88.69
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	88.68
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.65
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	88.63
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.54
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	88.5
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	88.49
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	88.43
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	88.35
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.32
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	88.27
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	88.24
2z43_A	324	DNA repair and recombination protein RADA; archaea	88.18
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	88.18
2cvh_A	220	DNA repair and recombination protein RADB; filamen	88.17
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	88.05
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	88.05
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	87.8
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	87.74
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	87.72
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	87.7
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	87.64
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	87.61
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	87.61
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	87.6
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	87.59
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	87.57
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	87.53
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	87.4
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	87.35
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	87.33
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	87.29
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	87.13
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	87.05
2chq_A	319	Replication factor C small subunit; DNA-binding pr	86.99
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	86.96
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	86.91
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	86.91
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	86.76
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	86.76
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	86.74
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	86.71
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	86.67
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	86.67
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	86.56
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	86.5
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	86.48
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	86.43
4gl2_A	699	Interferon-induced helicase C domain-containing P;	86.39
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	86.35
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	86.31
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	86.26
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	86.16
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	86.13
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	86.1
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	86.05
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	85.96
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	85.95
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	85.93
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	85.9
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	85.9
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	85.89
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	85.83
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	85.83
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	85.82
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	85.79
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	85.74
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	85.73
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	85.7
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	85.67
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	85.66
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	85.6
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	85.58
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	85.56
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	85.55
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	85.53
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	85.53
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	85.5
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	85.49
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	85.48
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	85.48
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	85.47
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	85.46
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	85.4
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	85.36
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	85.32
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	85.26
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	85.17
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	85.08
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	85.03
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	84.97
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	84.96
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	84.81
1via_A	175	Shikimate kinase; structural genomics, transferase	84.72
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	84.72
3u06_A	412	Protein claret segregational; motor domain, stalk	84.62
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	84.54
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	84.53
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	84.51
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	84.51
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	84.4
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	84.39
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	84.36
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	84.32
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	84.32
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	84.31
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	84.29
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	84.27
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	84.23
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	84.21
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	84.15
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	84.14
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	84.12
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	84.1
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	83.99
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	83.95
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	83.91
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	83.84
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	83.81
1u94_A	356	RECA protein, recombinase A; homologous recombinat	83.74
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	83.66
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	83.61
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	83.54
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	83.52
2r6a_A	454	DNAB helicase, replicative helicase; replication,	83.51
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	83.5
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	83.48
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	83.46
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	83.46
3kta_A	182	Chromosome segregation protein SMC; structural mai	83.4
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	83.31
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	83.31
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	83.3
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	83.27
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	83.26
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	83.2
1sgw_A	214	Putative ABC transporter; structural genomics, P p	83.15
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	83.15
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	83.08
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	83.02
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	82.97
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	82.91
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	82.82
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	82.78
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	82.73
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	82.69
3pvs_A	447	Replication-associated recombination protein A; ma	82.65
4a74_A	231	DNA repair and recombination protein RADA; hydrola	82.64
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	82.64
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	82.59
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	82.57
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	82.35
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	82.32
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	82.31
2ghi_A	260	Transport protein; multidrug resistance protein, M	82.16
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	82.15
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	82.14
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	82.12
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	82.1
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	82.07
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	82.04
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	82.03
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	81.96
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	81.91
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	81.86
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	81.61
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	81.59
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	81.58
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	81.54
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	81.35
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	81.33
1b0u_A	262	Histidine permease; ABC transporter, transport pro	81.22
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	81.21
1xp8_A	366	RECA protein, recombinase A; recombination, radior	81.18
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	81.14
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	81.13
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	81.12
1g6h_A	257	High-affinity branched-chain amino acid transport	81.11
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	81.11
1ji0_A	240	ABC transporter; ATP binding protein, structural g	81.09
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	81.08
2vli_A	183	Antibiotic resistance protein; transferase, tunica	81.07
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	81.05
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	81.02
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	80.99
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	80.98
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	80.97
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	80.92
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	80.88
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	80.86
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	80.84
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	80.82
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	80.73
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	80.69
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	80.52
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	80.51
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	80.38
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	80.38
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	80.3
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	80.28
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	80.11
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	80.05
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	80.04
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	80.02

>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=1e-33  Score=215.68  Aligned_cols=166  Identities=22%  Similarity=0.273  Sum_probs=148.9

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----C
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----D   80 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~   80 (175)
                      +...+.+...|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|++.++...     .
T Consensus        21 ~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~  100 (242)
T 3fe2_A           21 GHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERG  100 (242)
T ss_dssp             SSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTT
T ss_pred             CCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccC
Confidence            34457788999999999999999999999999999999999999999999999999999999999999988642     3


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVV  152 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~  152 (175)
                      .+++++|++||++|+.|+.+.++++.... ++++..++||.+...+.+.+.++++++|++.        +....++++++
T Consensus       101 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~  179 (242)
T 3fe2_A          101 DGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTY  179 (242)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCE
T ss_pred             CCCEEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccE
Confidence            57789999999999999999999999887 8999999999998888888999999999922        22567899999


Q ss_pred             EEEeCCC----CCCHHHHHHHHhh
Q psy1539         153 NVMDVRS----GGWWLDLEALILS  172 (175)
Q Consensus       153 lVlDEad----~~f~~~v~~il~~  172 (175)
                      +|+||||    .+|..+++.|+..
T Consensus       180 lViDEah~l~~~~~~~~~~~i~~~  203 (242)
T 3fe2_A          180 LVLDEADRMLDMGFEPQIRKIVDQ  203 (242)
T ss_dssp             EEETTHHHHHHTTCHHHHHHHHTT
T ss_pred             EEEeCHHHHhhhCcHHHHHHHHHh
Confidence            9999994    6899999998764

>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=5e-33  Score=228.23  Aligned_cols=162  Identities=23%  Similarity=0.322  Sum_probs=145.9

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-----CCCeE
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVY   84 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~   84 (175)
                      +.+..+|++++|++.+++++.+.||..|||+|+++||.+++|+|+++++|||||||++|++|++.++...     ..+++
T Consensus        52 p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~  131 (434)
T 2db3_A           52 PQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQ  131 (434)
T ss_dssp             CCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCS
T ss_pred             CCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCcc
Confidence            4567889999999999999999999999999999999999999999999999999999999999988643     24679


Q ss_pred             EEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEe
Q psy1539          85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMD  156 (175)
Q Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlD  156 (175)
                      +||++|||+|+.|+++.++++.... ++++..++||.+...+.+.+.++++++|++        .+....+++++++|+|
T Consensus       132 ~lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlD  210 (434)
T 2db3_A          132 VVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLD  210 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEE
T ss_pred             EEEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEc
Confidence            9999999999999999999998876 889999999999888888898999999992        2225678999999999


Q ss_pred             CC----CCCCHHHHHHHHhh
Q psy1539         157 VR----SGGWWLDLEALILS  172 (175)
Q Consensus       157 Ea----d~~f~~~v~~il~~  172 (175)
                      ||    +++|.++++.|+..
T Consensus       211 Eah~~~~~gf~~~~~~i~~~  230 (434)
T 2db3_A          211 EADRMLDMGFSEDMRRIMTH  230 (434)
T ss_dssp             THHHHTSTTTHHHHHHHHHC
T ss_pred             cHhhhhccCcHHHHHHHHHh
Confidence            99    67899999999864

>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=2e-32  Score=203.18  Aligned_cols=158  Identities=25%  Similarity=0.314  Sum_probs=141.8

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .+|+++++++++++++.+.||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..+.....+++++|++||++
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            46999999999999999999999999999999999999999999999999999999999998876667789999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCC----CC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRS----GG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad----~~  161 (175)
                      |+.|+.+.++++....+++++..++|+.+..++...+.++++++|++        .+....+++++++|+||||    .+
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            99999999999988776889999999998888888888888999982        2224578899999999994    68


Q ss_pred             CHHHHHHHHh
Q psy1539         162 WWLDLEALIL  171 (175)
Q Consensus       162 f~~~v~~il~  171 (175)
                      |..+++.++.
T Consensus       163 ~~~~l~~i~~  172 (206)
T 1vec_A          163 FVQIMEDIIL  172 (206)
T ss_dssp             THHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            9999988875

>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=2.5e-32  Score=206.52  Aligned_cols=164  Identities=25%  Similarity=0.294  Sum_probs=138.8

Q ss_pred             cccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEE
Q psy1539           8 FHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLV   87 (175)
Q Consensus         8 ~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~li   87 (175)
                      ..+.+...|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+.....+.+++|
T Consensus        18 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~li   97 (230)
T 2oxc_A           18 VLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILI   97 (230)
T ss_dssp             ------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEE
T ss_pred             CCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEE
Confidence            33456678999999999999999999999999999999999999999999999999999999999999876566789999


Q ss_pred             EecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC
Q psy1539          88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS  159 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad  159 (175)
                      ++||++|+.|+.+.++++....+++++..++||.+..++.+.+. +++++|++.        .....+++++++|+||||
T Consensus        98 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah  176 (230)
T 2oxc_A           98 LAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEAD  176 (230)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT-SCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHH
T ss_pred             EeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc-CCCEEEECHHHHHHHHhcCCcccccCCEEEeCCch
Confidence            99999999999999999987766889999999988766666554 689999822        224567889999999993


Q ss_pred             ----CC-CHHHHHHHHhh
Q psy1539         160 ----GG-WWLDLEALILS  172 (175)
Q Consensus       160 ----~~-f~~~v~~il~~  172 (175)
                          .+ |.++++.|+..
T Consensus       177 ~~~~~~~~~~~~~~i~~~  194 (230)
T 2oxc_A          177 KLLEEGSFQEQINWIYSS  194 (230)
T ss_dssp             HHHSTTSSHHHHHHHHHH
T ss_pred             HhhcCcchHHHHHHHHHh
Confidence                55 99999988753

>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=2.2e-32  Score=206.21  Aligned_cols=164  Identities=19%  Similarity=0.257  Sum_probs=137.3

Q ss_pred             Cccccccccccc-CCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC------
Q psy1539           7 MFHGVTVKVLSS-RNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT------   79 (175)
Q Consensus         7 ~~~~~~~~~~~~-~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~------   79 (175)
                      ...+.+...|++ +++++++++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|++..+...      
T Consensus        12 ~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~   91 (228)
T 3iuy_A           12 RLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQ   91 (228)
T ss_dssp             CCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC--------
T ss_pred             CcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhc
Confidence            345677888999 8999999999999999999999999999999999999999999999999999999887532      


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCce
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVV  151 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~  151 (175)
                      ..+++++|++||++|+.|+.+.++++..  .++++..++||.+...+.+.+.++++++|++        .+....+++++
T Consensus        92 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~  169 (228)
T 3iuy_A           92 RNGPGMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSIT  169 (228)
T ss_dssp             -CCCSEEEECSSHHHHHHHHHHHHHHCC--TTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCC
T ss_pred             cCCCcEEEEeCCHHHHHHHHHHHHHhcc--cCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccce
Confidence            3567899999999999999999999863  3788999999998888888888899999992        22256788999


Q ss_pred             EEEEeCC----CCCCHHHHHHHHhh
Q psy1539         152 VNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       152 ~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      ++|+|||    +.+|..+++.++..
T Consensus       170 ~lViDEah~~~~~~~~~~~~~i~~~  194 (228)
T 3iuy_A          170 YLVIDEADKMLDMEFEPQIRKILLD  194 (228)
T ss_dssp             EEEECCHHHHHHTTCHHHHHHHHHH
T ss_pred             EEEEECHHHHhccchHHHHHHHHHh
Confidence            9999999    46899999998754

>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=2.1e-32  Score=209.49  Aligned_cols=159  Identities=21%  Similarity=0.272  Sum_probs=142.1

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC---------CCC
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---------DSN   82 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---------~~~   82 (175)
                      +..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|++..+...         ..+
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            67789999999999999999999999999999999999999999999999999999999999987642         234


Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNV  154 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lV  154 (175)
                      +++||++||++|+.|+.+.++++.... ++++..++||.+...+.+.+.++++++|++        .+....+++++++|
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lV  179 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIV  179 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEE
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEE
Confidence            689999999999999999999998776 888999999998888888888889999992        22246788999999


Q ss_pred             EeCC----CCCCHHHHHHHHh
Q psy1539         155 MDVR----SGGWWLDLEALIL  171 (175)
Q Consensus       155 lDEa----d~~f~~~v~~il~  171 (175)
                      +|||    +.+|..+++.|+.
T Consensus       180 iDEah~~~~~~~~~~~~~i~~  200 (253)
T 1wrb_A          180 LDEADRMLDMGFEPQIRKIIE  200 (253)
T ss_dssp             EETHHHHHHTTCHHHHHHHHH
T ss_pred             EeCHHHHHhCchHHHHHHHHh
Confidence            9999    4689999999986

>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=4.5e-32  Score=207.75  Aligned_cols=161  Identities=27%  Similarity=0.363  Sum_probs=143.9

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .+..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.....+++++|++|
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            44677999999999999999999999999999999999999999999999999999999999999887667789999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------c-CccCCCCceEEEEeCCC--
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------N-YETNLSGVVVNVMDVRS--  159 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~-~~~~~~~~~~lVlDEad--  159 (175)
                      |++|+.|+.+.++++.... ++++..++||.+...+...+.++++++|++.        + ....+++++++|+||||  
T Consensus       120 tr~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l  198 (249)
T 3ber_A          120 TRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRI  198 (249)
T ss_dssp             SHHHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHH
T ss_pred             CHHHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhh
Confidence            9999999999999998877 8899999999988778888888899999921        1 24567899999999994  


Q ss_pred             --CCCHHHHHHHHhh
Q psy1539         160 --GGWWLDLEALILS  172 (175)
Q Consensus       160 --~~f~~~v~~il~~  172 (175)
                        .+|..+++.|+..
T Consensus       199 ~~~~~~~~l~~i~~~  213 (249)
T 3ber_A          199 LNMDFETEVDKILKV  213 (249)
T ss_dssp             HHTTCHHHHHHHHHS
T ss_pred             hccChHHHHHHHHHh
Confidence              6899999988753

>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=3.7e-32  Score=206.51  Aligned_cols=162  Identities=27%  Similarity=0.320  Sum_probs=131.9

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +.+..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.....+.+++|++
T Consensus        26 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  105 (237)
T 3bor_A           26 NEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLA  105 (237)
T ss_dssp             -CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             CCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEE
Confidence            45667899999999999999999999999999999999999999999999999999999999999987655677999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEEe--------ecCccCCCCceEEEEeCCC-
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVGL--------VNYETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~l--------~~~~~~~~~~~~lVlDEad-  159 (175)
                      ||++|+.|+.+.++++.... ++++..++|+.....+.+.+.++ ++++|++        .+....+++++++|+|||| 
T Consensus       106 Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~  184 (237)
T 3bor_A          106 PTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADE  184 (237)
T ss_dssp             SSHHHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHH
T ss_pred             CcHHHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchH
Confidence            99999999999999998776 78888899998877777777666 7889882        2224667899999999995 


Q ss_pred             ---CCCHHHHHHHHhh
Q psy1539         160 ---GGWWLDLEALILS  172 (175)
Q Consensus       160 ---~~f~~~v~~il~~  172 (175)
                         .+|..++..|+..
T Consensus       185 ~~~~~~~~~l~~i~~~  200 (237)
T 3bor_A          185 MLSRGFKDQIYEIFQK  200 (237)
T ss_dssp             HHHTTCHHHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHh
Confidence               6899999888753

>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=2.2e-32  Score=214.79  Aligned_cols=158  Identities=23%  Similarity=0.292  Sum_probs=137.8

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +..+|++++|++.+++++.++||..||++|.++||.+++|  +|+++++|||||||++|++|+++++.....++++||++
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            4678999999999999999999999999999999999997  99999999999999999999999998777788999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe-------e-c-CccCCCCceEEEEeCCC-
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL-------V-N-YETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l-------~-~-~~~~~~~~~~lVlDEad-  159 (175)
                      |||+|+.|+++.++.+....+++++...+|+.......   ..+++|+|++       + + ..+.+++++++|+|||| 
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            99999999999999998877789999999987654332   4567899992       1 2 24567899999999994 


Q ss_pred             ----CCCHHHHHHHHhh
Q psy1539         160 ----GGWWLDLEALILS  172 (175)
Q Consensus       160 ----~~f~~~v~~il~~  172 (175)
                          .+|.+++..|+..
T Consensus       247 l~~~~~~~~~~~~i~~~  263 (300)
T 3fmo_B          247 MIATQGHQDQSIRIQRM  263 (300)
T ss_dssp             HHHSTTHHHHHHHHHTT
T ss_pred             HhhccCcHHHHHHHHHh
Confidence                5888888887653

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=2.5e-32  Score=204.85  Aligned_cols=160  Identities=22%  Similarity=0.300  Sum_probs=138.5

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      ..+|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.....+.+++|++||+
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   82 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTR   82 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcH
Confidence            35799999999999999999999999999999999999999999999999999999999999987666678999999999


Q ss_pred             HHHHHHHHHHHHHHhhCC---CeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC--
Q psy1539          93 ELAFQISKEYERFSKYMS---NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS--  159 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~---~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad--  159 (175)
                      +|+.|+.+.++++....+   ++++..++|+.+...+.+.+.++++++|++.        +....+++++++|+||||  
T Consensus        83 ~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~  162 (219)
T 1q0u_A           83 ELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLM  162 (219)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHH
T ss_pred             HHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHH
Confidence            999999999999987653   5788889999877666666666788999822        224567899999999994  


Q ss_pred             --CCCHHHHHHHHhh
Q psy1539         160 --GGWWLDLEALILS  172 (175)
Q Consensus       160 --~~f~~~v~~il~~  172 (175)
                        .+|..+++.++..
T Consensus       163 ~~~~~~~~l~~i~~~  177 (219)
T 1q0u_A          163 LDMGFITDVDQIAAR  177 (219)
T ss_dssp             HHTTCHHHHHHHHHT
T ss_pred             hhhChHHHHHHHHHh
Confidence              6899999888754

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.98  E-value=1.2e-31  Score=201.04  Aligned_cols=165  Identities=52%  Similarity=0.733  Sum_probs=138.8

Q ss_pred             CcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEE
Q psy1539           7 MFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVL   86 (175)
Q Consensus         7 ~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~l   86 (175)
                      .+.+.....|+++++++++++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+....++.+++
T Consensus         7 ~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~l   86 (220)
T 1t6n_A            7 SYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVL   86 (220)
T ss_dssp             -------CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEE
T ss_pred             CcccccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEE
Confidence            34445556799999999999999999999999999999999999999999999999999999999999887655667999


Q ss_pred             EEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEEee--------cCccCCCCceEEEEeC
Q psy1539          87 VMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVGLV--------NYETNLSGVVVNVMDV  157 (175)
Q Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~l~--------~~~~~~~~~~~lVlDE  157 (175)
                      |++||++|+.|+.+.++++....+++++..++|+.+...+.+.+.++ ++++|++.        +....+++++++|+||
T Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDE  166 (220)
T 1t6n_A           87 VMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE  166 (220)
T ss_dssp             EECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEES
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcC
Confidence            99999999999999999998877789999999999877777777654 58888822        2246788999999999


Q ss_pred             CC-----CCCHHHHHHHHh
Q psy1539         158 RS-----GGWWLDLEALIL  171 (175)
Q Consensus       158 ad-----~~f~~~v~~il~  171 (175)
                      ||     .+|..++..++.
T Consensus       167 ah~~~~~~~~~~~~~~i~~  185 (220)
T 1t6n_A          167 CDKMLEQLDMRRDVQEIFR  185 (220)
T ss_dssp             HHHHHSSHHHHHHHHHHHH
T ss_pred             HHHHhcccCcHHHHHHHHH
Confidence            94     467788887764

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.97  E-value=3e-31  Score=199.30  Aligned_cols=161  Identities=27%  Similarity=0.332  Sum_probs=134.2

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +.....|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....+.+++|++
T Consensus        10 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (224)
T 1qde_A           10 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   89 (224)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             CcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEE
Confidence            45678899999999999999999999999999999999999999999999999999999999999987666778999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCC--
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRS--  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad--  159 (175)
                      ||++|+.|+.+.++++.... ++++..++|+.+..++.+.+.+ ++++|++        .+....+++++++|+||||  
T Consensus        90 Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~  167 (224)
T 1qde_A           90 PTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM  167 (224)
T ss_dssp             SSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHH
Confidence            99999999999999998776 8899999999887666666654 7899982        2235667899999999994  


Q ss_pred             --CCCHHHHHHHHhh
Q psy1539         160 --GGWWLDLEALILS  172 (175)
Q Consensus       160 --~~f~~~v~~il~~  172 (175)
                        .+|..++..++..
T Consensus       168 ~~~~~~~~l~~i~~~  182 (224)
T 1qde_A          168 LSSGFKEQIYQIFTL  182 (224)
T ss_dssp             HHTTCHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHh
Confidence              6899888888753

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.97  E-value=7.1e-31  Score=212.86  Aligned_cols=165  Identities=25%  Similarity=0.255  Sum_probs=145.4

Q ss_pred             CCcccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC-----
Q psy1539           6 GMFHGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-----   80 (175)
Q Consensus         6 ~~~~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~-----   80 (175)
                      +...+.+..+|+++++++.+++++.+.||..|||+|.++||.+++|+|+++++|||||||++|++|+++.+....     
T Consensus         7 ~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~   86 (417)
T 2i4i_A            7 GNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEAL   86 (417)
T ss_dssp             STTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHH
T ss_pred             CCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchh
Confidence            344567788899999999999999999999999999999999999999999999999999999999998875422     


Q ss_pred             -------------CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee------
Q psy1539          81 -------------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV------  141 (175)
Q Consensus        81 -------------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~------  141 (175)
                                   .+++++|++||++|+.|+++.++++.... ++++..++||.+..++.+.+.++++++|++.      
T Consensus        87 ~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~  165 (417)
T 2i4i_A           87 RAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDM  165 (417)
T ss_dssp             HHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHH
T ss_pred             hccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC-CceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHH
Confidence                         23689999999999999999999998776 8999999999998888888888899999922      


Q ss_pred             --cCccCCCCceEEEEeCCC----CCCHHHHHHHHh
Q psy1539         142 --NYETNLSGVVVNVMDVRS----GGWWLDLEALIL  171 (175)
Q Consensus       142 --~~~~~~~~~~~lVlDEad----~~f~~~v~~il~  171 (175)
                        .....+++++++|+||||    .+|..+++.++.
T Consensus       166 l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~  201 (417)
T 2i4i_A          166 MERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVE  201 (417)
T ss_dssp             HHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHT
T ss_pred             HHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHH
Confidence              224678899999999994    689999999876

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.97  E-value=4.9e-31  Score=203.35  Aligned_cols=157  Identities=23%  Similarity=0.257  Sum_probs=135.7

Q ss_pred             ccccCC--CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeEEEEE
Q psy1539          15 VLSSRN--RREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVM   88 (175)
Q Consensus        15 ~~~~~~--l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~~lil   88 (175)
                      .|++++  +++++++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|+++.+...    .++.+++|+
T Consensus        53 ~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil  132 (262)
T 3ly5_A           53 SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLIL  132 (262)
T ss_dssp             CC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEE
T ss_pred             ChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEE
Confidence            455665  99999999999999999999999999999999999999999999999999999987642    246789999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------C-ccCCCCceEEEEeCC-
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------Y-ETNLSGVVVNVMDVR-  158 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~-~~~~~~~~~lVlDEa-  158 (175)
                      +||++|+.|+++.++++.... +..+..++|+.....+...+.++++++|++..        . ...+++++++|+||| 
T Consensus       133 ~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah  211 (262)
T 3ly5_A          133 SPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEAD  211 (262)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHH
T ss_pred             eCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChH
Confidence            999999999999999998877 88899999999988888888888999999321        1 357889999999999 


Q ss_pred             ---CCCCHHHHHHHHhh
Q psy1539         159 ---SGGWWLDLEALILS  172 (175)
Q Consensus       159 ---d~~f~~~v~~il~~  172 (175)
                         +.+|..+++.|+..
T Consensus       212 ~l~~~~~~~~l~~i~~~  228 (262)
T 3ly5_A          212 RILDVGFEEELKQIIKL  228 (262)
T ss_dssp             HHHHTTCHHHHHHHHHH
T ss_pred             HHhhhhHHHHHHHHHHh
Confidence               46899999998754

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.97  E-value=2e-30  Score=196.42  Aligned_cols=161  Identities=24%  Similarity=0.303  Sum_probs=137.2

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeEE
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYV   85 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~~   85 (175)
                      ..+...|+++++++.+++++.+.||..|+++|.++++.+++|+|+++++|||||||++|++|+++.+...    ..++++
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~  100 (236)
T 2pl3_A           21 VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGV  100 (236)
T ss_dssp             GGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceE
Confidence            4567789999999999999999999999999999999999999999999999999999999999887532    346789


Q ss_pred             EEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee----c----C-ccCCCCceEEEEe
Q psy1539          86 LVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV----N----Y-ETNLSGVVVNVMD  156 (175)
Q Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~----~----~-~~~~~~~~~lVlD  156 (175)
                      +|++||++|+.|+.+.++++.... ++++..++|+.+...+.+.+ .+++++|++.    +    . ...+.+++++|+|
T Consensus       101 lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViD  178 (236)
T 2pl3_A          101 LIISPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLD  178 (236)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEET
T ss_pred             EEEeCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEe
Confidence            999999999999999999998776 78999999998877666666 4689999921    1    1 3567899999999


Q ss_pred             CC----CCCCHHHHHHHHhh
Q psy1539         157 VR----SGGWWLDLEALILS  172 (175)
Q Consensus       157 Ea----d~~f~~~v~~il~~  172 (175)
                      ||    +.+|..++..++..
T Consensus       179 Eah~~~~~~~~~~~~~i~~~  198 (236)
T 2pl3_A          179 EADRILDMGFADTMNAVIEN  198 (236)
T ss_dssp             THHHHHHTTTHHHHHHHHHT
T ss_pred             ChHHHhcCCcHHHHHHHHHh
Confidence            99    46899999888754

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.97  E-value=3e-30  Score=191.41  Aligned_cols=155  Identities=27%  Similarity=0.346  Sum_probs=135.6

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEecC
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHT   91 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~Pt   91 (175)
                      +|+++++++.+++++.+.||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..+...   ..+++++|++||
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            58999999999999999999999999999999999999999999999999999999999987642   356789999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC----
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS----  159 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad----  159 (175)
                      ++|+.|+.+.++++..   .+++..++|+.....+.+.+.++++++|++.        +....+++++++|+||||    
T Consensus        82 ~~L~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~  158 (207)
T 2gxq_A           82 RELALQVASELTAVAP---HLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLS  158 (207)
T ss_dssp             HHHHHHHHHHHHHHCT---TSCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHH
T ss_pred             HHHHHHHHHHHHHHhh---cceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhc
Confidence            9999999999988864   4678888999887788888888899999922        225678899999999994    


Q ss_pred             CCCHHHHHHHHhh
Q psy1539         160 GGWWLDLEALILS  172 (175)
Q Consensus       160 ~~f~~~v~~il~~  172 (175)
                      .+|..+++.++..
T Consensus       159 ~~~~~~~~~i~~~  171 (207)
T 2gxq_A          159 MGFEEEVEALLSA  171 (207)
T ss_dssp             TTCHHHHHHHHHT
T ss_pred             cchHHHHHHHHHh
Confidence            6899999888753

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.97  E-value=1.1e-29  Score=205.79  Aligned_cols=160  Identities=25%  Similarity=0.329  Sum_probs=143.4

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .+..+|+++++++.+++++.+.||..|+|+|.++++.+++|+|+++++|||||||++|++|+++.+.....+.++||++|
T Consensus        34 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P  113 (410)
T 2j0s_A           34 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP  113 (410)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             cCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcC
Confidence            45678999999999999999999999999999999999999999999999999999999999998875556779999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCC----
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVR----  158 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEa----  158 (175)
                      |++|+.|+.+.++++.... ++++..++|+....++.+.+..+++++|++        .+....+.+++++|+|||    
T Consensus       114 t~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~  192 (410)
T 2j0s_A          114 TRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEML  192 (410)
T ss_dssp             SHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHT
T ss_pred             cHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHH
Confidence            9999999999999998877 899999999999888888888889999982        222566788999999999    


Q ss_pred             CCCCHHHHHHHHh
Q psy1539         159 SGGWWLDLEALIL  171 (175)
Q Consensus       159 d~~f~~~v~~il~  171 (175)
                      +.+|...+..++.
T Consensus       193 ~~~~~~~~~~i~~  205 (410)
T 2j0s_A          193 NKGFKEQIYDVYR  205 (410)
T ss_dssp             STTTHHHHHHHHT
T ss_pred             hhhhHHHHHHHHH
Confidence            4688898888865

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.97  E-value=2.3e-30  Score=197.14  Aligned_cols=166  Identities=22%  Similarity=0.249  Sum_probs=135.7

Q ss_pred             CCcccccccccccC----CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-C
Q psy1539           6 GMFHGVTVKVLSSR----NRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-D   80 (175)
Q Consensus         6 ~~~~~~~~~~~~~~----~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~   80 (175)
                      +...+.+...|+++    ++++.+++++.+.||..|+|+|.++++.+++|+|+++++|||||||++|++|++..+... .
T Consensus        17 ~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~   96 (245)
T 3dkp_A           17 GTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPAN   96 (245)
T ss_dssp             SSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCS
T ss_pred             CCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhccc
Confidence            34456777888887    899999999999999999999999999999999999999999999999999999988642 4


Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH-HHHhcCCCeEEEe-------e-cC--ccCCCC
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE-EYLKTHNPQIVGL-------V-NY--ETNLSG  149 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~-~~l~~~~~iiv~l-------~-~~--~~~~~~  149 (175)
                      .+++++|++||++|+.|+.+.++++.... ++++..++|+....... .....+++++|++       . +.  ...+++
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~  175 (245)
T 3dkp_A           97 KGFRALIISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLAS  175 (245)
T ss_dssp             SSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCccccc
Confidence            56789999999999999999999998876 88887777665332221 1223467899982       1 22  367889


Q ss_pred             ceEEEEeCCC-------CCCHHHHHHHHhh
Q psy1539         150 VVVNVMDVRS-------GGWWLDLEALILS  172 (175)
Q Consensus       150 ~~~lVlDEad-------~~f~~~v~~il~~  172 (175)
                      ++++|+||||       .+|.+++..++..
T Consensus       176 ~~~lViDEah~~~~~~~~~~~~~~~~i~~~  205 (245)
T 3dkp_A          176 VEWLVVDESDKLFEDGKTGFRDQLASIFLA  205 (245)
T ss_dssp             CCEEEESSHHHHHHHC--CHHHHHHHHHHH
T ss_pred             CcEEEEeChHHhcccccccHHHHHHHHHHh
Confidence            9999999994       5899999988753

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.96  E-value=2.1e-28  Score=197.48  Aligned_cols=160  Identities=28%  Similarity=0.328  Sum_probs=136.3

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      .....+|+++++++.+++++.+.||..|+|+|.++++.+++|+++++.+|||+|||++|++|++..+.....+.+++|++
T Consensus        17 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   96 (400)
T 1s2m_A           17 NTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMV   96 (400)
T ss_dssp             ----CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEEC
T ss_pred             ccccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEc
Confidence            34556799999999999999999999999999999999999999999999999999999999999887655677899999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCCC-
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRSG-  160 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad~-  160 (175)
                      ||++|+.|+.+.++++.... ++++..++|+.....+...+..+++++|++.        +....+++++++|+||||. 
T Consensus        97 P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~  175 (400)
T 1s2m_A           97 PTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKM  175 (400)
T ss_dssp             SSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHH
T ss_pred             CCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHh
Confidence            99999999999999998877 8899999999987777777777889999822        2245688999999999953 


Q ss_pred             ---CCHHHHHHHH
Q psy1539         161 ---GWWLDLEALI  170 (175)
Q Consensus       161 ---~f~~~v~~il  170 (175)
                         +|...++.++
T Consensus       176 ~~~~~~~~~~~i~  188 (400)
T 1s2m_A          176 LSRDFKTIIEQIL  188 (400)
T ss_dssp             SSHHHHHHHHHHH
T ss_pred             hhhchHHHHHHHH
Confidence               4555555554

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.96  E-value=2.1e-28  Score=196.66  Aligned_cols=158  Identities=54%  Similarity=0.757  Sum_probs=137.4

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      ..|+++++++.++++|.+.||..|+|+|.++++.+++|+|+++.+|||+|||++|++|++..+.....+.++||++||++
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            56999999999999999999999999999999999999999999999999999999999998876666779999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEEee--------cCccCCCCceEEEEeCCC-----
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVGLV--------NYETNLSGVVVNVMDVRS-----  159 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~l~--------~~~~~~~~~~~lVlDEad-----  159 (175)
                      |+.|+.+.++++....+++++..++|+.+...+.+.+.++ ++++|++.        +....+++++++|+||||     
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            9999999999998887789999999999887777777665 58888822        224568899999999994     


Q ss_pred             CCCHHHHHHHHh
Q psy1539         160 GGWWLDLEALIL  171 (175)
Q Consensus       160 ~~f~~~v~~il~  171 (175)
                      .+|...+..++.
T Consensus       168 ~~~~~~~~~~~~  179 (391)
T 1xti_A          168 LDMRRDVQEIFR  179 (391)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             cchHHHHHHHHh
Confidence            366677776654

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.96  E-value=7.3e-28  Score=194.82  Aligned_cols=161  Identities=27%  Similarity=0.309  Sum_probs=141.3

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .....|+++++++.+++.+.+.||..|+++|.++++.+++|+|+++.+|||||||++|++|+++.+.....+.+++|++|
T Consensus        37 ~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  116 (414)
T 3eiq_A           37 EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAP  116 (414)
T ss_dssp             CCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             chhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeC
Confidence            44577999999999999999999999999999999999999999999999999999999999998876656778999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh-cCCCeEEEe--------ecCccCCCCceEEEEeCCC--
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK-THNPQIVGL--------VNYETNLSGVVVNVMDVRS--  159 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~-~~~~iiv~l--------~~~~~~~~~~~~lVlDEad--  159 (175)
                      |++|+.|+.+.++++.... +..+...+|+.....+.+.+. .+++++|++        .+....+.+++++|+||||  
T Consensus       117 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~  195 (414)
T 3eiq_A          117 TRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM  195 (414)
T ss_dssp             SHHHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHH
T ss_pred             hHHHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHh
Confidence            9999999999999998877 888999999998877777776 567888882        2224567889999999995  


Q ss_pred             --CCCHHHHHHHHhh
Q psy1539         160 --GGWWLDLEALILS  172 (175)
Q Consensus       160 --~~f~~~v~~il~~  172 (175)
                        .+|...+..++..
T Consensus       196 ~~~~~~~~~~~~~~~  210 (414)
T 3eiq_A          196 LSRGFKDQIYDIFQK  210 (414)
T ss_dssp             HHTTTHHHHHHHHTT
T ss_pred             hccCcHHHHHHHHHh
Confidence              5888888888754

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.96  E-value=4.5e-28  Score=194.73  Aligned_cols=161  Identities=27%  Similarity=0.333  Sum_probs=140.6

Q ss_pred             ccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539           9 HGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus         9 ~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      .......|+++++++.+++++.+.||..|+|+|.++++.+++|+++++.+|||+|||++|++|++..+.....+++++|+
T Consensus        16 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil   95 (394)
T 1fuu_A           16 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALML   95 (394)
T ss_dssp             SCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             cccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEE
Confidence            34556779999999999999999999999999999999999999999999999999999999999988766667899999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCC-
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad-  159 (175)
                      +||++|+.|+.+.++++.... ++++..++|+.+..++...+. +++++|++        .+....+.+++++|+|||| 
T Consensus        96 ~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~  173 (394)
T 1fuu_A           96 APTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADE  173 (394)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHH
T ss_pred             cCCHHHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHH
Confidence            999999999999999998776 889999999998777766665 47899982        2224567899999999994 


Q ss_pred             ---CCCHHHHHHHHh
Q psy1539         160 ---GGWWLDLEALIL  171 (175)
Q Consensus       160 ---~~f~~~v~~il~  171 (175)
                         .+|...+..++.
T Consensus       174 ~~~~~~~~~~~~~~~  188 (394)
T 1fuu_A          174 MLSSGFKEQIYQIFT  188 (394)
T ss_dssp             HHHTTCHHHHHHHHH
T ss_pred             hhCCCcHHHHHHHHH
Confidence               578888888764

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.95  E-value=2.1e-27  Score=190.59  Aligned_cols=156  Identities=19%  Similarity=0.218  Sum_probs=131.4

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      +..++|+++++++++++++.+.||..|+|+|.++++.+++|  +++++++|||+|||++|++|++..+.....+.+++|+
T Consensus         2 ~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil   81 (395)
T 3pey_A            2 AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICL   81 (395)
T ss_dssp             --CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             ccccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEE
Confidence            45688999999999999999999999999999999999998  9999999999999999999999998766677799999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCC-
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad-  159 (175)
                      +||++|+.|+.+.++++.... ++.+...+++......    ..+++++|++        .+....+++++++|+|||| 
T Consensus        82 ~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~  156 (395)
T 3pey_A           82 APSRELARQTLEVVQEMGKFT-KITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADN  156 (395)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHH
T ss_pred             CCCHHHHHHHHHHHHHHhccc-CeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhh
Confidence            999999999999999998776 7888888877543222    2357899982        2235678899999999995 


Q ss_pred             ----CCCHHHHHHHHh
Q psy1539         160 ----GGWWLDLEALIL  171 (175)
Q Consensus       160 ----~~f~~~v~~il~  171 (175)
                          .+|...+..++.
T Consensus       157 ~~~~~~~~~~~~~~~~  172 (395)
T 3pey_A          157 MLDQQGLGDQCIRVKR  172 (395)
T ss_dssp             HHHSTTHHHHHHHHHH
T ss_pred             hcCccccHHHHHHHHH
Confidence                677777776654

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.95  E-value=1e-27  Score=198.36  Aligned_cols=157  Identities=23%  Similarity=0.311  Sum_probs=133.1

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +..+|++++|++.+++++.++||..|+|+|.+++|.+++|  +|+++++|||||||++|++|++..+.....++++||++
T Consensus        90 ~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~  169 (479)
T 3fmp_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLS  169 (479)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEEC
T ss_pred             CcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEe
Confidence            3568999999999999999999999999999999999987  99999999999999999999999988766777999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE----eec-----CccCCCCceEEEEeCCC-
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVN-----YETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~-----~~~~~~~~~~lVlDEad-  159 (175)
                      ||++|+.|+.+.++++....+++.+....++.......   ..+++++|+    +.+     ..+.+++++++|+|||| 
T Consensus       170 Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~  246 (479)
T 3fmp_B          170 PTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV  246 (479)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHH
T ss_pred             ChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc---cCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHH
Confidence            99999999999999998877788888888876543322   335689998    211     14566899999999995 


Q ss_pred             ----CCCHHHHHHHHh
Q psy1539         160 ----GGWWLDLEALIL  171 (175)
Q Consensus       160 ----~~f~~~v~~il~  171 (175)
                          .+|...+..++.
T Consensus       247 ~~~~~~~~~~~~~i~~  262 (479)
T 3fmp_B          247 MIATQGHQDQSIRIQR  262 (479)
T ss_dssp             HHTSTTHHHHHHHHHT
T ss_pred             HhhcCCcHHHHHHHHh
Confidence                577777776654

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.95  E-value=4.5e-27  Score=189.88  Aligned_cols=158  Identities=23%  Similarity=0.289  Sum_probs=134.6

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      ...++|+++++++.+++++.+.||..|+|+|.++++.+++|  +++++++|||+|||++|++|++..+.....+++++|+
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil  101 (412)
T 3fht_A           22 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCL  101 (412)
T ss_dssp             CCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             cccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEE
Confidence            45678999999999999999999999999999999999987  9999999999999999999999998876677799999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------c-CccCCCCceEEEEeCCC
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------N-YETNLSGVVVNVMDVRS  159 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~-~~~~~~~~~~lVlDEad  159 (175)
                      +||++|+.|+.+.++++....+++.+....|+.......   ..+++++|++.        + ....+++++++|+||||
T Consensus       102 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah  178 (412)
T 3fht_A          102 SPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEAD  178 (412)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh---cCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHH
Confidence            999999999999999998887788898888887644332   34568888821        1 24556889999999994


Q ss_pred             -----CCCHHHHHHHHh
Q psy1539         160 -----GGWWLDLEALIL  171 (175)
Q Consensus       160 -----~~f~~~v~~il~  171 (175)
                           .+|...+..++.
T Consensus       179 ~~~~~~~~~~~~~~~~~  195 (412)
T 3fht_A          179 VMIATQGHQDQSIRIQR  195 (412)
T ss_dssp             HHHSTTTTHHHHHHHHH
T ss_pred             HHhhcCCcHHHHHHHHh
Confidence                 578777776654

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.95  E-value=3.7e-27  Score=199.48  Aligned_cols=161  Identities=21%  Similarity=0.269  Sum_probs=133.5

Q ss_pred             cccccccCC-CCHHHHHHHhhCCCCCCcHHHHHhHHHHh--cCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeE
Q psy1539          12 TVKVLSSRN-RREKEDRIGESQPFREQTSFQHECIPQAV--LGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVY   84 (175)
Q Consensus        12 ~~~~~~~~~-l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~--~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~   84 (175)
                      ++..|.+.+ |++++++++.++||..|+|+|.++++.++  .|+|+++++|||+|||++|++|+++.+...    ..+++
T Consensus        18 ~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~   97 (579)
T 3sqw_A           18 TLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVK   97 (579)
T ss_dssp             CHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCC
T ss_pred             CHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCe
Confidence            333443333 99999999999999999999999999999  789999999999999999999999988653    23568


Q ss_pred             EEEEecCHHHHHHHHHHHHHHHhh---CCCeEEEEEECCCchHHhHHHHhc-CCCeEEEeecC---------ccCCCCce
Q psy1539          85 VLVMCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKT-HNPQIVGLVNY---------ETNLSGVV  151 (175)
Q Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~---~~~i~v~~~~g~~~~~~~~~~l~~-~~~iiv~l~~~---------~~~~~~~~  151 (175)
                      +||++||++|+.|+.+.++++...   .+.+.+..++|+.....+.+.+.+ +++|+|++...         ...+++++
T Consensus        98 ~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~  177 (579)
T 3sqw_A           98 AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVD  177 (579)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCC
T ss_pred             EEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCC
Confidence            999999999999999999998753   246778889999988877777754 78999982221         34678999


Q ss_pred             EEEEeCC----CCCCHHHHHHHHhh
Q psy1539         152 VNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       152 ~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      ++|+|||    +.+|.++++.|+..
T Consensus       178 ~lViDEah~l~~~gf~~~~~~i~~~  202 (579)
T 3sqw_A          178 YKVLDEADRLLEIGFRDDLETISGI  202 (579)
T ss_dssp             EEEEETHHHHTSTTTHHHHHHHHHH
T ss_pred             EEEEEChHHhhcCCCHHHHHHHHHH
Confidence            9999999    57899999988753

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.95  E-value=1.7e-26  Score=183.54  Aligned_cols=157  Identities=25%  Similarity=0.366  Sum_probs=135.7

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ..+|+++++++.+++++.+.||..|+|+|.++++.+++| +++++.+|||+|||++|++|++..+... ++.+++|++|+
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~   83 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN-NGIEAIILTPT   83 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS-SSCCEEEECSC
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc-CCCcEEEEcCC
Confidence            457999999999999999999999999999999999988 7999999999999999999999877543 46689999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCC----C
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVR----S  159 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEa----d  159 (175)
                      ++|+.|+.+.++++.... ++++..++|+.....+...+. +++++|++.        +....+++++++|+|||    +
T Consensus        84 ~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~  161 (367)
T 1hv8_A           84 RELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLN  161 (367)
T ss_dssp             HHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHT
T ss_pred             HHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhh
Confidence            999999999999998765 888999999998777777666 579999822        22456789999999999    5


Q ss_pred             CCCHHHHHHHHhh
Q psy1539         160 GGWWLDLEALILS  172 (175)
Q Consensus       160 ~~f~~~v~~il~~  172 (175)
                      .+|...+..++..
T Consensus       162 ~~~~~~~~~~~~~  174 (367)
T 1hv8_A          162 MGFIKDVEKILNA  174 (367)
T ss_dssp             TTTHHHHHHHHHT
T ss_pred             hchHHHHHHHHHh
Confidence            6788888887653

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.95  E-value=9.2e-27  Score=196.01  Aligned_cols=151  Identities=21%  Similarity=0.272  Sum_probs=128.6

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHh--cCCcEEEEcCCCChHHHHHHHHHHHhhhcCC----CCeEEEEEecCHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAV--LGMDILCQAKSGMGKTAVFVLATLQQLETTD----SNVYVLVMCHTREL   94 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~--~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~----~~~~~lil~Pt~~L   94 (175)
                      +++.+++++.+.||..|+|+|.++++.++  .|+|+++++|||||||++|++|+++.+....    .++++||++||++|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            99999999999999999999999999999  6799999999999999999999999886532    34689999999999


Q ss_pred             HHHHHHHHHHHHhh---CCCeEEEEEECCCchHHhHHHHh-cCCCeEEEeecC---------ccCCCCceEEEEeCC---
Q psy1539          95 AFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLK-THNPQIVGLVNY---------ETNLSGVVVNVMDVR---  158 (175)
Q Consensus        95 ~~q~~~~~~~~~~~---~~~i~v~~~~g~~~~~~~~~~l~-~~~~iiv~l~~~---------~~~~~~~~~lVlDEa---  158 (175)
                      +.|+.+.++++...   .+...+..++|+.....+.+.+. .+++|+|++...         ...+++++++|+|||   
T Consensus       159 a~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l  238 (563)
T 3i5x_A          159 ALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRL  238 (563)
T ss_dssp             HHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHH
T ss_pred             HHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHH
Confidence            99999999998653   23567888899988777777664 478999992222         346789999999999   


Q ss_pred             -CCCCHHHHHHHHh
Q psy1539         159 -SGGWWLDLEALIL  171 (175)
Q Consensus       159 -d~~f~~~v~~il~  171 (175)
                       +.+|.++++.|+.
T Consensus       239 ~~~~f~~~~~~i~~  252 (563)
T 3i5x_A          239 LEIGFRDDLETISG  252 (563)
T ss_dssp             TSTTTHHHHHHHHH
T ss_pred             hccchHHHHHHHHH
Confidence             5789999998864

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.94  E-value=1.2e-25  Score=176.88  Aligned_cols=144  Identities=25%  Similarity=0.419  Sum_probs=125.1

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      |++++.+++.++||..|+|+|.++++.+++|+++++.+|||+|||++|++|++..      +.+++|++|+++|+.|+.+
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            5789999999999999999999999999999999999999999999999999874      4479999999999999999


Q ss_pred             HHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC----CCCHHHHHH
Q psy1539         101 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS----GGWWLDLEA  168 (175)
Q Consensus       101 ~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad----~~f~~~v~~  168 (175)
                      .++++.... +.++..++|+.....+.+.+.+ ++++|++.        +....+.+++++|+||||    .+|..++..
T Consensus        75 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~  152 (337)
T 2z0m_A           75 HIRDIGRYM-DTKVAEVYGGMPYKAQINRVRN-ADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKI  152 (337)
T ss_dssp             HHHHHTTTS-CCCEEEECTTSCHHHHHHHHTT-CSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHH
T ss_pred             HHHHHhhhc-CCcEEEEECCcchHHHHhhcCC-CCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHH
Confidence            999998776 8899999999987777777665 79999822        224567889999999994    678888888


Q ss_pred             HHhh
Q psy1539         169 LILS  172 (175)
Q Consensus       169 il~~  172 (175)
                      ++..
T Consensus       153 ~~~~  156 (337)
T 2z0m_A          153 ILAQ  156 (337)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            7653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.93  E-value=1.4e-25  Score=182.27  Aligned_cols=142  Identities=14%  Similarity=0.099  Sum_probs=118.8

Q ss_pred             HHHHHHhh-CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHH
Q psy1539          24 KEDRIGES-QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        24 ~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      ++.+.+++ .|| .|+|+|.++++.+++|+|+++++|||||||++|++|++....   .+++++|++||++|+.|+.+.+
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            34455555 356 799999999999999999999999999999999999888763   5668999999999999999999


Q ss_pred             HHHHhhCCCeEEEEEECCCch---HHhHHHHhcC-CCeEEEeecC------ccCCCCceEEEEeCCC-------------
Q psy1539         103 ERFSKYMSNIKVGVFFGGLPI---QKDEEYLKTH-NPQIVGLVNY------ETNLSGVVVNVMDVRS-------------  159 (175)
Q Consensus       103 ~~~~~~~~~i~v~~~~g~~~~---~~~~~~l~~~-~~iiv~l~~~------~~~~~~~~~lVlDEad-------------  159 (175)
                      +++.. . ++++..++|+.+.   ..+.+.+.++ ++++|++...      ...+.+++++|+||||             
T Consensus        85 ~~~~~-~-~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~iViDEaH~~~~~~~~~d~~l  162 (414)
T 3oiy_A           85 QKLAD-E-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLL  162 (414)
T ss_dssp             HHHCC-S-SCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSEEEESCHHHHHHCHHHHHHHH
T ss_pred             HHHcc-C-CceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccEEEEeChHhhhhccchhhhHH
Confidence            99877 4 8999999999987   5566777776 8999983322      3567899999999996             


Q ss_pred             --CCCHHH-HHHHHh
Q psy1539         160 --GGWWLD-LEALIL  171 (175)
Q Consensus       160 --~~f~~~-v~~il~  171 (175)
                        .+|.++ ++.++.
T Consensus       163 ~~~~~~~~~~~~i~~  177 (414)
T 3oiy_A          163 MMVGIPEEIIRKAFS  177 (414)
T ss_dssp             HHTTCCHHHHHHHHH
T ss_pred             hhcCCcHHHHHHHHH
Confidence              899999 777764

>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=99.90  E-value=8.3e-24  Score=183.00  Aligned_cols=151  Identities=15%  Similarity=0.164  Sum_probs=125.1

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHH-HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQ-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~-~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .|+++++++.+.+.+++.||..|+|+|.++++. +.+|+|+++++|||||||++|.+|+++.+..  ++.+++|++|+++
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 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILT--QGGKAVYIVPLKA   79 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHH--HCSEEEEECSSGG
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHh--CCCEEEEEcCcHH
Confidence            488999999999999999999999999999998 8899999999999999999999999988764  2458999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC----CC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS----GG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad----~~  161 (175)
                      |+.|+.+.++++.. . ++++..++|+......  . ...++++|++.        +....+++++++|+||++    ..
T Consensus        80 La~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~--~-~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~  154 (720)
T 2zj8_A           80 LAEEKFQEFQDWEK-I-GLRVAMATGDYDSKDE--W-LGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRD  154 (720)
T ss_dssp             GHHHHHHHTGGGGG-G-TCCEEEECSCSSCCCG--G-GGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTT
T ss_pred             HHHHHHHHHHHHHh-c-CCEEEEecCCCCcccc--c-cCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCc
Confidence            99999999976554 3 8899999998764432  1 23578999822        123447899999999996    36


Q ss_pred             CHHHHHHHHhh
Q psy1539         162 WWLDLEALILS  172 (175)
Q Consensus       162 f~~~v~~il~~  172 (175)
                      +...++.++..
T Consensus       155 r~~~~~~ll~~  165 (720)
T 2zj8_A          155 RGATLEVILAH  165 (720)
T ss_dssp             THHHHHHHHHH
T ss_pred             ccHHHHHHHHH
Confidence            77777777643

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.90  E-value=1.9e-23  Score=187.37  Aligned_cols=135  Identities=15%  Similarity=0.113  Sum_probs=116.0

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      ..|| .|||+|.+++|.+++|+|++++||||||||++|++|++..+.   +++++||++||++|+.|+.+.++++. .. 
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~---~~~~~Lil~PtreLa~Q~~~~l~~l~-~~-  147 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---KGKKSALVFPTVTLVKQTLERLQKLA-DE-  147 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT---TTCCEEEEESSHHHHHHHHHHHHTTS-CT-
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh---cCCeEEEEechHHHHHHHHHHHHHhh-CC-
Confidence            4678 699999999999999999999999999999999888888763   56789999999999999999999976 44 


Q ss_pred             CeEEEEEECCCch---HHhHHHHhcC-CCeEEEeecC------ccCCCCceEEEEeCCC---------------CCCHHH
Q psy1539         111 NIKVGVFFGGLPI---QKDEEYLKTH-NPQIVGLVNY------ETNLSGVVVNVMDVRS---------------GGWWLD  165 (175)
Q Consensus       111 ~i~v~~~~g~~~~---~~~~~~l~~~-~~iiv~l~~~------~~~~~~~~~lVlDEad---------------~~f~~~  165 (175)
                      ++++..++|+.+.   .++.+.+.++ ++++|++...      ...+++++++|+||||               .||.++
T Consensus       148 ~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~gf~~~  227 (1104)
T 4ddu_A          148 KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEE  227 (1104)
T ss_dssp             TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEEEESCHHHHTTSSHHHHHHHHTSSCCHH
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEEEEeCCCccccccccchhhhHhcCCCHH
Confidence            8999999999987   6677788877 8999983332      3557899999999994               789999


Q ss_pred             -HHHHHh
Q psy1539         166 -LEALIL  171 (175)
Q Consensus       166 -v~~il~  171 (175)
                       ++.|+.
T Consensus       228 ~i~~il~  234 (1104)
T 4ddu_A          228 IIRKAFS  234 (1104)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence             787775

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.90  E-value=3e-23  Score=179.27  Aligned_cols=152  Identities=14%  Similarity=0.125  Sum_probs=125.4

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHH-HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQ-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~-~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ..+|+++++++.+.+.+.+.||..|+|+|.++++. +.+|+|+++++|||||||++|.+|+++.+..  ++.+++|++|+
T Consensus         7 ~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~--~~~~il~i~P~   84 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK--NGGKAIYVTPL   84 (715)
T ss_dssp             CCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH--SCSEEEEECSC
T ss_pred             cCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH--CCCeEEEEeCc
Confidence            35699999999999999999999999999999999 7789999999999999999999999988764  24599999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCCC---
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRSG---  160 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad~---  160 (175)
                      |+|+.|+.+.++.+.. . ++++..++|+....+.  .+ .+++++|++.        +....+++++++|+||+|.   
T Consensus        85 r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~  159 (715)
T 2va8_A           85 RALTNEKYLTFKDWEL-I-GFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLND  159 (715)
T ss_dssp             HHHHHHHHHHHGGGGG-G-TCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGC
T ss_pred             HHHHHHHHHHHHHhhc-C-CCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCC
Confidence            9999999999865543 3 8899999998765433  12 3578999822        1234478999999999954   


Q ss_pred             -CCHHHHHHHHh
Q psy1539         161 -GWWLDLEALIL  171 (175)
Q Consensus       161 -~f~~~v~~il~  171 (175)
                       .+...++.++.
T Consensus       160 ~~~~~~l~~i~~  171 (715)
T 2va8_A          160 PERGPVVESVTI  171 (715)
T ss_dssp             TTTHHHHHHHHH
T ss_pred             cccchHHHHHHH
Confidence             67777777764

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.90  E-value=2.4e-23  Score=179.01  Aligned_cols=134  Identities=16%  Similarity=0.089  Sum_probs=110.2

Q ss_pred             HHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC--CCeEEEEEecCHHHHHHHHHHHH
Q psy1539          26 DRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD--SNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        26 ~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~--~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .+++..+||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....  .+.++||++||++|+.|+.+.++
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~   82 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFS   82 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999999999999998876543  23689999999999999999999


Q ss_pred             HHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------Ccc-CCCCceEEEEeCCCC
Q psy1539         104 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------YET-NLSGVVVNVMDVRSG  160 (175)
Q Consensus       104 ~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~~~-~~~~~~~lVlDEad~  160 (175)
                      ++.... ++++..++|+.+...+.+.+..+++++|++..        ... .+++++++|+||||.
T Consensus        83 ~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~  147 (696)
T 2ykg_A           83 KYFERH-GYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHN  147 (696)
T ss_dssp             HHTTTT-TCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGG
T ss_pred             HHhccC-CceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCc
Confidence            998765 88999999998766677777778899999221        123 578899999999965

>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=99.89  E-value=5.5e-23  Score=171.83  Aligned_cols=127  Identities=18%  Similarity=0.119  Sum_probs=103.3

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC--CCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          33 PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD--SNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~--~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      +...|+|+|.++++.+++|+|+++++|||+|||++|++|+++.+....  .+.++||++||++|+.|+.+.++++.... 
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-   82 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ-   82 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG-
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc-
Confidence            345799999999999999999999999999999999999999887543  26789999999999999999999998877 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------Ccc-CCCCceEEEEeCCCC
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------YET-NLSGVVVNVMDVRSG  160 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~~~-~~~~~~~lVlDEad~  160 (175)
                      ++++..++|+.+...+.+.+..+++++|++..        ... .+++++++|+||||.
T Consensus        83 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~  141 (556)
T 4a2p_A           83 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHN  141 (556)
T ss_dssp             TCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGG
T ss_pred             CceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcc
Confidence            89999999999877777777777899999222        234 688999999999953

>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=99.89  E-value=7.6e-24  Score=182.79  Aligned_cols=149  Identities=17%  Similarity=0.163  Sum_probs=120.2

Q ss_pred             ccccCC--CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          15 VLSSRN--RREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        15 ~~~~~~--l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      +|++++  +++.+.+.+++.||..|+|+|.++++.+.+|+|+++++|||||||++|.+|+++.+..   +.+++|++|++
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            477888  9999999999999999999999999999999999999999999999999999988763   45899999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEee-------cC-ccCCCCceEEEEeCCCC----
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV-------NY-ETNLSGVVVNVMDVRSG----  160 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~-------~~-~~~~~~~~~lVlDEad~----  160 (175)
                      +|+.|+.+.++++.. . ++++..++|+....+.  .+ .+++++|++.       +. ...+++++++|+||++.    
T Consensus        79 ~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~  153 (702)
T 2p6r_A           79 ALAGEKYESFKKWEK-I-GLRIGISTGDYESRDE--HL-GDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSE  153 (702)
T ss_dssp             HHHHHHHHHHTTTTT-T-TCCEEEECSSCBCCSS--CS-TTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCT
T ss_pred             HHHHHHHHHHHHHHh-c-CCEEEEEeCCCCcchh--hc-cCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCC
Confidence            999999999865543 3 8899999998764432  12 3578998832       22 33478999999999964    


Q ss_pred             CCHHHHHHHHh
Q psy1539         161 GWWLDLEALIL  171 (175)
Q Consensus       161 ~f~~~v~~il~  171 (175)
                      ++...++.++.
T Consensus       154 ~r~~~~~~ll~  164 (702)
T 2p6r_A          154 KRGATLEILVT  164 (702)
T ss_dssp             TTHHHHHHHHH
T ss_pred             CcccHHHHHHH
Confidence            67777777654

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.89  E-value=8.4e-23  Score=170.40  Aligned_cols=124  Identities=17%  Similarity=0.161  Sum_probs=107.8

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC--CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD--SNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~--~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .|+|+|.++++.+++|+|+++++|||+|||++|++|+++.+....  .+.++||++||++|+.|+.+.++++.... +++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~   82 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERL-GYN   82 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTT-TCC
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccC-CcE
Confidence            699999999999999999999999999999999999999887543  26789999999999999999999998877 899


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEEeecC--------cc-CCCCceEEEEeCCCC
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVGLVNY--------ET-NLSGVVVNVMDVRSG  160 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~--------~~-~~~~~~~lVlDEad~  160 (175)
                      +..++|+.+...+.+.+..+++++|++...        .. .+.+++++|+||||.
T Consensus        83 ~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~  138 (555)
T 3tbk_A           83 IASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHN  138 (555)
T ss_dssp             EEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGG
T ss_pred             EEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccc
Confidence            999999998777777777778999992221        23 678899999999964

>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=99.89  E-value=1.8e-22  Score=169.16  Aligned_cols=145  Identities=14%  Similarity=0.086  Sum_probs=116.9

Q ss_pred             cccccCCCCHHHHHHHhh-CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          14 KVLSSRNRREKEDRIGES-QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      ..|+++++++.+.+.|++ +||..|+|+|.++|+.+++|+|+++.+|||+|||++|.+|++..      ...++|++|++
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            578999999999999998 89999999999999999999999999999999999999999853      23799999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEEeec----C----ccCCCCceEEEEeCCC-
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVGLVN----Y----ETNLSGVVVNVMDVRS-  159 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~l~~----~----~~~~~~~~~lVlDEad-  159 (175)
                      +|+.|+.+.++.+     ++.+..+.|+.+..+...   .+.+ ..+++++...    .    .+...++.++|+|||| 
T Consensus        76 aL~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~  150 (523)
T 1oyw_A           76 SLMKDQVDQLQAN-----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHC  150 (523)
T ss_dssp             HHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGG
T ss_pred             HHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccc
Confidence            9999988888764     778888888877554432   2333 4677777221    1    3455799999999994 


Q ss_pred             ---CC--CHHHHHHH
Q psy1539         160 ---GG--WWLDLEAL  169 (175)
Q Consensus       160 ---~~--f~~~v~~i  169 (175)
                         .|  |.++...+
T Consensus       151 i~~~g~~fr~~~~~l  165 (523)
T 1oyw_A          151 ISQWGHDFRPEYAAL  165 (523)
T ss_dssp             GCTTSSCCCHHHHGG
T ss_pred             cCcCCCccHHHHHHH
Confidence               23  77766543

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.88  E-value=1.3e-22  Score=172.18  Aligned_cols=141  Identities=15%  Similarity=0.117  Sum_probs=115.1

Q ss_pred             ccCCCCHHHHHHHhh-CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          17 SSRNRREKEDRIGES-QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        17 ~~~~l~~~l~~~l~~-~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      .++++++.+.+.|++ +||..|+|+|.++|+.+++|+|+++.+|||+|||++|.+|++..      ..++||++|+++|+
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            458899999999998 69999999999999999999999999999999999999999753      23899999999999


Q ss_pred             HHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH------hcCCCeEEEeecC-------------ccCCCCceEEEEe
Q psy1539          96 FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL------KTHNPQIVGLVNY-------------ETNLSGVVVNVMD  156 (175)
Q Consensus        96 ~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l------~~~~~iiv~l~~~-------------~~~~~~~~~lVlD  156 (175)
                      .|+.+.++++     ++++..+.|+.+..+....+      ..+.+++++....             ...+.++.++|+|
T Consensus        98 ~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViD  172 (591)
T 2v1x_A           98 EDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVD  172 (591)
T ss_dssp             HHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEE
T ss_pred             HHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEE
Confidence            9999988876     67888899988765443322      2457888882221             2346799999999


Q ss_pred             CCC----CC--CHHHHHH
Q psy1539         157 VRS----GG--WWLDLEA  168 (175)
Q Consensus       157 Ead----~~--f~~~v~~  168 (175)
                      |||    .|  |.+++..
T Consensus       173 EAH~is~~g~dfr~~~~~  190 (591)
T 2v1x_A          173 EVHCCSQWGHDFRPDYKA  190 (591)
T ss_dssp             TGGGGSTTCTTCCGGGGG
T ss_pred             CcccccccccccHHHHHH
Confidence            994    34  7777654

>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=99.88  E-value=2.5e-22  Score=173.61  Aligned_cols=133  Identities=13%  Similarity=0.087  Sum_probs=111.2

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      ..|| .|||+|..++|.+++|+  +..++||+|||++|.+|++....   .+.+++|++||++||.|+.+++..+.+.. 
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL---~g~~vlVltptreLA~qd~e~~~~l~~~l-  151 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL---TGKGVHVVTVNEYLASRDAEQMGKIFEFL-  151 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT---TSSCEEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHH---cCCCEEEEeCCHHHHHHHHHHHHHHHhhc-
Confidence            5799 99999999999999999  89999999999999999985433   35589999999999999999999999988 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEe---------ecC------ccCCCCceEEEEeCCC-----CC---------
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGL---------VNY------ETNLSGVVVNVMDVRS-----GG---------  161 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l---------~~~------~~~~~~~~~lVlDEad-----~~---------  161 (175)
                      ++++.+++||.+...  +....+++|++|+         .++      ...++++.++|+||||     .+         
T Consensus       152 gl~v~~i~gg~~~~~--r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg~  229 (844)
T 1tf5_A          152 GLTVGLNLNSMSKDE--KREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQ  229 (844)
T ss_dssp             TCCEEECCTTSCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEEE
T ss_pred             CCeEEEEeCCCCHHH--HHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcCC
Confidence            999999999987543  3344578999992         222      3567899999999994     43         


Q ss_pred             ------CHHHHHHHHhh
Q psy1539         162 ------WWLDLEALILS  172 (175)
Q Consensus       162 ------f~~~v~~il~~  172 (175)
                            |..+++.|+..
T Consensus       230 ~~~~~~~~~~i~~iv~~  246 (844)
T 1tf5_A          230 AAKSTKLYVQANAFVRT  246 (844)
T ss_dssp             EECCCHHHHHHHHHHTT
T ss_pred             cccchhHHHHHHHHHHh
Confidence                  56788888754

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.87  E-value=4.7e-22  Score=173.81  Aligned_cols=129  Identities=18%  Similarity=0.111  Sum_probs=104.4

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC--CCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD--SNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~--~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      -.|+..|+|+|.++++.+++|+|+++++|||+|||++|++|++..+....  .+.++||++||++|+.|+.+.++++...
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~  322 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGG
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhccc
Confidence            44688999999999999999999999999999999999999999887542  2668999999999999999999999887


Q ss_pred             CCCeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------Ccc-CCCCceEEEEeCCCC
Q psy1539         109 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------YET-NLSGVVVNVMDVRSG  160 (175)
Q Consensus       109 ~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~~~-~~~~~~~lVlDEad~  160 (175)
                      . ++++..++|+.+...+.+.+..+++++|++..        ... .+++++++|+||||.
T Consensus       323 ~-~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~  382 (797)
T 4a2q_A          323 Q-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHN  382 (797)
T ss_dssp             G-TCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGG
T ss_pred             C-CceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccc
Confidence            7 89999999999877777777788999999221        233 677899999999963

>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=99.87  E-value=1e-21  Score=170.74  Aligned_cols=132  Identities=23%  Similarity=0.270  Sum_probs=111.0

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcC------CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHH
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ   97 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g------~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q   97 (175)
                      .+.+.+.+++| .||++|.++++.++++      +|+++++|||||||++|++|++..+..   +.+++|++||++|+.|
T Consensus       357 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---g~qvlvlaPtr~La~Q  432 (780)
T 1gm5_A          357 LAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAIQ  432 (780)
T ss_dssp             HHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHHH
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHH
Confidence            44455678899 8999999999999875      699999999999999999999998764   4589999999999999


Q ss_pred             HHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhcC-CCeEEE---eecCccCCCCceEEEEeCCCC
Q psy1539          98 ISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus        98 ~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad~  160 (175)
                      +++.++++.... ++++..++|+.+.++.   .+.+.++ ++++|+   ++.....+++++++|+||+|.
T Consensus       433 ~~~~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVIDEaHr  501 (780)
T 1gm5_A          433 HYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHR  501 (780)
T ss_dssp             HHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCC
T ss_pred             HHHHHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEecccch
Confidence            999999998877 8999999999876553   3445555 788888   333357789999999999964

>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=99.87  E-value=1.1e-21  Score=175.65  Aligned_cols=136  Identities=16%  Similarity=0.194  Sum_probs=112.2

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      ++.+||. | ++|.++||.+++|+|+++++|||||||+ |.+|++..+..  .+++++|++||++|+.|+.+.++++...
T Consensus        51 ~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~--~~~~~lil~PtreLa~Q~~~~l~~l~~~  125 (1054)
T 1gku_B           51 RKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRKYAEK  125 (1054)
T ss_dssp             HTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHHHHTT
T ss_pred             HHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh--cCCeEEEEeccHHHHHHHHHHHHHHHhh
Confidence            3457999 9 9999999999999999999999999998 88999888764  5679999999999999999999999987


Q ss_pred             CCCe----EEEEEECCCchHHh---HHHHhcCCCeEEE----eecCccCCCCceEEEEeCCCC--CCHHHHHHHHh
Q psy1539         109 MSNI----KVGVFFGGLPIQKD---EEYLKTHNPQIVG----LVNYETNLSGVVVNVMDVRSG--GWWLDLEALIL  171 (175)
Q Consensus       109 ~~~i----~v~~~~g~~~~~~~---~~~l~~~~~iiv~----l~~~~~~~~~~~~lVlDEad~--~f~~~v~~il~  171 (175)
                      . ++    ++..++|+.+...+   .+.+.+ ++|+|+    +.+....+++++++|+||||.  .|..+++.++.
T Consensus       126 ~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~L~~l~~lViDEah~~l~~~~~~~~i~~  199 (1054)
T 1gku_B          126 A-GVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLH  199 (1054)
T ss_dssp             T-CCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTTSCCCSEEEESCHHHHHTSTHHHHHHHH
T ss_pred             c-CCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHHhccCCEEEEeChhhhhhccccHHHHHH
Confidence            7 77    89999999887653   444555 899999    333333377999999999953  35567766654

>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=99.87  E-value=4.7e-22  Score=147.62  Aligned_cols=130  Identities=21%  Similarity=0.217  Sum_probs=100.7

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEecCHHHHHH-HHHHHHH
Q psy1539          29 GESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTRELAFQ-ISKEYER  104 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~Pt~~L~~q-~~~~~~~  104 (175)
                      ........|+++|.++++.+++++++++.+|||+|||++++.+++..+...   ..+.+++|++|+++|+.| +.+.+++
T Consensus        26 ~~~~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~  105 (216)
T 3b6e_A           26 ASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQP  105 (216)
T ss_dssp             TCCSCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHH
T ss_pred             cCccCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHH
Confidence            344445689999999999999999999999999999999999998876532   235689999999999999 7788888


Q ss_pred             HHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC--------------ccCCCCceEEEEeCCCC
Q psy1539         105 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY--------------ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       105 ~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~--------------~~~~~~~~~lVlDEad~  160 (175)
                      +...  ++++..+.|+.........+.++++++|+..+.              ...+.+++++|+||||.
T Consensus       106 ~~~~--~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~  173 (216)
T 3b6e_A          106 FLKK--WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHH  173 (216)
T ss_dssp             HHTT--TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC--
T ss_pred             Hhcc--CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchh
Confidence            8764  678888888877666665565678999982222              14567899999999964

>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=99.85  E-value=1.9e-21  Score=172.52  Aligned_cols=129  Identities=19%  Similarity=0.128  Sum_probs=102.8

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC--CCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD--SNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~--~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      -.|+..|+|+|.++++.+++|+|+++.+|||+|||++|++|++..+....  .+.++||++||++|+.|+.+.++++...
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~  322 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFER  322 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            34677899999999999999999999999999999999999998876542  1568999999999999999999999887


Q ss_pred             CCCeEEEEEECCCchHHhHHHHhcCCCeEEEe----e----cCcc-CCCCceEEEEeCCCC
Q psy1539         109 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL----V----NYET-NLSGVVVNVMDVRSG  160 (175)
Q Consensus       109 ~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l----~----~~~~-~~~~~~~lVlDEad~  160 (175)
                      . ++++..++|+.+...+.+.+..+++++|++    .    +... .+++++++|+||||.
T Consensus       323 ~-~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~  382 (936)
T 4a2w_A          323 Q-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHN  382 (936)
T ss_dssp             T-TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGG
T ss_pred             c-CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccc
Confidence            6 899999999987766666676778999992    1    1223 577899999999963

>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=99.85  E-value=1.7e-21  Score=168.24  Aligned_cols=119  Identities=14%  Similarity=0.090  Sum_probs=101.3

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .|. .|+++|..++|.+++|+  +..++||||||++|.+|++....   .+.+++|++||++||.|+.+++..+.+.+ +
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l---~g~~vlVltPTreLA~Q~~e~~~~l~~~l-g  143 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNAL---TGKGVHVVTVNDYLAQRDAENNRPLFEFL-G  143 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHT---TSSCCEEEESSHHHHHHHHHHHHHHHHHT-T
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHH---cCCcEEEEcCCHHHHHHHHHHHHHHHHhc-C
Confidence            454 79999999999999998  89999999999999999986544   35689999999999999999999999998 9


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEEee---------cC------ccCCCCceEEEEeCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVGLV---------NY------ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~---------~~------~~~~~~~~~lVlDEad  159 (175)
                      +++..++||.+..  .+.+..+++|+||+.         ++      ...+++++++|+||||
T Consensus       144 l~v~~i~GG~~~~--~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD  204 (853)
T 2fsf_A          144 LTVGINLPGMPAP--AKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVD  204 (853)
T ss_dssp             CCEEECCTTCCHH--HHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHH
T ss_pred             CeEEEEeCCCCHH--HHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchH
Confidence            9999999998753  444555789999932         11      2566899999999994

>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=99.85  E-value=1.4e-21  Score=175.47  Aligned_cols=143  Identities=19%  Similarity=0.105  Sum_probs=116.8

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      ..|+..++++.+...+.+.++..|+|+|.++++.+.+|+|+++++|||||||++|.+|++..+.   .+.+++|++||++
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~---~g~rvlvl~Ptra  238 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK---NKQRVIYTSPIKA  238 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH---TTCEEEEEESSHH
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh---cCCeEEEEcCcHH
Confidence            3567788888888888777777899999999999999999999999999999999999999875   3558999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeec--------CccCCCCceEEEEeCCCC----C
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVN--------YETNLSGVVVNVMDVRSG----G  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~--------~~~~~~~~~~lVlDEad~----~  161 (175)
                      |+.|+++.++++..     .++.++|+.+..       .+++++|++..        ....+++++++|+||||+    +
T Consensus       239 La~Q~~~~l~~~~~-----~VglltGd~~~~-------~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~  306 (1108)
T 3l9o_A          239 LSNQKYRELLAEFG-----DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKE  306 (1108)
T ss_dssp             HHHHHHHHHHHHTS-----SEEEECSSCBCC-------CSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHH
T ss_pred             HHHHHHHHHHHHhC-----CccEEeCccccC-------CCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccc
Confidence            99999999888753     577788988743       34789998322        234477899999999964    5


Q ss_pred             CHHHHHHHHh
Q psy1539         162 WWLDLEALIL  171 (175)
Q Consensus       162 f~~~v~~il~  171 (175)
                      |...++.++.
T Consensus       307 rg~~~e~ii~  316 (1108)
T 3l9o_A          307 RGVVWEETII  316 (1108)
T ss_dssp             HHHHHHHHHH
T ss_pred             hHHHHHHHHH
Confidence            6666776654

>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=99.84  E-value=8.5e-21  Score=175.80  Aligned_cols=145  Identities=19%  Similarity=0.122  Sum_probs=114.5

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      |+++..+++.+.+|+.++|+|.++++.+++ ++|++++||||||||++|.+|+++.+... ++.+++|++|+|+||.|++
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~-~~~kavyi~P~raLa~q~~  989 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS-SEGRCVYITPMEALAEQVY  989 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC-TTCCEEEECSCHHHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC-CCCEEEEEcChHHHHHHHH
Confidence            456788899999999999999999999986 58899999999999999999999998764 3458999999999999999


Q ss_pred             HHHHHH-HhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe-------ecC---ccCCCCceEEEEeCCCC---CCHHH
Q psy1539         100 KEYERF-SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL-------VNY---ETNLSGVVVNVMDVRSG---GWWLD  165 (175)
Q Consensus       100 ~~~~~~-~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l-------~~~---~~~~~~~~~lVlDEad~---~f~~~  165 (175)
                      +.+++. .+.. ++++..++|+.+.  +.+.+. +++|+|++       .++   ...+++++++|+||+|+   .....
T Consensus       990 ~~~~~~f~~~~-g~~V~~ltGd~~~--~~~~~~-~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~rg~~ 1065 (1724)
T 4f92_B          990 MDWYEKFQDRL-NKKVVLLTGETST--DLKLLG-KGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPV 1065 (1724)
T ss_dssp             HHHHHHHTTTS-CCCEEECCSCHHH--HHHHHH-HCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGSTTHHH
T ss_pred             HHHHHHhchhc-CCEEEEEECCCCc--chhhcC-CCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCCCCcc
Confidence            998764 4445 8999999998753  333343 46999992       222   23467899999999952   34444


Q ss_pred             HHHHH
Q psy1539         166 LEALI  170 (175)
Q Consensus       166 v~~il  170 (175)
                      ++.++
T Consensus      1066 le~il 1070 (1724)
T 4f92_B         1066 LEVIC 1070 (1724)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44444

>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=99.84  E-value=6e-21  Score=165.34  Aligned_cols=133  Identities=17%  Similarity=0.195  Sum_probs=110.1

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      ..|+ .|+++|..++|.+++|+  +..++||+|||++|.+|++.....   +.+++|++||++||.|..+++..+.+.+ 
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~---g~~v~VvTpTreLA~Qdae~m~~l~~~l-  179 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA---GNGVHIVTVNDYLAKRDSEWMGRVHRFL-  179 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT---TSCEEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh---CCCeEEEeCCHHHHHHHHHHHHHHHhhc-
Confidence            4688 89999999999999998  999999999999999999754432   4579999999999999999999999998 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEee---------cC------ccCCCCceEEEEeCCCC---------------
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV---------NY------ETNLSGVVVNVMDVRSG---------------  160 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~---------~~------~~~~~~~~~lVlDEad~---------------  160 (175)
                      ++++++++||.+...  +....+++|++|+.         ++      ...++++.++|+||||.               
T Consensus       180 GLsv~~i~gg~~~~~--r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg~  257 (922)
T 1nkt_A          180 GLQVGVILATMTPDE--RRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISGP  257 (922)
T ss_dssp             TCCEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEEE
T ss_pred             CCeEEEEeCCCCHHH--HHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecCC
Confidence            999999999987543  33444689999922         22      35678999999999952               


Q ss_pred             -----CCHHHHHHHHhh
Q psy1539         161 -----GWWLDLEALILS  172 (175)
Q Consensus       161 -----~f~~~v~~il~~  172 (175)
                           +|..+++.|+..
T Consensus       258 ~~~~~~~y~~i~~iv~~  274 (922)
T 1nkt_A          258 ADGASNWYTEFARLAPL  274 (922)
T ss_dssp             CCCCHHHHHHHHHHHHH
T ss_pred             CCcchhHHHHHHHHHHh
Confidence                 466788888754

>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=99.83  E-value=2e-20  Score=173.32  Aligned_cols=123  Identities=19%  Similarity=0.238  Sum_probs=103.1

Q ss_pred             CCCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhhcC--------CCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          33 PFREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLETT--------DSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~~~--------~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      ||++++++|++++|.+++ ++|++++||||||||++|.+|+++.+...        .++.+++|++|+|+|++|+++.++
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            799999999999998875 79999999999999999999999988642        346799999999999999999999


Q ss_pred             HHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-------eecC---ccCCCCceEEEEeCCC
Q psy1539         104 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-------LVNY---ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       104 ~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~---~~~~~~~~~lVlDEad  159 (175)
                      +..+.. |++|..++|+.+.....   ..+++|+|+       +.++   ...+++++++|+||++
T Consensus       156 ~~~~~~-gi~V~~~tGd~~~~~~~---~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH  217 (1724)
T 4f92_B          156 KRLATY-GITVAELTGDHQLCKEE---ISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIH  217 (1724)
T ss_dssp             HHHTTT-TCCEEECCSSCSSCCTT---GGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGG
T ss_pred             HHHhhC-CCEEEEEECCCCCCccc---cCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecch
Confidence            888877 99999999998754321   245799999       2332   2246799999999993

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.82  E-value=5e-20  Score=159.57  Aligned_cols=120  Identities=17%  Similarity=0.023  Sum_probs=101.1

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      ..|+ .|+++|..++|.+++|+  +..+.||+|||++|.+|++....   .+.+++|++||++||.|.++++..+.+.+ 
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL---~G~qv~VvTPTreLA~Qdae~m~~l~~~l-  147 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNAL---TGKGVHVVTVNDYLARRDAEWMGPVYRGL-  147 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHT---TCSCCEEEESSHHHHHHHHHHHHHHHHTT-
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHH---hCCCEEEEeCCHHHHHHHHHHHHHHHHhc-
Confidence            3688 89999999999999999  89999999999999999965443   24579999999999999999999999988 


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEee---------cC------ccCCC---CceEEEEeCCC
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV---------NY------ETNLS---GVVVNVMDVRS  159 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~---------~~------~~~~~---~~~~lVlDEad  159 (175)
                      ++++.+++||.+.+  .+....+++|++|+.         ++      ...++   ++.++|+||+|
T Consensus       148 GLsv~~i~Gg~~~~--~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaD  212 (997)
T 2ipc_A          148 GLSVGVIQHASTPA--ERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVD  212 (997)
T ss_dssp             TCCEEECCTTCCHH--HHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHH
T ss_pred             CCeEEEEeCCCCHH--HHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechH
Confidence            99999999998743  344445789999921         11      24577   89999999996

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.82  E-value=6.1e-20  Score=152.76  Aligned_cols=132  Identities=15%  Similarity=0.199  Sum_probs=108.3

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEE
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKV  114 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v  114 (175)
                      ..|+|+|.++++.+++++++++++|||+|||++|+.++...+..  ...+++|++||++|+.|+.+.++++... ++.++
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~--~~~~vlvl~P~~~L~~Q~~~~~~~~~~~-~~~~v  188 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLF-SHAMI  188 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH--CSSEEEEEESSHHHHHHHHHHHHHTTSS-CGGGE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC--CCCeEEEEECcHHHHHHHHHHHHHhhcC-Cccce
Confidence            37999999999999999999999999999999999999887754  2348999999999999999999888544 36788


Q ss_pred             EEEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         115 GVFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       115 ~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      ..++|+.+..++   +..+.+++|++.+.     ...+++++++|+||++.....+.+.++..
T Consensus       189 ~~~~~~~~~~~~---~~~~~~I~i~T~~~l~~~~~~~~~~~~liIiDE~H~~~~~~~~~il~~  248 (510)
T 2oca_A          189 KKIGGGASKDDK---YKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISG  248 (510)
T ss_dssp             EECGGGCCTTGG---GCTTCSEEEEEHHHHTTSCGGGGGGEEEEEEETGGGCCHHHHHHHGGG
T ss_pred             EEEecCCccccc---cccCCcEEEEeHHHHhhchhhhhhcCCEEEEECCcCCCcccHHHHHHh
Confidence            888888775544   34567899983332     35578899999999988777888887654

>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=99.81  E-value=5.9e-20  Score=142.45  Aligned_cols=131  Identities=15%  Similarity=0.191  Sum_probs=103.4

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|.++++.++++.+.++++|||+|||++++.++...+..  +..++||++||++|+.|+.+.++++.... ...+.
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~--~~~~~lil~Pt~~L~~q~~~~l~~~~~~~-~~~~~  189 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLFS-HAMIK  189 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH--CSSEEEEECSSHHHHHHHHHHHHHHTSCC-GGGEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc--CCCeEEEEECCHHHHHHHHHHHHHhcccc-cceEE
Confidence            7999999999999988889999999999999998888776653  23389999999999999999999886543 66777


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      .++||.....   ....+.+++|++.+.     ...+++++++|+||||....+.++.++..
T Consensus       190 ~~~~~~~~~~---~~~~~~~I~v~T~~~l~~~~~~~~~~~~~vIiDEaH~~~~~~~~~il~~  248 (282)
T 1rif_A          190 KIGGGASKDD---KYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISG  248 (282)
T ss_dssp             ECSTTCSSTT---CCCTTCSEEEECHHHHTTSCGGGGGGEEEEEEETGGGCCHHHHHHHTTT
T ss_pred             EEeCCCcchh---hhccCCcEEEEchHHHHhhHHHHHhhCCEEEEECCccCCcccHHHHHHH
Confidence            7888765332   122357888883322     33567899999999987777778777664

>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=99.81  E-value=6.8e-19  Score=158.69  Aligned_cols=147  Identities=16%  Similarity=0.177  Sum_probs=114.6

Q ss_pred             CCCCHHHHHHH-hhCCCCCCcHHHHHhHHHHhc----CC--cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          19 RNRREKEDRIG-ESQPFREQTSFQHECIPQAVL----GM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        19 ~~l~~~l~~~l-~~~g~~~~t~~Q~~~i~~~~~----g~--~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ++.++...+.+ ..++|. +||+|.++++.+++    |+  |+++++|||+|||++|+.+++..+.   .+.+++|++||
T Consensus       586 ~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~---~g~~vlvlvPt  661 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD---NHKQVAVLVPT  661 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT---TTCEEEEECSS
T ss_pred             CCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH---hCCeEEEEech
Confidence            45566666665 455775 69999999999886    65  9999999999999999988887654   35599999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhcC-CCeEEE---eecCccCCCCceEEEEeCCCCCCHH
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTH-NPQIVG---LVNYETNLSGVVVNVMDVRSGGWWL  164 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEad~~f~~  164 (175)
                      ++|+.|+++.+++..... ++++..+.|..+.++.   .+.+.++ ++++|+   +++....+++++++|+||+|. |..
T Consensus       662 ~~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvIiDEaH~-~g~  739 (1151)
T 2eyq_A          662 TLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHR-FGV  739 (1151)
T ss_dssp             HHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGG-SCH
T ss_pred             HHHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEEEechHh-cCh
Confidence            999999999999887766 7888888887664443   3445554 788988   444567889999999999975 444


Q ss_pred             HHHHHHh
Q psy1539         165 DLEALIL  171 (175)
Q Consensus       165 ~v~~il~  171 (175)
                      +.+.++.
T Consensus       740 ~~~~~l~  746 (1151)
T 2eyq_A          740 RHKERIK  746 (1151)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4555554

>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=99.81  E-value=1.7e-20  Score=161.33  Aligned_cols=123  Identities=22%  Similarity=0.233  Sum_probs=100.0

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEecCHHHHHHH-HHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTRELAFQI-SKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~Pt~~L~~q~-~~~~~~~~~~~~~  111 (175)
                      .|+|+|.++++.+++|+|+++.+|||+|||++|++|++..+...   ..+.++||++|+++|+.|+ .+.++++...  +
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~--~   84 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK--W   84 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT--T
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc--C
Confidence            68999999999999999999999999999999999999887643   2235899999999999999 9999998764  4


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEE----ee----------cCccCCCCceEEEEeCCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVG----LV----------NYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~----------~~~~~~~~~~~lVlDEad~  160 (175)
                      +++..++|+....+....+..+.+++|+    +.          .....+.+++++|+||||.
T Consensus        85 ~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~  147 (699)
T 4gl2_A           85 YRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHH  147 (699)
T ss_dssp             SCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGG
T ss_pred             ceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccc
Confidence            8899999998777666777778899998    21          1235678899999999963

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.80  E-value=3.7e-19  Score=158.58  Aligned_cols=127  Identities=22%  Similarity=0.212  Sum_probs=102.9

Q ss_pred             HhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          29 GESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      ....+|. |+|+|.++++.+.+|+++++++|||||||++|.+|++..+.   .+.+++|++||++|+.|+++.++++.. 
T Consensus        80 ~~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~---~g~rvL~l~PtkaLa~Q~~~~l~~~~~-  154 (1010)
T 2xgj_A           80 ARTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK---NKQRVIYTSPIKALSNQKYRELLAEFG-  154 (1010)
T ss_dssp             SCCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH---TTCEEEEEESSHHHHHHHHHHHHHHHS-
T ss_pred             HHhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc---cCCeEEEECChHHHHHHHHHHHHHHhC-
Confidence            4455675 99999999999999999999999999999999999998875   346999999999999999999888763 


Q ss_pred             CCCeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC----CCCHHHHHHHHh
Q psy1539         109 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS----GGWWLDLEALIL  171 (175)
Q Consensus       109 ~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad----~~f~~~v~~il~  171 (175)
                          +++.++|+.+...       .++++|++.        +....+++++++|+||+|    .++....+.++.
T Consensus       155 ----~vglltGd~~~~~-------~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~  218 (1010)
T 2xgj_A          155 ----DVGLMTGDITINP-------DAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETII  218 (1010)
T ss_dssp             ----CEEEECSSCEECT-------TCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHH
T ss_pred             ----CEEEEeCCCccCC-------CCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHH
Confidence                5778889886543       468888832        224567899999999995    456666665543

>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=99.78  E-value=1.5e-18  Score=141.57  Aligned_cols=120  Identities=18%  Similarity=0.202  Sum_probs=98.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+|+|.++++.++++ ++++.+|||+|||++++.+++..+.  ..+.++||++|+++|+.|+.+.++++... +..++.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~-~~~~v~   84 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNL-PPEKIV   84 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCS-CGGGEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCc-chhheE
Confidence            6899999999999999 9999999999999999999988776  24558999999999999999999988632 255888


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCCC
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad~  160 (175)
                      .++|+....+....+ .+++++|+..        .....+.+++++|+|||+.
T Consensus        85 ~~~g~~~~~~~~~~~-~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~  136 (494)
T 1wp9_A           85 ALTGEKSPEERSKAW-ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHR  136 (494)
T ss_dssp             EECSCSCHHHHHHHH-HHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGG
T ss_pred             EeeCCcchhhhhhhc-cCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcc
Confidence            999988765544443 3578999822        2245678999999999964

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.78  E-value=5e-19  Score=157.60  Aligned_cols=127  Identities=18%  Similarity=0.235  Sum_probs=100.7

Q ss_pred             hCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          31 SQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        31 ~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      ..+| .|+++|.++++.+++|+|+++.+|||||||++|.+|+...+.   .+.+++|++|+++|+.|+++.++++.   +
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~---~g~~vlvl~PtraLa~Q~~~~l~~~~---~  107 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR---NMTKTIYTSPIKALSNQKFRDFKETF---D  107 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH---TTCEEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh---cCCeEEEEeCCHHHHHHHHHHHHHHc---C
Confidence            4456 489999999999999999999999999999999999987754   45689999999999999988887654   3


Q ss_pred             CeEEEEEECCCchHHhHHHHhcCCCeEEEee--------cCccCCCCceEEEEeCCC----CCCHHHHHHHHh
Q psy1539         111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS----GGWWLDLEALIL  171 (175)
Q Consensus       111 ~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad----~~f~~~v~~il~  171 (175)
                      ++++..++|+.+...       ..+++|++.        .....+++++++|+||||    .+|....+.++.
T Consensus       108 ~~~v~~l~G~~~~~~-------~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~  173 (997)
T 4a4z_A          108 DVNIGLITGDVQINP-------DANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVII  173 (997)
T ss_dssp             -CCEEEECSSCEECT-------TSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHH
T ss_pred             CCeEEEEeCCCccCC-------CCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHH
Confidence            678999999886443       368888822        224457899999999994    456666666654

>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=99.76  E-value=4.9e-18  Score=128.50  Aligned_cols=127  Identities=15%  Similarity=0.125  Sum_probs=90.2

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCC--CeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      ...++++|.++++.+.+|++++++||||||||+++.++++........  +.++++++|+++++.|+.+.+........+
T Consensus        59 ~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~  138 (235)
T 3llm_A           59 LLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPG  138 (235)
T ss_dssp             TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTT
T ss_pred             cCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccC
Confidence            345799999999999999999999999999999999999887654332  458999999999999998877665432213


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEEee----cC-ccCCCCceEEEEeCCCC-CCHHH
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVGLV----NY-ETNLSGVVVNVMDVRSG-GWWLD  165 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~----~~-~~~~~~~~~lVlDEad~-~f~~~  165 (175)
                      ..++.-......     ....+++++|++.    +. ...+++++++|+||||. ++..+
T Consensus       139 ~~~g~~~~~~~~-----~~~~~~~Ivv~Tpg~l~~~l~~~l~~~~~lVlDEah~~~~~~~  193 (235)
T 3llm_A          139 KSCGYSVRFESI-----LPRPHASIMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINTD  193 (235)
T ss_dssp             SSEEEEETTEEE-----CCCSSSEEEEEEHHHHHHHHHHCCTTCCEEEECCTTSCCHHHH
T ss_pred             ceEEEeechhhc-----cCCCCCeEEEECHHHHHHHHHhhhcCCcEEEEECCccCCcchH
Confidence            344332221110     0113467888833    22 22589999999999975 34433

>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=99.73  E-value=1.2e-17  Score=137.62  Aligned_cols=105  Identities=19%  Similarity=0.171  Sum_probs=85.8

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE-E
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK-V  114 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~-v  114 (175)
                      .|+|+|.++++.+++++++++++|||+|||++|+.++...      +.++||++|+++|+.|+.+.++++     +++ +
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~-----~~~~v  161 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-----GEEYV  161 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG-----CGGGE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC-----CCcce
Confidence            5899999999999999999999999999999999988764      347999999999999988888773     677 8


Q ss_pred             EEEECCCchHHhHHHHhcCCCeEEEeecC----c-cCCCCceEEEEeCCCC
Q psy1539         115 GVFFGGLPIQKDEEYLKTHNPQIVGLVNY----E-TNLSGVVVNVMDVRSG  160 (175)
Q Consensus       115 ~~~~g~~~~~~~~~~l~~~~~iiv~l~~~----~-~~~~~~~~lVlDEad~  160 (175)
                      ..++|+.+.         ..+++|++.+.    . ....+++++|+||++.
T Consensus       162 ~~~~g~~~~---------~~~Ivv~T~~~l~~~~~~~~~~~~liIvDEaH~  203 (472)
T 2fwr_A          162 GEFSGRIKE---------LKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHH  203 (472)
T ss_dssp             EEBSSSCBC---------CCSEEEEEHHHHHHTHHHHTTTCSEEEEETGGG
T ss_pred             EEECCCcCC---------cCCEEEEEcHHHHHHHHHhcCCCCEEEEECCcC
Confidence            888887652         36888883332    1 1125699999999954

>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=99.73  E-value=4.7e-17  Score=123.45  Aligned_cols=115  Identities=18%  Similarity=0.122  Sum_probs=88.3

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE-E
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK-V  114 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~-v  114 (175)
                      .|+++|.++++.+++++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.++++     +++ +
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~-----~~~~v  161 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-----GEEYV  161 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG-----CGGGE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC-----CCCeE
Confidence            6899999999999999999999999999999988877653      347999999999999988887763     566 7


Q ss_pred             EEEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         115 GVFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       115 ~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      ..+.|+...         ..+++|++.+.     .....+++++|+||++.......+.++
T Consensus       162 ~~~~g~~~~---------~~~i~v~T~~~l~~~~~~~~~~~~llIiDEaH~l~~~~~~~i~  213 (237)
T 2fz4_A          162 GEFSGRIKE---------LKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIA  213 (237)
T ss_dssp             EEESSSCBC---------CCSEEEEEHHHHHHTHHHHTTTCSEEEEECSSCCCTTTHHHHH
T ss_pred             EEEeCCCCC---------cCCEEEEeHHHHHhhHHHhcccCCEEEEECCccCCChHHHHHH
Confidence            777776642         46888883332     112256899999999765444444443

>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=99.71  E-value=1.1e-18  Score=148.76  Aligned_cols=135  Identities=11%  Similarity=0.015  Sum_probs=90.9

Q ss_pred             CCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHH
Q psy1539          19 RNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI   98 (175)
Q Consensus        19 ~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~   98 (175)
                      +++++.+.+++... ...++|+|+.++|.+++|+|+++++|||||||++|++|+++.+..  ++.++||++|||+|+.|+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~--~~~~vLvl~PtreLa~Qi  231 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK--RRLRTLILAPTRVVAAEM  231 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh--CCCeEEEEcChHHHHHHH
Confidence            56777777777764 478999999999999999999999999999999999999998765  457899999999999998


Q ss_pred             HHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-eecC--------ccCCCCceEEEEeCCCCC---CHHHH
Q psy1539          99 SKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-LVNY--------ETNLSGVVVNVMDVRSGG---WWLDL  166 (175)
Q Consensus        99 ~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-l~~~--------~~~~~~~~~lVlDEad~~---f~~~v  166 (175)
                      .+.++       +..+. +.++. ..    .. ..+.-++- +...        ...+++++++|+||||..   |..++
T Consensus       232 ~~~l~-------~~~v~-~~~~~-l~----~~-~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~  297 (618)
T 2whx_A          232 EEALR-------GLPIR-YQTPA-VK----SD-HTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAAR  297 (618)
T ss_dssp             HHHTT-------TSCEE-ECCTT-SS----CC-CCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEESTTCCSHHHHHHH
T ss_pred             HHHhc-------CCcee-Eeccc-ce----ec-cCCCceEEEEChHHHHHHHhccccccCCeEEEEECCCCCCccHHHHH
Confidence            87765       22232 22211 00    00 11111221 1111        234789999999999753   55555


Q ss_pred             HHHH
Q psy1539         167 EALI  170 (175)
Q Consensus       167 ~~il  170 (175)
                      ..|+
T Consensus       298 ~~i~  301 (618)
T 2whx_A          298 GYIS  301 (618)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>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=99.70  E-value=4.1e-18  Score=140.36  Aligned_cols=114  Identities=11%  Similarity=0.039  Sum_probs=81.5

Q ss_pred             CCCCCcHHHHHhHHHHhcCCcE-EEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          33 PFREQTSFQHECIPQAVLGMDI-LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g~~~-ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      |+..|+|+|+ ++|.+++|+++ ++++|||||||++|++|++..+..  .+.+++|++|||+|+.|+.+.+.       +
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~-------g   70 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL--RRLRTLILAPTRVVAAEMEEALR-------G   70 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT-------T
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh--cCCcEEEECCCHHHHHHHHHHhc-------C
Confidence            7889999985 79999999877 999999999999999999987664  45689999999999999988774       3


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEE----eecC---ccCCCCceEEEEeCCCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY---ETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~---~~~~~~~~~lVlDEad~~  161 (175)
                      ..+....+...  .   ....+..+.++    +.+.   ...+++++++|+||||..
T Consensus        71 ~~v~~~~~~~~--~---~~~~~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~  122 (451)
T 2jlq_A           71 LPIRYQTPAVK--S---DHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFT  122 (451)
T ss_dssp             SCEEECCTTCS--C---CCCSSCCEEEEEHHHHHHHHHHCSCCCCCSEEEEETTTCC
T ss_pred             ceeeeeecccc--c---cCCCCceEEEEChHHHHHHhhCcccccCCCEEEEeCCccC
Confidence            33322111111  0   01112234443    1111   245789999999999853

>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=99.67  E-value=1e-17  Score=142.95  Aligned_cols=118  Identities=14%  Similarity=0.019  Sum_probs=90.1

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEE
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGV  116 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~  116 (175)
                      +.++|.++++.+.++++++++||||||||.+|.+|+++.      +.+++|++|||+|+.|+.+.+.+..    +..+..
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~----g~~vg~  287 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH----GIDPNI  287 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH----SCCCEE
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh----CCCeeE
Confidence            445666666666688999999999999999999998762      4589999999999999988766554    555667


Q ss_pred             EECCCchHHhHHHHhcCCCeEEE-----eecCccCCCCceEEEEeCC---CCCCHHHHHHHHh
Q psy1539         117 FFGGLPIQKDEEYLKTHNPQIVG-----LVNYETNLSGVVVNVMDVR---SGGWWLDLEALIL  171 (175)
Q Consensus       117 ~~g~~~~~~~~~~l~~~~~iiv~-----l~~~~~~~~~~~~lVlDEa---d~~f~~~v~~il~  171 (175)
                      .+|+..       +..+.+++|+     +.+..+.+++++++|+|||   +.+|..++..|+.
T Consensus       288 ~vG~~~-------~~~~~~IlV~TPGrLl~~~~l~l~~l~~lVlDEAH~l~~~~~~~l~~Il~  343 (666)
T 3o8b_A          288 RTGVRT-------ITTGAPVTYSTYGKFLADGGCSGGAYDIIICDECHSTDSTTILGIGTVLD  343 (666)
T ss_dssp             ECSSCE-------ECCCCSEEEEEHHHHHHTTSCCTTSCSEEEETTTTCCSHHHHHHHHHHHH
T ss_pred             EECcEe-------ccCCCCEEEECcHHHHhCCCcccCcccEEEEccchhcCccHHHHHHHHHH
Confidence            777764       2346789998     3333677889999999999   3456666666654

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.67  E-value=2.3e-16  Score=132.86  Aligned_cols=80  Identities=19%  Similarity=0.249  Sum_probs=68.4

Q ss_pred             CCCCCcHHHHHhHHH----HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhh
Q psy1539          33 PFREQTSFQHECIPQ----AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  108 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~----~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  108 (175)
                      || .++|.|.+.+..    +.+|+++++.+|||+|||++|++|++.      .+.+++|++||++|+.|+.+.+..+.+.
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~------~~~~v~i~~pt~~l~~q~~~~~~~l~~~   73 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE------VKPKVLFVVRTHNEFYPIYRDLTKIREK   73 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH------HCSEEEEEESSGGGHHHHHHHHTTCCCS
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh------CCCeEEEEcCCHHHHHHHHHHHHHHhhh
Confidence            45 689999997764    457899999999999999999999997      2458999999999999999999888766


Q ss_pred             CCCeEEEEEECC
Q psy1539         109 MSNIKVGVFFGG  120 (175)
Q Consensus       109 ~~~i~v~~~~g~  120 (175)
                      . ++++..+.|.
T Consensus        74 ~-~~~~~~l~gr   84 (551)
T 3crv_A           74 R-NITFSFLVGK   84 (551)
T ss_dssp             S-CCCEEECCCH
T ss_pred             c-CccEEEEccc
Confidence            6 7888877774

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.67  E-value=3.3e-18  Score=146.88  Aligned_cols=118  Identities=14%  Similarity=0.115  Sum_probs=83.0

Q ss_pred             HHhhCCCC-----CCcHHHH-----HhHHHHh------cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          28 IGESQPFR-----EQTSFQH-----ECIPQAV------LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        28 ~l~~~g~~-----~~t~~Q~-----~~i~~~~------~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      ++...||.     .||++|+     ++||.++      +|+|+++++|||||||++|++|+++.+..  ++.+++|++||
T Consensus       202 ~l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~--~~~~~lilaPT  279 (673)
T 2wv9_A          202 GLYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ--KRLRTAVLAPT  279 (673)
T ss_dssp             EEEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH--TTCCEEEEESS
T ss_pred             EeeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEccH
Confidence            56677777     8999999     9999888      89999999999999999999999988765  45789999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE-eecC--------ccCCCCceEEEEeCCCCC
Q psy1539          92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG-LVNY--------ETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus        92 ~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~-l~~~--------~~~~~~~~~lVlDEad~~  161 (175)
                      ++|+.|+++.++.+     ++.  ...+..  .    .. ..+.-++. +.+.        ...+++++++|+||||..
T Consensus       280 r~La~Q~~~~l~~~-----~i~--~~~~~l--~----~v-~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~  344 (673)
T 2wv9_A          280 RVVAAEMAEALRGL-----PVR--YLTPAV--Q----RE-HSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFT  344 (673)
T ss_dssp             HHHHHHHHHHTTTS-----CCE--ECCC---------CC-CCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEESTTCC
T ss_pred             HHHHHHHHHHHhcC-----Cee--eecccc--c----cc-CCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCCccc
Confidence            99999998877643     222  111100  0    01 11222222 1111        136889999999999864

>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=99.60  E-value=4.5e-15  Score=129.32  Aligned_cols=143  Identities=13%  Similarity=0.074  Sum_probs=98.6

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhc-CCcEEEEcCCCChHHHHHHHHHHHhhh--cCCCCeEEEE
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVL-GMDILCQAKSGMGKTAVFVLATLQQLE--TTDSNVYVLV   87 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~-g~~~ii~a~TGsGKT~~~~~~~l~~l~--~~~~~~~~li   87 (175)
                      .+...|+++++++.+.+.+.+.+ ..|++.|+++|+.++. |+++++++|||||||+  ++|++....  ....+.++++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~~~g~~ilv  145 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPHLENTQVAC  145 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGGGGTCEEEE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccccCCCceEEe
Confidence            34667999999999999999988 7899999999988775 5789999999999998  455552221  1122568999


Q ss_pred             EecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCC-chHHhHHHHhcCCCeEEEe----ec---CccCCCCceEEEEeCCC
Q psy1539          88 MCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYLKTHNPQIVGL----VN---YETNLSGVVVNVMDVRS  159 (175)
Q Consensus        88 l~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~-~~~~~~~~l~~~~~iiv~l----~~---~~~~~~~~~~lVlDEad  159 (175)
                      ++|+|+|+.|+.+.+....    +..+...+|.. .....   ...+.++++++    .+   ....+.+++++|+||++
T Consensus       146 l~P~r~La~q~~~~l~~~~----~~~v~~~vG~~i~~~~~---~~~~~~I~v~T~G~l~r~l~~~~~l~~~~~lIlDEah  218 (773)
T 2xau_A          146 TQPRRVAAMSVAQRVAEEM----DVKLGEEVGYSIRFENK---TSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAH  218 (773)
T ss_dssp             EESCHHHHHHHHHHHHHHT----TCCBTTTEEEEETTEEE---CCTTCSEEEEEHHHHHHHHHHSTTCTTEEEEEECSGG
T ss_pred             cCchHHHHHHHHHHHHHHh----CCchhheecceeccccc---cCCCCCEEEECHHHHHHHHhhCccccCCCEEEecCcc
Confidence            9999999999887665443    22222222211 00000   11245777772    11   13568899999999997


Q ss_pred             C-CCH
Q psy1539         160 G-GWW  163 (175)
Q Consensus       160 ~-~f~  163 (175)
                      . +..
T Consensus       219 ~R~ld  223 (773)
T 2xau_A          219 ERTLA  223 (773)
T ss_dssp             GCCHH
T ss_pred             ccccc
Confidence            4 443

>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=99.58  E-value=3.9e-15  Score=132.78  Aligned_cols=122  Identities=19%  Similarity=0.162  Sum_probs=90.1

Q ss_pred             CCcHHHHHhHHHHhc--------------CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVL--------------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~--------------g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      .|+|+|.+|++.+++              +++.+++++||||||+++ ++++..+.......++|||+|+++|+.|+.+.
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            599999999998875              378999999999999997 66666554433446999999999999999998


Q ss_pred             HHHHHhhCCCeEEEEEECCCchHHhHHHHh-cCCCeEEEeecC----------ccCCCCceEEEEeCCCCCCHHH
Q psy1539         102 YERFSKYMSNIKVGVFFGGLPIQKDEEYLK-THNPQIVGLVNY----------ETNLSGVVVNVMDVRSGGWWLD  165 (175)
Q Consensus       102 ~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~-~~~~iiv~l~~~----------~~~~~~~~~lVlDEad~~f~~~  165 (175)
                      ++.+...  .     +.++.+.....+.+. .+.+++|++.+.          ...+++..++|+||||.+...+
T Consensus       350 f~~f~~~--~-----v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~~  417 (1038)
T 2w00_A          350 YQRFSPD--S-----VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGE  417 (1038)
T ss_dssp             HHTTSTT--C-----SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHHH
T ss_pred             HHHhccc--c-----cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcchH
Confidence            8877542  1     234455455555664 467888884333          1135678999999998765443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.57  E-value=2.5e-15  Score=127.23  Aligned_cols=113  Identities=19%  Similarity=0.150  Sum_probs=68.6

Q ss_pred             CCcHHHHHhHHHHhc----C-CcEEEEcCCCChHHHHHHHHHHHhhhcCC-------CCeEEEEEecCHHHHHHHH-HHH
Q psy1539          36 EQTSFQHECIPQAVL----G-MDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVYVLVMCHTRELAFQIS-KEY  102 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~----g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~-------~~~~~lil~Pt~~L~~q~~-~~~  102 (175)
                      .|+++|.++++.+++    | +++++++|||||||++++. ++..+....       .+.++||++||++|+.|+. +.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~-~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQ-ISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHH-HHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            699999999998876    4 6799999999999999654 444443333       5679999999999999988 666


Q ss_pred             HHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecC------------ccCCCCceEEEEeCCCCCC
Q psy1539         103 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY------------ETNLSGVVVNVMDVRSGGW  162 (175)
Q Consensus       103 ~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~------------~~~~~~~~~lVlDEad~~f  162 (175)
                      +.+.     ..+..+.++.        ...+.+++|++.+.            .+...+++++|+||||...
T Consensus       257 ~~~~-----~~~~~~~~~~--------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~  315 (590)
T 3h1t_A          257 TPFG-----DARHKIEGGK--------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGS  315 (590)
T ss_dssp             TTTC-----SSEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC---
T ss_pred             Hhcc-----hhhhhhhccC--------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCcccc
Confidence            6443     2333333332        12356888883322            2345678999999997554

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.56  E-value=9.9e-15  Score=125.31  Aligned_cols=133  Identities=12%  Similarity=0.010  Sum_probs=89.9

Q ss_pred             CHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          22 REKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        22 ~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      ..+.++++.++.+    |.|.......++|++++++||||||||+    +++..+....   +++|++|||+||.|+++.
T Consensus       130 ~~d~l~~i~dl~~----p~~~~p~ar~l~rk~vlv~apTGSGKT~----~al~~l~~~~---~gl~l~PtR~LA~Qi~~~  198 (677)
T 3rc3_A          130 CKDDLRKISDLRI----PPNWYPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSAK---SGVYCGPLKLLAHEIFEK  198 (677)
T ss_dssp             CHHHHHHHTBCCC----GGGGCHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHSS---SEEEEESSHHHHHHHHHH
T ss_pred             CHHHHHHHhhccC----hhhhCHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhcC---CeEEEeCHHHHHHHHHHH
Confidence            3344455544332    3444444566789999999999999998    3444444332   459999999999999998


Q ss_pred             HHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCC----CCCHHHHHHHHhh
Q psy1539         102 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRS----GGWWLDLEALILS  172 (175)
Q Consensus       102 ~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad----~~f~~~v~~il~~  172 (175)
                      +++.     ++++..++|+...-..  .-....+++++........++++++|+||+|    .+|..+++.++..
T Consensus       199 l~~~-----g~~v~lltG~~~~iv~--TpGr~~~il~~T~e~~~l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~  266 (677)
T 3rc3_A          199 SNAA-----GVPCDLVTGEERVTVQ--PNGKQASHVSCTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALLG  266 (677)
T ss_dssp             HHHT-----TCCEEEECSSCEECCS--TTCCCCSEEEEEGGGCCSSSCEEEEEECSGGGGGCTTTHHHHHHHHHH
T ss_pred             HHhc-----CCcEEEEECCeeEEec--CCCcccceeEecHhHhhhcccCCEEEEecceecCCccchHHHHHHHHc
Confidence            7764     7788899998754100  0001145666654443445788999999994    5788888877764

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.56  E-value=4.6e-15  Score=124.69  Aligned_cols=67  Identities=24%  Similarity=0.277  Sum_probs=54.0

Q ss_pred             CCCCCCcHHHHHhHHH----HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          32 QPFREQTSFQHECIPQ----AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~----~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      .|| .|+|+|.+++..    +.+|+++++.+|||+|||++|++|++..      +.+++|++||++|+.|+.+.+.++
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~------~~~~~~~~~t~~l~~q~~~~~~~l   74 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL------KKKVLIFTRTHSQLDSIYKNAKLL   74 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH------TCEEEEEESCHHHHHHHHHHHGGG
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC------CCcEEEEcCCHHHHHHHHHHHHhc
Confidence            467 799999998654    4578999999999999999999999764      358999999999999998877664

>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=99.55  E-value=2.4e-15  Score=124.10  Aligned_cols=99  Identities=13%  Similarity=0.094  Sum_probs=66.4

Q ss_pred             HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  126 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~  126 (175)
                      .+.+|+++++++|||||||++|++|+++.+..  .+.++||++|||+|+.|+.+.++       +..+....+.....  
T Consensus        17 ~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~-------g~~v~~~~~~~~~~--   85 (459)
T 2z83_A           17 MLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ--QRLRTAVLAPTRVVAAEMAEALR-------GLPVRYQTSAVQRE--   85 (459)
T ss_dssp             GGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH--TTCCEEEEECSHHHHHHHHHHTT-------TSCEEECC--------
T ss_pred             HHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEECchHHHHHHHHHHhc-------CceEeEEecccccC--
Confidence            45678999999999999999999999988764  45689999999999999888776       22222211111100  


Q ss_pred             HHHHhcCCCeEEEeecC--------ccCCCCceEEEEeCCCC
Q psy1539         127 EEYLKTHNPQIVGLVNY--------ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       127 ~~~l~~~~~iiv~l~~~--------~~~~~~~~~lVlDEad~  160 (175)
                          .....++..+...        ...+++++++|+||||.
T Consensus        86 ----~t~~~~i~~~~~~~l~~~l~~~~~l~~~~~iViDEaH~  123 (459)
T 2z83_A           86 ----HQGNEIVDVMCHATLTHRLMSPNRVPNYNLFVMDEAHF  123 (459)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHSCC-CCCCSEEEESSTTC
T ss_pred             ----CCCCcEEEEEchHHHHHHhhccccccCCcEEEEECCcc
Confidence                1111222211111        24578999999999985

>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=99.55  E-value=3.5e-15  Score=122.50  Aligned_cols=99  Identities=17%  Similarity=0.222  Sum_probs=69.2

Q ss_pred             HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  126 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~  126 (175)
                      .+++|+|+++++|||||||++|++|+++.+..  ++.+++|++||++|+.|+++.++.+     +  +....+....   
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~--~~~~~lil~Ptr~La~Q~~~~l~~~-----~--v~~~~~~~~~---   71 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFHGL-----D--VKFHTQAFSA---   71 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTS-----C--EEEESSCCCC---
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh--cCCeEEEEcchHHHHHHHHHHHhcC-----C--eEEeccccee---
Confidence            35689999999999999999999999998765  4578999999999999998877633     2  2222221110   


Q ss_pred             HHHHhcCCCeEEE-eecC--------ccCCCCceEEEEeCCCCC
Q psy1539         127 EEYLKTHNPQIVG-LVNY--------ETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       127 ~~~l~~~~~iiv~-l~~~--------~~~~~~~~~lVlDEad~~  161 (175)
                          ...+..++. +.+.        ...+++++++|+||+|..
T Consensus        72 ----v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~  111 (440)
T 1yks_A           72 ----HGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL  111 (440)
T ss_dssp             ----CCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC
T ss_pred             ----ccCCccceeeecccchhHhhhCcccccCccEEEEECcccc
Confidence                111222222 2211        234789999999999864

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.53  E-value=8.3e-15  Score=119.97  Aligned_cols=97  Identities=11%  Similarity=0.070  Sum_probs=65.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  129 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~  129 (175)
                      +|+++++++|||||||++|++|+++.+..  ++.+++|++||++|+.|+++.++       ++.+....|+...      
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~--~g~~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~~~------   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK--KRLRTVILAPTRVVASEMYEALR-------GEPIRYMTPAVQS------   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT-------TSCEEEC------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEECcHHHHHHHHHHHhC-------CCeEEEEecCccc------
Confidence            47899999999999999999999976654  45689999999999999887664       4445544443221      


Q ss_pred             HhcCCCeEEEeecC--------ccCCCCceEEEEeCCCCC
Q psy1539         130 LKTHNPQIVGLVNY--------ETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       130 l~~~~~iiv~l~~~--------~~~~~~~~~lVlDEad~~  161 (175)
                      ......++..+...        ...+++++++|+||+|..
T Consensus        66 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~l~~vViDEaH~~  105 (431)
T 2v6i_A           66 ERTGNEIVDFMCHSTFTMKLLQGVRVPNYNLYIMDEAHFL  105 (431)
T ss_dssp             ---CCCSEEEEEHHHHHHHHHHTCCCCCCSEEEEESTTCC
T ss_pred             cCCCCceEEEEchHHHHHHHhcCccccCCCEEEEeCCccC
Confidence            11111222221111        334889999999999753

>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=3.9e-13  Score=114.60  Aligned_cols=83  Identities=24%  Similarity=0.285  Sum_probs=70.6

Q ss_pred             CCcHHHHHhHH----HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIP----QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~----~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .|+|.|.+.+.    .+.+|+++++.||||+|||++|++|++..+..  .+.+++|++||++++.|+.+.++.+.... +
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~--~~~kvli~t~T~~l~~Qi~~el~~l~~~~-~   79 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE--RKLKVLYLVRTNSQEEQVIKELRSLSSTM-K   79 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH--HTCEEEEEESSHHHHHHHHHHHHHHHHHS-C
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh--cCCeEEEECCCHHHHHHHHHHHHHHhhcc-C
Confidence            57999999885    44579999999999999999999999998764  34689999999999999999999998876 7


Q ss_pred             eEEEEEECCC
Q psy1539         112 IKVGVFFGGL  121 (175)
Q Consensus       112 i~v~~~~g~~  121 (175)
                      +++..+.|+.
T Consensus        80 ~~~~~l~gr~   89 (620)
T 4a15_A           80 IRAIPMQGRV   89 (620)
T ss_dssp             CCEEECCCHH
T ss_pred             eEEEEEECCC
Confidence            8888777753

>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=99.38  E-value=7.5e-13  Score=109.71  Aligned_cols=114  Identities=16%  Similarity=0.167  Sum_probs=81.9

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .|+|+|.++++.+.    .+.+.++..+||+|||+.++..+ ..+.......++||+||+ +|+.|+.+.++++.   |+
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i-~~~~~~~~~~~~LIv~P~-~l~~qw~~e~~~~~---~~  111 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICPL-SVLKNWEEELSKFA---PH  111 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEECS-TTHHHHHHHHHHHC---TT
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHH-HHHHhcCCCCCEEEEccH-HHHHHHHHHHHHHC---CC
Confidence            68999999998763    57899999999999999875444 444433344579999995 68899999988875   35


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad  159 (175)
                      .++..+.|+....     ...+.+++|+..+.     .+...+.+++|+|||+
T Consensus       112 ~~v~~~~g~~~~~-----~~~~~~ivi~t~~~l~~~~~l~~~~~~~vIvDEaH  159 (500)
T 1z63_A          112 LRFAVFHEDRSKI-----KLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQ  159 (500)
T ss_dssp             SCEEECSSSTTSC-----CGGGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGG
T ss_pred             ceEEEEecCchhc-----cccCCcEEEeeHHHHhccchhcCCCcCEEEEeCcc
Confidence            6777776665321     12346788882222     2334578999999995

>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=99.26  E-value=5.1e-12  Score=112.56  Aligned_cols=118  Identities=16%  Similarity=0.052  Sum_probs=82.0

Q ss_pred             CCcHHHHHhHHHHhc--CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVL--GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~--g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .|+|+|.+++..++.  +.+++++.+||+|||+.++..+...+... ...++||+||+ +|+.|+.+.+.+..    ++.
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-~~~rvLIVvP~-sLl~Qw~~E~~~~f----~l~  226 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-AAERVLIIVPE-TLQHQWLVEMLRRF----NLR  226 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-SCCCEEEECCT-TTHHHHHHHHHHHS----CCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-CCCeEEEEeCH-HHHHHHHHHHHHHh----CCC
Confidence            689999999988876  46899999999999999877776665443 33479999999 99999888776543    556


Q ss_pred             EEEEECCCchHHhHHH---HhcCCCeEEE----eecC-----ccCCCCceEEEEeCCCC
Q psy1539         114 VGVFFGGLPIQKDEEY---LKTHNPQIVG----LVNY-----ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~---l~~~~~iiv~----l~~~-----~~~~~~~~~lVlDEad~  160 (175)
                      +..+.|+... .....   .....+++|+    +.+.     .+...++.++|+|||+.
T Consensus       227 v~v~~~~~~~-~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~  284 (968)
T 3dmq_A          227 FALFDDERYA-EAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHH  284 (968)
T ss_dssp             CEECCHHHHH-HHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSC
T ss_pred             EEEEccchhh-hhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHh
Confidence            6555543321 11110   1123578888    2121     24456899999999953

>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=99.26  E-value=6.9e-11  Score=101.32  Aligned_cols=81  Identities=16%  Similarity=0.055  Sum_probs=71.2

Q ss_pred             CCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          32 QPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        32 ~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .|. .|+++|......+.+|+  +....||+|||+++.+|++-...   .|..+.|++|++.||.|-.+++..+.+.+ |
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL---~G~~vhVvT~ndyLA~rdae~m~~l~~~L-g  144 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNAL---IGKGVHLVTVNDYLARRDALWMGPVYLFL-G  144 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHT---TSSCEEEEESSHHHHHHHHHHHHHHHHHT-T
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHh---cCCceEEEeccHHHHHhHHHHHHHHHHHh-C
Confidence            455 58999999998888888  89999999999999999975544   34579999999999999999999999999 9


Q ss_pred             eEEEEEEC
Q psy1539         112 IKVGVFFG  119 (175)
Q Consensus       112 i~v~~~~g  119 (175)
                      +++++++.
T Consensus       145 lsvg~i~~  152 (822)
T 3jux_A          145 LRVGVINS  152 (822)
T ss_dssp             CCEEEEET
T ss_pred             CEEEEEcC
Confidence            99999988

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.19  E-value=3.9e-11  Score=105.03  Aligned_cols=121  Identities=13%  Similarity=0.091  Sum_probs=85.4

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .++|+|.+++..+.    .+.+.++..++|+|||+..+..+...+........+||||| .+|+.|+.+.+.++.   |+
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~---p~  311 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWA---PD  311 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHS---TT
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHC---CC
Confidence            68899999998665    78999999999999998876655544433333446899999 678889888888775   57


Q ss_pred             eEEEEEECCCchHHhHHHHh------------cCCCeEEEeecC------ccCCCCceEEEEeCCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLK------------THNPQIVGLVNY------ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~------------~~~~iiv~l~~~------~~~~~~~~~lVlDEad~  160 (175)
                      +++..++|+.......+...            ...+++|+..+.      .+.-.+..++|+|||+.
T Consensus       312 ~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~l~~~~w~~vIvDEaH~  378 (800)
T 3mwy_W          312 LNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHR  378 (800)
T ss_dssp             CCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHHHHTSEEEEEEETTGGG
T ss_pred             ceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHHHhcCCcceeehhhhhh
Confidence            78888888765444433321            234677772221      22223678999999953

>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=99.17  E-value=5.3e-11  Score=101.30  Aligned_cols=126  Identities=18%  Similarity=0.143  Sum_probs=83.3

Q ss_pred             cHHHHHhHHHHhcCCcEEEEcCCCChHH--HHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          38 TSFQHECIPQAVLGMDILCQAKSGMGKT--AVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~~~ii~a~TGsGKT--~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      ++.|++|++.++.++++++.+++|||||  ++++++.+..+.. ..+.++++++||.+.+.++.+.+....... ++...
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~-~~~~~vll~APTg~AA~~L~e~~~~~~~~l-~l~~~  228 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGKALRQL-PLTDE  228 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTHHHHHS-SCCSC
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh-cCCCeEEEEeCChhHHHHHHHHHHHHHhcC-CCCHH
Confidence            7899999999999999999999999999  6677887776532 245689999999999999988887766554 32110


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE-------eecCccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG-------LVNYETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      .. .+..  ...    ...+-+++       +........+++++|+|||++.-.++++.++..
T Consensus       229 ~~-~~~~--~~~----~Tih~ll~~~~~~~~~~~~~~~~l~~d~lIIDEAsml~~~~~~~Ll~~  285 (608)
T 1w36_D          229 QK-KRIP--EDA----STLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDA  285 (608)
T ss_dssp             CC-CSCS--CCC----BTTTSCC-----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHT
T ss_pred             HH-hccc--hhh----hhhHhhhccCCCchHHHhccCCCCCCCEEEEechhhCCHHHHHHHHHh
Confidence            00 0000  000    00011111       111112223789999999987777788887753

>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=99.15  E-value=4.1e-10  Score=96.38  Aligned_cols=122  Identities=13%  Similarity=0.055  Sum_probs=83.8

Q ss_pred             CCcHHHHHhHHHHh---------cCCcEEEEcCCCChHHHHHHHHHHHhhhcCC----CCeEEEEEecCHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAV---------LGMDILCQAKSGMGKTAVFVLATLQQLETTD----SNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~---------~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      .+.|+|.+++..+.         .+.+.++..++|+|||+..+..+...+....    ...++||++|+ +|+.|+.+.+
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            58999999998764         4578999999999999987766655544321    23468999997 8899999999


Q ss_pred             HHHHhhCCCeEEEEEECCCchHH--hHHHHhc------CCCeEEEeecC------ccCCCCceEEEEeCCCC
Q psy1539         103 ERFSKYMSNIKVGVFFGGLPIQK--DEEYLKT------HNPQIVGLVNY------ETNLSGVVVNVMDVRSG  160 (175)
Q Consensus       103 ~~~~~~~~~i~v~~~~g~~~~~~--~~~~l~~------~~~iiv~l~~~------~~~~~~~~~lVlDEad~  160 (175)
                      .++...  .+.+..++||.....  ....+..      ..+++|+..+.      .+.-.+..++|+|||+.
T Consensus       134 ~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~~l~~~~~~~vI~DEaH~  203 (644)
T 1z3i_X          134 GKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHR  203 (644)
T ss_dssp             HHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTTTTTSCCCEEEETTGGG
T ss_pred             HHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHHHhhcCCccEEEEECcee
Confidence            998754  456666777654221  1222221      35777772221      23335788999999954

>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=98.55  E-value=1.1e-06  Score=74.88  Aligned_cols=69  Identities=19%  Similarity=0.145  Sum_probs=53.7

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      ...+++.|.+|+..++.+.-.+|.||+|+|||.+.. .++..+... .+.++++.+||..-+.++.+.+.+
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHHTS-SSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHHHc-CCCeEEEEeCcHHHHHHHHHHHHh
Confidence            346799999999998888889999999999997643 333444321 345899999999999888777654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.47  E-value=1.2e-06  Score=75.06  Aligned_cols=66  Identities=18%  Similarity=0.139  Sum_probs=51.5

Q ss_pred             CCcHHHHHhHHHHhcCC-cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~-~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      .+++-|.+|+..++..+ -.+|+||+|||||.+..-.+.+.+.   .+.++|+.+||..=+.++.+.+..
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~---~~~~ILv~a~TN~AvD~i~erL~~  255 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVK---QGLKVLCCAPSNIAVDNLVERLAL  255 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEcCchHHHHHHHHHHHh
Confidence            57899999999888765 4689999999999875544444443   345899999999988887776654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.41  E-value=2.7e-06  Score=74.51  Aligned_cols=70  Identities=17%  Similarity=0.183  Sum_probs=53.9

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHH
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  105 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  105 (175)
                      +..+++.|.+|+..++.+.-.+|.||+|||||.+..- ++..+... .+.++++++||..-+.++.+.+.+.
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~-~i~~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSAT-IVYHLSKI-HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHH-HHHHHHHH-HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHH-HHHHHHhC-CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            3457899999999998888899999999999976543 33333221 2347999999999999988877654

>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=98.39  E-value=3.4e-06  Score=73.86  Aligned_cols=68  Identities=19%  Similarity=0.138  Sum_probs=53.1

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHH
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      ..+++.|.+|+..++.+.-.+|.||+|+|||.+.. .++..+... .+.++++++||..-+.++.+.+.+
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHH
Confidence            45799999999999888889999999999997643 344444332 345899999999999887776654

>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=98.31  E-value=5.5e-06  Score=70.05  Aligned_cols=113  Identities=13%  Similarity=0.000  Sum_probs=72.1

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .+++.|.+++..++.+..+++.++.|+|||... ..++..+..  .+.++++++||...+..+.+..        +....
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~--~g~~Vl~~ApT~~Aa~~L~e~~--------~~~a~  257 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES--LGLEVGLCAPTGKAARRLGEVT--------GRTAS  257 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH--TTCCEEEEESSHHHHHHHHHHH--------TSCEE
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh--cCCeEEEecCcHHHHHHhHhhh--------cccHH
Confidence            579999999999999999999999999999653 334444433  3457899999998887765432        11111


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .++         +.+.....   ............+++|+||+.+.-...+..++.
T Consensus       258 Tih---------~ll~~~~~---~~~~~~~~~~~~dvlIIDEasml~~~~~~~Ll~  301 (574)
T 3e1s_A          258 TVH---------RLLGYGPQ---GFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLA  301 (574)
T ss_dssp             EHH---------HHTTEETT---EESCSSSSCCSCSEEEECCGGGCCHHHHHHHHT
T ss_pred             HHH---------HHHcCCcc---hhhhhhcccccCCEEEEcCccCCCHHHHHHHHH
Confidence            100         00000000   111112233467899999998777777777664

>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=98.19  E-value=2.7e-05  Score=63.89  Aligned_cols=70  Identities=16%  Similarity=0.154  Sum_probs=50.0

Q ss_pred             hhCCCCCCcHHHHHhHHHHhc----C-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHH
Q psy1539          30 ESQPFREQTSFQHECIPQAVL----G-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  101 (175)
Q Consensus        30 ~~~g~~~~t~~Q~~~i~~~~~----g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  101 (175)
                      ..+.|..+++-|++++..++.    + ..+++.|+.|||||... ..++..+.... ...+++++||..-+..+.+.
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~-~~~il~~a~T~~Aa~~l~~~   93 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTG-ETGIILAAPTHAAKKILSKL   93 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTT-CCCEEEEESSHHHHHHHHHH
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcC-CceEEEecCcHHHHHHHHhh
Confidence            445688999999999987653    2 39999999999999543 44555554322 23689999998887665543

>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=97.75  E-value=8.9e-05  Score=63.01  Aligned_cols=71  Identities=18%  Similarity=0.197  Sum_probs=54.6

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ..+++-|.+++.  ..+..++|.|+.|||||.+..--+...+... ....+++++++|+..+.++.+.+.++..
T Consensus         8 ~~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A            8 DSLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             TTCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             hcCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            468999999996  2357899999999999987655555444432 1234799999999999999999887743

>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=97.61  E-value=0.00015  Score=62.36  Aligned_cols=68  Identities=22%  Similarity=0.229  Sum_probs=52.3

Q ss_pred             CCCCCcHHHHHhHHHHhc----C-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          33 PFREQTSFQHECIPQAVL----G-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~----g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      +| .|++.|..++..+.+    | +...+.+.||||||+++.- ++....     ..+|||+|+..+|.|+++.++.+..
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~~-----~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEALG-----RPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHT-----CCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHhC-----CCEEEEecCHHHHHHHHHHHHHHCC
Confidence            56 799999999876653    4 3567899999999976643 233321     1489999999999999999998853

>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=97.60  E-value=0.00013  Score=62.65  Aligned_cols=80  Identities=14%  Similarity=0.104  Sum_probs=57.8

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHHhhC--CCe
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSKYM--SNI  112 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~--~~i  112 (175)
                      .+++-|++++..  .+.+++|.|+.|||||.+..--+...+.. .-...++++++.|+..+.++.+.+.+.....  .++
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~~~~~~~~   79 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGL   79 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSCTTTTTTS
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcCcccccCC
Confidence            478999999875  36789999999999998765555444433 2233479999999999999999888764321  235


Q ss_pred             EEEEE
Q psy1539         113 KVGVF  117 (175)
Q Consensus       113 ~v~~~  117 (175)
                      .+..+
T Consensus        80 ~v~Tf   84 (673)
T 1uaa_A           80 MISTF   84 (673)
T ss_dssp             EEEEH
T ss_pred             EEEeH
Confidence            55443

>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=97.46  E-value=0.00032  Score=64.18  Aligned_cols=69  Identities=28%  Similarity=0.315  Sum_probs=55.7

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCC---CCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD---SNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~---~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .+|+-|.++|..-  +.+++|.|+.|||||.+.+--++..+....   ..-+.+++++|+..+.++.+.+....
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            5799999998653  889999999999999887666666665432   33479999999999999998887743

>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=97.39  E-value=0.00074  Score=58.48  Aligned_cols=81  Identities=16%  Similarity=0.168  Sum_probs=58.2

Q ss_pred             CCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHhh-CCCe
Q psy1539          35 REQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSKY-MSNI  112 (175)
Q Consensus        35 ~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~-~~~i  112 (175)
                      ..+++-|++|+..  .+..++|.|+.|||||.+...-+...+... -...++++++.|+..+.++.+.+.++... ..++
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~~~~~   87 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDV   87 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHGGGGTTS
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhcccccCc
Confidence            4689999999865  356899999999999987665555544432 23347999999999999999888776432 1244


Q ss_pred             EEEEE
Q psy1539         113 KVGVF  117 (175)
Q Consensus       113 ~v~~~  117 (175)
                      .+..+
T Consensus        88 ~v~Tf   92 (724)
T 1pjr_A           88 WISTF   92 (724)
T ss_dssp             EEEEH
T ss_pred             EEeeH
Confidence            44443

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.02  E-value=0.001  Score=54.32  Aligned_cols=93  Identities=14%  Similarity=0.060  Sum_probs=53.3

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhC-CCeEEEEEECCCchHHhHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM-SNIKVGVFFGGLPIQKDEEYL  130 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~i~v~~~~g~~~~~~~~~~l  130 (175)
                      +=.++.|+.|+|||....    +.+..    ...++++||++++..+.+.+.+..... .+.++..         -...+
T Consensus       162 ~v~~I~G~aGsGKTt~I~----~~~~~----~~~lVlTpT~~aa~~l~~kl~~~~~~~~~~~~V~T---------~dsfL  224 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL----SRVNF----EEDLILVPGRQAAEMIRRRANASGIIVATKDNVRT---------VDSFL  224 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH----HHCCT----TTCEEEESCHHHHHHHHHHHTTTSCCCCCTTTEEE---------HHHHH
T ss_pred             cEEEEEcCCCCCHHHHHH----HHhcc----CCeEEEeCCHHHHHHHHHHhhhcCccccccceEEE---------eHHhh
Confidence            346899999999997542    22221    246999999999988777664321000 0111111         11122


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHH
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALI  170 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il  170 (175)
                      .+..         .......+.+|+||+.+.....+..++
T Consensus       225 ~~~~---------~~~~~~~d~liiDE~sm~~~~~l~~l~  255 (446)
T 3vkw_A          225 MNYG---------KGARCQFKRLFIDEGLMLHTGCVNFLV  255 (446)
T ss_dssp             HTTT---------SSCCCCCSEEEEETGGGSCHHHHHHHH
T ss_pred             cCCC---------CCCCCcCCEEEEeCcccCCHHHHHHHH
Confidence            2210         111124789999999777777776654

>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=96.82  E-value=0.008  Score=50.85  Aligned_cols=74  Identities=11%  Similarity=0.186  Sum_probs=58.8

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .++|+|...+..+...+.+++..+-|+|||.....-++..+... .+..+++++|+++.+..+.+.++.+.+..|
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~~p  236 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHhCh
Confidence            47999999998775668899999999999987664444444332 355899999999999999988888887664

>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=96.80  E-value=0.0099  Score=47.73  Aligned_cols=74  Identities=11%  Similarity=0.193  Sum_probs=58.6

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCC
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  110 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  110 (175)
                      .++|+|...+..+...+-+++..+-+.|||.....-++..+.. ..+..+++++|+++-|..+.+.++.+.+..|
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~-~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~P  236 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-NKDKAVGILAHKGSMSAEVLDRTKQAIELLP  236 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS-SSSCEEEEEESSHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh-CCCCeEEEEeCCHHHHHHHHHHHHHHHHhCh
Confidence            6799999999876555778999999999998766555543333 2456899999999999999988888877664

>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=96.72  E-value=0.0037  Score=53.65  Aligned_cols=66  Identities=24%  Similarity=0.316  Sum_probs=50.0

Q ss_pred             CCcHHHHHhHHHHhc----CC-cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVL----GM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~----g~-~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|+..|..++..+.+    |. ...+.+.||||||++..- ++....    . .+|||+|+..+|.|+++.++.|..
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~~----~-~~lvv~~~~~~A~~l~~el~~~~~   82 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEVN----K-PTLVIAHNKTLAGQLYSEFKEFFP   82 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHC----C-CEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHhC----C-CEEEEECCHHHHHHHHHHHHHHcC
Confidence            689999998875543    43 477889999999976543 233321    1 489999999999999999999853

>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=96.39  E-value=0.065  Score=37.58  Aligned_cols=73  Identities=14%  Similarity=0.177  Sum_probs=53.2

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++++..+..+.+.++..     ++.+..++|+.+..+..+   .++++ ..++|+  +....++++++.++|
T Consensus        33 ~~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi  107 (175)
T 2rb4_A           33 TIGQAIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVV  107 (175)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEE
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecchhcCCCcccCCEEE
Confidence            4458999999999998877766543     778999999987654433   34443 567777  555588899999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       108 ~~d~  111 (175)
T 2rb4_A          108 NFDL  111 (175)
T ss_dssp             ESSC
T ss_pred             EeCC
Confidence            6443

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=96.31  E-value=0.031  Score=38.86  Aligned_cols=72  Identities=13%  Similarity=0.216  Sum_probs=52.9

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.++||.++++.-+..+.+.++..     ++.+..++|+.+..+..+   .++++ ..++|+  .....+++++++++|.
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~  109 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVIN  109 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTTTCCCSCCSEEEE
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCchhcCCEEEE
Confidence            347999999999998887777653     778999999987554433   34444 467777  4555788888998887


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      -+.
T Consensus       110 ~~~  112 (163)
T 2hjv_A          110 YDL  112 (163)
T ss_dssp             SSC
T ss_pred             eCC
Confidence            655

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=96.22  E-value=0.16  Score=42.13  Aligned_cols=99  Identities=13%  Similarity=0.074  Sum_probs=67.4

Q ss_pred             ChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeE
Q psy1539          62 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQI  137 (175)
Q Consensus        62 sGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~ii  137 (175)
                      ..+....+-.+...+.....+.++||.++|+.-+..+.+.+++....  ++.+..++|+.+..+..+   .++++ .+++
T Consensus       319 ~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~--~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vL  396 (563)
T 3i5x_A          319 ANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGIL  396 (563)
T ss_dssp             THHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEE
T ss_pred             HhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcCCCCEE
Confidence            34443333344444443345668999999999999999888876542  678889999987654433   34444 4677


Q ss_pred             EE--eecCccCCCCceEEEEeCCCCCC
Q psy1539         138 VG--LVNYETNLSGVVVNVMDVRSGGW  162 (175)
Q Consensus       138 v~--l~~~~~~~~~~~~lVlDEad~~f  162 (175)
                      |+  +....+++++++++|.-..-...
T Consensus       397 vaT~~~~~GiDip~v~~VI~~~~p~s~  423 (563)
T 3i5x_A          397 VCTDVGARGMDFPNVHEVLQIGVPSEL  423 (563)
T ss_dssp             EECGGGTSSCCCTTCCEEEEESCCSST
T ss_pred             EEcchhhcCCCcccCCEEEEECCCCch
Confidence            77  56668899999999887764333

>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=96.19  E-value=0.01  Score=41.87  Aligned_cols=59  Identities=20%  Similarity=0.306  Sum_probs=33.5

Q ss_pred             cHHHHHhHHHHh---------cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          38 TSFQHECIPQAV---------LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        38 t~~Q~~~i~~~~---------~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      ++.|.+++..+.         .|+.+++.+|+|+|||... -.+...+... .+..+++ .+..++..++.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~-~~i~~~~~~~-~g~~~~~-~~~~~~~~~~~   83 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLA-VATLKAIYEK-KGIRGYF-FDTKDLIFRLK   83 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHH-HHHHHHHHHH-SCCCCCE-EEHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHH-HHHHHHHHHH-cCCeEEE-EEHHHHHHHHH
Confidence            456666665443         4789999999999999643 3344443321 2222333 44555554433

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=95.99  E-value=0.22  Score=41.64  Aligned_cols=86  Identities=14%  Similarity=0.115  Sum_probs=61.8

Q ss_pred             HHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCcc
Q psy1539          72 TLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYET  145 (175)
Q Consensus        72 ~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~  145 (175)
                      +...+.....+.++||.++|+.-+..+.+.+++....  ++.+..++|+.+..+..   +.++++ ..++|+  +....+
T Consensus       278 l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~--~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~~~~Gi  355 (579)
T 3sqw_A          278 IKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGM  355 (579)
T ss_dssp             HHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGGGTSSC
T ss_pred             HHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhcC--CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcchhhcCC
Confidence            3333333345568999999999999999988876542  67888999998755443   334444 466777  556688


Q ss_pred             CCCCceEEEEeCCC
Q psy1539         146 NLSGVVVNVMDVRS  159 (175)
Q Consensus       146 ~~~~~~~lVlDEad  159 (175)
                      ++++++++|.-..-
T Consensus       356 Dip~v~~VI~~~~p  369 (579)
T 3sqw_A          356 DFPNVHEVLQIGVP  369 (579)
T ss_dssp             CCTTCCEEEEESCC
T ss_pred             CcccCCEEEEcCCC
Confidence            99999999987763

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=95.94  E-value=0.068  Score=37.09  Aligned_cols=85  Identities=13%  Similarity=0.235  Sum_probs=56.4

Q ss_pred             HHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE
Q psy1539          64 KTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG  139 (175)
Q Consensus        64 KT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~  139 (175)
                      |. ..+..++...    .+.++||.+++++-+..+.+.++..     ++.+..++|+.+..+..+   .++++ ..++|+
T Consensus        17 K~-~~l~~ll~~~----~~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~   86 (165)
T 1fuk_A           17 KY-ECLTDLYDSI----SVTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILIS   86 (165)
T ss_dssp             HH-HHHHHHHHHT----TCSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEE
T ss_pred             HH-HHHHHHHHhC----CCCCEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEE
Confidence            54 3344444432    3457999999999998877776653     678889999987554433   33443 467777


Q ss_pred             --eecCccCCCCceEEEEeCC
Q psy1539         140 --LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       140 --l~~~~~~~~~~~~lVlDEa  158 (175)
                        .....+++++++++|.-+.
T Consensus        87 T~~~~~G~d~~~~~~Vi~~~~  107 (165)
T 1fuk_A           87 TDLLARGIDVQQVSLVINYDL  107 (165)
T ss_dssp             EGGGTTTCCCCSCSEEEESSC
T ss_pred             cChhhcCCCcccCCEEEEeCC
Confidence              4444677778888776544

>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=95.88  E-value=0.077  Score=37.21  Aligned_cols=87  Identities=13%  Similarity=0.122  Sum_probs=58.9

Q ss_pred             ChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeE
Q psy1539          62 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQI  137 (175)
Q Consensus        62 sGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~ii  137 (175)
                      ..|. ..+..++...    .+.++||.++++.-+..+.+.++..     ++.+..++|+.+..+..+   .+++ ...++
T Consensus        16 ~~K~-~~L~~ll~~~----~~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vL   85 (172)
T 1t5i_A           16 NEKN-RKLFDLLDVL----EFNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRIL   85 (172)
T ss_dssp             GGHH-HHHHHHHHHS----CCSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEE
T ss_pred             HHHH-HHHHHHHHhC----CCCcEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEE
Confidence            4554 3344444432    3447999999999998877777653     778889999987554433   3444 35677


Q ss_pred             EE--eecCccCCCCceEEEEeCC
Q psy1539         138 VG--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       138 v~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      |+  .....+++++++++|.-+.
T Consensus        86 vaT~~~~~Gldi~~~~~Vi~~d~  108 (172)
T 1t5i_A           86 VATNLFGRGMDIERVNIAFNYDM  108 (172)
T ss_dssp             EESSCCSTTCCGGGCSEEEESSC
T ss_pred             EECCchhcCcchhhCCEEEEECC
Confidence            77  4455778888888887655

>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=95.79  E-value=0.057  Score=39.32  Aligned_cols=71  Identities=14%  Similarity=0.131  Sum_probs=52.0

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.++||.+++++-+..+.+.+...     ++.+..++|+.+..++.+   .++++ ..++|+  +....+++++++++|.
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~  105 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVH  105 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTTTTCSSSCCCBSEEEE
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecChhhcCCCCccCcEEEE
Confidence            348999999999998888777654     778889999987655443   34444 467777  4555788888888775


Q ss_pred             eC
Q psy1539         156 DV  157 (175)
Q Consensus       156 DE  157 (175)
                      =+
T Consensus       106 ~~  107 (212)
T 3eaq_A          106 YR  107 (212)
T ss_dssp             SS
T ss_pred             CC
Confidence            33

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=95.57  E-value=0.04  Score=47.29  Aligned_cols=102  Identities=14%  Similarity=0.044  Sum_probs=65.4

Q ss_pred             CCcHHHHHhHHHHhc--CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVL--GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~--g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      .+|.-|.+++..+.+  ..-.++.|+-|.|||.+.-+.+.. +..     .++|-+|+.+=+..+.+    +...  .++
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~-~~~-----~~~vtAP~~~a~~~l~~----~~~~--~i~  242 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISR-IAG-----RAIVTAPAKASTDVLAQ----FAGE--KFR  242 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHH-SSS-----CEEEECSSCCSCHHHHH----HHGG--GCC
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHH-HHh-----CcEEECCCHHHHHHHHH----HhhC--CeE
Confidence            578999999988876  234789999999999655444433 221     35888999876654333    2221  111


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEEeecCccCCCCceEEEEeCCCCCCHHHHHHHHhh
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDLEALILS  172 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~~  172 (175)
                      .      ...++   .+.              ...+.+++|+|||.+.-.+-++.++..
T Consensus       243 ~------~~Pd~---~~~--------------~~~~~dlliVDEAAaIp~pll~~ll~~  278 (671)
T 2zpa_A          243 F------IAPDA---LLA--------------SDEQADWLVVDEAAAIPAPLLHQLVSR  278 (671)
T ss_dssp             B------CCHHH---HHH--------------SCCCCSEEEEETGGGSCHHHHHHHHTT
T ss_pred             E------eCchh---hhh--------------CcccCCEEEEEchhcCCHHHHHHHHhh
Confidence            0      01111   111              235689999999988888888877754

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=95.40  E-value=0.25  Score=35.29  Aligned_cols=71  Identities=8%  Similarity=0.068  Sum_probs=50.3

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEEEe
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNVMD  156 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lVlD  156 (175)
                      .++||.+++++-+..+.+.++..     ++.+..++|+.+..+..+   .+++ ...++|+  .....+++++++++|.=
T Consensus        55 ~~~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~  129 (191)
T 2p6n_A           55 PPVLIFAEKKADVDAIHEYLLLK-----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINY  129 (191)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEES
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEe
Confidence            47999999999999888777654     678889999987554433   3343 3567777  34446677777777664


Q ss_pred             CC
Q psy1539         157 VR  158 (175)
Q Consensus       157 Ea  158 (175)
                      +.
T Consensus       130 d~  131 (191)
T 2p6n_A          130 DM  131 (191)
T ss_dssp             SC
T ss_pred             CC
Confidence            44

>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=95.37  E-value=0.17  Score=35.89  Aligned_cols=16  Identities=38%  Similarity=0.526  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      .++++.||+|+|||..
T Consensus        39 ~~~ll~G~~G~GKT~l   54 (226)
T 2chg_A           39 PHLLFSGPPGTGKTAT   54 (226)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999964

>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=95.28  E-value=0.056  Score=42.15  Aligned_cols=39  Identities=28%  Similarity=0.324  Sum_probs=26.2

Q ss_pred             cHHHHHhHHHHh----cC---CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          38 TSFQHECIPQAV----LG---MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        38 t~~Q~~~i~~~~----~g---~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .|+|.+++..+.    +|   +.+++.||.|+|||... ..+...+.
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a-~~la~~l~   49 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI-YALSRYLL   49 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH-HHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH-HHHHHHHh
Confidence            577777765544    34   34999999999999654 33444443

>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=95.21  E-value=0.13  Score=36.56  Aligned_cols=89  Identities=15%  Similarity=0.121  Sum_probs=49.8

Q ss_pred             CChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhc-CCCe
Q psy1539          61 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKT-HNPQ  136 (175)
Q Consensus        61 GsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~-~~~i  136 (175)
                      .+.|. ..+.-++...   ..+.++||.++++.-+..+.+.++..     ++.+..++|+.+..+.   .+.+++ ...+
T Consensus        29 ~~~K~-~~L~~ll~~~---~~~~k~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~v   99 (185)
T 2jgn_A           29 ESDKR-SFLLDLLNAT---GKDSLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPI   99 (185)
T ss_dssp             GGGHH-HHHHHHHHHC----CCSCEEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSE
T ss_pred             cHHHH-HHHHHHHHhc---CCCCeEEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeE
Confidence            45664 3344444442   23458999999999998877776653     7788889998764432   334444 3567


Q ss_pred             EEE--eecCccCCCCceEEEEeCC
Q psy1539         137 IVG--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       137 iv~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      +|+  .....++++++.++|.=+.
T Consensus       100 LvaT~~~~~Gldi~~~~~VI~~d~  123 (185)
T 2jgn_A          100 LVATAVAARGLDISNVKHVINFDL  123 (185)
T ss_dssp             EEEEC------CCCSBSEEEESSC
T ss_pred             EEEcChhhcCCCcccCCEEEEeCC
Confidence            777  4444677778877776444

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=95.00  E-value=0.34  Score=37.79  Aligned_cols=74  Identities=11%  Similarity=0.117  Sum_probs=54.7

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.+++++-+..+.+.++..     ++.+..++|+.+..+..+   .++++ ..++|+  .....+++++++++|
T Consensus       249 ~~~~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi  323 (391)
T 1xti_A          249 EFNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAF  323 (391)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSCBCCTTEEEEE
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcCCCcccCCEEE
Confidence            3458999999999998887777653     678888999987554433   34443 467777  555688999999999


Q ss_pred             EeCCC
Q psy1539         155 MDVRS  159 (175)
Q Consensus       155 lDEad  159 (175)
                      .-+..
T Consensus       324 ~~~~p  328 (391)
T 1xti_A          324 NYDMP  328 (391)
T ss_dssp             ESSCC
T ss_pred             EeCCC
Confidence            87663

>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=94.67  E-value=0.42  Score=37.16  Aligned_cols=73  Identities=11%  Similarity=0.143  Sum_probs=54.4

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.+++++-+..+.+.+++.     +..+..++|+.+..+..   +.++++ .+++|+  +....+++++++++|
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi  316 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE-----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVV  316 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGGSSSCCCTTEEEEE
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc-----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChhhcCCCcccCCEEE
Confidence            4468999999999998877777653     67788899998755443   344443 467777  556688999999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       317 ~~~~  320 (395)
T 3pey_A          317 NYDL  320 (395)
T ss_dssp             ESSC
T ss_pred             EcCC
Confidence            7655

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.63  E-value=0.03  Score=38.13  Aligned_cols=20  Identities=15%  Similarity=0.101  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEcCCCChHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~   67 (175)
                      ...+.++++.+++|+|||..
T Consensus        24 ~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHH
T ss_pred             hCCCCcEEEECCCCccHHHH
Confidence            34568999999999999964

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=94.56  E-value=0.25  Score=42.28  Aligned_cols=81  Identities=19%  Similarity=0.222  Sum_probs=60.4

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH---HhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY---LKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~---l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++|+.-+..+.+.++..     ++++..++|+.+..+..+.   +++| .+++|+  +....+++.+++++|
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi  518 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEI-----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVA  518 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEE
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhc-----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEE
Confidence            4558999999999998877766653     7788888988775544443   4444 578888  777899999999999


Q ss_pred             EeCCC-CCCHHHH
Q psy1539         155 MDVRS-GGWWLDL  166 (175)
Q Consensus       155 lDEad-~~f~~~v  166 (175)
                      +=++| .||-.+.
T Consensus       519 ~~d~d~~G~p~s~  531 (661)
T 2d7d_A          519 ILDADKEGFLRSE  531 (661)
T ss_dssp             ETTTTCCTTTTSH
T ss_pred             EeCcccccCCCCH
Confidence            99985 4553333

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=94.50  E-value=0.037  Score=37.67  Aligned_cols=20  Identities=10%  Similarity=0.144  Sum_probs=17.0

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+.++++.+|+|+|||..+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            45689999999999999754

>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=94.49  E-value=0.56  Score=36.73  Aligned_cols=73  Identities=10%  Similarity=0.081  Sum_probs=53.7

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.+++++-+..+.+.+++.     ++.+..++|+.+..+..   +.++++ ..++|+  .....+++++++++|
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi  331 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVI  331 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEE
T ss_pred             CCCcEEEEEecHHHHHHHHHHHHhc-----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCCCccCCCEEE
Confidence            3458999999999999888877765     67788899998755443   344444 467777  555688889999888


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       332 ~~~~  335 (400)
T 1s2m_A          332 NFDF  335 (400)
T ss_dssp             ESSC
T ss_pred             EeCC
Confidence            6554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.44  E-value=0.092  Score=36.09  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|+.+++.+|+|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            688999999999999954

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=94.31  E-value=0.49  Score=37.26  Aligned_cols=72  Identities=15%  Similarity=0.137  Sum_probs=51.7

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.+++++-+..+.+.+++.     +..+..++|+.+..+..+   .+++ ...++|+  +....+++++++++|
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi  349 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVI  349 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEE
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC-----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEE
Confidence            4568999999999998887777653     778899999987554433   3444 3567777  555577778888777


Q ss_pred             EeC
Q psy1539         155 MDV  157 (175)
Q Consensus       155 lDE  157 (175)
                      .=+
T Consensus       350 ~~~  352 (417)
T 2i4i_A          350 NFD  352 (417)
T ss_dssp             ESS
T ss_pred             EEc
Confidence            543

>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=94.22  E-value=0.52  Score=39.79  Aligned_cols=73  Identities=10%  Similarity=0.171  Sum_probs=55.0

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++|+.-+.++.+.++..     ++.+..++|+.+..+..+   .+.+ ..+++|+  .....+++++++++|
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~-----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI  340 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNL-----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVI  340 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEE
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHC-----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEE
Confidence            4568999999999999988877653     788999999987654433   3333 3577787  555588999999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .=..
T Consensus       341 ~~~~  344 (591)
T 2v1x_A          341 HHSM  344 (591)
T ss_dssp             ESSC
T ss_pred             EeCC
Confidence            7554

>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=94.09  E-value=0.32  Score=39.69  Aligned_cols=59  Identities=20%  Similarity=0.157  Sum_probs=34.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEEEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVF  117 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~~~  117 (175)
                      .-+++.+++|+|||.... -+...+..  .+.+++++.  |.|.-+   .++++.+.... ++.+...
T Consensus       101 ~vIlivG~~G~GKTTt~~-kLA~~l~~--~G~kVllv~~D~~R~aa---~eqL~~~~~~~-gvpv~~~  161 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVA-KLARYFQK--RGYKVGVVCSDTWRPGA---YHQLRQLLDRY-HIEVFGN  161 (443)
T ss_dssp             EEEEEECCTTSSHHHHHH-HHHHHHHT--TTCCEEEEECCCSSTHH---HHHHHHHHGGG-TCEEECC
T ss_pred             eEEEEECcCCCCHHHHHH-HHHHHHHH--CCCeEEEEeCCCcchhH---HHHHHHHHHhc-CCcEEec
Confidence            357889999999997543 23333332  344666665  445443   34566666655 6665443

>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=94.05  E-value=0.31  Score=39.64  Aligned_cols=57  Identities=16%  Similarity=0.086  Sum_probs=30.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe--cCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .-+++.+++|+|||....- +...+..  .+.+++++.  +.|.-+   .+++..+.... ++.+.
T Consensus        98 ~vI~lvG~~GsGKTTt~~k-LA~~l~~--~G~kVllv~~D~~r~~a---~eqL~~~~~~~-gv~~~  156 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGK-LAYFYKK--RGYKVGLVAADVYRPAA---YDQLLQLGNQI-GVQVY  156 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHH-HHHHHHH--TTCCEEEEEECCSCHHH---HHHHHHHHHTT-TCCEE
T ss_pred             eEEEEECCCCCCHHHHHHH-HHHHHHH--cCCeEEEEecCccchhH---HHHHHHHHHhc-CCcee
Confidence            3578889999999975432 2223322  234565555  334333   23455555544 55443

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=93.91  E-value=0.42  Score=36.79  Aligned_cols=72  Identities=13%  Similarity=0.116  Sum_probs=51.6

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.++||.+++++-+..+.+.+...     ++.+..++|+.+..++.+   .++++ ..++|+  +....+++++++++|.
T Consensus        28 ~~~~LVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~va~~Gidi~~v~~VI~  102 (300)
T 3i32_A           28 PDRAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVH  102 (300)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECSTTTCSTTCCCCSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEechhhcCccccceeEEEE
Confidence            447999999999988877666532     778999999987655443   33443 567887  5555788888888875


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      =+.
T Consensus       103 ~d~  105 (300)
T 3i32_A          103 YRM  105 (300)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            333

>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=93.87  E-value=0.27  Score=38.65  Aligned_cols=72  Identities=15%  Similarity=0.230  Sum_probs=53.7

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.++||.++++.-+..+.+.+++.     +..+..++|+.+..+..+   .++++ ..++|+  +....+++++++++|.
T Consensus       266 ~~~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~  340 (412)
T 3fht_A          266 IAQAMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVIN  340 (412)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhC-----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEE
Confidence            358999999999999888777654     677888999987554433   34443 467777  6666889999999885


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      -..
T Consensus       341 ~~~  343 (412)
T 3fht_A          341 FDL  343 (412)
T ss_dssp             SSC
T ss_pred             ECC
Confidence            444

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=93.73  E-value=0.14  Score=42.54  Aligned_cols=48  Identities=10%  Similarity=-0.080  Sum_probs=29.4

Q ss_pred             HHHHhhCCCCCCcHHHHHhHH-HHhcCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          26 DRIGESQPFREQTSFQHECIP-QAVLGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        26 ~~~l~~~g~~~~t~~Q~~~i~-~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +..+.+.|.  +++.+..-+. .+..|.++++.+|||||||... -.++..+
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            344555552  3444444443 3457899999999999999643 3344433

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=93.67  E-value=0.45  Score=40.74  Aligned_cols=83  Identities=16%  Similarity=0.143  Sum_probs=61.0

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH---HhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY---LKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~---l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++|+.-+..+.+.+.+.     ++++..++|+.+..+..+.   +++| .+++|+  +....+++.+++++|
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI  512 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVA  512 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEE
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhc-----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEE
Confidence            3458999999999998877766653     7788888988775544443   4444 578888  777799999999999


Q ss_pred             EeCCC-CCCHHHHHH
Q psy1539         155 MDVRS-GGWWLDLEA  168 (175)
Q Consensus       155 lDEad-~~f~~~v~~  168 (175)
                      +=++| .||-.+...
T Consensus       513 ~~d~d~~G~p~s~~~  527 (664)
T 1c4o_A          513 ILDADKEGFLRSERS  527 (664)
T ss_dssp             ETTTTSCSGGGSHHH
T ss_pred             EeCCcccCCCCCHHH
Confidence            98885 455444443

>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=93.63  E-value=0.38  Score=36.84  Aligned_cols=16  Identities=44%  Similarity=0.499  Sum_probs=11.9

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.+|+|+|||...
T Consensus        50 ~~L~~G~~G~GKT~la   65 (324)
T 3u61_B           50 IILHSPSPGTGKTTVA   65 (324)
T ss_dssp             EEEECSSTTSSHHHHH
T ss_pred             EEEeeCcCCCCHHHHH
Confidence            3566677999999653

>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=93.61  E-value=0.035  Score=42.64  Aligned_cols=58  Identities=14%  Similarity=0.076  Sum_probs=32.4

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHH-HHhcCCcEEEEcCCCChHHHHH
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIP-QAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~-~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+-..|++++-.....+.+.+. ...|......... .+..++.+++.+|+|+|||...
T Consensus         8 ~~~~~~~~di~G~~~~~~~l~~~-v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A            8 EVPQVTWEDIGGLEDVKRELQEL-VQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHH-HHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHH-HHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            34455677776666666666543 1111000011011 1234688999999999999654

>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=93.60  E-value=0.54  Score=37.01  Aligned_cols=71  Identities=11%  Similarity=0.233  Sum_probs=52.3

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEEe
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVMD  156 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVlD  156 (175)
                      .++||.+++++-+..+.+.+++.     ++.+..++|+.+..+..+   .++++ ..++|+  +....+++++++++|.-
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~  351 (410)
T 2j0s_A          277 TQAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINY  351 (410)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEES
T ss_pred             CcEEEEEcCHHHHHHHHHHHHhC-----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhCcCCcccCCEEEEE
Confidence            48999999999998877776653     678888999987554433   34443 567777  55568889999998875


Q ss_pred             CC
Q psy1539         157 VR  158 (175)
Q Consensus       157 Ea  158 (175)
                      +.
T Consensus       352 ~~  353 (410)
T 2j0s_A          352 DL  353 (410)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=93.47  E-value=0.082  Score=41.93  Aligned_cols=40  Identities=13%  Similarity=0.127  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      |.-+.+.+|+|+|||.. ++.++..+..  .+..++++.....
T Consensus        61 G~i~~I~GppGsGKSTL-al~la~~~~~--~gg~VlyId~E~s  100 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTL-ALHAIAEAQK--MGGVAAFIDAEHA  100 (356)
T ss_dssp             TEEEEEEESTTSSHHHH-HHHHHHHHHH--TTCCEEEEESSCC
T ss_pred             CcEEEEECCCCCCHHHH-HHHHHHHHHh--cCCeEEEEecccc
Confidence            46789999999999954 4444444333  2336777775443

>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=93.44  E-value=0.025  Score=42.57  Aligned_cols=17  Identities=29%  Similarity=0.415  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.+|+|+|||...
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            68999999999999654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.42  E-value=0.24  Score=35.21  Aligned_cols=25  Identities=24%  Similarity=0.360  Sum_probs=18.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +++++.+|+|+|||... -.+...+.
T Consensus        55 ~~~~l~G~~GtGKT~la-~~i~~~~~   79 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL-AAIANELA   79 (202)
T ss_dssp             CEEEEECSTTSSHHHHH-HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHH
Confidence            78999999999999643 34444443

>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=93.36  E-value=0.1  Score=42.25  Aligned_cols=45  Identities=27%  Similarity=0.321  Sum_probs=27.3

Q ss_pred             HhhCCCCCCcHHHHHhHHHHh--cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          29 GESQPFREQTSFQHECIPQAV--LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        29 l~~~g~~~~t~~Q~~~i~~~~--~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +.+.|+   ++-+..++..++  .|.-+++.+|||||||.. +-.++..+.
T Consensus       146 l~~Lg~---~~~~~~~L~~l~~~~ggii~I~GpnGSGKTTl-L~allg~l~  192 (418)
T 1p9r_A          146 LHSLGM---TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTT-LYAGLQELN  192 (418)
T ss_dssp             GGGSCC---CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHH-HHHHHHHHC
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHH-HHHHHhhcC
Confidence            445554   334455555444  355689999999999964 344444443

>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=93.35  E-value=0.85  Score=36.61  Aligned_cols=70  Identities=9%  Similarity=0.021  Sum_probs=50.9

Q ss_pred             EEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEEeC
Q psy1539          84 YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVMDV  157 (175)
Q Consensus        84 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVlDE  157 (175)
                      ++||.++++.-+..+.+.+++.     ++.+..++|+.+..+..+   .++++ .+++|+  +....+++.+++++|.=+
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d  376 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK-----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYD  376 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESS
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEEC
Confidence            3999999999998877776643     778899999987554443   34443 577887  555678888888877644


Q ss_pred             C
Q psy1539         158 R  158 (175)
Q Consensus       158 a  158 (175)
                      .
T Consensus       377 ~  377 (434)
T 2db3_A          377 M  377 (434)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=93.20  E-value=0.073  Score=50.95  Aligned_cols=46  Identities=11%  Similarity=0.017  Sum_probs=31.4

Q ss_pred             HHHHhc------CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          45 IPQAVL------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        45 i~~~~~------g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      +..++.      |+++++.+|+|+|||.....-+.+...   .+.+++++.....
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~---~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDAEHA 1466 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHT---TTCCEEEECTTSC
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEEcccc
Confidence            555555      689999999999999765444433332   4557888876543

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=93.07  E-value=0.85  Score=37.77  Aligned_cols=73  Identities=12%  Similarity=0.122  Sum_probs=54.2

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++|+.-+.++.+.++..     ++.+..++|+.+..+..+   .+.+ ...++|+  .....+++++++++|
T Consensus       235 ~~~~~IVf~~sr~~~e~l~~~L~~~-----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI  309 (523)
T 1oyw_A          235 RGKSGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV  309 (523)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEE
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHC-----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEechhhCCCCccCccEEE
Confidence            4457999999999999888777653     778999999987544332   3333 3577777  555588999999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-..
T Consensus       310 ~~~~  313 (523)
T 1oyw_A          310 HFDI  313 (523)
T ss_dssp             ESSC
T ss_pred             EECC
Confidence            7555

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=93.05  E-value=0.034  Score=42.00  Aligned_cols=56  Identities=16%  Similarity=0.008  Sum_probs=32.6

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHH--HhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQ--AVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~--~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+...|+++.-.++.++.+.+. ...+.. ..+.+..  +..++++++.+|+|+|||...
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~-~~~~~~-~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREV-VELPLK-HPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHH-THHHHH-CHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCCHHHhcCHHHHHHHHHHH-HHHHhh-CHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            3345677777777777776653 111100 0111111  234588999999999999643

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.03  E-value=0.088  Score=38.41  Aligned_cols=35  Identities=20%  Similarity=0.151  Sum_probs=28.2

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      +..-+.-|..++..+..|.-+.+.+|+|+|||..+
T Consensus         5 i~pk~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            5 IRPKTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CCCCSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             cccCCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            34445667788888889999999999999999654

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=92.88  E-value=0.19  Score=35.75  Aligned_cols=40  Identities=15%  Similarity=0.024  Sum_probs=26.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      .|+=.++.+|.|+|||...+-- +.++..  .+.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~-~~~~~~--~g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSF-VEIYKL--GKKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHH-HHHHHH--TTCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHHH-HHHHHH--CCCeEEEEeecc
Confidence            3566789999999999765433 333322  334788888874

>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=92.87  E-value=0.14  Score=41.25  Aligned_cols=43  Identities=9%  Similarity=0.101  Sum_probs=27.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      ...++++.|+||||||... -+++..+..  .+..++|+=|..++.
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~--~g~~viv~Dpkge~~   94 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLL--RGDRMVIVDPNGDML   94 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHH--TTCEEEEEEETTHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHH--CCCcEEEEeCCCchh
Confidence            4589999999999999864 334433332  223455555655553

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=92.84  E-value=0.16  Score=37.45  Aligned_cols=41  Identities=15%  Similarity=0.020  Sum_probs=26.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .|.=.++.++-|+|||...+-- +.+...  .+.+++++.|...
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~-~~r~~~--~g~kvli~kp~~D   67 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRR-LRRGIY--AKQKVVVFKPAID   67 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHH-HHHHHH--TTCCEEEEEEC--
T ss_pred             CceEEEEECCCCCCHHHHHHHH-HHHHHH--cCCceEEEEeccC
Confidence            3566788999999999655443 444433  3457899988653

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.77  E-value=0.09  Score=39.72  Aligned_cols=21  Identities=24%  Similarity=0.186  Sum_probs=17.4

Q ss_pred             HhcCCcEEEEcCCCChHHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      +..|.-+.+.+|||||||...
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            446788999999999999643

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.74  E-value=0.14  Score=40.56  Aligned_cols=21  Identities=29%  Similarity=0.409  Sum_probs=17.8

Q ss_pred             HHhcCCcEEEEcCCCChHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~   67 (175)
                      .+..|..+.+.+|||||||..
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHH
Confidence            344789999999999999963

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.60  E-value=0.041  Score=44.83  Aligned_cols=56  Identities=16%  Similarity=0.087  Sum_probs=35.3

Q ss_pred             cccccccccCCCCHHHHHHHhhCC---CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQP---FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g---~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..|-.+|++.+-.++..+.+.+.=   +.+|.-++..-+   ..-+.+++.||+|+|||+..
T Consensus       174 ~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          174 EKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            355667888887777777776531   112222222211   12389999999999999653

>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=92.58  E-value=0.17  Score=39.75  Aligned_cols=19  Identities=32%  Similarity=0.302  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.++++.+|+|+|||...
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3578999999999999754

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=92.57  E-value=0.25  Score=38.10  Aligned_cols=26  Identities=19%  Similarity=0.327  Sum_probs=19.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      ++++++.||+|+|||... ..+...+.
T Consensus       152 ~~~lll~G~~GtGKT~La-~aia~~~~  177 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLL-AAMAHELS  177 (308)
T ss_dssp             CCEEEEECSTTSSHHHHH-HHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHH-HHHHHHHH
Confidence            589999999999999643 34444443

>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=92.39  E-value=0.16  Score=37.49  Aligned_cols=40  Identities=20%  Similarity=0.069  Sum_probs=27.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      .|.-+++.+++|+|||.+.+--+.+...   .+.+++++.|..
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~---~g~kVli~~~~~   50 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEY---ADVKYLVFKPKI   50 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHH---TTCCEEEEEECC
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHh---cCCEEEEEEecc
Confidence            3567888999999999766444433332   344788887764

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=91.51  E-value=0.025  Score=39.61  Aligned_cols=73  Identities=14%  Similarity=0.073  Sum_probs=48.3

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++++.-+..+.+.++..     ++.+..++|+.+..+..+   .++++ ..++|+  +....+++.++.++|
T Consensus        29 ~~~~~iVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi  103 (170)
T 2yjt_D           29 EATRSIVFVRKRERVHELANWLREA-----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVF  103 (170)
Confidence            3458999999999998877776654     667888888876443332   33333 456666  444467777777776


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       104 ~~~~  107 (170)
T 2yjt_D          104 NFDM  107 (170)
Confidence            5443

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.24  E-value=0.2  Score=36.57  Aligned_cols=50  Identities=14%  Similarity=0.057  Sum_probs=29.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  103 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  103 (175)
                      .|.-+++.+|+|+|||.....-+.....   .+..++++.-.. -..++.+.+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~---~~~~v~~~~~e~-~~~~~~~~~~   71 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLK---MGEPGIYVALEE-HPVQVRQNMA   71 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHH---TTCCEEEEESSS-CHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh---cCCeEEEEEccC-CHHHHHHHHH
Confidence            5688999999999999654333333222   233577766432 2344444443

>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=92.14  E-value=0.57  Score=35.98  Aligned_cols=73  Identities=15%  Similarity=0.285  Sum_probs=51.1

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.+++++-+..+.+.+++.     +..+..++|+.+..+..+   .++++ ..++|+  .....+++++++++|
T Consensus       237 ~~~~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi  311 (367)
T 1hv8_A          237 KEFYGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVI  311 (367)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEE
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc-----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCCCcccCCEEE
Confidence            4557999999999998887777654     678888999987554433   34443 467777  333467777788777


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-+.
T Consensus       312 ~~~~  315 (367)
T 1hv8_A          312 NYHL  315 (367)
T ss_dssp             ESSC
T ss_pred             EecC
Confidence            6554

>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=92.10  E-value=0.76  Score=36.44  Aligned_cols=94  Identities=18%  Similarity=0.155  Sum_probs=59.3

Q ss_pred             CCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEEC--------CCchHHh---HH
Q psy1539          60 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFG--------GLPIQKD---EE  128 (175)
Q Consensus        60 TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g--------~~~~~~~---~~  128 (175)
                      ..++|.. .+.-++........+.++||.+++++-+..+.+.++..     ++.+..++|        +.+..+.   .+
T Consensus       340 ~~~~k~~-~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~  413 (494)
T 1wp9_A          340 LDHPKMD-KLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILD  413 (494)
T ss_dssp             CSCHHHH-HHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHH
T ss_pred             CCChHHH-HHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHc-----CCCcEEEeccccccccccCCHHHHHHHHH
Confidence            4455643 33444444332234568999999999998877776654     678888888        5544333   33


Q ss_pred             HHhcC-CCeEEE--eecCccCCCCceEEEEeCCC
Q psy1539         129 YLKTH-NPQIVG--LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       129 ~l~~~-~~iiv~--l~~~~~~~~~~~~lVlDEad  159 (175)
                      .+.++ ..++|+  .....+++.+++++|.-+..
T Consensus       414 ~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~  447 (494)
T 1wp9_A          414 EFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPV  447 (494)
T ss_dssp             HHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCC
T ss_pred             HHhcCCceEEEECCccccCCCchhCCEEEEeCCC
Confidence            44444 467777  44447889999999876653

>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=92.01  E-value=0.26  Score=38.61  Aligned_cols=42  Identities=7%  Similarity=-0.064  Sum_probs=27.6

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      -+.+.+|+|+|||...+..+.+.... ..+.+++++.....+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~-g~g~~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQ-YPDAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHH-CTTCEEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEeccchhh
Confidence            47899999999997655444433322 1244788988765554

>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=91.99  E-value=0.2  Score=35.97  Aligned_cols=40  Identities=10%  Similarity=0.053  Sum_probs=27.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      .|+=.++.++.|||||.+.+- ++.+...  .+.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~-~a~r~~~--~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIR-RIRRAKI--AKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHH-HHHHHHH--TTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHH-HHHHHHH--CCCEEEEEEecc
Confidence            355678899999999976554 3444332  455789998874

>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=91.98  E-value=0.35  Score=36.49  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.++++.+|+|+|||...
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            578999999999999654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=91.72  E-value=0.093  Score=36.98  Aligned_cols=20  Identities=10%  Similarity=0.270  Sum_probs=16.5

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..|+-+++.+|+|+|||...
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35778999999999999643

>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=91.72  E-value=0.037  Score=42.88  Aligned_cols=52  Identities=13%  Similarity=0.047  Sum_probs=31.5

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHh-----cCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAV-----LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~-----~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+...|+++.-.....+.+.+.= .  .|..   .|...     ..+++++.+|+|+|||...
T Consensus        12 ~~~~~~~di~G~~~~~~~l~~~i-~--~~~~---~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           12 KPNVKWEDVAGLEGAKEALKEAV-I--LPVK---FPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHT-H--HHHH---CGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCCCHHHhcChHHHHHHHHHHH-H--HHHh---CHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            34455777777777777776531 1  1111   11111     2368999999999999654

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=91.60  E-value=0.27  Score=40.74  Aligned_cols=42  Identities=17%  Similarity=0.248  Sum_probs=27.9

Q ss_pred             HHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHH
Q psy1539          25 EDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        25 l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~   67 (175)
                      +.+.+.+ ++..-...-..+.-.+..|.++++.||+|+|||..
T Consensus        16 l~~~l~~-~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           16 LSSSLEK-GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHT-TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHh-hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            3444443 23333444445555667889999999999999964

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=91.48  E-value=0.1  Score=36.14  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=18.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +.++++.+|+|+|||... -.+.+.+
T Consensus        43 ~~~~ll~G~~G~GKT~l~-~~~~~~~   67 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV-EGLAQRI   67 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCceEEECCCCCCHHHHH-HHHHHHH
Confidence            378999999999999653 3334443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=91.40  E-value=0.092  Score=40.99  Aligned_cols=26  Identities=8%  Similarity=-0.018  Sum_probs=19.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +.++++.+|+|+|||.+. -.++..+.
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            478999999999999654 33444443

>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=91.39  E-value=0.9  Score=41.45  Aligned_cols=77  Identities=6%  Similarity=0.098  Sum_probs=58.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.+++|++|+++-+..+.+.+++.   .|+.++..++|+.+..+..+   .+.+ ..+++|+  +....+++++++++|
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~---~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v~e~GiDip~v~~VI  887 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII  887 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHH---CTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEE
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHh---CCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCcceeeecccCCcEEE
Confidence            4568999999999888877777765   45788999999987554433   3443 4578888  666689999999999


Q ss_pred             EeCCCC
Q psy1539         155 MDVRSG  160 (175)
Q Consensus       155 lDEad~  160 (175)
                      +..++.
T Consensus       888 i~~~~~  893 (1151)
T 2eyq_A          888 IERADH  893 (1151)
T ss_dssp             ETTTTS
T ss_pred             EeCCCC
Confidence            988853

>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=91.26  E-value=0.11  Score=37.63  Aligned_cols=19  Identities=16%  Similarity=0.020  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+++.+|+|+|||...
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            3689999999999999643

>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=91.07  E-value=0.4  Score=36.83  Aligned_cols=36  Identities=19%  Similarity=0.167  Sum_probs=22.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +..+++.||+|+|||... -.+...+...  +..++++.
T Consensus        37 ~~~lll~G~~GtGKT~la-~~i~~~~~~~--~~~~~~i~   72 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL-QAAGNEAKKR--GYRVIYSS   72 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH-HHHHHHHHHT--TCCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHHHHC--CCEEEEEE
Confidence            468999999999999643 3444444332  33455554

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=91.00  E-value=0.15  Score=39.30  Aligned_cols=24  Identities=25%  Similarity=0.300  Sum_probs=19.2

Q ss_pred             HHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ...+..+.++++.+|+|+|||...
T Consensus        40 ~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           40 LIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHcCCeEEEECCCCCcHHHHH
Confidence            344556899999999999999643

>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=90.98  E-value=0.24  Score=39.21  Aligned_cols=27  Identities=26%  Similarity=0.316  Sum_probs=18.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+..+++.+|||||||... -.++..+.
T Consensus       122 ~~g~i~I~GptGSGKTTlL-~~l~g~~~  148 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL-AAMLDYLN  148 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH-HHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHhccc
Confidence            4568999999999999643 33444443

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=90.96  E-value=0.12  Score=36.85  Aligned_cols=19  Identities=26%  Similarity=0.239  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .++.+++.+++|||||...
T Consensus        24 ~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            5789999999999999754

>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=90.91  E-value=0.12  Score=40.37  Aligned_cols=19  Identities=26%  Similarity=0.562  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEcCCCChHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~   66 (175)
                      +..|..+.+.+|||||||.
T Consensus       168 i~~g~~v~i~G~~GsGKTT  186 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTT  186 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHH
T ss_pred             ccCCCEEEEECCCCCCHHH
Confidence            3468999999999999996

>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=90.89  E-value=0.21  Score=37.20  Aligned_cols=19  Identities=26%  Similarity=0.403  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.++++.+++|+|||...
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            4689999999999999643

>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=90.87  E-value=1.3  Score=34.12  Aligned_cols=17  Identities=18%  Similarity=0.057  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ...++.+|.|+|||...
T Consensus        19 ~~~Lf~Gp~G~GKtt~a   35 (305)
T 2gno_A           19 ISILINGEDLSYPREVS   35 (305)
T ss_dssp             EEEEEECSSSSHHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            47899999999998654

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=90.85  E-value=0.4  Score=35.12  Aligned_cols=50  Identities=10%  Similarity=0.072  Sum_probs=30.4

Q ss_pred             HHHHHHhhCCCCCCcHHHHHhHHHHhcC----CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          24 KEDRIGESQPFREQTSFQHECIPQAVLG----MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        24 ~l~~~l~~~g~~~~t~~Q~~~i~~~~~g----~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .+.+-|+=.|+. +... ..++..+.++    +.+++.+|+|+|||..+ .++++.+
T Consensus        29 ~I~~~l~yq~~~-~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~l   82 (212)
T 1tue_A           29 PIVQFLRYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHFI   82 (212)
T ss_dssp             HHHHHHHHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHcCcC-HHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHHh
Confidence            555555544432 3333 3445555555    35999999999999543 5566554

>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=90.77  E-value=0.45  Score=36.62  Aligned_cols=55  Identities=11%  Similarity=0.020  Sum_probs=31.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcC---------CCC----eEEEEEecCHHH-HHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETT---------DSN----VYVLVMCHTREL-AFQISKEYERF  105 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---------~~~----~~~lil~Pt~~L-~~q~~~~~~~~  105 (175)
                      |.-+++.+++|+|||...+.-+.+.....         ..+    .+++|+.-...+ ..++.+.++++
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~  166 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHA  166 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHc
Confidence            36789999999999965544333322111         122    578888755432 44444444443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=90.69  E-value=0.13  Score=36.86  Aligned_cols=19  Identities=21%  Similarity=0.333  Sum_probs=15.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+-+.+.+|+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999743

>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=90.63  E-value=0.1  Score=36.50  Aligned_cols=20  Identities=35%  Similarity=0.438  Sum_probs=16.9

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..++.+++.+++|||||...
T Consensus         9 ~~~~~i~i~G~~GsGKst~~   28 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLG   28 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHH
Confidence            45688999999999999754

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=90.56  E-value=0.1  Score=36.13  Aligned_cols=18  Identities=28%  Similarity=0.436  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ..++++.+|+|+|||...
T Consensus        43 ~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCEEEEESCGGGCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            478999999999999643

>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=90.52  E-value=0.54  Score=35.70  Aligned_cols=48  Identities=15%  Similarity=0.022  Sum_probs=32.9

Q ss_pred             HHHHHHHhhCCCCCCcHHHHHh-HHHHhcCC-----cEEEEcCCCChHHHHHHHHHHH
Q psy1539          23 EKEDRIGESQPFREQTSFQHEC-IPQAVLGM-----DILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        23 ~~l~~~l~~~g~~~~t~~Q~~~-i~~~~~g~-----~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      .++.+-|+-.||.   +++-.. +..+++|+     .+++.+|+|+|||+.+. ++..
T Consensus        73 n~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~-ala~  126 (267)
T 1u0j_A           73 NRIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE-AIAH  126 (267)
T ss_dssp             CHHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH-HHHH
T ss_pred             HHHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH-HHHh
Confidence            3778888877764   555443 45566553     59999999999997654 3443

>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=90.47  E-value=0.25  Score=44.95  Aligned_cols=39  Identities=15%  Similarity=0.252  Sum_probs=28.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      -+|.|+.|||||.+.+--+...+.....+.+++++||..
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q   42 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQ   42 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGG
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCc
Confidence            368899999999877666655555444446889998865

>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=90.46  E-value=0.15  Score=35.48  Aligned_cols=18  Identities=22%  Similarity=0.307  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ++-+++.+++|||||...
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            567899999999999754

>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=90.44  E-value=0.47  Score=37.31  Aligned_cols=73  Identities=8%  Similarity=0.139  Sum_probs=44.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.+++++-+..+.+.+++.     ++.+..++|+.+..+..+   .++++ ..++|+  +....+++.+++++|
T Consensus       279 ~~~~~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi  353 (414)
T 3eiq_A          279 TITQAVIFINTRRKVDWLTEKMHAR-----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVI  353 (414)
T ss_dssp             CCSSCEEECSCHHHHHHHHHHHHTT-----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSCC--CCGGGCSCEE
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHhc-----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCccccCCCccCCCEEE
Confidence            3447999999999998877766542     677888999887554433   34443 457777  444567777777776


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .-..
T Consensus       354 ~~~~  357 (414)
T 3eiq_A          354 NYDL  357 (414)
T ss_dssp             ESSC
T ss_pred             EeCC
Confidence            5444

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=90.42  E-value=0.13  Score=39.09  Aligned_cols=18  Identities=28%  Similarity=0.434  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.++++.+|+|+|||...
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            357999999999999654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=90.42  E-value=0.14  Score=36.35  Aligned_cols=21  Identities=33%  Similarity=0.404  Sum_probs=16.8

Q ss_pred             HhcCCcEEEEcCCCChHHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      +..|.-+.+.+|+|||||...
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            346788999999999999743

>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=90.38  E-value=0.79  Score=40.00  Aligned_cols=75  Identities=11%  Similarity=0.177  Sum_probs=53.5

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHh------hCCCeEEEEEECCCchHHhHHHHhc--------C-CCeEEE--eecC
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSK------YMSNIKVGVFFGGLPIQKDEEYLKT--------H-NPQIVG--LVNY  143 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~------~~~~i~v~~~~g~~~~~~~~~~l~~--------~-~~iiv~--l~~~  143 (175)
                      .+.++||.+|++.-+.++.+.+++...      ...++.+..++|+.+..++.+.+..        | ..+||+  +...
T Consensus       302 ~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~iae~  381 (773)
T 2xau_A          302 EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTNIAET  381 (773)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECTHHHH
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCcHHHh
Confidence            345899999999999999888876332      1248899999999986665544432        2 245666  4445


Q ss_pred             ccCCCCceEEEE
Q psy1539         144 ETNLSGVVVNVM  155 (175)
Q Consensus       144 ~~~~~~~~~lVl  155 (175)
                      .+++.++++||-
T Consensus       382 GidIp~v~~VId  393 (773)
T 2xau_A          382 SLTIDGIVYVVD  393 (773)
T ss_dssp             TCCCTTEEEEEE
T ss_pred             CcCcCCeEEEEe
Confidence            788889987763

>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=90.34  E-value=0.15  Score=36.77  Aligned_cols=19  Identities=37%  Similarity=0.483  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+-+++.+|+|+|||...
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            4677999999999999743

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=90.24  E-value=0.72  Score=46.24  Aligned_cols=49  Identities=18%  Similarity=0.194  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHhhCCCCCCcHHHHH-hH---HHHhcCCcEEEEcCCCChHHHHHH
Q psy1539          20 NRREKEDRIGESQPFREQTSFQHE-CI---PQAVLGMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        20 ~l~~~l~~~l~~~g~~~~t~~Q~~-~i---~~~~~g~~~ii~a~TGsGKT~~~~   69 (175)
                      .|...+.+.+.+.|+. +++.+.. ++   ..+...+.+++.||||||||.++-
T Consensus       872 ~l~~ai~~~~~~~~L~-~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          872 QLRKKIQEIAKQRHLV-TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHHHTTCC-CCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHHcCCc-cCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            3456777788888875 5554433 22   233346889999999999998874

>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=90.21  E-value=0.1  Score=36.80  Aligned_cols=20  Identities=25%  Similarity=0.416  Sum_probs=16.7

Q ss_pred             HhcCCcEEEEcCCCChHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~   67 (175)
                      +..|.-+++.+|+|||||..
T Consensus         6 i~~g~~i~l~G~~GsGKSTl   25 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTI   25 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHH
Confidence            34577899999999999974

>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=90.19  E-value=0.35  Score=38.34  Aligned_cols=21  Identities=24%  Similarity=0.221  Sum_probs=17.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~   70 (175)
                      .+.++++.++||+|||...-.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~   54 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKM   54 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHH
Confidence            567999999999999965433

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=90.04  E-value=0.17  Score=35.45  Aligned_cols=18  Identities=33%  Similarity=0.230  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ++.+++.+++|||||...
T Consensus         5 ~~~i~l~G~~GsGKst~a   22 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVG   22 (185)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            578999999999999754

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=90.01  E-value=0.28  Score=35.78  Aligned_cols=50  Identities=20%  Similarity=0.177  Sum_probs=28.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      .|.-+++.|++|+|||...+--+.+....  .+..+++++-. +-..++.+.+
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~--~~~~v~~~s~E-~~~~~~~~~~   78 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEE--YGEPGVFVTLE-ERARDLRREM   78 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHH--HCCCEEEEESS-SCHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCCceeeccc-CCHHHHHHHH
Confidence            35789999999999996544333332222  12246666533 2234444443

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=89.89  E-value=0.17  Score=35.89  Aligned_cols=19  Identities=32%  Similarity=0.358  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+.+.+|+|||||...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~   24 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLV   24 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            5778899999999999743

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=89.75  E-value=0.1  Score=39.65  Aligned_cols=54  Identities=11%  Similarity=0.015  Sum_probs=27.2

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHH-HhHHHHh--cCCcEEEEcCCCChHHHHH
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQH-ECIPQAV--LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~-~~i~~~~--~g~~~ii~a~TGsGKT~~~   68 (175)
                      +-..|++++-..++.+.+.+. +.  .|+.. .++..+-  -.+.+++.+|+|+|||...
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~-i~--~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMA-IL--APVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             -------CCHHHHHHHHHHHH-HT--HHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHH-HH--HHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            345677777767777777653 11  22211 1222211  1255999999999999643

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=89.75  E-value=0.16  Score=38.46  Aligned_cols=18  Identities=28%  Similarity=0.320  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ++.+++.||+|+|||...
T Consensus        54 ~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            589999999999999654

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=89.71  E-value=0.19  Score=34.67  Aligned_cols=18  Identities=22%  Similarity=0.309  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ++.+.+.+++|||||...
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            567999999999999743

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.68  E-value=0.16  Score=40.96  Aligned_cols=55  Identities=13%  Similarity=0.049  Sum_probs=31.0

Q ss_pred             ccccccccCCCCHHHHHHHhhCC---CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP---FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g---~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|-..|++.+=-.+..+.+.+.=   +.+|--++..-   +..-+.+++.+|+|+|||+.+
T Consensus       142 ~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          142 VPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHHH
Confidence            34456777765556666565431   11111121111   112389999999999999753

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=89.63  E-value=4.7  Score=33.53  Aligned_cols=83  Identities=11%  Similarity=0.080  Sum_probs=55.9

Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhC---CCeEEEEEECCCch--HHhHHHHhcCC---C-eEEE--eecCccCCC
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYM---SNIKVGVFFGGLPI--QKDEEYLKTHN---P-QIVG--LVNYETNLS  148 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~---~~i~v~~~~g~~~~--~~~~~~l~~~~---~-iiv~--l~~~~~~~~  148 (175)
                      ..+.++||.|++++-+..+.+.+++.....   .+-.+..++|+.+.  .+.++.++++.   + ++++  +....++++
T Consensus       437 ~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip  516 (590)
T 3h1t_A          437 DRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGKIGKGHLSRFQELETSTPVILTTSQLLTTGVDAP  516 (590)
T ss_dssp             CTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHHHHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCT
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChHHHHHHHHHHhCCCCCCCEEEEECChhhcCccch
Confidence            345689999999999999999988764321   12235667777643  23345565532   2 4455  566689999


Q ss_pred             CceEEEEeCCCCCC
Q psy1539         149 GVVVNVMDVRSGGW  162 (175)
Q Consensus       149 ~~~~lVlDEad~~f  162 (175)
                      ++.++|++..-.+.
T Consensus       517 ~v~~Vi~~~~~~s~  530 (590)
T 3h1t_A          517 TCKNVVLARVVNSM  530 (590)
T ss_dssp             TEEEEEEESCCCCH
T ss_pred             heeEEEEEecCCCh
Confidence            99999998874443

>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=89.51  E-value=0.17  Score=37.35  Aligned_cols=18  Identities=28%  Similarity=0.257  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+++++.+|+|+|||...
T Consensus        39 ~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999643

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.46  E-value=0.13  Score=42.18  Aligned_cols=55  Identities=15%  Similarity=-0.023  Sum_probs=33.1

Q ss_pred             ccccccccCCCCHHHHHHHhhCC---CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP---FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g---~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|-.+|++.+=-.+..+.|.+.=   +.+|-.++..   -+.--+.+++.+|+|+|||+..
T Consensus       203 ~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~---Gi~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATL---GIDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHH---TCCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHC---CCCCCCceEeeCCCCCcHHHHH
Confidence            44566888877777777776531   1111111111   1112489999999999999653

>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=89.42  E-value=0.73  Score=37.24  Aligned_cols=66  Identities=12%  Similarity=0.032  Sum_probs=44.7

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      +.+++|+||+++-+.++.+.++..     +.++..++|+.. .+..+.++++ .+++|+  +....++++ ++++|
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~-----~~~v~~lhg~~R-~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI  245 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTF-EREYPTIKQKKPDFILATDIAEMGANLC-VERVL  245 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSC-C--------CCCSEEEESSSTTCCTTCC-CSEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc-----CCCEEEecchhH-HHHHhhhcCCCceEEEECChhheeeccC-ceEEE
Confidence            458999999999999988777654     678888888543 4455556554 567777  566688888 88877

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=89.36  E-value=0.18  Score=39.38  Aligned_cols=24  Identities=33%  Similarity=0.497  Sum_probs=17.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +.+++.||+|+|||... -.+...+
T Consensus        71 ~~vLl~GppGtGKT~la-~~la~~l   94 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIA-MGMAQAL   94 (368)
T ss_dssp             CEEEEEESTTSSHHHHH-HHHHHHH
T ss_pred             CEEEEECCCCCCHHHHH-HHHHHHh
Confidence            58999999999999653 3344443

>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=89.26  E-value=0.18  Score=34.44  Aligned_cols=16  Identities=31%  Similarity=0.372  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.|++|||||...
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            4789999999999744

>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=89.20  E-value=0.22  Score=35.12  Aligned_cols=19  Identities=37%  Similarity=0.629  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .++.+++.+++|||||...
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            4678999999999999754

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=89.20  E-value=0.22  Score=35.63  Aligned_cols=20  Identities=20%  Similarity=0.222  Sum_probs=16.9

Q ss_pred             HhcCCcEEEEcCCCChHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~   67 (175)
                      +..|+-+++++|+|||||..
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl   28 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTL   28 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHH
T ss_pred             cccCCEEEEECCCCCCHHHH
Confidence            34678899999999999964

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=89.17  E-value=0.23  Score=36.18  Aligned_cols=21  Identities=19%  Similarity=0.196  Sum_probs=16.6

Q ss_pred             HhcCCcEEEEcCCCChHHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      +..|+-+.+.+|+|+|||...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            346888999999999999643

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.04  E-value=0.12  Score=42.07  Aligned_cols=55  Identities=15%  Similarity=0.046  Sum_probs=30.6

Q ss_pred             ccccccccCCCCHHHHHHHhhCC---CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP---FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g---~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|-.+|++.+=-.+..+.+.+.=   +.+|.-++..-   +.--+.+++.+|+|+|||+..
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHHH
Confidence            34455777765555555554430   11111111111   112389999999999999753

>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=88.99  E-value=0.23  Score=35.71  Aligned_cols=22  Identities=27%  Similarity=0.445  Sum_probs=16.9

Q ss_pred             HHhcCCcEEEEcCCCChHHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..|+-+.+.+|+|+|||...
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            5667899999999999999743

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=88.98  E-value=0.2  Score=37.21  Aligned_cols=55  Identities=16%  Similarity=0.173  Sum_probs=30.0

Q ss_pred             ccccccccCCCCHHHHHHHhhCC--CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP--FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g--~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+...|+++.-.+...+.+.+.-  +..+..++..   .....+.+++.+|+|+|||...
T Consensus         6 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A            6 QIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHc---CCCCCCeEEEECcCCCCHHHHH
Confidence            34456777766666666655420  1111111110   0112367999999999999643

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.96  E-value=0.14  Score=41.67  Aligned_cols=55  Identities=9%  Similarity=0.028  Sum_probs=30.3

Q ss_pred             ccccccccCCCCHHHHHHHhhCC---CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP---FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g---~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|-..|++.+=-.+..+.+.+.=   +.+|--++..-   +..-+.+++.||+|+|||+..
T Consensus       166 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            34456777765555555554420   11111111111   112378999999999999653

>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=88.95  E-value=0.22  Score=34.80  Aligned_cols=18  Identities=17%  Similarity=0.281  Sum_probs=15.0

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .+.-+++.+++|||||..
T Consensus         2 ~~~~I~i~G~~GsGKsT~   19 (192)
T 1kht_A            2 KNKVVVVTGVPGVGSTTS   19 (192)
T ss_dssp             -CCEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            356799999999999964

>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=88.88  E-value=0.43  Score=38.67  Aligned_cols=47  Identities=11%  Similarity=0.188  Sum_probs=27.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      +..+++.||+|+|||... -.+.+.+.....+..++++.. .++..+..
T Consensus       130 ~~~lll~Gp~G~GKTtLa-~aia~~l~~~~~~~~v~~v~~-~~~~~~~~  176 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITS-EKFLNDLV  176 (440)
T ss_dssp             SCCEEEECSSSSSHHHHH-HHHHHHHHHHCCSSCEEEEEH-HHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEeeH-HHHHHHHH
Confidence            368999999999999643 344444433222334555543 33444433

>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=88.85  E-value=0.16  Score=40.42  Aligned_cols=19  Identities=26%  Similarity=0.202  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|..+.+.+|||||||..
T Consensus       134 ~~g~~i~ivG~~GsGKTTl  152 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTT  152 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4578899999999999964

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=88.85  E-value=0.19  Score=35.14  Aligned_cols=20  Identities=20%  Similarity=0.084  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~   69 (175)
                      .|.-+.+.+|+|||||..+-
T Consensus         8 ~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHH
Confidence            56778999999999997554

>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=88.72  E-value=0.24  Score=35.90  Aligned_cols=20  Identities=15%  Similarity=0.222  Sum_probs=16.9

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..|+-+++.+|+|+|||...
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~   36 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIK   36 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECcCCCCHHHHH
Confidence            46788999999999999643

>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=88.71  E-value=1.3  Score=36.44  Aligned_cols=51  Identities=14%  Similarity=0.193  Sum_probs=38.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|....+.+-||||||++..- +...     .+...|+|+|+...|.|+++.++.+.
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~-l~~~-----~~~p~lvv~~~~~~A~~l~~~l~~~~   63 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAE-IAER-----HAGPVVLIAPDMQNALRLHDEISQFT   63 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHH-HHHH-----SSSCEEEEESSHHHHHHHHHHHHHTC
T ss_pred             CCCeEEEeCCCchHHHHHHHH-HHHH-----hCCCEEEEeCCHHHHHHHHHHHHhhC
Confidence            466788999999999864322 2222     12248999999999999999998875

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=88.71  E-value=0.2  Score=39.40  Aligned_cols=25  Identities=12%  Similarity=0.218  Sum_probs=17.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ++-++|.+|||+|||... ..+..++
T Consensus        40 ~~lIvI~GPTgsGKTtLa-~~LA~~l   64 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLS-IDLAAHF   64 (339)
T ss_dssp             CEEEEEECSTTSSHHHHH-HHHHTTS
T ss_pred             CceEEEECCCCCCHHHHH-HHHHHHC
Confidence            356899999999999543 3444443

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=88.70  E-value=0.21  Score=37.38  Aligned_cols=16  Identities=25%  Similarity=0.092  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.+|+|||||...
T Consensus         3 li~I~G~~GSGKSTla   18 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMA   18 (253)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            4689999999999644

>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=88.69  E-value=1.1  Score=40.90  Aligned_cols=56  Identities=21%  Similarity=0.154  Sum_probs=41.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcC---------CCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETT---------DSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---------~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      .|.+ +|.|+-|||||.+..-=++..+...         -.-.+.|+|+=|++=+.+..+.++...
T Consensus        16 ~g~~-lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L   80 (1180)
T 1w36_B           16 QGER-LIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (1180)
T ss_dssp             SSCE-EEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCE-EEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHH
Confidence            4555 9999999999988776666666431         122379999999988888888776654

>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=88.68  E-value=0.43  Score=36.63  Aligned_cols=18  Identities=28%  Similarity=0.386  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |+-+.+.+++|+|||...
T Consensus       105 g~vi~lvG~~GsGKTTl~  122 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTL  122 (296)
T ss_dssp             SSEEEEEESTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            567899999999999754

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.65  E-value=0.24  Score=35.31  Aligned_cols=19  Identities=26%  Similarity=0.337  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+++.+|+|||||...
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            4788999999999999753

>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=88.63  E-value=0.69  Score=33.54  Aligned_cols=21  Identities=19%  Similarity=0.028  Sum_probs=17.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~   70 (175)
                      .|.-+.+.+|+|+|||.....
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~   43 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHT   43 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHH
Confidence            467899999999999965543

>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=88.54  E-value=0.25  Score=35.42  Aligned_cols=16  Identities=31%  Similarity=0.507  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      +-++++||+|+|||..
T Consensus         2 RpIVi~GPSG~GK~Tl   17 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            5689999999999964

>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=88.50  E-value=0.25  Score=36.22  Aligned_cols=22  Identities=27%  Similarity=0.431  Sum_probs=16.7

Q ss_pred             HHhcCCcEEEEcCCCChHHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..|+-+++.+|+|+|||...
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTLl   33 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSLI   33 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHHH
T ss_pred             cCCCCcEEEEECCCCCCHHHHH
Confidence            3456888999999999999743

>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=88.49  E-value=0.21  Score=36.40  Aligned_cols=18  Identities=33%  Similarity=0.708  Sum_probs=15.1

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|+-+++.+|||+|||..
T Consensus        33 ~g~~ilI~GpsGsGKStL   50 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSET   50 (205)
T ss_dssp             TTEEEEEECCCTTTTHHH
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            467799999999999843

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=88.43  E-value=0.36  Score=37.08  Aligned_cols=19  Identities=32%  Similarity=0.410  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.++++.+++|+|||...
T Consensus        24 ~~~~vLi~Ge~GtGKt~lA   42 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVA   42 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHH
T ss_pred             CCCcEEEECCCCchHHHHH
Confidence            4689999999999999653

>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=88.35  E-value=0.82  Score=37.99  Aligned_cols=19  Identities=16%  Similarity=0.193  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.+++|.++||||||.+.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L  184 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGV  184 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHH
T ss_pred             cCceEEEECCCCCCHHHHH
Confidence            3578999999999999654

>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=88.32  E-value=0.23  Score=38.73  Aligned_cols=23  Identities=13%  Similarity=0.120  Sum_probs=16.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      +-++|.+|||||||... ..+...
T Consensus         4 ~~i~i~GptgsGKt~la-~~La~~   26 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTS-VMLAKR   26 (322)
T ss_dssp             EEEEEECCTTSCHHHHH-HHHHHT
T ss_pred             cEEEEECCCcCCHHHHH-HHHHHh
Confidence            45788999999999543 344443

>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=88.27  E-value=0.94  Score=35.03  Aligned_cols=25  Identities=36%  Similarity=0.414  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +..+++.||+|+|||... -.+...+
T Consensus        45 ~~~vli~G~~G~GKTtl~-~~l~~~~   69 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV-KFVLSKL   69 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            578999999999999643 3344443

>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=88.24  E-value=0.22  Score=34.56  Aligned_cols=19  Identities=32%  Similarity=0.162  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+++.+++|||||...
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            3567899999999999754

>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=88.18  E-value=0.72  Score=35.66  Aligned_cols=54  Identities=9%  Similarity=-0.066  Sum_probs=30.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcC---CCCeEEEEEecCHHH-HHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTREL-AFQISKEYER  104 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---~~~~~~lil~Pt~~L-~~q~~~~~~~  104 (175)
                      |.-+++.+++|+|||.....-+.+.....   ..+.+++++.-...+ ..++.+.++.
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~  164 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKA  164 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999965444333322210   013467887754322 3344444433

>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=88.18  E-value=0.24  Score=38.55  Aligned_cols=22  Identities=23%  Similarity=0.256  Sum_probs=15.6

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      -+++++|||||||... ..+...
T Consensus        12 ~i~i~GptgsGKt~la-~~La~~   33 (316)
T 3foz_A           12 AIFLMGPTASGKTALA-IELRKI   33 (316)
T ss_dssp             EEEEECCTTSCHHHHH-HHHHHH
T ss_pred             EEEEECCCccCHHHHH-HHHHHh
Confidence            4788999999999543 334443

>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=88.17  E-value=0.35  Score=34.56  Aligned_cols=35  Identities=20%  Similarity=0.063  Sum_probs=22.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.+|+|+|||.....-+.   .   .+..++++.-
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~---~---~~~~v~~i~~   53 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL---L---SGKKVAYVDT   53 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH---H---HCSEEEEEES
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH---H---cCCcEEEEEC
Confidence            457789999999999965433222   1   2335666653

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=88.05  E-value=2.9  Score=32.17  Aligned_cols=17  Identities=29%  Similarity=0.409  Sum_probs=13.8

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +-+.+.+++|+|||...
T Consensus       105 ~vi~ivG~~GsGKTTl~  121 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSC  121 (306)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEEcCCCChHHHHH
Confidence            35789999999999654

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=88.05  E-value=0.77  Score=32.89  Aligned_cols=19  Identities=32%  Similarity=0.357  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+.+.+|+|+|||...
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4688999999999999543

>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=87.80  E-value=0.61  Score=35.31  Aligned_cols=39  Identities=26%  Similarity=0.181  Sum_probs=24.0

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      ..|.-+++.+|+|+|||.... -++..+... .+..++++.
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~-~ia~~~~~~-~G~~v~~~~   71 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVR-QQALQWGTA-MGKKVGLAM   71 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHH-HHHHHHHHT-SCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHH-HHHHHHHHH-cCCeEEEEe
Confidence            357889999999999996443 333333322 232465654

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=87.74  E-value=0.42  Score=37.89  Aligned_cols=24  Identities=38%  Similarity=0.732  Sum_probs=18.1

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      +..+++|.|  ++..+.||||||.+.
T Consensus        97 v~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           97 VSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            345567866  677889999999775

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=87.72  E-value=0.26  Score=38.15  Aligned_cols=50  Identities=16%  Similarity=0.044  Sum_probs=29.3

Q ss_pred             ccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHh-----cCCcEEEEcCCCChHHHHH
Q psy1539          13 VKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAV-----LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        13 ~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~-----~g~~~ii~a~TGsGKT~~~   68 (175)
                      -..|++++=.....+.+.+.= .  .|.+.   |.+.     ..+.+++.+|+|+|||...
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v-~--~p~~~---~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAV-I--LPIKF---PHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHH-H--HHHHC---GGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHH-H--HHHhC---HHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            346777766666666665420 0  11110   1121     2378999999999999643

>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=87.70  E-value=0.75  Score=35.84  Aligned_cols=25  Identities=24%  Similarity=0.250  Sum_probs=17.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ++.+++.+|+|+|||... -.+.+.+
T Consensus        45 ~~~vll~G~~G~GKT~la-~~l~~~~   69 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS-KYIFNEI   69 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH-HHHHHHH
Confidence            367999999999999653 3334433

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=87.64  E-value=0.99  Score=31.78  Aligned_cols=25  Identities=28%  Similarity=0.236  Sum_probs=16.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +-+.+.+++|+|||. ++-.++..+.
T Consensus         7 ~~i~i~G~sGsGKTT-l~~~l~~~l~   31 (174)
T 1np6_A            7 PLLAFAAWSGTGKTT-LLKKLIPALC   31 (174)
T ss_dssp             CEEEEECCTTSCHHH-HHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHH-HHHHHHHhcc
Confidence            357889999999995 3344444443

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=87.61  E-value=0.28  Score=33.90  Aligned_cols=16  Identities=31%  Similarity=0.254  Sum_probs=13.4

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.+++|||||...
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            4789999999999643

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=87.61  E-value=2  Score=34.93  Aligned_cols=95  Identities=15%  Similarity=0.179  Sum_probs=53.9

Q ss_pred             ChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEEC--------CCchHHh---HHHH
Q psy1539          62 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFG--------GLPIQKD---EEYL  130 (175)
Q Consensus        62 sGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g--------~~~~~~~---~~~l  130 (175)
                      ++|.. .+.-++........+.++||.+++++-+..+.+.++...... .+++..++|        +.+..+.   .+.+
T Consensus       370 ~~k~~-~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F  447 (555)
T 3tbk_A          370 NPKLR-DLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALS-FLKPGILTGRGRTNRATGMTLPAQKCVLEAF  447 (555)
T ss_dssp             CHHHH-HHHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGT-TCCEEECCC----------------------
T ss_pred             CHHHH-HHHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcC-ceeeeEEEecCCcccccccCHHHHHHHHHHH
Confidence            55643 334444444333345689999999999999999888764322 455555554        4443332   3345


Q ss_pred             hc-C-CCeEEE--eecCccCCCCceEEEEeCC
Q psy1539         131 KT-H-NPQIVG--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       131 ~~-~-~~iiv~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      ++ + .+++|+  .....+++.+++++|.=+.
T Consensus       448 ~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~  479 (555)
T 3tbk_A          448 RASGDNNILIATSVADEGIDIAECNLVILYEY  479 (555)
T ss_dssp             ----CCSEEEECCCTTCCEETTSCSEEEEESC
T ss_pred             hcCCCeeEEEEcchhhcCCccccCCEEEEeCC
Confidence            54 3 478887  5555788888888876544

>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=87.60  E-value=0.28  Score=33.64  Aligned_cols=16  Identities=19%  Similarity=0.038  Sum_probs=13.6

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.|+.|||||...
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            4789999999999754

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=87.59  E-value=0.25  Score=37.70  Aligned_cols=24  Identities=13%  Similarity=0.130  Sum_probs=17.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +.+++.+|+|+|||... -.+...+
T Consensus        37 ~~lLl~GppGtGKT~la-~aiA~~l   60 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQC-ELVFRKM   60 (293)
T ss_dssp             SEEEEEECTTSCHHHHH-HHHHHHH
T ss_pred             eEEEEECCCCCCHHHHH-HHHHHHh
Confidence            57899999999999643 3344443

>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=87.57  E-value=0.52  Score=33.63  Aligned_cols=16  Identities=31%  Similarity=0.526  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.+|+|+|||...
T Consensus        47 ~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            6899999999999643

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=87.53  E-value=0.21  Score=34.97  Aligned_cols=19  Identities=21%  Similarity=0.392  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+++.+++|||||...
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            4567899999999999753

>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=87.40  E-value=0.46  Score=34.13  Aligned_cols=31  Identities=19%  Similarity=0.159  Sum_probs=22.6

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .++.++.. .....|..+++.+++|||||...
T Consensus        12 ~~~~~r~~-~~~~~~~~i~~~G~~GsGKsT~~   42 (211)
T 1m7g_A           12 LTRSERTE-LRNQRGLTIWLTGLSASGKSTLA   42 (211)
T ss_dssp             CCHHHHHH-HHTSSCEEEEEECSTTSSHHHHH
T ss_pred             cCHHHhhc-ccCCCCCEEEEECCCCCCHHHHH
Confidence            34555555 34556888999999999999643

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=87.35  E-value=0.79  Score=33.11  Aligned_cols=39  Identities=13%  Similarity=-0.036  Sum_probs=28.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      .|+=.++.+|.|||||...+-.+-+....   +.+++++.|.
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            36778999999999996655544444332   3578999887

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=87.33  E-value=0.84  Score=32.12  Aligned_cols=24  Identities=13%  Similarity=-0.055  Sum_probs=16.4

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      -+.+.+++|||||.. +.-++..+.
T Consensus         6 ~i~i~G~sGsGKTTl-~~~L~~~l~   29 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTL-MEKWVAAAV   29 (169)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHHH
T ss_pred             EEEEECCCCCCHHHH-HHHHHHhhH
Confidence            467899999999953 334444444

>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=87.29  E-value=0.87  Score=33.39  Aligned_cols=40  Identities=10%  Similarity=-0.018  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      |+=.++.++-|||||.+.+--+.+...   .+.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~---~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQF---AKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHH---TTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHH---CCCEEEEEEeccC
Confidence            444567888899999765544444333   3457999998764

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=87.13  E-value=0.29  Score=38.07  Aligned_cols=19  Identities=37%  Similarity=0.331  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.++++.||+|+|||...
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            3578999999999999643

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=87.05  E-value=0.3  Score=36.07  Aligned_cols=55  Identities=11%  Similarity=0.016  Sum_probs=30.8

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHh--cCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAV--LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~--~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+...|+++.-.+...+.+++.-..  .. ...++..+.  -.+.+++.+|+|+|||...
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~~--~~-~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVEF--LK-NPSRFHEMGARIPKGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHHH--HH-CHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHH--HH-CHHHHHHcCCCCCCeEEEECCCCCCHHHHH
Confidence            3455677776666666666543110  00 012222221  1256999999999999643

>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=86.99  E-value=1.4  Score=33.27  Aligned_cols=17  Identities=35%  Similarity=0.450  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.||+|+|||...
T Consensus        39 ~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           39 PHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CCEEEESSSSSSHHHHH
T ss_pred             CeEEEECcCCcCHHHHH
Confidence            36999999999999643

>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=86.96  E-value=0.52  Score=36.81  Aligned_cols=23  Identities=22%  Similarity=0.413  Sum_probs=17.9

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus        71 ~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           71 KDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCeEEEEEECCCCCCCceEe
Confidence            34567866  677889999999875

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=86.91  E-value=0.37  Score=36.52  Aligned_cols=17  Identities=29%  Similarity=0.413  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ..+++.+|+|+|||...
T Consensus        48 ~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             EEEEEESCSSSSHHHHH
T ss_pred             eEEEEECCCCcCHHHHH
Confidence            47999999999999654

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=86.91  E-value=0.19  Score=40.83  Aligned_cols=18  Identities=28%  Similarity=0.246  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.+++.+|+|+|||...
T Consensus       167 ~~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          167 WRGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             CSEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            378999999999999654

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=86.76  E-value=0.32  Score=39.53  Aligned_cols=25  Identities=44%  Similarity=0.581  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ++++++.+|+|+|||... -.+...+
T Consensus        63 ~~~iLl~GppGtGKT~la-~ala~~l   87 (456)
T 2c9o_A           63 GRAVLLAGPPGTGKTALA-LAIAQEL   87 (456)
T ss_dssp             TCEEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCcCCHHHHH-HHHHHHh
Confidence            368999999999999654 3344433

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=86.74  E-value=0.88  Score=35.07  Aligned_cols=38  Identities=21%  Similarity=0.197  Sum_probs=24.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.|++|+|||...+ -++.....  ++..+++++.
T Consensus        67 ~G~l~li~G~pG~GKTtl~l-~ia~~~a~--~g~~vl~~sl  104 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFAL-KQAKNMSD--NDDVVNLHSL  104 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHH-HHHHHHHT--TTCEEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHHH-HHHHHHHH--cCCeEEEEEC
Confidence            45779999999999995443 33333222  2346777764

>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=86.71  E-value=0.36  Score=38.02  Aligned_cols=18  Identities=33%  Similarity=0.396  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ..++++.+|+|+|||...
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            468999999999999654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=86.67  E-value=0.35  Score=37.31  Aligned_cols=17  Identities=35%  Similarity=0.542  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.+|+|+|||...
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            68999999999999654

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=86.67  E-value=0.36  Score=37.93  Aligned_cols=18  Identities=28%  Similarity=0.322  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+++++.+|+|+|||...
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            368999999999999654

>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=86.56  E-value=0.49  Score=37.26  Aligned_cols=23  Identities=22%  Similarity=0.420  Sum_probs=17.5

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
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            34567866  577889999999875

>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=86.50  E-value=0.9  Score=34.98  Aligned_cols=18  Identities=33%  Similarity=0.545  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |.-+.+.+|+|+|||...
T Consensus       102 g~vi~lvG~nGsGKTTll  119 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTI  119 (304)
T ss_dssp             SSEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            567889999999999743

>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=86.48  E-value=0.32  Score=34.65  Aligned_cols=31  Identities=19%  Similarity=0.219  Sum_probs=21.2

Q ss_pred             CcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          37 QTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        37 ~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+.... ....|.-+.+.+|+|||||...
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            444544433 2345788999999999999653

>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=86.43  E-value=0.79  Score=35.81  Aligned_cols=42  Identities=7%  Similarity=-0.105  Sum_probs=25.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCC---CCeEEEEEecCH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTD---SNVYVLVMCHTR   92 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~---~~~~~lil~Pt~   92 (175)
                      |.-+.+.+|+|+|||.....-+........   .+.+++++....
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            356899999999999654433333222210   244678887543

>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=86.39  E-value=1.2  Score=37.92  Aligned_cols=76  Identities=11%  Similarity=0.147  Sum_probs=50.3

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHH--HhhCCCeEEEEEECC--------CchHHhHH---HHhcC-CCeEEE--eecCcc
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERF--SKYMSNIKVGVFFGG--------LPIQKDEE---YLKTH-NPQIVG--LVNYET  145 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~--~~~~~~i~v~~~~g~--------~~~~~~~~---~l~~~-~~iiv~--l~~~~~  145 (175)
                      +.++||.++++..+..+.+.++..  .... ++++..++|+        .+..++.+   .+++| .+++|+  +....+
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~-g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~GI  478 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEV-GVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEEGL  478 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC------CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCTTS
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCcccccc-CcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEccccccCC
Confidence            568999999999999988887754  1111 6788889998        66554443   34443 477887  555578


Q ss_pred             CCCCceEEEEeCC
Q psy1539         146 NLSGVVVNVMDVR  158 (175)
Q Consensus       146 ~~~~~~~lVlDEa  158 (175)
                      ++++++++|.=+.
T Consensus       479 Dip~v~~VI~~d~  491 (699)
T 4gl2_A          479 DIKECNIVIRYGL  491 (699)
T ss_dssp             CCCSCCCCEEESC
T ss_pred             ccccCCEEEEeCC
Confidence            8888888876554

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=86.35  E-value=0.44  Score=35.69  Aligned_cols=20  Identities=30%  Similarity=0.297  Sum_probs=17.4

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      +.|+.+++.+++|||||...
T Consensus        46 l~g~~i~l~G~~GsGKSTl~   65 (250)
T 3nwj_A           46 LNGRSMYLVGMMGSGKTTVG   65 (250)
T ss_dssp             HTTCCEEEECSTTSCHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            34999999999999999754

>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=86.31  E-value=1.8  Score=38.77  Aligned_cols=82  Identities=18%  Similarity=0.147  Sum_probs=58.2

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh---HHHHhcC---CCeEEE--eecCccCCCCceE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTH---NPQIVG--LVNYETNLSGVVV  152 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~---~~~l~~~---~~iiv~--l~~~~~~~~~~~~  152 (175)
                      .+.+++|.|+++.-+..+.+.++.   .. ++++..++|+.+..+.   .+.++++   .+++|+  +....+++.++.+
T Consensus       502 ~~~k~iVF~~~~~~~~~l~~~L~~---~~-g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~  577 (968)
T 3dmq_A          502 RSQKVLVICAKAATALQLEQVLRE---RE-GIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASH  577 (968)
T ss_dssp             SSSCCCEECSSTHHHHHHHHHHHT---TT-CCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCE
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHHH---Hc-CCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcE
Confidence            455899999999988877666653   23 7889999999775433   3456665   566666  4445889999999


Q ss_pred             EEEeCCCCCCHHHH
Q psy1539         153 NVMDVRSGGWWLDL  166 (175)
Q Consensus       153 lVlDEad~~f~~~v  166 (175)
                      +|+-+...+....+
T Consensus       578 VI~~d~p~~~~~~~  591 (968)
T 3dmq_A          578 MVMFDLPFNPDLLE  591 (968)
T ss_dssp             EECSSCCSSHHHHH
T ss_pred             EEEecCCCCHHHHH
Confidence            99888765444333

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.26  E-value=0.21  Score=40.60  Aligned_cols=55  Identities=15%  Similarity=0.134  Sum_probs=31.2

Q ss_pred             ccccccccCCCCHHHHHHHhhC---CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQ---PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~---g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+-.+|++.+=-.+..+.+.+.   -+.+|--++..-+   .--+.+++.+|+|+|||+..
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi---~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI---KPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTC---CCCSEEEEESSTTTTHHHHH
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCCCceECCCCchHHHHH
Confidence            4455677775445555555442   1112222222211   12388999999999999743

>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=86.16  E-value=4.1  Score=31.02  Aligned_cols=18  Identities=22%  Similarity=0.084  Sum_probs=14.2

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ++-+.+.+++|+|||...
T Consensus        98 ~~~i~i~g~~G~GKTT~~  115 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTA  115 (295)
T ss_dssp             SEEEEEECCTTTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456778899999999643

>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=86.13  E-value=0.61  Score=36.71  Aligned_cols=23  Identities=22%  Similarity=0.421  Sum_probs=17.5

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
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            34567866  577789999999875

>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=86.10  E-value=2  Score=42.62  Aligned_cols=48  Identities=17%  Similarity=0.101  Sum_probs=32.8

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhH----HHHhcCCcEEEEcCCCChHHHHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECI----PQAVLGMDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i----~~~~~g~~~ii~a~TGsGKT~~~~   69 (175)
                      +...+.+.+.+.|+. +++.+..-+    ..+...+.+++.||||||||.++-
T Consensus       890 l~~~i~~~~~~~~l~-~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~  941 (2695)
T 4akg_A          890 IVQCLKDAGQRSGFS-MSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWK  941 (2695)
T ss_dssp             HHHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHH
Confidence            345566777777775 555543322    333456899999999999998763

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=86.05  E-value=2  Score=36.43  Aligned_cols=95  Identities=15%  Similarity=0.195  Sum_probs=49.3

Q ss_pred             ChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEEC--------CCchHHhH---HHH
Q psy1539          62 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFG--------GLPIQKDE---EYL  130 (175)
Q Consensus        62 sGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g--------~~~~~~~~---~~l  130 (175)
                      +.|. ..+.-++........+.++||.+++++-+..+.+.++..... +++++..++|        +.+..++.   +.+
T Consensus       379 ~~k~-~~L~~ll~~~~~~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~-~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F  456 (696)
T 2ykg_A          379 NPKL-EDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKL-SFLKPGILTGRGKTNQNTGMTLPAQKCILDAF  456 (696)
T ss_dssp             CHHH-HHHHHHHHHHHTTCTTCCEEEECSCHHHHHHHHHHHHHCTTC-CSCCEEC-------------------------
T ss_pred             CHHH-HHHHHHHHHHhccCCCCcEEEEeCcHHHHHHHHHHHHhCCCc-cccceeEEEccCCCccccCCCHHHHHHHHHHH
Confidence            4443 233334443322234568999999999999988888765322 1367777755        55443333   334


Q ss_pred             hc--CCCeEEE--eecCccCCCCceEEEEeCC
Q psy1539         131 KT--HNPQIVG--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       131 ~~--~~~iiv~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      ++  ...++|+  .....+++.+++++|.=+.
T Consensus       457 ~~~g~~~vLVaT~v~~~GiDip~v~~VI~~d~  488 (696)
T 2ykg_A          457 KASGDHNILIATSVADEGIDIAQCNLVILYEY  488 (696)
T ss_dssp             ----CCSCSEEEESSCCC---CCCSEEEEESC
T ss_pred             HhcCCccEEEEechhhcCCcCccCCEEEEeCC
Confidence            43  3578888  5555888899999887555

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=85.96  E-value=0.62  Score=36.86  Aligned_cols=22  Identities=18%  Similarity=0.478  Sum_probs=17.2

Q ss_pred             HHhcCCc--EEEEcCCCChHHHHH
Q psy1539          47 QAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+++|.|  ++..+.||||||.+.
T Consensus        75 ~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           75 DILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCcceEEEECCCCCCcceEe
Confidence            4567865  677889999999875

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=85.95  E-value=0.62  Score=36.99  Aligned_cols=23  Identities=22%  Similarity=0.446  Sum_probs=17.7

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
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            34567865  677889999999875

>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=85.93  E-value=0.28  Score=34.49  Aligned_cols=17  Identities=18%  Similarity=0.313  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .-+++.+|+|+|||...
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            45789999999999754

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=85.90  E-value=0.65  Score=36.62  Aligned_cols=25  Identities=24%  Similarity=0.458  Sum_probs=19.1

Q ss_pred             hHHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          44 CIPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        44 ~i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+..+++|.|  ++..+.||||||.+.
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            3455678876  567789999999876

>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=85.90  E-value=0.61  Score=37.16  Aligned_cols=23  Identities=26%  Similarity=0.525  Sum_probs=17.4

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
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            34567865  567889999999874

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=85.89  E-value=0.63  Score=36.73  Aligned_cols=22  Identities=27%  Similarity=0.513  Sum_probs=17.2

Q ss_pred             HHhcCCc--EEEEcCCCChHHHHH
Q psy1539          47 QAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+++|.|  ++..+.||||||.+.
T Consensus        84 ~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           84 AVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCCceeEEeecCCCCCCCEEe
Confidence            4567865  677889999999875

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=85.83  E-value=0.46  Score=33.31  Aligned_cols=20  Identities=20%  Similarity=0.096  Sum_probs=16.6

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+..+++.+++|||||...
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~   26 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQC   26 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35678999999999999753

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=85.83  E-value=0.29  Score=35.73  Aligned_cols=20  Identities=35%  Similarity=0.516  Sum_probs=12.7

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..|+-+.+.+|+|||||...
T Consensus        25 ~~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           25 SVGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             ECCCEEEEECSCC----CHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35788999999999999653

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=85.82  E-value=0.4  Score=37.65  Aligned_cols=18  Identities=33%  Similarity=0.303  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.+++.+|+|+|||...
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999654

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=85.79  E-value=0.63  Score=37.45  Aligned_cols=25  Identities=24%  Similarity=0.457  Sum_probs=19.2

Q ss_pred             hHHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          44 CIPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        44 ~i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+..+++|.|  ++..+.||||||.+.
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            3455678876  567789999999876

>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=85.74  E-value=0.63  Score=36.78  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=17.6

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
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            34567865  677889999999875

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=85.73  E-value=0.71  Score=36.13  Aligned_cols=25  Identities=24%  Similarity=0.505  Sum_probs=19.3

Q ss_pred             hHHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          44 CIPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        44 ~i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+..+++|.|  ++..+.||||||.+.
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            3455678876  667889999999775

>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=85.70  E-value=0.61  Score=35.90  Aligned_cols=17  Identities=29%  Similarity=0.446  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.||+|+|||...
T Consensus        59 ~~~ll~G~~G~GKT~la   75 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTI   75 (353)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            56999999999999643

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=85.67  E-value=0.36  Score=33.73  Aligned_cols=18  Identities=17%  Similarity=0.270  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.-+++.+++|||||...
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            456899999999999754

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=85.66  E-value=2.3  Score=34.17  Aligned_cols=65  Identities=9%  Similarity=-0.000  Sum_probs=45.8

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEE--eecCccCCCCceEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVG--LVNYETNLSGVVVN  153 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~--l~~~~~~~~~~~~l  153 (175)
                      +.+++|++|+++-+..+.+.+++.     +.++..++|+.. .+..+.+++| .+++|+  +....++++ +..+
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~v~~lhg~~r-~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~V  238 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKA-----GKKVLYLNRKTF-ESEYPKCKSEKWDFVITTDISEMGANFK-ADRV  238 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTTH-HHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc-----CCeEEEeCCccH-HHHHHhhcCCCCeEEEECchHHcCcccC-CcEE
Confidence            347999999999999888777654     677888998743 3444555554 577887  555667776 4443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=85.60  E-value=0.4  Score=37.99  Aligned_cols=18  Identities=28%  Similarity=0.324  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+++++.+|+|+|||...
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            479999999999999654

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=85.58  E-value=0.34  Score=34.82  Aligned_cols=18  Identities=17%  Similarity=0.180  Sum_probs=15.2

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|.-+.+.+|+|||||..
T Consensus        21 ~g~~v~I~G~sGsGKSTl   38 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTL   38 (208)
T ss_dssp             SCEEEEEECCTTSCTHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            467788999999999964

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=85.56  E-value=0.93  Score=36.83  Aligned_cols=38  Identities=21%  Similarity=0.193  Sum_probs=24.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.|++|+|||...+ -++......  +..+++++.
T Consensus       196 ~G~liiIaG~pG~GKTtlal-~ia~~~a~~--g~~vl~fSl  233 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFAL-KQAKNMSDN--DDVVNLHSL  233 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHH-HHHHHHHHT--TCEEEEECS
T ss_pred             CCcEEEEEeCCCCChHHHHH-HHHHHHHHc--CCEEEEEEC
Confidence            35679999999999996544 333333322  446777764

>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=85.55  E-value=0.71  Score=36.64  Aligned_cols=23  Identities=26%  Similarity=0.496  Sum_probs=17.6

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus        83 ~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           83 QHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhcCCeeEEEEeCCCCCCCceEe
Confidence            44567865  677889999999765

>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=85.53  E-value=0.69  Score=37.31  Aligned_cols=23  Identities=22%  Similarity=0.312  Sum_probs=17.6

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
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            34567865  677889999999875

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=85.53  E-value=0.18  Score=37.52  Aligned_cols=18  Identities=28%  Similarity=0.337  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.+++.+|+|+|||...
T Consensus        44 ~~~vll~G~~GtGKT~la   61 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            467999999999999654

>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=85.50  E-value=0.37  Score=35.63  Aligned_cols=18  Identities=28%  Similarity=0.255  Sum_probs=15.8

Q ss_pred             hcCCcEEEEcCCCChHHH
Q psy1539          49 VLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~   66 (175)
                      ..|.-+.+.+|+|||||.
T Consensus        29 ~~Ge~~~iiG~nGsGKST   46 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKST   46 (235)
T ss_dssp             CTTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCcHHH
Confidence            357889999999999996

>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=85.49  E-value=0.38  Score=33.69  Aligned_cols=18  Identities=22%  Similarity=0.257  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.-+++.+++|||||...
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            456899999999999753

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=85.48  E-value=0.4  Score=37.75  Aligned_cols=16  Identities=25%  Similarity=0.231  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -++|.+|||||||...
T Consensus         9 lI~I~GptgSGKTtla   24 (340)
T 3d3q_A            9 LIVIVGPTASGKTELS   24 (340)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             eEEEECCCcCcHHHHH
Confidence            5789999999999643

>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=85.48  E-value=0.7  Score=36.44  Aligned_cols=23  Identities=26%  Similarity=0.452  Sum_probs=17.7

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus        71 ~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           71 DSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHcCCccceeeecCCCCCCCeEE
Confidence            34567865  667889999999876

>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=85.46  E-value=0.7  Score=36.53  Aligned_cols=24  Identities=25%  Similarity=0.481  Sum_probs=18.4

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      +..+++|.|  ++..+.||||||.+.
T Consensus        85 v~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           85 LQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHhCCceeEEEeeCCCCCCCceEE
Confidence            345567876  577789999999875

>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=85.40  E-value=1.2  Score=32.26  Aligned_cols=35  Identities=20%  Similarity=0.097  Sum_probs=27.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      -.+++..++|.|||.+++--.+..+.   .|.+++++-
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g---~G~rV~~vQ   63 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVG---HGKNVGVVQ   63 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHH---TTCCEEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEE
Confidence            58999999999999888776666665   355777773

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=85.36  E-value=0.4  Score=37.48  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=14.1

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++++|||||||...
T Consensus         6 ~~i~i~GptGsGKTtla   22 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLA   22 (323)
T ss_dssp             EEEEEECCTTSCHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            36899999999999643

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=85.32  E-value=0.45  Score=33.58  Aligned_cols=16  Identities=31%  Similarity=0.652  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+.+.+|+|+|||...
T Consensus         2 ~i~l~G~nGsGKTTLl   17 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLV   17 (178)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4678999999999643

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=85.26  E-value=0.43  Score=33.93  Aligned_cols=17  Identities=35%  Similarity=0.366  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +-+++.|++|||||...
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            57999999999999754

>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=85.17  E-value=0.32  Score=37.15  Aligned_cols=18  Identities=28%  Similarity=0.350  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ..++++.+|+|+|||...
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            378999999999999653

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=85.08  E-value=0.44  Score=35.79  Aligned_cols=54  Identities=11%  Similarity=0.015  Sum_probs=30.8

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHh--cCCcEEEEcCCCChHHHHH
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAV--LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~--~g~~~ii~a~TGsGKT~~~   68 (175)
                      +...|+++.-.++..+.+.+.-..  .. ....+..+.  -.+.+++.+|+|+|||...
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~--~~-~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF--LK-NPSRFHEMGARIPKGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH--HH-CHHHHHHTTCCCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH--HH-CHHHHHHcCCCCCCeEEEECCCcChHHHHH
Confidence            456677777777776666553110  00 011222211  1246999999999999643

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=85.03  E-value=0.4  Score=34.24  Aligned_cols=19  Identities=21%  Similarity=0.102  Sum_probs=15.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+.+.+|+|||||...
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            3556789999999999743

>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=84.97  E-value=0.72  Score=36.53  Aligned_cols=23  Identities=26%  Similarity=0.602  Sum_probs=17.5

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus        82 ~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           82 DEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHhCCCceEEEEeCCCCCCCceEE
Confidence            34567865  677889999999765

>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=84.96  E-value=0.43  Score=33.23  Aligned_cols=19  Identities=37%  Similarity=0.429  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+++.++.|||||...
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            4677899999999999743

>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=84.81  E-value=0.69  Score=36.46  Aligned_cols=24  Identities=25%  Similarity=0.497  Sum_probs=18.1

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      +..+++|.|  ++..+.||||||.+.
T Consensus        77 v~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           77 VQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHhcCCceeEEEEECCCCCCCcEec
Confidence            334567866  667889999999875

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=84.72  E-value=0.52  Score=32.63  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.+++|||||...
T Consensus         5 ~~i~i~G~~GsGKsTla   21 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLA   21 (175)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CEEEEEcCCCCCHHHHH
Confidence            36899999999999654

>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=84.72  E-value=0.54  Score=33.19  Aligned_cols=19  Identities=26%  Similarity=0.237  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+.+++.++.|||||...
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            4678999999999999743

>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=84.62  E-value=0.73  Score=37.21  Aligned_cols=25  Identities=32%  Similarity=0.488  Sum_probs=19.1

Q ss_pred             hHHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          44 CIPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        44 ~i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+..+++|.|  ++..+.||||||.+.
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            3456678876  577789999999875

>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=84.54  E-value=0.75  Score=36.86  Aligned_cols=22  Identities=27%  Similarity=0.502  Sum_probs=17.3

Q ss_pred             HHhcCCc--EEEEcCCCChHHHHH
Q psy1539          47 QAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+++|.|  ++..+.||||||.+.
T Consensus        93 ~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           93 HLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             HHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             HhhcCceeeEeeecCCCCCCCeEe
Confidence            4567866  667889999999875

>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=84.53  E-value=0.68  Score=36.82  Aligned_cols=24  Identities=33%  Similarity=0.528  Sum_probs=18.6

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      +..+++|.|  ++..+.||||||.+.
T Consensus        72 v~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           72 VQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHhhhcCCceEEEEECCCCCCCeEee
Confidence            455678876  566789999999875

>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=84.51  E-value=0.83  Score=35.26  Aligned_cols=15  Identities=33%  Similarity=0.328  Sum_probs=12.7

Q ss_pred             cEEEEcCCCChHHHH
Q psy1539          53 DILCQAKSGMGKTAV   67 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~   67 (175)
                      -+++.++.|||||..
T Consensus         6 v~~i~G~~GaGKTTl   20 (318)
T 1nij_A            6 VTLLTGFLGAGKTTL   20 (318)
T ss_dssp             EEEEEESSSSSCHHH
T ss_pred             EEEEEecCCCCHHHH
Confidence            367899999999964

>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=84.51  E-value=1.3  Score=34.70  Aligned_cols=38  Identities=18%  Similarity=0.076  Sum_probs=24.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      |+-+.+.+|+|+|||...+.-+.....   .+.+++++...
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~---~g~~vlyi~~E   98 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQA---AGGIAAFIDAE   98 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHH---TTCCEEEEESS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEECC
Confidence            477999999999999654443333322   23357777643

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=84.40  E-value=0.52  Score=33.77  Aligned_cols=16  Identities=25%  Similarity=0.329  Sum_probs=13.6

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.|++|||||...
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            4789999999999754

>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=84.39  E-value=0.26  Score=35.23  Aligned_cols=22  Identities=18%  Similarity=0.093  Sum_probs=17.0

Q ss_pred             HHhcCCcEEEEcCCCChHHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+.-+.+.+++|||||...
T Consensus        17 ~~~~~~~i~i~G~~GsGKSTl~   38 (207)
T 2qt1_A           17 RGSKTFIIGISGVTNSGKTTLA   38 (207)
T ss_dssp             CSCCCEEEEEEESTTSSHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHH
Confidence            3445667889999999999643

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=84.36  E-value=0.52  Score=36.58  Aligned_cols=17  Identities=29%  Similarity=0.489  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ..+++.+|+|+|||...
T Consensus        52 ~~~ll~Gp~G~GKTTLa   68 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLA   68 (334)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            67999999999999653

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=84.32  E-value=0.6  Score=32.78  Aligned_cols=19  Identities=21%  Similarity=0.102  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.-+++.+++|||||...
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            4678999999999999653

>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=84.32  E-value=1.9  Score=33.50  Aligned_cols=17  Identities=29%  Similarity=0.315  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      |.-+.+.+|+|+|||..
T Consensus       129 g~vi~lvG~nGaGKTTl  145 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTT  145 (328)
T ss_dssp             SEEEEEECCTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            56788999999999974

>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=84.31  E-value=0.7  Score=35.98  Aligned_cols=35  Identities=11%  Similarity=0.151  Sum_probs=21.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      .+++.||+|+|||... -.+...+.... +...+.+.
T Consensus        46 ~~li~G~~G~GKTtl~-~~l~~~~~~~~-~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL-RKLWELYKDKT-TARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHHTTSC-CCEEEEEE
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHhhhc-CeeEEEEe
Confidence            7999999999999654 33444443211 23445544

>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=84.29  E-value=1.8  Score=36.50  Aligned_cols=41  Identities=20%  Similarity=0.176  Sum_probs=24.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecC
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHT   91 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt   91 (175)
                      +.+++|.+.||||||.+.-.-++..+.. .....+.+++=|.
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~~sP~ev~lilIDpK  255 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFKSTPSEARLIMIDPK  255 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTTCCTTTEEEEEECSS
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHhCCCcceEEEEeCCC
Confidence            4689999999999996644333333322 1234445544444

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=84.27  E-value=0.41  Score=36.51  Aligned_cols=18  Identities=28%  Similarity=0.364  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.-++++||+|||||...
T Consensus        33 ~~livl~G~sGsGKSTla   50 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLR   50 (287)
T ss_dssp             CEEEEEECCTTSCTHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            356899999999999643

>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=84.23  E-value=0.78  Score=36.51  Aligned_cols=22  Identities=23%  Similarity=0.542  Sum_probs=17.0

Q ss_pred             HHhcCCc--EEEEcCCCChHHHHH
Q psy1539          47 QAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        47 ~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .+++|.|  ++..+.||||||.+.
T Consensus        95 ~~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           95 EVLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhCCceEEEEeecCCCCCcceec
Confidence            4567865  677889999999764

>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=84.21  E-value=0.78  Score=36.72  Aligned_cols=23  Identities=22%  Similarity=0.312  Sum_probs=17.7

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus       128 ~~~l~G~N~tifAYGQTGSGKTyTM  152 (387)
T 2heh_A          128 QTIFEGGKATCFAYGQTGSGKTHTM  152 (387)
T ss_dssp             HHHHTTCEEEEEEESCTTSSHHHHH
T ss_pred             HHHhcCCceEEEEecCCCCCCCeEe
Confidence            34567865  677889999999875

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=84.15  E-value=0.49  Score=38.19  Aligned_cols=22  Identities=23%  Similarity=0.400  Sum_probs=15.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      -++|.+|||||||... ..+...
T Consensus         4 ~i~i~GptgsGKttla-~~La~~   25 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLS-IQLAQK   25 (409)
T ss_dssp             EEEEEECSSSSHHHHH-HHHHHH
T ss_pred             EEEEECcchhhHHHHH-HHHHHH
Confidence            3689999999999543 334443

>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=84.14  E-value=0.59  Score=33.70  Aligned_cols=19  Identities=16%  Similarity=0.219  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+++.++.|||||...
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            3567999999999999653

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=84.12  E-value=0.56  Score=34.25  Aligned_cols=19  Identities=21%  Similarity=0.272  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+++.+++|||||...
T Consensus        15 ~~~~I~l~G~~GsGKsT~a   33 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQA   33 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4578999999999999643

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=84.10  E-value=1.5  Score=37.55  Aligned_cols=66  Identities=8%  Similarity=0.010  Sum_probs=47.3

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      +.++||++|+++-++.+.+.+++.     ++++..++|+. ..+..+.++++ .+++|+  +....++++ ++++|
T Consensus       410 ~~~~lVF~~s~~~~e~la~~L~~~-----g~~v~~lHg~e-R~~v~~~F~~g~~~VLVaTdv~e~GIDip-v~~VI  478 (673)
T 2wv9_A          410 AGKTVWFVASVKMSNEIAQCLQRA-----GKRVIQLNRKS-YDTEYPKCKNGDWDFVITTDISEMGANFG-ASRVI  478 (673)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSS-HHHHGGGGGTCCCSEEEECGGGGTTCCCC-CSEEE
T ss_pred             CCCEEEEECCHHHHHHHHHHHHhC-----CCeEEEeChHH-HHHHHHHHHCCCceEEEECchhhcceeeC-CcEEE
Confidence            458999999999998877766543     77888899853 23344455544 467787  666678888 87766

>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=83.99  E-value=0.64  Score=32.37  Aligned_cols=17  Identities=18%  Similarity=0.196  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ..+++.+++|||||...
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            46899999999999754

>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=83.95  E-value=0.56  Score=33.65  Aligned_cols=16  Identities=19%  Similarity=0.243  Sum_probs=13.7

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.+++|||||...
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            4789999999999754

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=83.91  E-value=1.7  Score=36.67  Aligned_cols=23  Identities=22%  Similarity=0.221  Sum_probs=19.1

Q ss_pred             HHHhcCCcEEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+..|..+++.+|+|+|||..+
T Consensus        55 ~~i~~g~~vll~Gp~GtGKTtla   77 (604)
T 3k1j_A           55 TAANQKRHVLLIGEPGTGKSMLG   77 (604)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHHH
T ss_pred             ccccCCCEEEEEeCCCCCHHHHH
Confidence            45567899999999999999643

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=83.84  E-value=0.92  Score=36.97  Aligned_cols=23  Identities=22%  Similarity=0.414  Sum_probs=17.7

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus       130 ~~~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          130 DHNFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHhhcCCceEEEEeCCCCCCCCEEe
Confidence            34567866  677889999999875

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=83.81  E-value=0.49  Score=35.02  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        29 ~~Ge~~~i~G~nGsGKSTL   47 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSL   47 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3578899999999999963

>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=83.74  E-value=1.6  Score=34.46  Aligned_cols=37  Identities=11%  Similarity=0.031  Sum_probs=24.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      |+-+++.+++|+|||...+.-+.. ...  .+..++++..
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~-~~~--~g~~vlyid~   99 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAA-AQR--EGKTCAFIDA   99 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHH-HHH--TTCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHH--CCCeEEEEeC
Confidence            477999999999999655433333 222  2335777765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=83.66  E-value=1.2  Score=35.98  Aligned_cols=39  Identities=28%  Similarity=0.210  Sum_probs=24.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.|++|+|||... +-++...... .+..++++..
T Consensus       199 ~G~l~ii~G~pg~GKT~la-l~ia~~~a~~-~g~~vl~~sl  237 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFA-LTIAQNAALK-EGVGVGIYSL  237 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHH-HHHHHHHHHT-TCCCEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHH-HHHHHHHHHh-CCCeEEEEEC
Confidence            3567899999999999544 4343333221 2335777764

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=83.61  E-value=0.59  Score=33.92  Aligned_cols=19  Identities=21%  Similarity=0.184  Sum_probs=15.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+++.|++|||||...
T Consensus         6 ~~~~I~l~G~~GsGKsT~a   24 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVS   24 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHH
T ss_pred             cCcEEEEECCCCCCHHHHH
Confidence            3467999999999999753

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=83.54  E-value=1.5  Score=34.36  Aligned_cols=38  Identities=21%  Similarity=0.272  Sum_probs=25.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.|++|+|||... +-++..+..  .+..++|++.
T Consensus        45 ~G~LiiIaG~pG~GKTt~a-l~ia~~~a~--~g~~Vl~fSl   82 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLM-MNMVLSALN--DDRGVAVFSL   82 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHH-HHHHHHHHH--TTCEEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHH-HHHHHHHHH--cCCeEEEEeC
Confidence            4577999999999999544 333333332  3446777764

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=83.52  E-value=0.51  Score=33.47  Aligned_cols=19  Identities=26%  Similarity=0.326  Sum_probs=15.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+++.++.|||||...
T Consensus         3 ~~~~I~i~G~~GsGKsT~~   21 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQA   21 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHH
Confidence            4567899999999999643

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=83.51  E-value=1.2  Score=36.10  Aligned_cols=39  Identities=28%  Similarity=0.297  Sum_probs=24.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.|++|+|||... +-++..+... .+..++++..
T Consensus       202 ~G~liiI~G~pG~GKTtl~-l~ia~~~~~~-~g~~Vl~~s~  240 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFA-LNIAQNVATK-TNENVAIFSL  240 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHH-HHHHHHHHHH-SSCCEEEEES
T ss_pred             CCCEEEEECCCCCCHHHHH-HHHHHHHHHh-CCCcEEEEEC
Confidence            4578999999999999544 4343333221 2335777764

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=83.50  E-value=0.9  Score=36.00  Aligned_cols=19  Identities=26%  Similarity=0.350  Sum_probs=16.0

Q ss_pred             cCCc--EEEEcCCCChHHHHH
Q psy1539          50 LGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .|.|  ++..+.||||||.+.
T Consensus        82 ~G~n~tifAYGqTGSGKTyTM  102 (360)
T 1ry6_A           82 NGCVCSCFAYGQTGSGKTYTM  102 (360)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             CCceeEEEeeCCCCCCCCEEE
Confidence            4776  689999999999775

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=83.48  E-value=0.61  Score=31.98  Aligned_cols=17  Identities=18%  Similarity=0.266  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.++.|||||...
T Consensus         8 ~~i~l~G~~GsGKSTva   24 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLA   24 (168)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            68999999999999754

>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=83.46  E-value=2.6  Score=31.75  Aligned_cols=70  Identities=11%  Similarity=0.125  Sum_probs=47.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.+++++-+..+.+.++         .+..++|+.+..+..+   .++++ ..++|+  .....+++++++++|
T Consensus       219 ~~~~~lvf~~~~~~~~~l~~~l~---------~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi  289 (337)
T 2z0m_A          219 KDKGVIVFVRTRNRVAKLVRLFD---------NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVI  289 (337)
T ss_dssp             CCSSEEEECSCHHHHHHHHTTCT---------TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEE
T ss_pred             CCCcEEEEEcCHHHHHHHHHHhh---------hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEE
Confidence            45579999999988876554433         3567788877554433   33443 467777  555688899999998


Q ss_pred             EeCCC
Q psy1539         155 MDVRS  159 (175)
Q Consensus       155 lDEad  159 (175)
                      .-...
T Consensus       290 ~~~~~  294 (337)
T 2z0m_A          290 NFDAP  294 (337)
T ss_dssp             ESSCC
T ss_pred             EecCC
Confidence            86654

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=83.46  E-value=1  Score=34.58  Aligned_cols=18  Identities=28%  Similarity=0.292  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |.-+.+.+|+|+|||...
T Consensus       100 g~vi~lvG~nGsGKTTll  117 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSL  117 (302)
T ss_dssp             CEEEEEECCTTSCHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHH
Confidence            456789999999999753

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=83.40  E-value=0.56  Score=32.59  Aligned_cols=16  Identities=19%  Similarity=0.131  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -.++.+|+|+|||..+
T Consensus        28 ~~~i~G~NGsGKStll   43 (182)
T 3kta_A           28 FTAIVGANGSGKSNIG   43 (182)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             cEEEECCCCCCHHHHH
Confidence            5678999999999653

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=83.31  E-value=0.55  Score=37.11  Aligned_cols=16  Identities=25%  Similarity=0.563  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -.++.+|||+|||..+
T Consensus        25 ~~~i~G~NGaGKTTll   40 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLF   40 (365)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4678999999999765

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=83.31  E-value=0.63  Score=33.51  Aligned_cols=18  Identities=28%  Similarity=0.298  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +..+.+.+|+|||||...
T Consensus         5 ~~~i~i~G~~GsGKSTl~   22 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLC   22 (227)
T ss_dssp             SCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            356889999999999754

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=83.30  E-value=0.55  Score=32.85  Aligned_cols=19  Identities=26%  Similarity=0.399  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+++.++.|||||...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~   30 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIA   30 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHH
Confidence            4677999999999999654

>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=83.27  E-value=0.67  Score=31.77  Aligned_cols=17  Identities=29%  Similarity=0.256  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.+++|||||...
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            46899999999999754

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=83.26  E-value=0.62  Score=31.81  Aligned_cols=15  Identities=27%  Similarity=0.373  Sum_probs=12.6

Q ss_pred             cEEEEcCCCChHHHH
Q psy1539          53 DILCQAKSGMGKTAV   67 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~   67 (175)
                      -.++.+|+|+|||..
T Consensus        25 ~~~I~G~NGsGKSti   39 (149)
T 1f2t_A           25 INLIIGQNGSGKSSL   39 (149)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            357899999999965

>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=83.20  E-value=0.32  Score=37.55  Aligned_cols=18  Identities=22%  Similarity=0.289  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ..++++.||+|+|||...
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            467999999999999653

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=83.15  E-value=0.56  Score=34.24  Aligned_cols=27  Identities=19%  Similarity=0.048  Sum_probs=21.6

Q ss_pred             CCCCceEEEEeCC----CCCCHHHHHHHHhh
Q psy1539         146 NLSGVVVNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       146 ~~~~~~~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      ...+-+++++||.    |......+.++|.+
T Consensus       148 L~~~p~lllLDEPts~LD~~~~~~l~~~l~~  178 (214)
T 1sgw_A          148 LLVNAEIYVLDDPVVAIDEDSKHKVLKSILE  178 (214)
T ss_dssp             TTSCCSEEEEESTTTTSCTTTHHHHHHHHHH
T ss_pred             HHhCCCEEEEECCCcCCCHHHHHHHHHHHHH
Confidence            4567899999999    77788888877764

>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=83.15  E-value=0.7  Score=32.75  Aligned_cols=18  Identities=28%  Similarity=0.340  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +..+++.+++|||||...
T Consensus        20 ~~~I~l~G~~GsGKST~a   37 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQA   37 (201)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            457999999999999753

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=83.08  E-value=0.69  Score=33.36  Aligned_cols=18  Identities=11%  Similarity=0.248  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +..+++.+++|||||...
T Consensus         5 ~~~I~l~G~~GsGKsT~~   22 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQC   22 (222)
T ss_dssp             SCCEEEEESTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            467999999999999754

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=83.02  E-value=0.71  Score=32.92  Aligned_cols=18  Identities=22%  Similarity=0.501  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |.-+.+.+|+|+|||...
T Consensus         1 G~~i~i~G~nG~GKTTll   18 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLI   18 (189)
T ss_dssp             CCCEEEESCCSSCHHHHH
T ss_pred             CCEEEEECCCCChHHHHH
Confidence            456789999999999743

>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=82.97  E-value=0.69  Score=40.58  Aligned_cols=57  Identities=14%  Similarity=0.041  Sum_probs=33.4

Q ss_pred             ccccccccCCCCHHHHHHHhhCC-CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP-FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g-~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+-..|++.+.-.+..+.|.+.= +....|.+..-+ .+...+.+++.+|+|+|||+.+
T Consensus       471 ~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~-g~~~~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          471 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKF-GMTPSKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSS-CCCCCSCCEEESSTTSSHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhc-CCCCCceEEEecCCCCCchHHH
Confidence            34456778887888888877652 111111110000 0112378999999999999654

>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=82.91  E-value=0.9  Score=36.22  Aligned_cols=24  Identities=29%  Similarity=0.475  Sum_probs=18.0

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      +..+++|.|  ++..+.||||||.+.
T Consensus       108 v~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          108 VQSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HHGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhcCCCceEEEEeCCCCCCCceEe
Confidence            345567865  667789999999765

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=82.82  E-value=0.6  Score=32.48  Aligned_cols=16  Identities=25%  Similarity=0.393  Sum_probs=13.4

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.++.|||||...
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            4789999999999643

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=82.78  E-value=0.69  Score=32.85  Aligned_cols=19  Identities=21%  Similarity=0.167  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+++.++.|||||...
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            4678999999999999753

>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=82.73  E-value=0.61  Score=38.46  Aligned_cols=18  Identities=33%  Similarity=0.368  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+++++.+|+|+|||...
T Consensus       238 ~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          238 PRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCcEEEECcCCCCHHHHH
Confidence            478999999999999754

>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=82.69  E-value=1.2  Score=38.28  Aligned_cols=65  Identities=11%  Similarity=0.178  Sum_probs=47.2

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++|++-++++.+.+++.     ++++..++|+.+..+.   .+.+.+++|+  +....++++ ++++|
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~-----g~~v~~lHG~l~q~er---~~~~~~VLVATdVaerGIDId-V~~VI  461 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGL-----GINAVAYYRGLDVSVI---PTIGDVVVVATDALMTGYTGD-FDSVI  461 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTT-----TCCEEEECTTSCGGGS---CSSSCEEEEECTTHHHHCCCC-BSEEE
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhC-----CCcEEEecCCCCHHHH---HhCCCcEEEECChHHccCCCC-CcEEE
Confidence            3458999999999998877777642     7889999999875432   2345577777  455567775 88776

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=82.65  E-value=0.62  Score=37.93  Aligned_cols=17  Identities=24%  Similarity=0.374  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.+|+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            47999999999999654

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=82.64  E-value=0.65  Score=33.33  Aligned_cols=19  Identities=21%  Similarity=0.053  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+.+.+|+|+|||...
T Consensus        24 ~G~~~~l~G~nGsGKSTll   42 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLA   42 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4678999999999999644

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=82.64  E-value=3.2  Score=32.25  Aligned_cols=16  Identities=19%  Similarity=0.113  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+.+.||+|||||...
T Consensus        94 iigI~GpsGSGKSTl~  109 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTS  109 (321)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3788999999999753

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=82.59  E-value=1.8  Score=32.06  Aligned_cols=18  Identities=28%  Similarity=0.477  Sum_probs=15.2

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~   70 (175)
                      ++++.++.|+|||...+-
T Consensus         8 ~I~~~~kgGvGKTt~a~~   25 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQ   25 (228)
T ss_dssp             EEEEESSTTSSHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            689999999999976543

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=82.57  E-value=0.73  Score=32.76  Aligned_cols=19  Identities=21%  Similarity=0.193  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.-+++.++.|||||...
T Consensus         8 ~~~~I~l~G~~GsGKsT~~   26 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQS   26 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            5678999999999999754

>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=82.35  E-value=0.99  Score=34.17  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.5

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.||+|+|||...
T Consensus        47 ~~~ll~G~~G~GKT~la   63 (327)
T 1iqp_A           47 PHLLFAGPPGVGKTTAA   63 (327)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            37999999999999653

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=82.32  E-value=0.57  Score=35.61  Aligned_cols=19  Identities=21%  Similarity=0.274  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        32 ~~Ge~~~iiGpnGsGKSTL   50 (275)
T 3gfo_A           32 KRGEVTAILGGNGVGKSTL   50 (275)
T ss_dssp             ETTSEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3578899999999999973

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=82.31  E-value=0.59  Score=34.82  Aligned_cols=19  Identities=32%  Similarity=0.347  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        33 ~~Ge~~~i~G~nGsGKSTL   51 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTL   51 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3578899999999999974

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=82.16  E-value=0.62  Score=35.00  Aligned_cols=19  Identities=21%  Similarity=0.345  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        44 ~~Ge~~~i~G~nGsGKSTL   62 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTI   62 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3578899999999999974

>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=82.15  E-value=16  Score=29.44  Aligned_cols=95  Identities=12%  Similarity=0.125  Sum_probs=59.6

Q ss_pred             CCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC--C
Q psy1539          60 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH--N  134 (175)
Q Consensus        60 TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~--~  134 (175)
                      ..++|... +.-++.....  .+.+++|.+.+++.+..+.+.++...    +..+..++|+.+..+..   +.++++  .
T Consensus       322 ~~s~K~~~-l~~~l~~~~~--~~~k~lvF~~~~~~~~~l~~~l~~~~----~~~~~~~~g~~~~~~R~~~~~~F~~~~~~  394 (500)
T 1z63_A          322 RRSGKMIR-TMEIIEEALD--EGDKIAIFTQFVDMGKIIRNIIEKEL----NTEVPFLYGELSKKERDDIISKFQNNPSV  394 (500)
T ss_dssp             TTCHHHHH-HHHHHHHHHT--TTCCEEEECSCHHHHHHHHHHHHHHH----TCCCCEEETTSCHHHHHHHHHHHHHCTTC
T ss_pred             hcchhHHH-HHHHHHHHHc--cCCcEEEEEehHHHHHHHHHHHHHhh----CCCeEEEECCCCHHHHHHHHHHhcCCCCC
Confidence            34666533 3333433332  45589999999999888777776532    56677889998754443   345555  3


Q ss_pred             C-eEEE--eecCccCCCCceEEEEeCCCCC
Q psy1539         135 P-QIVG--LVNYETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       135 ~-iiv~--l~~~~~~~~~~~~lVlDEad~~  161 (175)
                      . ++++  .....+++...+.+|+=+....
T Consensus       395 ~vil~st~~~~~Glnl~~~~~vi~~d~~~~  424 (500)
T 1z63_A          395 KFIVLSVKAGGFGINLTSANRVIHFDRWWN  424 (500)
T ss_dssp             CCCEEECCCC-CCCCCTTCSEEEESSCCSC
T ss_pred             CEEEEecccccCCCchhhCCEEEEeCCCCC
Confidence            3 3444  3344788888988888776433

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=82.14  E-value=1.1  Score=32.31  Aligned_cols=17  Identities=35%  Similarity=0.366  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFV   69 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~   69 (175)
                      -.++.|+.|||||....
T Consensus         7 i~l~tG~pGsGKT~~a~   23 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMV   23 (199)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHH
Confidence            46899999999997543

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=82.12  E-value=0.7  Score=32.76  Aligned_cols=16  Identities=31%  Similarity=0.335  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+.+.+++|||||...
T Consensus         3 ~i~i~G~~GsGKSTl~   18 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVA   18 (204)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             EEEEECCCCcCHHHHH
Confidence            4789999999999753

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=82.10  E-value=0.68  Score=32.18  Aligned_cols=17  Identities=18%  Similarity=0.206  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +-+++.+++|||||...
T Consensus         7 ~~I~l~G~~GsGKsT~~   23 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEEEESTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35889999999999753

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=82.07  E-value=0.74  Score=31.42  Aligned_cols=16  Identities=25%  Similarity=0.061  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.++.|||||...
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVG   17 (168)
T ss_dssp             EEEEESCTTSCHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5789999999999753

>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=82.04  E-value=1.9  Score=32.01  Aligned_cols=41  Identities=12%  Similarity=0.014  Sum_probs=28.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .|+=.++.++-|+|||.+.+--+.+...   .+.+++++-|...
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~---~g~kvli~kp~~D   58 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI---AQYKCLVIKYAKD   58 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT---TTCCEEEEEETTC
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH---CCCeEEEEeecCC
Confidence            3666778888899999766554444433   4557888888653

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=82.03  E-value=0.76  Score=33.80  Aligned_cols=18  Identities=22%  Similarity=0.257  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.-+.+.+|+|||||...
T Consensus        27 ~~~i~l~G~~GsGKSTl~   44 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVC   44 (246)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            578999999999999643

>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=81.96  E-value=2.2  Score=34.50  Aligned_cols=65  Identities=8%  Similarity=-0.066  Sum_probs=46.4

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .++||.+|++.-++++.+.+++.     ++.+..++|+.. .+..+.++++ .+++|+  +....+++++ +++|
T Consensus       189 ~~~lVF~~s~~~a~~l~~~L~~~-----g~~~~~lh~~~~-~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI  256 (451)
T 2jlq_A          189 GKTVWFVPSIKAGNDIANCLRKS-----GKRVIQLSRKTF-DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVI  256 (451)
T ss_dssp             SCEEEECSSHHHHHHHHHHHHTT-----TCCEEEECTTTH-HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEE
T ss_pred             CCEEEEcCCHHHHHHHHHHHHHc-----CCeEEECCHHHH-HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEE
Confidence            37999999999998877776543     677888888765 3344445544 467777  6666788888 6665

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=81.91  E-value=0.78  Score=34.08  Aligned_cols=19  Identities=26%  Similarity=0.350  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+.+.+|+|||||...
T Consensus        26 ~g~~I~I~G~~GsGKSTl~   44 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLC   44 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4678999999999999754

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=81.86  E-value=0.8  Score=33.62  Aligned_cols=19  Identities=26%  Similarity=0.389  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|+-+.+.+|+|+|||..
T Consensus        32 ~~Ge~~~i~G~nGsGKSTL   50 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTSL   50 (229)
T ss_dssp             ETTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3578899999999999963

>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=81.61  E-value=0.8  Score=34.39  Aligned_cols=24  Identities=21%  Similarity=0.192  Sum_probs=19.3

Q ss_pred             HHhcCCcEEEEcCCCChHHHHHHH
Q psy1539          47 QAVLGMDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        47 ~~~~g~~~ii~a~TGsGKT~~~~~   70 (175)
                      -+..|.-+.+.+|+|+|||.....
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~   49 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQ   49 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHH
Confidence            455788999999999999965443

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=81.59  E-value=0.74  Score=32.71  Aligned_cols=16  Identities=25%  Similarity=0.208  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+.+.++.|||||...
T Consensus         4 ~i~l~G~~GsGKST~~   19 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIA   19 (206)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4678999999999754

>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=81.58  E-value=1.3  Score=36.65  Aligned_cols=17  Identities=24%  Similarity=0.333  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.||+|+|||...
T Consensus        78 ~~lLL~GppGtGKTtla   94 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAA   94 (516)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            68999999999999654

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=81.54  E-value=0.63  Score=35.10  Aligned_cols=19  Identities=21%  Similarity=0.333  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        35 ~~Ge~~~liG~nGsGKSTL   53 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTL   53 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3578899999999999973

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=81.35  E-value=0.82  Score=35.35  Aligned_cols=18  Identities=11%  Similarity=0.054  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|+-+.+.+|+|+|||..
T Consensus       125 ~Ge~vaIvGpsGsGKSTL  142 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSML  142 (305)
T ss_dssp             TCSEEEEECSSSSSHHHH
T ss_pred             CCCEEEEECCCCCcHHHH
Confidence            578999999999999964

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=81.33  E-value=0.55  Score=34.81  Aligned_cols=18  Identities=28%  Similarity=0.278  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|.-+.+.+|+|||||..
T Consensus        27 ~Ge~~~i~G~nGsGKSTL   44 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTI   44 (243)
T ss_dssp             TTEEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            577899999999999974

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=81.22  E-value=0.69  Score=34.77  Aligned_cols=18  Identities=33%  Similarity=0.342  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|.-+.+.+|+|+|||..
T Consensus        31 ~Ge~~~liG~nGsGKSTL   48 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTF   48 (262)
T ss_dssp             TTCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            578889999999999973

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=81.21  E-value=0.83  Score=33.42  Aligned_cols=19  Identities=26%  Similarity=0.274  Sum_probs=16.0

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|+|||..
T Consensus        28 ~~Ge~~~iiG~nGsGKSTL   46 (224)
T 2pcj_A           28 KKGEFVSIIGASGSGKSTL   46 (224)
T ss_dssp             ETTCEEEEEECTTSCHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3578889999999999963

>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=81.18  E-value=2.1  Score=33.81  Aligned_cols=38  Identities=18%  Similarity=0.078  Sum_probs=24.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT   91 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   91 (175)
                      |.-+++.+++|+|||... +.++.....  .+..++++...
T Consensus        74 G~li~I~G~pGsGKTtla-l~la~~~~~--~g~~vlyi~~E  111 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLA-LAIVAQAQK--AGGTCAFIDAE  111 (366)
T ss_dssp             TSEEEEEESTTSSHHHHH-HHHHHHHHH--TTCCEEEEESS
T ss_pred             CcEEEEEcCCCCChHHHH-HHHHHHHHH--CCCeEEEEECC
Confidence            467899999999999644 444433322  23356666643

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=81.14  E-value=0.85  Score=32.86  Aligned_cols=18  Identities=17%  Similarity=0.274  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +..+++.+++|||||...
T Consensus         5 ~~~I~l~G~~GsGKsT~a   22 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQC   22 (217)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            467899999999999643

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=81.13  E-value=1.1  Score=36.51  Aligned_cols=25  Identities=28%  Similarity=0.320  Sum_probs=18.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ..++++.+|+|+|||... -.+...+
T Consensus       201 ~~~~LL~G~pG~GKT~la-~~la~~l  225 (468)
T 3pxg_A          201 KNNPVLIGEPGVGKTAIA-EGLAQQI  225 (468)
T ss_dssp             SCEEEEESCTTTTTHHHH-HHHHHHH
T ss_pred             CCCeEEECCCCCCHHHHH-HHHHHHH
Confidence            478999999999999654 3344444

>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=81.12  E-value=0.9  Score=35.06  Aligned_cols=42  Identities=17%  Similarity=0.065  Sum_probs=25.6

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+++--++.+.+.+.+.-+..            -...++++.||+|+|||...
T Consensus        12 ~~~~~vg~~~~~~~l~~~~~~~------------~~~~~~ll~Gp~G~GKTtl~   53 (354)
T 1sxj_E           12 SLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRC   53 (354)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHHHhhC------------CCCCeEEEECCCCCCHHHHH
Confidence            3555545666666665531010            12245999999999999653

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=81.11  E-value=0.88  Score=34.02  Aligned_cols=19  Identities=26%  Similarity=0.291  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        31 ~~Ge~~~liG~nGsGKSTL   49 (257)
T 1g6h_A           31 NKGDVTLIIGPNGSGKSTL   49 (257)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             eCCCEEEEECCCCCCHHHH
Confidence            3578899999999999973

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=81.11  E-value=1.3  Score=34.22  Aligned_cols=19  Identities=16%  Similarity=0.155  Sum_probs=15.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|.-+.|.||+|||||...
T Consensus        89 ~g~ivgI~G~sGsGKSTL~  107 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTA  107 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHH
T ss_pred             CCEEEEEECCCCchHHHHH
Confidence            3556889999999999643

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=81.09  E-value=0.89  Score=33.63  Aligned_cols=18  Identities=28%  Similarity=0.331  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|.-+.+.+|+|+|||..
T Consensus        31 ~Ge~~~l~G~nGsGKSTL   48 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTT   48 (240)
T ss_dssp             TTCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            578899999999999974

>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=81.08  E-value=0.31  Score=39.56  Aligned_cols=68  Identities=18%  Similarity=0.319  Sum_probs=0.0

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ..+++|.||++.-+..+.+.+...     +..+..++|+.+..+..   +.++++ .+++|+  +....+++++++++|
T Consensus       333 ~~~~lvF~~s~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~~~~~GlDip~v~~VI  406 (479)
T 3fmp_B          333 IAQAMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVI  406 (479)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             CCceEEEeCcHHHHHHHHHHHHhC-----CccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEccccccCCccccCCEEE
Confidence            357999999999988877776654     56788888887654333   233333 467777  566678888888887

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=81.07  E-value=0.58  Score=32.42  Aligned_cols=19  Identities=26%  Similarity=0.167  Sum_probs=11.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.-+++.++.|||||...
T Consensus         4 ~~~~I~l~G~~GsGKST~a   22 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTA   22 (183)
T ss_dssp             -CCEEEEECCC----CHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3567899999999999754

>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=81.05  E-value=0.74  Score=37.86  Aligned_cols=55  Identities=16%  Similarity=0.127  Sum_probs=30.2

Q ss_pred             ccccccccCCCCHHHHHHHhhCC--CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQP--FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g--~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+...|+++.=..+..+.+.+.-  +..+..++...   +.-.+.+++.+|+|+|||+..
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g---~~~p~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIG---ARMPKGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTT---CCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcC---CCCCCeEEEECCCCCCHHHHH
Confidence            34556777766666555554420  11111111100   011267999999999999754

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=81.02  E-value=0.7  Score=34.43  Aligned_cols=20  Identities=20%  Similarity=0.120  Sum_probs=16.6

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..|.-+.+.+|+|+|||..+
T Consensus        27 ~~Ge~~~l~G~nGsGKSTLl   46 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTLG   46 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35788999999999999743

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=80.99  E-value=0.64  Score=35.94  Aligned_cols=26  Identities=27%  Similarity=0.376  Sum_probs=19.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .|.-+.+.+|+|||||..  +-++..+.
T Consensus        79 ~Ge~vaivG~sGsGKSTL--l~ll~gl~  104 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTI--LRLLFRFY  104 (306)
T ss_dssp             TTCEEEEESSSCHHHHHH--HHHHTTSS
T ss_pred             CCCEEEEECCCCchHHHH--HHHHHcCC
Confidence            578899999999999973  34444443

>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=80.98  E-value=0.8  Score=38.19  Aligned_cols=19  Identities=26%  Similarity=0.340  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+++.+|+|+|||...
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            3678999999999999643

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=80.97  E-value=0.71  Score=34.80  Aligned_cols=19  Identities=21%  Similarity=0.205  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|+|||..
T Consensus        44 ~~Ge~~~l~G~NGsGKSTL   62 (267)
T 2zu0_C           44 HPGEVHAIMGPNGSGKSTL   62 (267)
T ss_dssp             CTTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3578899999999999974

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=80.92  E-value=0.82  Score=32.34  Aligned_cols=17  Identities=24%  Similarity=0.253  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +-+++.++.|||||...
T Consensus        16 ~~I~l~G~~GsGKsT~~   32 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQC   32 (203)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            46899999999999754

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=80.88  E-value=0.73  Score=34.70  Aligned_cols=19  Identities=26%  Similarity=0.434  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        31 ~~Ge~~~liG~nGsGKSTL   49 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTL   49 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3578889999999999974

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=80.86  E-value=0.9  Score=33.51  Aligned_cols=19  Identities=16%  Similarity=0.080  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+..+++.+|.|||||...
T Consensus        28 ~~~~I~l~G~~GsGKsT~a   46 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQS   46 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            3567999999999999653

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=80.84  E-value=5.5  Score=34.18  Aligned_cols=68  Identities=15%  Similarity=0.301  Sum_probs=50.9

Q ss_pred             EEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchH---HhHHHHhc--C-CCeEEE--eecCccCCCCceEEEEe
Q psy1539          85 VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ---KDEEYLKT--H-NPQIVG--LVNYETNLSGVVVNVMD  156 (175)
Q Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~---~~~~~l~~--~-~~iiv~--l~~~~~~~~~~~~lVlD  156 (175)
                      .+++++++.-+.++.+.+++.     +..+..++|+.+..   +..+.+++  + .+++|+  +....+++ +++++|.-
T Consensus       323 ~iIf~~s~~~ie~la~~L~~~-----g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~  396 (677)
T 3rc3_A          323 DCIVCFSKNDIYSVSRQIEIR-----GLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFY  396 (677)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEES
T ss_pred             CEEEEcCHHHHHHHHHHHHhc-----CCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEEC
Confidence            477799998887777766652     77899999999866   45556664  3 578888  66668888 89998886


Q ss_pred             CC
Q psy1539         157 VR  158 (175)
Q Consensus       157 Ea  158 (175)
                      ..
T Consensus       397 ~~  398 (677)
T 3rc3_A          397 SL  398 (677)
T ss_dssp             CS
T ss_pred             Cc
Confidence            65

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=80.82  E-value=0.73  Score=34.57  Aligned_cols=19  Identities=26%  Similarity=0.158  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|+|||..
T Consensus        39 ~~Gei~~l~G~NGsGKSTL   57 (256)
T 1vpl_A           39 EEGEIFGLIGPNGAGKTTT   57 (256)
T ss_dssp             CTTCEEEEECCTTSSHHHH
T ss_pred             cCCcEEEEECCCCCCHHHH
Confidence            3578899999999999974

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=80.73  E-value=0.72  Score=34.45  Aligned_cols=19  Identities=21%  Similarity=0.281  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|+|||..
T Consensus        24 ~~Ge~~~liG~NGsGKSTL   42 (249)
T 2qi9_C           24 RAGEILHLVGPNGAGKSTL   42 (249)
T ss_dssp             ETTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3578889999999999964

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=80.69  E-value=0.86  Score=32.01  Aligned_cols=15  Identities=27%  Similarity=0.448  Sum_probs=13.0

Q ss_pred             cEEEEcCCCChHHHH
Q psy1539          53 DILCQAKSGMGKTAV   67 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~   67 (175)
                      .+++.+++|||||..
T Consensus         2 ~I~i~G~~GsGKsT~   16 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTI   16 (205)
T ss_dssp             EEEEECCTTSCHHHH
T ss_pred             EEEEECCCccCHHHH
Confidence            478999999999964

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=80.52  E-value=0.86  Score=32.70  Aligned_cols=16  Identities=19%  Similarity=0.115  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.+++|||||...
T Consensus         2 ~I~l~G~~GsGKsT~a   17 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQA   17 (214)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999653

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=80.51  E-value=0.76  Score=34.74  Aligned_cols=19  Identities=26%  Similarity=0.272  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        43 ~~Ge~~~i~G~nGsGKSTL   61 (271)
T 2ixe_A           43 YPGKVTALVGPNGSGKSTV   61 (271)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3578899999999999963

>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=80.38  E-value=3.9  Score=33.31  Aligned_cols=99  Identities=19%  Similarity=0.233  Sum_probs=43.9

Q ss_pred             CChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEE--------ECCCchHHh---HHH
Q psy1539          61 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF--------FGGLPIQKD---EEY  129 (175)
Q Consensus        61 GsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~--------~g~~~~~~~---~~~  129 (175)
                      .++|-.. +.-++........+.++||.++++.-+..+.+.+++.... +++++..+        +|+.+..+.   .+.
T Consensus       370 ~~~K~~~-L~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~  447 (556)
T 4a2p_A          370 ENPKLEE-LVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPIL-NYIKPGVLMGRGRRDQTTGMTLPSQKGVLDA  447 (556)
T ss_dssp             CCHHHHH-HHHHHHHHHHHCTTCCEEEEESSHHHHHHHHHHHTTCSGG-GSCCEEC------------------------
T ss_pred             CChHHHH-HHHHHHHHhcCCCCceEEEEEccHHHHHHHHHHHHhCCCc-ceeeeeEEEccCCcccccccCHHHHHHHHHH
Confidence            4666533 3334433322234568999999999999988877654211 13344333        344443332   334


Q ss_pred             Hhc-C-CCeEEE--eecCccCCCCceEEEEeCCCCC
Q psy1539         130 LKT-H-NPQIVG--LVNYETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       130 l~~-~-~~iiv~--l~~~~~~~~~~~~lVlDEad~~  161 (175)
                      +++ + ..++|+  .....+++.+++++|.=+....
T Consensus       448 F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s  483 (556)
T 4a2p_A          448 FKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGN  483 (556)
T ss_dssp             ------CCEEEEEC-----------CEEEEETCCSC
T ss_pred             hcccCceEEEEEcCchhcCCCchhCCEEEEeCCCCC
Confidence            444 3 477887  5555889999999988666433

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=80.38  E-value=0.78  Score=36.17  Aligned_cols=16  Identities=25%  Similarity=0.530  Sum_probs=13.1

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      =.++.++||+|||..+
T Consensus        27 l~vi~G~NGaGKT~il   42 (371)
T 3auy_A           27 IVAIIGENGSGKSSIF   42 (371)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            3578999999999753

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=80.30  E-value=0.95  Score=38.23  Aligned_cols=15  Identities=27%  Similarity=0.432  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChHHHH
Q psy1539          53 DILCQAKSGMGKTAV   67 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~   67 (175)
                      ++++.||+|+|||..
T Consensus       329 ~vLL~GppGtGKT~L  343 (595)
T 3f9v_A          329 HILIIGDPGTAKSQM  343 (595)
T ss_dssp             CEEEEESSCCTHHHH
T ss_pred             ceEEECCCchHHHHH
Confidence            899999999999964

>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=80.28  E-value=5.2  Score=33.87  Aligned_cols=65  Identities=8%  Similarity=-0.081  Sum_probs=46.0

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcC-CCeEEE--eecCccCCCCceEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH-NPQIVG--LVNYETNLSGVVVN  153 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~-~~iiv~--l~~~~~~~~~~~~l  153 (175)
                      +.++||.++|++-+..+.+.+++.     +.++..++|+.. .+..+.++++ ..++|+  +....++++ ++++
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~-----g~~v~~lhg~~R-~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~~V  422 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKS-----GKRVIQLSRKTF-DTEYPKTKLTDWDFVVTTDISEMGANFR-AGRV  422 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTTH-HHHTTHHHHSCCSEEEECGGGGTTCCCC-CSEE
T ss_pred             CCCEEEEECChhHHHHHHHHHHHc-----CCcEEEEChHHH-HHHHHhhcCCCcEEEEECcHHHcCcccC-ceEE
Confidence            347999999999999888777654     677888888643 3344455544 567787  555677775 7665

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=80.11  E-value=0.72  Score=31.92  Aligned_cols=18  Identities=22%  Similarity=0.298  Sum_probs=15.4

Q ss_pred             hcCCcEEEEcCCCChHHH
Q psy1539          49 VLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~   66 (175)
                      ..|.-+.+.+|.|+|||.
T Consensus        31 ~~Ge~v~L~G~nGaGKTT   48 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTT   48 (158)
T ss_dssp             SSCEEEEEECSTTSSHHH
T ss_pred             CCCCEEEEECCCCCCHHH
Confidence            457778999999999995

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=80.05  E-value=0.8  Score=34.52  Aligned_cols=18  Identities=28%  Similarity=0.394  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~   67 (175)
                      .|.-+.+.+|+|+|||..
T Consensus        49 ~Gei~~liG~NGsGKSTL   66 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTF   66 (263)
T ss_dssp             TTCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEEcCCCCcHHHH
Confidence            577889999999999974

>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=80.04  E-value=1.2  Score=34.50  Aligned_cols=16  Identities=31%  Similarity=0.530  Sum_probs=13.7

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      ++++.||+|+|||...
T Consensus        48 ~~ll~Gp~G~GKTtla   63 (340)
T 1sxj_C           48 HLLFYGPPGTGKTSTI   63 (340)
T ss_dssp             CEEEECSSSSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            3999999999999654

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=80.02  E-value=0.88  Score=33.92  Aligned_cols=18  Identities=28%  Similarity=0.322  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      +.-++++|++|||||...
T Consensus         4 ~~lIvl~G~pGSGKSTla   21 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFS   21 (260)
T ss_dssp             CEEEEEECCTTSSHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHH
Confidence            456899999999999643

---

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	175
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	4e-12
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-10
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-08
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	8e-07
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-06
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-05
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	2e-04
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	5e-04

>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 = 60.3 bits (145), Expect = 4e-12
 Identities = 14/138 (10%), Positives = 39/138 (28%), Gaps = 10/138 (7%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
             E  + Q     + +        A +G+GKT+  +  +L             V+  T  
Sbjct: 41  VGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSL 97

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVN 153
           L  Q ++   ++++    +      G    +  +   +     +       T    +  +
Sbjct: 98  LVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH 156

Query: 154 VMDVRSGGWWLDLEALIL 171
                        + + +
Sbjct: 157 YR------ELGHFDFIFV 168

>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 = 55.7 bits (133), Expect = 1e-10
 Identities = 81/105 (77%), Positives = 87/105 (82%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           F   +  QHECIPQA+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRE
Sbjct: 21  FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE 80

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
           LAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IV
Sbjct: 81  LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIV 125

>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 = 49.1 bits (116), Expect = 4e-08
 Identities = 9/64 (14%), Positives = 23/64 (35%), Gaps = 2/64 (3%)

Query: 51  GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 110
               +     G GKT  ++ A +++       +  L++  TR +A ++ +          
Sbjct: 9   KRLTIMDLHPGAGKTKRYLPAIVREA--IKRGLRTLILAPTRVVAAEMEEALRGLPIRYQ 66

Query: 111 NIKV 114
              +
Sbjct: 67  TPAI 70

>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 = 45.0 bits (105), Expect = 8e-07
 Identities = 34/106 (32%), Positives = 58/106 (54%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
           + + +  Q E IP A+ G DIL +AK+G GK+  +++  L++L+    N+  +V+  TRE
Sbjct: 23  WEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE 82

Query: 94  LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG 139
           LA Q+S+   + SK+M   KV    GG  ++ D   L      ++ 
Sbjct: 83  LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIA 128

>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 = 44.2 bits (103), Expect = 1e-06
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 30  ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC 89
           + +   E    Q E + +   G ++L    +  GKT +  +A +++      ++Y   + 
Sbjct: 19  KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLY---VV 75

Query: 90  HTRELAFQISKEYERFSKYMSNIKV 114
             R LA +  + ++++ K    I +
Sbjct: 76  PLRALAGEKYESFKKWEKIGLRIGI 100

>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 = 40.7 bits (94), Expect = 3e-05
 Identities = 31/115 (26%), Positives = 50/115 (43%), Gaps = 10/115 (8%)

Query: 34  FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---------VY 84
           ++  T  Q   IP  +   DI+  A++G GKTA F++  +  L   D N           
Sbjct: 41  YQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK 100

Query: 85  VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG 139
            L++  TRELA QI  E ++FS     ++  V +GG         ++     +V 
Sbjct: 101 CLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVA 154

>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 = 38.1 bits (87), Expect = 2e-04
 Identities = 17/104 (16%), Positives = 32/104 (30%), Gaps = 10/104 (9%)

Query: 16  LSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQ 75
           L S  ++  ++  G  Q        Q E I   + G D L    +G GK+  + +  L  
Sbjct: 9   LESGAKQVLQETFGYQQF----RPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL 64

Query: 76  LETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFG 119
              T      +V+     L      + +      + +       
Sbjct: 65  NGLT------VVVSPLISLMKDQVDQLQANGVAAACLNSTQTRE 102

>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 = 36.7 bits (83), Expect = 5e-04
 Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 1/55 (1%)

Query: 36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH 90
          +   +Q     +     + L    +G+GKT + ++    +L      V +L    
Sbjct: 9  QPRIYQEVIYAKC-KETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTK 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	175
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	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
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.93
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.9
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.9
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.84
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.8
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.8
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.67
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.64
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.64
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.46
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.39
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.76
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.75
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.58
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.5
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.49
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.3
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	98.1
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.76
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	97.07
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	96.97
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.89
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.87
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	96.66
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.64
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.63
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.57
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.56
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	96.28
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.14
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.1
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.1
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.03
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	95.98
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.93
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	95.92
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.91
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.5
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.35
d1okkd2	207	GTPase domain of the signal recognition particle r	95.21
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	95.18
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	95.06
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.83
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.5
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.37
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.0
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.98
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.96
d2awna2	232	Maltose transport protein MalK, N-terminal domain	93.85
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.82
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	93.68
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	93.64
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	93.6
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.34
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	93.28
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	93.25
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	93.21
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	93.1
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.86
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	92.85
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	92.81
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	92.71
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	92.61
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	92.55
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	92.39
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	92.25
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	92.14
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	92.12
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	91.87
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	91.79
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.72
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	91.65
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	91.47
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	91.18
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	91.07
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	91.06
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	90.98
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	90.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	90.55
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	90.48
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	90.26
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	89.9
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	89.87
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	89.8
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	89.69
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	89.67
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	89.63
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	89.6
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	89.39
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	89.36
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	89.36
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	89.24
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	89.14
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	89.05
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	89.03
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	88.93
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	88.92
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	88.8
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	88.48
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	88.46
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	88.41
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	88.36
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	88.32
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	88.03
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	87.84
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	87.35
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	87.29
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	87.16
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	87.08
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	87.03
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	86.98
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	86.98
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	86.38
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	86.13
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	85.8
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	85.69
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	85.57
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	85.53
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	85.51
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	85.41
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	85.25
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	85.23
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	85.15
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	85.02
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	84.86
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	84.85
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	84.73
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	84.58
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	84.57
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.47
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	84.25
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	84.12
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	83.75
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	83.61
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	83.57
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	83.42
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	82.88
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	82.84
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	82.42
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	82.34
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	82.07
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	82.06
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	81.79
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	81.75
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	81.58
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	81.52
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	81.16
d1g2912	240	Maltose transport protein MalK, N-terminal domain	81.07
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	81.01
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	80.15

>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=3.9e-40  Score=246.91  Aligned_cols=161  Identities=25%  Similarity=0.331  Sum_probs=149.5

Q ss_pred             ccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          11 VTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        11 ~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      ....+|+++||+++++++|++.||..|||+|++|||.+++|+|+++.||||||||+||++|+++++......++++|++|
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~P   93 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAP   93 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECS
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecc
Confidence            45568999999999999999999999999999999999999999999999999999999999999988888899999999


Q ss_pred             CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC----
Q psy1539          91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR----  158 (175)
Q Consensus        91 t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa----  158 (175)
                      ||||+.|+++.++++.+.. ++++..++|+....++...++.+++++|+        +.+....+++++++|+|||    
T Consensus        94 treLa~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll  172 (222)
T d2j0sa1          94 TRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEML  172 (222)
T ss_dssp             SHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHT
T ss_pred             hHHHHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhh
Confidence            9999999999999999887 99999999999999999999999999999        2233678899999999999    


Q ss_pred             CCCCHHHHHHHHhh
Q psy1539         159 SGGWWLDLEALILS  172 (175)
Q Consensus       159 d~~f~~~v~~il~~  172 (175)
                      |.+|.+++..|+..
T Consensus       173 ~~~f~~~i~~I~~~  186 (222)
T d2j0sa1         173 NKGFKEQIYDVYRY  186 (222)
T ss_dssp             STTTHHHHHHHHTT
T ss_pred             hcCcHHHHHHHHHh
Confidence            68999999999864

>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=6e-39  Score=238.07  Aligned_cols=159  Identities=26%  Similarity=0.328  Sum_probs=147.1

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      ++|++++|++++++++.++||..|||+|++|||.+++|+|++++||||||||+||++|+++++..+.++++++|++||++
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            68999999999999999999999999999999999999999999999999999999999999988888999999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC----CCC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR----SGG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa----d~~  161 (175)
                      |+.|+++.+..+.+...+..+....|+.....+...+.++++++|+        +......+++++++|+|||    |.+
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            9999999999998877678888899999888888888999999999        3333678899999999999    589


Q ss_pred             CHHHHHHHHhh
Q psy1539         162 WWLDLEALILS  172 (175)
Q Consensus       162 f~~~v~~il~~  172 (175)
                      |.++++.|+..
T Consensus       163 f~~~i~~I~~~  173 (206)
T d1veca_         163 FVQIMEDIILT  173 (206)
T ss_dssp             THHHHHHHHHH
T ss_pred             hHHHHHHHHHh
Confidence            99999999864

>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=3.4e-38  Score=234.17  Aligned_cols=159  Identities=54%  Similarity=0.744  Sum_probs=142.9

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      +.|++++|++++++++.++||+.|||+|++|||.+++|+|++++||||||||++|++|+++++....++++++|++|||+
T Consensus         1 s~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptre   80 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   80 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccch
Confidence            46999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHh-cCCCeEEE--------eecCccCCCCceEEEEeCCC-----
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK-THNPQIVG--------LVNYETNLSGVVVNVMDVRS-----  159 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~-~~~~iiv~--------l~~~~~~~~~~~~lVlDEad-----  159 (175)
                      |+.|+++.++.+....+.+++..++|+.+...+.+.+. .+++++|+        +.++.+.+++++++|+||||     
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~  160 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  160 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhc
Confidence            99999999999998876788889999998887777764 56788898        33336789999999999994     


Q ss_pred             CCCHHHHHHHHhh
Q psy1539         160 GGWWLDLEALILS  172 (175)
Q Consensus       160 ~~f~~~v~~il~~  172 (175)
                      .+|.++++.|+..
T Consensus       161 ~~~~~~i~~I~~~  173 (207)
T d1t6na_         161 LDMRRDVQEIFRM  173 (207)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHh
Confidence            4788999988754

>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=1.4e-37  Score=235.39  Aligned_cols=163  Identities=21%  Similarity=0.266  Sum_probs=147.6

Q ss_pred             ccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC---------
Q psy1539           9 HGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---------   79 (175)
Q Consensus         9 ~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~---------   79 (175)
                      .+.+..+|++++|+++++++|.+.||..|||+|.++||.+++|+|++++||||||||++|++|+++++...         
T Consensus        16 ~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~   95 (238)
T d1wrba1          16 ATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSK   95 (238)
T ss_dssp             CCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------C
T ss_pred             CCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccC
Confidence            34567899999999999999999999999999999999999999999999999999999999999998532         


Q ss_pred             CCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCce
Q psy1539          80 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVV  151 (175)
Q Consensus        80 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~  151 (175)
                      ..+++++|++||++|+.|+.+.+..+.... ++++..++|+.....+.+....+++++|+        +..+...+++++
T Consensus        96 ~~~~~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~  174 (238)
T d1wrba1          96 TAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCK  174 (238)
T ss_dssp             CBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCC
T ss_pred             CCCceEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccc
Confidence            356889999999999999999999999887 89999999999888888889999999999        333367899999


Q ss_pred             EEEEeCC----CCCCHHHHHHHHhh
Q psy1539         152 VNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       152 ~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      ++|+|||    +.+|.++++.|+.+
T Consensus       175 ~lViDEaD~ll~~~f~~~i~~Il~~  199 (238)
T d1wrba1         175 YIVLDEADRMLDMGFEPQIRKIIEE  199 (238)
T ss_dssp             EEEEETHHHHHHTTCHHHHHHHHHS
T ss_pred             eeeeehhhhhhhhccHHHHHHHHHH
Confidence            9999999    47999999999864

>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=1.3e-37  Score=232.65  Aligned_cols=163  Identities=27%  Similarity=0.306  Sum_probs=142.3

Q ss_pred             ccccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539           9 HGVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus         9 ~~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      .+.++.+|++++|++.++++|.+.||..|||+|++|||.+++|+|++++||||||||++|++|+++++..+..+++++|+
T Consensus         7 ~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil   86 (218)
T d2g9na1           7 WNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVL   86 (218)
T ss_dssp             CCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             CCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEE
Confidence            35788999999999999999999999999999999999999999999999999999999999999999888889999999


Q ss_pred             ecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH-HHhcCCCeEEE--------eecCccCCCCceEEEEeCC-
Q psy1539          89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE-YLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR-  158 (175)
Q Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~-~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa-  158 (175)
                      +||++||.|+++.++++.... +.++..+.++....++.. ...++++++|+        +.+....+++++++|+||| 
T Consensus        87 ~Pt~eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD  165 (218)
T d2g9na1          87 APTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEAD  165 (218)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHH
T ss_pred             cccchhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecc
Confidence            999999999999999999888 788877777765544433 33356788898        3334678899999999999 


Q ss_pred             ---CCCCHHHHHHHHhh
Q psy1539         159 ---SGGWWLDLEALILS  172 (175)
Q Consensus       159 ---d~~f~~~v~~il~~  172 (175)
                         |.+|.+++..|+..
T Consensus       166 ~ll~~~f~~~~~~Il~~  182 (218)
T d2g9na1         166 EMLSRGFKDQIYDIFQK  182 (218)
T ss_dssp             HHHHTTCHHHHHHHHHH
T ss_pred             hhhcCchHHHHHHHHHh
Confidence               47999999999864

>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=4.4e-37  Score=228.86  Aligned_cols=161  Identities=28%  Similarity=0.345  Sum_probs=138.6

Q ss_pred             cccccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +++..+|++++|+++++++|.++||.+|||+|+++||.+++|+|++++||||||||++|++|+++++.....+++++|++
T Consensus         6 ~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~   85 (212)
T d1qdea_           6 DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLA   85 (212)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             cccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEc
Confidence            56789999999999999999999999999999999999999999999999999999999999999998888899999999


Q ss_pred             cCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC---
Q psy1539          90 HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR---  158 (175)
Q Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa---  158 (175)
                      ||++|+.|++..+..+.... ..++....++....++...++ +++++|+        +..+...+++++++|+|||   
T Consensus        86 pt~el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~l  163 (212)
T d1qdea_          86 PTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM  163 (212)
T ss_dssp             SSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHH
T ss_pred             ccHHHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCceecCcceEEeehhhhhh
Confidence            99999999999999998877 888888888887766666654 6799998        3333678999999999999   


Q ss_pred             -CCCCHHHHHHHHhh
Q psy1539         159 -SGGWWLDLEALILS  172 (175)
Q Consensus       159 -d~~f~~~v~~il~~  172 (175)
                       |.+|.+++..|+..
T Consensus       164 ld~~f~~~v~~I~~~  178 (212)
T d1qdea_         164 LSSGFKEQIYQIFTL  178 (212)
T ss_dssp             HHTTCHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHh
Confidence             58999999999864

>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=3.8e-35  Score=217.36  Aligned_cols=158  Identities=28%  Similarity=0.333  Sum_probs=145.8

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      .+|++++|+++++++|++.||..|||+|+++||.+++|+|+++.||||||||++|++|+++++....++.++++++|+++
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            37999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC----CCC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR----SGG  161 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa----d~~  161 (175)
                      ++.|....+..+.... ++++...+|+.....+...+.++++++|+        +......+++++++|+|||    +.+
T Consensus        81 ~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~  159 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD  159 (206)
T ss_dssp             HHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH
T ss_pred             hhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhh
Confidence            9999999999988877 99999999999988888899999999999        3333678899999999999    467


Q ss_pred             CHHHHHHHHhh
Q psy1539         162 WWLDLEALILS  172 (175)
Q Consensus       162 f~~~v~~il~~  172 (175)
                      |.++++.|+..
T Consensus       160 f~~~v~~I~~~  170 (206)
T d1s2ma1         160 FKTIIEQILSF  170 (206)
T ss_dssp             HHHHHHHHHTT
T ss_pred             hHHHHHHHHHh
Confidence            89999999864

>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=1.8e-34  Score=214.07  Aligned_cols=156  Identities=25%  Similarity=0.373  Sum_probs=139.6

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR   92 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~   92 (175)
                      -+|++++|++++++++.+.||.+|||+|+++||.+++| +|+++++|||||||++|++|+++.... .++++++|++||+
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 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-NNGIEAIILTPTR   82 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS-SSSCCEEEECSCH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc-ccCcceEEEeecc
Confidence            38999999999999999999999999999999999998 599999999999999999999987654 5678999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEEe--------ecCccCCCCceEEEEeCCC----C
Q psy1539          93 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL--------VNYETNLSGVVVNVMDVRS----G  160 (175)
Q Consensus        93 ~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~l--------~~~~~~~~~~~~lVlDEad----~  160 (175)
                      +|+.|+++.++.+.... +.++..++|+.+..++.+.++ +++++|++        .+...++++++++|+||||    .
T Consensus        83 ~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~  160 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNM  160 (208)
T ss_dssp             HHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT
T ss_pred             ccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcC
Confidence            99999999999999887 889999999998888877765 68999992        2336789999999999994    6


Q ss_pred             CCHHHHHHHHhh
Q psy1539         161 GWWLDLEALILS  172 (175)
Q Consensus       161 ~f~~~v~~il~~  172 (175)
                      +|.++++.|+..
T Consensus       161 ~~~~~i~~I~~~  172 (208)
T d1hv8a1         161 GFIKDVEKILNA  172 (208)
T ss_dssp             TTHHHHHHHHHT
T ss_pred             CChHHHHHHHHh
Confidence            899999999864

>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=8.4e-33  Score=204.72  Aligned_cols=159  Identities=22%  Similarity=0.312  Sum_probs=138.3

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      +.|+++||++.++++|++.||.+|||+|++|||.+++|+|++++||||||||++|++|+++.+.........++++|+++
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~   80 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   80 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccc
Confidence            47999999999999999999999999999999999999999999999999999999999999988778889999999999


Q ss_pred             HHHHHHHHHHHHHhhC---CCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCC----
Q psy1539          94 LAFQISKEYERFSKYM---SNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVR----  158 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~---~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEa----  158 (175)
                      ++.+..+.+.......   ....+..+.++.+...+.+....+++++|+        +.+....+++++++|+|||    
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll  160 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLML  160 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHH
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeeccccc
Confidence            9999999888776554   245566677777766666667778999999        2223567789999999999    


Q ss_pred             CCCCHHHHHHHHhh
Q psy1539         159 SGGWWLDLEALILS  172 (175)
Q Consensus       159 d~~f~~~v~~il~~  172 (175)
                      |.+|.++++.|+..
T Consensus       161 ~~~f~~~v~~I~~~  174 (209)
T d1q0ua_         161 DMGFITDVDQIAAR  174 (209)
T ss_dssp             HTTCHHHHHHHHHT
T ss_pred             ccccHHHHHHHHHH
Confidence            57999999999864

>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=99.93  E-value=4.5e-26  Score=171.26  Aligned_cols=140  Identities=14%  Similarity=0.153  Sum_probs=107.7

Q ss_pred             ccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          15 VLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      .|.+..+.+.+.+ +.+.++.+|+++|+++++.++.|+|+++++|||+|||++++++++....   ++.+++|++||++|
T Consensus        23 ~~~~~~~~~~~~~-~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~---~~~rvliv~Pt~~L   98 (237)
T d1gkub1          23 LFPEDFLLKEFVE-FFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL---KGKRCYVIFPTSLL   98 (237)
T ss_dssp             CCTTHHHHHHHHH-HHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT---TSCCEEEEESCHHH
T ss_pred             cCccchhHHHHHH-HHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH---hcCeEEEEeccHHH
Confidence            3444444555544 5555788999999999999999999999999999999999999987665   34589999999999


Q ss_pred             HHHHHHHHHHHHhhCCCeE----EEEEECCCchHHhHHHHh--cCCCeEEE----eecCccCCCCceEEEEeCCC
Q psy1539          95 AFQISKEYERFSKYMSNIK----VGVFFGGLPIQKDEEYLK--THNPQIVG----LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus        95 ~~q~~~~~~~~~~~~~~i~----v~~~~g~~~~~~~~~~l~--~~~~iiv~----l~~~~~~~~~~~~lVlDEad  159 (175)
                      +.|+++.++++.+.. ++.    +....++.......+.+.  .+++++|+    +.++...+++++++|+||+|
T Consensus        99 a~Q~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~~~~~~~~vVvDE~d  172 (237)
T d1gkub1          99 VIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVD  172 (237)
T ss_dssp             HHHHHHHHHHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTTSCCCSEEEESCHH
T ss_pred             HHHHHHHHHHHHHHc-CCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhhhhcCCCCEEEEEChh
Confidence            999999999998776 443    344445544444444433  34688888    44445677899999999997

>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=99.90  E-value=1.1e-24  Score=160.23  Aligned_cols=134  Identities=12%  Similarity=0.012  Sum_probs=102.0

Q ss_pred             ccccCCCCHHHHHHHhhC-CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          15 VLSSRNRREKEDRIGESQ-PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        15 ~~~~~~l~~~l~~~l~~~-g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      ..+.++|++...+.|++. ||..++|+|.+|++.+++|+|+++++|||||||++|.+|++..      ..++++++|+++
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            457789999999999988 9999999999999999999999999999999999999998764      337999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchH---HhHHH-HhcCCCeEEEee--------cCccCCCCceEEEEeCCC
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQ---KDEEY-LKTHNPQIVGLV--------NYETNLSGVVVNVMDVRS  159 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~---~~~~~-l~~~~~iiv~l~--------~~~~~~~~~~~lVlDEad  159 (175)
                      |++|+.+.++.+...     .....+.....   ..... .....+++++..        .......+++++|+||+|
T Consensus        77 L~~q~~~~l~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH  149 (206)
T d1oywa2          77 LMKDQVDQLQANGVA-----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAH  149 (206)
T ss_dssp             HHHHHHHHHHHTTCC-----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGG
T ss_pred             hhhhHHHHHHhhccc-----ccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeee
Confidence            999999888776432     33333332222   22222 333455666511        114567789999999994

>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=99.90  E-value=3.7e-24  Score=157.05  Aligned_cols=131  Identities=18%  Similarity=0.182  Sum_probs=102.2

Q ss_pred             CCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHH
Q psy1539          21 RREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  100 (175)
Q Consensus        21 l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  100 (175)
                      +++.+...|++.||.+|+|+|.++++.+++|+|+++++|||||||.++.++++..+..   +.++++++|+++|+.|+.+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~---~~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---GGKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc---cCcceeecccHHHHHHHHH
Confidence            6788999999999999999999999999999999999999999999999999887764   3479999999999999999


Q ss_pred             HHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCCC
Q psy1539         101 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       101 ~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEad  159 (175)
                      .++++...  ..++....|+......   ..+.++++++        +.+....+.+++++|+||++
T Consensus        87 ~~~~~~~~--~~~v~~~~~~~~~~~~---~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h  148 (202)
T d2p6ra3          87 SFKKWEKI--GLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIH  148 (202)
T ss_dssp             HHTTTTTT--TCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGG
T ss_pred             HHHHHhhc--cccceeeccCcccccc---cccccceeeeccHHHHHHHhccchhhhhhhhccccHHH
Confidence            99877654  4556666666543221   1234567666        22234567789999999995

>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=99.84  E-value=1.2e-20  Score=137.34  Aligned_cols=121  Identities=18%  Similarity=0.220  Sum_probs=96.4

Q ss_pred             CCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        34 ~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      +-+|+++|.+++..+. ++|+++++|||+|||+++++++...+..  .+.++++++|+++|+.|+.+.++++.... +.+
T Consensus         7 ~~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~--~~~~il~i~P~~~L~~q~~~~~~~~~~~~-~~~   82 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLP-PEK   82 (200)
T ss_dssp             HHCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSC-GGG
T ss_pred             CCCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHh--cCCcEEEEcCchHHHHHHHHHHHHhhccc-ccc
Confidence            3479999999998775 5689999999999999999888776654  23479999999999999999999987655 777


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEE--------eecCccCCCCceEEEEeCCC
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVG--------LVNYETNLSGVVVNVMDVRS  159 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~--------l~~~~~~~~~~~~lVlDEad  159 (175)
                      +....++.......+.+.. .+++++        +......+++++++|+|||+
T Consensus        83 v~~~~~~~~~~~~~~~~~~-~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H  135 (200)
T d1wp9a1          83 IVALTGEKSPEERSKAWAR-AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAH  135 (200)
T ss_dssp             EEEECSCSCHHHHHHHHHH-CSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGG
T ss_pred             eeeeecccchhHHHHhhhc-ccccccccchhHHHHhhhhhhccccceEEEEehh
Confidence            8888887776555555544 577777        23335677899999999995

>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=99.80  E-value=1.1e-18  Score=129.91  Aligned_cols=142  Identities=16%  Similarity=0.134  Sum_probs=113.8

Q ss_pred             CCCHHHHHHHhhCCCCCCcHHHHHhHHHHhc----C--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          20 NRREKEDRIGESQPFREQTSFQHECIPQAVL----G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        20 ~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~----g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      ..+++..+.+.+.-...+|+-|..++..+.+    +  .+.+++|.||||||.+|+.++...+.   ++.++++++||..
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~---~g~qv~~l~Pt~~  115 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD---NHKQVAVLVPTTL  115 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT---TTCEEEEECSSHH
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH---cCCceEEEccHHH
Confidence            3456666665554333689999999987763    2  58999999999999999999988876   4569999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE---eecCccCCCCceEEEEeCC-CCCCHHH
Q psy1539          94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG---LVNYETNLSGVVVNVMDVR-SGGWWLD  165 (175)
Q Consensus        94 L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEa-d~~f~~~  165 (175)
                      |+.|+++.++++...+ ++++.+++|+.+..+..+   .+.+| .+++||   ++...+.++++.++|+||- ++|+.+.
T Consensus       116 La~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIiDEeH~fg~kQ~  194 (233)
T d2eyqa3         116 LAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHK  194 (233)
T ss_dssp             HHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGGSCHHHH
T ss_pred             hHHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceeeechhhhhhHHH
Confidence            9999999999998887 899999999988655433   44454 578888   5555778899999999999 5677665

>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=99.80  E-value=4.8e-19  Score=134.16  Aligned_cols=137  Identities=24%  Similarity=0.241  Sum_probs=107.6

Q ss_pred             HHHHHH-HhhCCCCCCcHHHHHhHHHHhc----C--CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHH
Q psy1539          23 EKEDRI-GESQPFREQTSFQHECIPQAVL----G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA   95 (175)
Q Consensus        23 ~~l~~~-l~~~g~~~~t~~Q~~~i~~~~~----g--~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~   95 (175)
                      .++.+. ..++.| .+|+-|.+|+..+.+    +  .+.+++|.||||||.+|+.+++..+..   +.++++++||..|+
T Consensus        70 ~~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---g~q~~~m~Pt~~La  145 (264)
T d1gm5a3          70 GKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILA  145 (264)
T ss_dssp             THHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHH
T ss_pred             hHHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---ccceeEEeehHhhh
Confidence            344443 455566 589999999988864    2  588999999999999999999888774   45899999999999


Q ss_pred             HHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE---eecCccCCCCceEEEEeCC-CCCCHH
Q psy1539          96 FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG---LVNYETNLSGVVVNVMDVR-SGGWWL  164 (175)
Q Consensus        96 ~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~---l~~~~~~~~~~~~lVlDEa-d~~f~~  164 (175)
                      .|+++.++++...+ ++++..++|+.+.++..+   .+.+| .++|||   +....+.|+++.++|+||- +.|+.+
T Consensus       146 ~Qh~~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDEqH~fgv~Q  221 (264)
T d1gm5a3         146 IQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQ  221 (264)
T ss_dssp             HHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCCC----
T ss_pred             HHHHHHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeeccccccchhh
Confidence            99999999999887 899999999988655443   44443 678888   5555678899999999998 456654

>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=99.67  E-value=1e-16  Score=122.82  Aligned_cols=130  Identities=13%  Similarity=0.185  Sum_probs=95.0

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|+++|.+|+..+++++..++.+|||+|||+.....+ ..+... ...++||+||+++|+.|+.+.+.++.... ...+.
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~-~~~~~~-~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~-~~~~~  189 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLA-RYYLEN-YEGKILIIVPTTALTTQMADDFVDYRLFS-HAMIK  189 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHH-HHHHHH-CSSEEEEECSSHHHHHHHHHHHHHHTSCC-GGGEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHH-HHhhhc-ccceEEEEEcCchhHHHHHHHHHHhhccc-cccce
Confidence            5899999999999998899999999999998765433 333222 33489999999999999999999886543 44566


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .+.+|......   .....++++++.+.     ...+++++++|+|||+..-......|+.
T Consensus       190 ~~~~g~~~~~~---~~~~~~i~i~t~qs~~~~~~~~~~~f~~VIvDEaH~~~a~~~~~il~  247 (282)
T d1rifa_         190 KIGGGASKDDK---YKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIIS  247 (282)
T ss_dssp             ECSTTCSSTTC---CCTTCSEEEECHHHHTTSCGGGGGGEEEEEEETGGGCCHHHHHHHTT
T ss_pred             eecceeccccc---ccccceEEEEeeehhhhhcccccCCCCEEEEECCCCCCchhHHHHHH
Confidence            66666542211   12345777773333     3456789999999998777777777764

>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=99.64  E-value=6.8e-17  Score=123.87  Aligned_cols=101  Identities=11%  Similarity=0.030  Sum_probs=68.5

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  127 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~  127 (175)
                      +.+|+++++.+|||||||++|+.|++.....  ++.+++|++||++|+.|+.+.++.+..........            
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~--~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~------------   71 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIR------------   71 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--HTCCEEEEESSHHHHHHHHHHTTTSCCBCCC----------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHh--cCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEe------------
Confidence            4578999999999999999998888876654  35689999999999999888766543222111110            


Q ss_pred             HHHhcCCCeEEE-------eecCccCCCCceEEEEeCCCCCC
Q psy1539         128 EYLKTHNPQIVG-------LVNYETNLSGVVVNVMDVRSGGW  162 (175)
Q Consensus       128 ~~l~~~~~iiv~-------l~~~~~~~~~~~~lVlDEad~~f  162 (175)
                      ........++++       .......+++++++|+||++...
T Consensus        72 ~~~~~~~~i~~~t~~~l~~~~~~~~~~~~~~~vViDE~H~~~  113 (305)
T d2bmfa2          72 AEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTD  113 (305)
T ss_dssp             ----CCCSEEEEEHHHHHHHHTSSSCCCCCSEEEEESTTCCS
T ss_pred             ecccCccccccCCcHHHHHHHhcCccccceeEEEeeeeeecc
Confidence            111122345555       12224567899999999997553

>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=99.64  E-value=8.3e-16  Score=112.47  Aligned_cols=117  Identities=19%  Similarity=0.143  Sum_probs=83.7

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .++++|.+++..+.++++.++.+|||+|||+.++..+ ..+     +.++||+||+++|+.|+.+.++++...    .+.
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~-----~~~~Liv~p~~~L~~q~~~~~~~~~~~----~~~  139 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL-----STPTLIVVPTLALAEQWKERLGIFGEE----YVG  139 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS-----CSCEEEEESSHHHHHHHHHHHGGGCGG----GEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh-----cCceeEEEcccchHHHHHHHHHhhccc----chh
Confidence            5899999999999999899999999999998765443 332     236899999999999999888776433    344


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEEeecC-----ccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVGLVNY-----ETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~l~~~-----~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      ...|+..         ...+++++..+.     ....++++++|+|||+..-.+....++.
T Consensus       140 ~~~~~~~---------~~~~i~i~t~~~~~~~~~~~~~~~~lvIiDEaH~~~a~~~~~i~~  191 (206)
T d2fz4a1         140 EFSGRIK---------ELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQ  191 (206)
T ss_dssp             EESSSCB---------CCCSEEEEEHHHHHHTHHHHTTTCSEEEEECSSCCCTTTHHHHHH
T ss_pred             hcccccc---------cccccccceehhhhhhhHhhCCcCCEEEEECCeeCCcHHHHHHHh
Confidence            4444432         234677762222     2335688999999997554445555554

>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=99.46  E-value=2.4e-14  Score=97.12  Aligned_cols=99  Identities=18%  Similarity=0.123  Sum_probs=65.1

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  128 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~  128 (175)
                      .+|+++++++|||||||..++.+++.....  .+.++++++|+++++.|..+.+...     +..+....+......   
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~--~~~~vli~~p~~~l~~q~~~~~~~~-----~~~~~~~~~~~~~~~---   74 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFHGL-----DVKFHTQAFSAHGSG---   74 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTS-----CEEEESSCCCCCCCS---
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhh--cCceeeeeecchhHHHHHHHHhhhh-----hhhhccccccccccc---
Confidence            468999999999999998887777766554  3568999999999999977665322     333322222111111   


Q ss_pred             HHhcCCCeEEE----e---ecCccCCCCceEEEEeCCCCC
Q psy1539         129 YLKTHNPQIVG----L---VNYETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       129 ~l~~~~~iiv~----l---~~~~~~~~~~~~lVlDEad~~  161 (175)
                          .......    +   ......+.+++++|+|||+..
T Consensus        75 ----~~~~~~~~~~~l~~~~~~~~~~~~~~lvIiDEaH~~  110 (140)
T d1yksa1          75 ----REVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL  110 (140)
T ss_dssp             ----SCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC
T ss_pred             ----ccchhhhhHHHHHHHHhccccccceeEEEEcccccc
Confidence                1223332    1   112566789999999999754

>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=99.39  E-value=6.2e-13  Score=90.45  Aligned_cols=94  Identities=14%  Similarity=0.024  Sum_probs=62.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  130 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l  130 (175)
                      .+..++.+|||||||+.+...+.      ..+.+++|++|+++|++|+.+.+.+.....    .....++.....     
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~------~~~~~vli~~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~~~-----   72 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA------AQGYKVLVLNPSVAATLGFGAYMSKAHGVD----PNIRTGVRTITT-----   72 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH------TTTCCEEEEESCHHHHHHHHHHHHHHHSCC----CEEECSSCEECC-----
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH------HcCCcEEEEcChHHHHHHHHHHHHHHhhcc----cccccccccccc-----
Confidence            36679999999999975433221      234589999999999999999888775432    333334432111     


Q ss_pred             hcCCCeEEE-----eecCccCCCCceEEEEeCCCCC
Q psy1539         131 KTHNPQIVG-----LVNYETNLSGVVVNVMDVRSGG  161 (175)
Q Consensus       131 ~~~~~iiv~-----l~~~~~~~~~~~~lVlDEad~~  161 (175)
                        ...+++.     .......+++++++|+||++..
T Consensus        73 --~~~~~~~~~~~~~~~~~~~~~~~~~vIiDE~H~~  106 (136)
T d1a1va1          73 --GSPITYSTYGKFLADGGCSGGAYDIIICDECHST  106 (136)
T ss_dssp             --CCSEEEEEHHHHHHTTGGGGCCCSEEEEETTTCC
T ss_pred             --ccceEEEeeeeeccccchhhhcCCEEEEeccccc
Confidence              2345554     2222556789999999999753

>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=98.76  E-value=8.6e-08  Score=72.65  Aligned_cols=121  Identities=14%  Similarity=0.082  Sum_probs=74.1

Q ss_pred             CCcHHHHHhHHHHh---------cCCcEEEEcCCCChHHHHHHHHHHHhhhcC----CCCeEEEEEecCHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAV---------LGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEY  102 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~---------~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~----~~~~~~lil~Pt~~L~~q~~~~~  102 (175)
                      .+.|+|.+++..+.         ++...++.-..|.|||+..+.-+...+...    .....+||+||.. |..|+.+.+
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHHH
Confidence            57899999997553         356789999999999975433222222221    1223689999975 889999999


Q ss_pred             HHHHhhCCCeEEEEEECCCchHHhHH--HHhc------CCCeEEE----eecC--ccCCCCceEEEEeCCC
Q psy1539         103 ERFSKYMSNIKVGVFFGGLPIQKDEE--YLKT------HNPQIVG----LVNY--ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       103 ~~~~~~~~~i~v~~~~g~~~~~~~~~--~l~~------~~~iiv~----l~~~--~~~~~~~~~lVlDEad  159 (175)
                      +++...  ...+..++|+...+...+  ....      ..+++++    +...  ...--+..++|+||++
T Consensus       134 ~k~~~~--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~l~~~~~~~vI~DEaH  202 (298)
T d1z3ix2         134 GKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGH  202 (298)
T ss_dssp             HHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTTTTTSCCCEEEETTGG
T ss_pred             HhhcCC--ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhcccccceeeeeccccc
Confidence            988764  345556666654322211  1111      1245554    1111  2222357899999995

>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=98.75  E-value=1.2e-07  Score=70.44  Aligned_cols=116  Identities=16%  Similarity=0.108  Sum_probs=91.3

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  115 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~  115 (175)
                      .|.++|...--.+.+|+  +....||-|||++..+|+.-....   |..+-+++..--||..=.+++..+.+.+ |++|+
T Consensus        80 RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~---g~~vhvvTvNdyLA~RDae~m~~iy~~l-Glsvg  153 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGKIFEFL-GLTVG  153 (273)
T ss_dssp             CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHHHHT-TCCEE
T ss_pred             EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhc---CCCceEEecCccccchhhhHHhHHHHHc-CCCcc
Confidence            57788877776676774  789999999999998888766553   3468899999999999999999999999 99999


Q ss_pred             EEECCCchHHhHHHHhcCCCeEEE---------eecC------ccCCCCceEEEEeCCC
Q psy1539         116 VFFGGLPIQKDEEYLKTHNPQIVG---------LVNY------ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       116 ~~~g~~~~~~~~~~l~~~~~iiv~---------l~~~------~~~~~~~~~lVlDEad  159 (175)
                      ....+.+..+..+..  .|+|+.+         |.++      ....+.+.+.|+||+|
T Consensus       154 ~~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvD  210 (273)
T d1tf5a3         154 LNLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVD  210 (273)
T ss_dssp             ECCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHH
T ss_pred             ccccccCHHHHHHHh--hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcch
Confidence            998887765555555  3789988         2222      3345679999999986

>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=98.58  E-value=1.1e-07  Score=69.45  Aligned_cols=114  Identities=18%  Similarity=0.218  Sum_probs=71.6

Q ss_pred             CCcHHHHHhHHHHh----cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCC
Q psy1539          36 EQTSFQHECIPQAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  111 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  111 (175)
                      .+.|+|.+++..+.    .+.+.++...+|.|||+..+. ++..+.......++||++| ..+..|+.+.+.++...   
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~-~~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~---   86 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPH---   86 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTT---
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHH-hhhhhhhcccccccceecc-hhhhhHHHHHHHhhccc---
Confidence            57899999997543    357799999999999988644 4444443334447899999 46778888888877643   


Q ss_pred             eEEEEEECCCchHHhHHHHhcCCCeEEE----eecC-ccCCCCceEEEEeCCC
Q psy1539         112 IKVGVFFGGLPIQKDEEYLKTHNPQIVG----LVNY-ETNLSGVVVNVMDVRS  159 (175)
Q Consensus       112 i~v~~~~g~~~~~~~~~~l~~~~~iiv~----l~~~-~~~~~~~~~lVlDEad  159 (175)
                      ..+....+......    . .+.++++.    +.+. ...--+..++|+||++
T Consensus        87 ~~~~~~~~~~~~~~----~-~~~~vvi~~~~~~~~~~~l~~~~~~~vI~DEah  134 (230)
T d1z63a1          87 LRFAVFHEDRSKIK----L-EDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQ  134 (230)
T ss_dssp             SCEEECSSSTTSCC----G-GGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGG
T ss_pred             ccceeeccccchhh----c-cCcCEEEeeHHHHHhHHHHhcccceEEEEEhhh
Confidence            33333322221111    1 13467666    1111 2222367889999993

>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=98.49  E-value=3.7e-07  Score=71.05  Aligned_cols=127  Identities=17%  Similarity=0.099  Sum_probs=75.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHH--HHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeE
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFV--LATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  113 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~--~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~  113 (175)
                      ..+..|.+|+..++.++-.+|.+|.|||||....  +..+.... ...+.++++.+||..=+..+.+.........+...
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~-~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~~~~~  226 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMA-DGERCRIRLAAPTGKAAARLTESLGKALRQLPLTD  226 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTC-SSCCCCEEEEBSSHHHHHHHHHHHTHHHHHSSCCS
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHH-hccCCeEEEecCcHHHHHHHHHHHHHHHhhcCchh
Confidence            3577899999999999999999999999997642  22222222 23456899999998888887776655443331100


Q ss_pred             EEEEECCCchHHhHHHHhcCCCeEEE-------eecCccCCCCceEEEEeCCCCCCHHHHHHHHh
Q psy1539         114 VGVFFGGLPIQKDEEYLKTHNPQIVG-------LVNYETNLSGVVVNVMDVRSGGWWLDLEALIL  171 (175)
Q Consensus       114 v~~~~g~~~~~~~~~~l~~~~~iiv~-------l~~~~~~~~~~~~lVlDEad~~f~~~v~~il~  171 (175)
                      .. .....   ...    ...+-+.+       +.....+...++++|+||+.+.-.+.+..++.
T Consensus       227 ~~-~~~~~---~~~----~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~~~l~~~ll~  283 (359)
T d1w36d1         227 EQ-KKRIP---EDA----STLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLID  283 (359)
T ss_dssp             CC-CCSCS---CCC----BTTTSCC-----------CTTSCCSCSEEEECSGGGCBHHHHHHHHH
T ss_pred             hh-hhhhh---hhh----hHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccCHHHHHHHHH
Confidence            00 00000   000    00011111       12223344578899999998776666666654

>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=98.30  E-value=1e-06  Score=65.94  Aligned_cols=69  Identities=14%  Similarity=0.082  Sum_probs=51.3

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHHHHHHHHHHHHHHH
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFS  106 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~  106 (175)
                      +++|-|++|+..  ...+++|.|+.|||||.+.+.-+...+.. ..+..+++++++|+.++..+.+.+.+..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            478999999964  34568999999999998765444333322 1233479999999999999888887664

>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=98.10  E-value=8.4e-06  Score=61.40  Aligned_cols=70  Identities=17%  Similarity=0.160  Sum_probs=53.2

Q ss_pred             CCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC-CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .+++-|.+++..  .+..++|.|+.|||||.+.+--+...+... ...-+++++++|+..+..+.+.+.....
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            478999999974  345699999999999988766555444332 1223799999999999999998876543

>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=97.07  E-value=0.00067  Score=53.11  Aligned_cols=66  Identities=27%  Similarity=0.305  Sum_probs=49.8

Q ss_pred             CCcHHHHHhHHHHhc----C-CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAVL----G-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~~----g-~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|+.-|=+||..+.+    | ++.++.+-||||||+... .++....     ..+|||+|+..+|.|+++.++.+..
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~~-----rp~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQVN-----KPTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHHT-----CCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHhC-----CCEEEEeCCHHHHHHHHHHHHHHcC
Confidence            477788777776654    4 678999999999995432 2333321     2489999999999999999998864

>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=96.97  E-value=0.0031  Score=43.39  Aligned_cols=75  Identities=16%  Similarity=0.115  Sum_probs=58.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.|+|+.-+..+.+.+++.     |+++..++|+.+..+..+   .+++| .+++|+  +....+++++++++|
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi  104 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVA  104 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEE
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEE
Confidence            4558999999999998877766643     899999999998655443   44444 578888  778899999999999


Q ss_pred             EeCCCC
Q psy1539         155 MDVRSG  160 (175)
Q Consensus       155 lDEad~  160 (175)
                      +=.++.
T Consensus       105 ~~~~~~  110 (174)
T d1c4oa2         105 ILDADK  110 (174)
T ss_dssp             ETTTTS
T ss_pred             Eecccc
Confidence            977643

>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=96.89  E-value=0.0028  Score=44.89  Aligned_cols=86  Identities=8%  Similarity=0.080  Sum_probs=65.1

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhH---HHHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~---~~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.|+.+++|..+-.....+.++   +.+|+.++.+++|..+.++..   ..+.++ .+++|+  ++...++.++..++|
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~---~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA~~ii  106 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLA---ELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII  106 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHH---HHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTEEEEE
T ss_pred             cCCeEEEEEcCccchhhHHHHHH---HhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCCcEEE
Confidence            56699999998877766655554   446789999999998755433   344444 789998  677799999999999


Q ss_pred             EeCCCCCCHHHHHHH
Q psy1539         155 MDVRSGGWWLDLEAL  169 (175)
Q Consensus       155 lDEad~~f~~~v~~i  169 (175)
                      +..|+..-..++.++
T Consensus       107 I~~a~rfGLaQLhQL  121 (211)
T d2eyqa5         107 IERADHFGLAQLHQL  121 (211)
T ss_dssp             ETTTTSSCHHHHHHH
T ss_pred             Eecchhccccccccc
Confidence            999986555666654

>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=96.87  E-value=0.0017  Score=45.71  Aligned_cols=39  Identities=28%  Similarity=0.324  Sum_probs=26.7

Q ss_pred             CcHHHHHhHHHHh----cC---CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          37 QTSFQHECIPQAV----LG---MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        37 ~t~~Q~~~i~~~~----~g---~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .+|+|..++..+.    ++   +.+++.||.|+|||... ..++..+
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a-~~~a~~l   48 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI-YALSRYL   48 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH-HHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHH-HHHHHhc
Confidence            3578888776554    33   34999999999999654 3344444

>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=96.66  E-value=0.0067  Score=40.95  Aligned_cols=73  Identities=14%  Similarity=0.276  Sum_probs=53.7

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH---HhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY---LKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~---l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.|.++.-+.++.+.++..     ++.+..++|+.+.++..+.   ++++ ..++|+  +....+++++++++|
T Consensus        26 ~~~k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~v~~VI  100 (162)
T d1fuka_          26 SVTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVI  100 (162)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEE
T ss_pred             CCCcEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeeccccccccccCCCceEEE
Confidence            3457999999999999877765543     7789999999886655443   3333 467777  566678888888888


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .=+.
T Consensus       101 ~~d~  104 (162)
T d1fuka_         101 NYDL  104 (162)
T ss_dssp             ESSC
T ss_pred             Eecc
Confidence            7655

>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=96.64  E-value=0.0014  Score=49.62  Aligned_cols=65  Identities=17%  Similarity=0.279  Sum_probs=38.5

Q ss_pred             HHHHhhCCCCC---CcHHHHHhHH-HHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          26 DRIGESQPFRE---QTSFQHECIP-QAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        26 ~~~l~~~g~~~---~t~~Q~~~i~-~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      +..+.+.|+..   ..+-+...+. .+..++|++|+++||||||.. +-+++..+..   ..+.+.+=-+.||
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~---~~rivtiEd~~El  205 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPK---EERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCT---TCCEEEEESSCCC
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccc---ccceeeccchhhh
Confidence            34455555433   2344444443 445679999999999999954 4556555432   2355555555554

>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=96.63  E-value=0.0076  Score=41.56  Aligned_cols=74  Identities=19%  Similarity=0.200  Sum_probs=58.0

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhc-CCCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKT-HNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~-~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ++.+++|.+++++-+..+...+++.     ++++..++|+.+..+..+   .+++ ..+++|+  +....+++++++++|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI  104 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVA  104 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEE
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEE
Confidence            3458999999999988766665533     899999999998665544   4444 4678888  777899999999999


Q ss_pred             EeCCC
Q psy1539         155 MDVRS  159 (175)
Q Consensus       155 lDEad  159 (175)
                      .-++.
T Consensus       105 ~~d~p  109 (181)
T d1t5la2         105 ILDAD  109 (181)
T ss_dssp             ETTTT
T ss_pred             EecCC
Confidence            98874

>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=96.57  E-value=0.023  Score=38.34  Aligned_cols=77  Identities=9%  Similarity=0.064  Sum_probs=56.8

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHH---HhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY---LKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~---l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      ...++||.|+++.-+..+...++..     ++.+..++|+.+..+..+.   ++++ ..++|+  .....+++.+++++|
T Consensus        31 ~~~k~iVF~~~~~~~~~l~~~L~~~-----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI  105 (171)
T d1s2ma2          31 QINQAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVI  105 (171)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSCCCTTEEEEE
T ss_pred             CCCceEEEEeeeehhhHhHHhhhcc-----cccccccccccchhhhhhhhhhcccCccccccchhHhhhccccceeEEEE
Confidence            3458999999999998877777654     7788889999886554443   3333 567777  666689999999999


Q ss_pred             EeCCCCCC
Q psy1539         155 MDVRSGGW  162 (175)
Q Consensus       155 lDEad~~f  162 (175)
                      .=+.....
T Consensus       106 ~~d~p~~~  113 (171)
T d1s2ma2         106 NFDFPKTA  113 (171)
T ss_dssp             ESSCCSSH
T ss_pred             ecCCcchH
Confidence            87764333

>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=96.56  E-value=0.0024  Score=45.64  Aligned_cols=51  Identities=20%  Similarity=0.141  Sum_probs=33.9

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +.|+++--++++.+.|++. +...           ....++++.||+|+|||... ..+++.+.
T Consensus         8 ~~~~diig~~~~~~~L~~~-~~~~-----------~~~~~lll~Gp~G~GKTt~~-~~la~~l~   58 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSL-SDQP-----------RDLPHLLLYGPNGTGKKTRC-MALLESIF   58 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTT-TTCT-----------TCCCCEEEECSTTSSHHHHH-HTHHHHHS
T ss_pred             CCHHHccCcHHHHHHHHHH-HHcC-----------CCCCeEEEECCCCCCHHHHH-HHHHHhhc
Confidence            4577887788888888754 1110           11246999999999999644 44555543

>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=96.28  E-value=0.014  Score=40.70  Aligned_cols=73  Identities=12%  Similarity=0.122  Sum_probs=53.6

Q ss_pred             CCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEE
Q psy1539          81 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      .+.++||.++|+.-+..+...++..     ++.+..++|+.+..+..+   .+.++ .+++|+  .....+++.+++++|
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~~~GiD~p~v~~VI  103 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV  103 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEE
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecchhhhccCCCCCCEEE
Confidence            4457999999999998877665543     788999999988654443   33343 567887  666689999999998


Q ss_pred             EeCC
Q psy1539         155 MDVR  158 (175)
Q Consensus       155 lDEa  158 (175)
                      .=+.
T Consensus       104 ~~~~  107 (200)
T d1oywa3         104 HFDI  107 (200)
T ss_dssp             ESSC
T ss_pred             ECCC
Confidence            6444

>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=96.14  E-value=0.051  Score=38.23  Aligned_cols=80  Identities=16%  Similarity=0.161  Sum_probs=42.9

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecC-HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHh-----H
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT-RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD-----E  127 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~-----~  127 (175)
                      +++.+|||+|||.+.. =+..++.. .+..-++|=+-| |.=+.+   +++.+.+.. ++.+.....+.+...-     .
T Consensus        14 i~lvGptGvGKTTTiA-KLAa~~~~-~~~kV~lit~Dt~R~gA~e---QL~~~a~~l-~i~~~~~~~~~d~~~~~~~~~~   87 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCG-KLAKMFVD-EGKSVVLAAADTFRAAAIE---QLKIWGERV-GATVISHSEGADPAAVAFDAVA   87 (213)
T ss_dssp             EEEECCTTSSHHHHHH-HHHHHHHH-TTCCEEEEEECTTCHHHHH---HHHHHHHHH-TCEEECCSTTCCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHHH-CCCceEEEeecccccchhH---HHHHHhhhc-CccccccCCCCcHHHHHHHHHH
Confidence            5679999999997643 22223332 223234444444 555533   566666655 7776554444433221     1


Q ss_pred             HHHhcCCCeEEE
Q psy1539         128 EYLKTHNPQIVG  139 (175)
Q Consensus       128 ~~l~~~~~iiv~  139 (175)
                      ....++.++|+.
T Consensus        88 ~~~~~~~d~ilI   99 (213)
T d1vmaa2          88 HALARNKDVVII   99 (213)
T ss_dssp             HHHHTTCSEEEE
T ss_pred             HHHHcCCCEEEE
Confidence            223346677776

>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=96.10  E-value=0.0076  Score=46.67  Aligned_cols=39  Identities=28%  Similarity=0.415  Sum_probs=27.8

Q ss_pred             cHHHHHhHHHHhcCC--cEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          38 TSFQHECIPQAVLGM--DILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        38 t~~Q~~~i~~~~~g~--~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .+.|.+.+..+....  -+++.+|||||||.+. ..+++.+.
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            577777777666543  4788999999999664 45666654

>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=96.10  E-value=0.026  Score=38.08  Aligned_cols=72  Identities=11%  Similarity=0.117  Sum_probs=52.6

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      ..++||.|+++.-+..+.+.+++.     +..+..++|+.+..+..+   .++++ .+++|+  +....+++.++.++|.
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~~~Gid~~~~~~vi~  101 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFN  101 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCCSTTCCGGGCSEEEE
T ss_pred             CCeEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeeccccccchhhcccchhhhh
Confidence            447999999999988877666543     778899999988665544   34443 567777  5556788888888887


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      =+.
T Consensus       102 ~~~  104 (168)
T d1t5ia_         102 YDM  104 (168)
T ss_dssp             SSC
T ss_pred             hhc
Confidence            666

>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=96.03  E-value=0.058  Score=38.14  Aligned_cols=48  Identities=19%  Similarity=0.184  Sum_probs=31.0

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC---CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG---MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g---~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      +.|+++-.+.++.+.|.+.               +.++   +.+++.||+|+|||.... .++..+.
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~-~~~~~l~   59 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIAR-LLAKGLN   59 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHH-HHHHHHH
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHH-HHHHHhc
Confidence            4677776677776665432               2222   358999999999997544 4455544

>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=95.93  E-value=0.003  Score=42.36  Aligned_cols=26  Identities=19%  Similarity=0.410  Sum_probs=19.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      +++++.+|+|+|||. .+-.++..+..
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHH
Confidence            689999999999996 44455555543

>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=95.92  E-value=0.022  Score=38.46  Aligned_cols=94  Identities=11%  Similarity=0.157  Sum_probs=64.6

Q ss_pred             EEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHh
Q psy1539          55 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLK  131 (175)
Q Consensus        55 ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~  131 (175)
                      ++.-+....|. .++..++...    .+.++||.|++++-+..+.+.++..     ++.+..++|+.+.++..+   .++
T Consensus        12 ~v~v~~~~~K~-~~L~~ll~~~----~~~k~iiF~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2          12 FVAVEREEWKF-DTLCDLYDTL----TITQAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             EEEESSTTHHH-HHHHHHHHHH----TSSEEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEecChHHHH-HHHHHHHHhC----CCCceEEEeeeHHHHHHHHHHhhhc-----ccchhhhhhhhhHHHHHHHHHHHh
Confidence            34444555664 3344455442    3458999999999998877766644     677888999988665544   334


Q ss_pred             cC-CCeEEE--eecCccCCCCceEEEEeCC
Q psy1539         132 TH-NPQIVG--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       132 ~~-~~iiv~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      ++ .+++|+  +....+++++++++|.=++
T Consensus        82 ~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~  111 (168)
T d2j0sa2          82 SGASRVLISTDVWARGLDVPQVSLIINYDL  111 (168)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSC
T ss_pred             cCCccEEeccchhcccccccCcceEEEecC
Confidence            44 578888  6777899999999886554

>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=95.91  E-value=0.023  Score=40.05  Aligned_cols=79  Identities=20%  Similarity=0.162  Sum_probs=44.3

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec-C-HHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH-
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-T-RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL-  130 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l-  130 (175)
                      +++.+|||+|||.+..= +..++..  .+.++.+++- | |.=+   .++++.+.+.. ++.+.....+.+.....+.. 
T Consensus        12 i~lvGptGvGKTTTiAK-LA~~~~~--~g~kV~lit~Dt~R~gA---~eQL~~~a~~l-~v~~~~~~~~~d~~~~l~~~~   84 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGK-LARQFEQ--QGKSVMLAAGDTFRAAA---VEQLQVWGQRN-NIPVIAQHTGADSASVIFDAI   84 (211)
T ss_dssp             EEEECCTTSCHHHHHHH-HHHHHHT--TTCCEEEECCCTTCHHH---HHHHHHHHHHT-TCCEECCSTTCCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH-HHHHHHH--CCCcEEEEecccccccc---hhhhhhhhhhc-CCcccccccCCCHHHHHHHHH
Confidence            55799999999976431 2223332  2334555553 3 5444   34677777776 77776555555544333221 


Q ss_pred             ----hcCCCeEEE
Q psy1539         131 ----KTHNPQIVG  139 (175)
Q Consensus       131 ----~~~~~iiv~  139 (175)
                          .++.++|+.
T Consensus        85 ~~a~~~~~d~ilI   97 (211)
T d2qy9a2          85 QAAKARNIDVLIA   97 (211)
T ss_dssp             HHHHHTTCSEEEE
T ss_pred             HHHHHcCCCEEEe
Confidence                235666665

>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=95.50  E-value=0.048  Score=36.06  Aligned_cols=72  Identities=15%  Similarity=0.289  Sum_probs=48.2

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH---HHhcC-CCeEEE--eecCccCCCCceEEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YLKTH-NPQIVG--LVNYETNLSGVVVNVM  155 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~---~l~~~-~~iiv~--l~~~~~~~~~~~~lVl  155 (175)
                      +.++||.|++++-+.++.+.+++.     ++.+..++|+.+..+..+   .++++ ..++|+  .....+++.+++++|.
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~~Vi~  102 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVIN  102 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEEEE
T ss_pred             CCCEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehhHHhhhhhhccCcEEEE
Confidence            347999999999998877776643     778899999987655544   33344 467776  2333556666666655


Q ss_pred             eCC
Q psy1539         156 DVR  158 (175)
Q Consensus       156 DEa  158 (175)
                      =+.
T Consensus       103 ~d~  105 (155)
T d1hv8a2         103 YHL  105 (155)
T ss_dssp             SSC
T ss_pred             ecC
Confidence            433

>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=95.35  E-value=0.033  Score=39.20  Aligned_cols=62  Identities=15%  Similarity=0.112  Sum_probs=28.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe-cC-HHHHHHHHHHHHHHHhhCCCeEEEEEECCCc
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC-HT-RELAFQISKEYERFSKYMSNIKVGVFFGGLP  122 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~-Pt-~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~  122 (175)
                      +++.+|||+|||.+.. =+..++.. . +.++.+++ -| |.=+.   ++++.+.+.. ++.+.......+
T Consensus        15 i~lvGptGvGKTTTiA-KLA~~~~~-~-g~kV~lit~Dt~R~ga~---eQL~~~a~~l-~v~~~~~~~~~~   78 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAG-KLAYFYKK-K-GFKVGLVGADVYRPAAL---EQLQQLGQQI-GVPVYGEPGEKD   78 (211)
T ss_dssp             EEEECSCCC----HHH-HHHHHHHH-T-TCCEEEEECCCSSHHHH---HHHHHHHHHH-TCCEECCTTCCC
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHHH-C-CCceEEEEeeccccchh---HHHHHhcccc-Ccceeecccchh
Confidence            5568999999997643 11223332 2 22444444 33 54443   3455555555 666554433333

>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=95.21  E-value=0.036  Score=38.83  Aligned_cols=82  Identities=15%  Similarity=0.035  Sum_probs=44.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec--CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH--TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  128 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~  128 (175)
                      ++-+++.+|||+|||.+..= +..++..  .+.++.+++-  .|.=+.+   +++.+.+.. ++.+.....+.+......
T Consensus         6 ~~vi~lvGptGvGKTTTiaK-LA~~~~~--~g~kV~lit~Dt~R~gA~e---QL~~~a~~l-~i~~~~~~~~~d~~~~~~   78 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAK-LGRYYQN--LGKKVMFCAGDTFRAAGGT---QLSEWGKRL-SIPVIQGPEGTDPAALAY   78 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHH-HHHHHHT--TTCCEEEECCCCSSTTHHH---HHHHHHHHH-TCCEECCCTTCCHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHH-HHHHHHH--CCCcEEEEEeccccccchh---hHhhccccc-CceEEeccCCccHHHHHH
Confidence            35577899999999976431 1223332  2335555552  3666644   455555555 666655444444333322


Q ss_pred             -----HHhcCCCeEEE
Q psy1539         129 -----YLKTHNPQIVG  139 (175)
Q Consensus       129 -----~l~~~~~iiv~  139 (175)
                           .-.++.++|+.
T Consensus        79 ~~~~~~~~~~~d~ilI   94 (207)
T d1okkd2          79 DAVQAMKARGYDLLFV   94 (207)
T ss_dssp             HHHHHHHHHTCSEEEE
T ss_pred             HHHHHHHHCCCCEEEc
Confidence                 12245677776

>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=95.18  E-value=0.03  Score=43.37  Aligned_cols=66  Identities=23%  Similarity=0.264  Sum_probs=46.1

Q ss_pred             CCcHHHHHhHHHHh----cCC-cEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          36 EQTSFQHECIPQAV----LGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        36 ~~t~~Q~~~i~~~~----~g~-~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      .|+.-|-+||..+.    +|. ...+.+.+||+|++... .+.....     ..+|||+|+...|.++++.++.+..
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~~-----rp~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA-KVIEALG-----RPALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHT-----CCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHH-HHHHHhC-----CCEEEEeCCHHHHHHHHHHHHHhcC
Confidence            44556666666544    454 57899999999985322 2222221     1489999999999999999998864

>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=95.06  E-value=0.065  Score=37.05  Aligned_cols=59  Identities=19%  Similarity=0.082  Sum_probs=34.6

Q ss_pred             HHHhHHHHhc---CCcEEEEcCCCChHHHHHHHHHHHhhhc-CCCCeEEEEEecCHH--HHHHHHH
Q psy1539          41 QHECIPQAVL---GMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRE--LAFQISK  100 (175)
Q Consensus        41 Q~~~i~~~~~---g~~~ii~a~TGsGKT~~~~~~~l~~l~~-~~~~~~~lil~Pt~~--L~~q~~~  100 (175)
                      |.+.+..+.+   +.++++.+|.|+|||..... +.+.+.. ..+.+-.+++.|...  -+.|+.+
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~-l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~   66 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLE-LPEYVEKFPPKASDVLEIDPEGENIGIDDIRT   66 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHH-HHHHHHTSCCCTTTEEEECCSSSCBCHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHH-HHHHHhccccCCCCEEEEeCCcCCCCHHHHHH
Confidence            4555555543   47899999999999965432 3333332 223445777777422  2445444

>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=94.83  E-value=0.045  Score=38.32  Aligned_cols=66  Identities=14%  Similarity=0.087  Sum_probs=37.1

Q ss_pred             CCc-EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec--CHHHHHHHHHHHHHHHhhCCCeEEEEEECCCch
Q psy1539          51 GMD-ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH--TRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  123 (175)
Q Consensus        51 g~~-~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~  123 (175)
                      .++ +++.+|||+|||.+..= +..++..  ++.++.+++.  .|.=+.+   +++.+.+.. ++.+.......+.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaK-LA~~~~~--~g~kV~lit~Dt~R~gA~e---QL~~~a~~l-~v~~~~~~~~~~~   77 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAK-LALYYKG--KGRRPLLVAADTQRPAARE---QLRLLGEKV-GVPVLEVMDGESP   77 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHH-HHHHHHH--TTCCEEEEECCSSCHHHHH---HHHHHHHHH-TCCEEECCTTCCH
T ss_pred             CCcEEEEECCCCCCHHHHHHH-HHHHHHH--CCCcEEEEecccccchHHH---HHHHHHHhc-CCccccccccchh
Confidence            345 45699999999976432 1222222  2335555553  4666644   455555555 6766665555443

>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=94.50  E-value=0.008  Score=47.22  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+|+++.+|||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            369999999999999744

>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=94.37  E-value=0.061  Score=37.94  Aligned_cols=25  Identities=16%  Similarity=0.173  Sum_probs=18.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      .++++.||+|+|||.+. -.++..+.
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l~   68 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELYK   68 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHHT
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHHh
Confidence            68999999999999654 33444443

>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=94.00  E-value=0.024  Score=43.51  Aligned_cols=46  Identities=11%  Similarity=0.168  Sum_probs=28.7

Q ss_pred             HHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHH
Q psy1539          46 PQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL   94 (175)
Q Consensus        46 ~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (175)
                      |.=...++++|.|+||||||.+. ..++..+..  .+..++|+=|.-++
T Consensus        45 ~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~--~g~~~iiiD~kge~   90 (433)
T d1e9ra_          45 PRDAEPRHLLVNGATGTGKSVLL-RELAYTGLL--RGDRMVIVDPNGDM   90 (433)
T ss_dssp             CGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHH--TTCEEEEEEETTHH
T ss_pred             CCCcccceEEEEeCCCCcHHHHH-HHHHHHHHh--CCCCEEEEeCChhH
Confidence            33345689999999999999764 333433332  23345666666554

>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=93.98  E-value=0.013  Score=38.14  Aligned_cols=18  Identities=22%  Similarity=0.309  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+++++.||+|||||...
T Consensus         2 ~k~I~l~G~~GsGKSTva   19 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIG   19 (169)
T ss_dssp             CCCEEEECCTTSCHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            478999999999999754

>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=93.96  E-value=0.034  Score=41.22  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      .+++++.+|||+|||..+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            589999999999999765

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, 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: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.85  E-value=0.05  Score=38.79  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=19.1

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ..|.-+.+.+|+|+|||..  +-++.-+
T Consensus        24 ~~Gei~~liGpsGsGKSTL--l~~i~Gl   49 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTL--LRMIAGL   49 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHH--HHHHHTS
T ss_pred             cCCCEEEEECCCCChHHHH--HHHHhcC
Confidence            3678899999999999963  3344433

>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=93.82  E-value=0.015  Score=38.54  Aligned_cols=19  Identities=37%  Similarity=0.629  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.++++.||+|||||...
T Consensus         4 k~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            3578999999999999754

>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=93.68  E-value=0.088  Score=34.24  Aligned_cols=64  Identities=11%  Similarity=0.210  Sum_probs=46.8

Q ss_pred             CeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--eecCccCCCCceEEE
Q psy1539          82 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--LVNYETNLSGVVVNV  154 (175)
Q Consensus        82 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--l~~~~~~~~~~~~lV  154 (175)
                      +.++||.|+|+.-|+++.+.+++.     ++++..++|+.+.++..   ....+++|+  +....++ .+++++|
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~-----G~~~~~~H~~~~~~~~~---~~~~~vlvaTd~~~~GiD-~~v~~Vi  100 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVAL-----GINAVAYYRGLDVSVIP---TNGDVVVVATDALMTGFT-GDFDSVI  100 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHH-----TCEEEEECTTCCSCCCT---TSSCEEEEESSSSCSSSC-CCBSEEE
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhcc-----ccchhhhhccchhhhhh---hhhcceeehhHHHHhccc-cccceEE
Confidence            347999999999999988887655     78899999998754321   234567777  5555677 6787765

>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=93.64  E-value=0.016  Score=40.88  Aligned_cols=18  Identities=28%  Similarity=0.425  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      .++++.||+|+|||...-
T Consensus        36 ~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            589999999999997553

>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=93.60  E-value=0.039  Score=36.25  Aligned_cols=33  Identities=21%  Similarity=0.218  Sum_probs=21.8

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +.++++.|||||. ++-.++.++..  ++.++.++.
T Consensus         5 i~itG~~GSGKTT-L~~~L~~~l~~--~g~~v~v~~   37 (170)
T d1np6a_           5 LAFAAWSGTGKTT-LLKKLIPALCA--RGIRPGLIK   37 (170)
T ss_dssp             EEEECCTTSCHHH-HHHHHHHHHHH--TTCCEEEEE
T ss_pred             EEEEcCCCCCHHH-HHHHHHHHHHH--CCCeEEEec
Confidence            6789999999994 45555665554  344455554

>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=93.34  E-value=0.02  Score=37.75  Aligned_cols=18  Identities=33%  Similarity=0.383  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      -.++++.||+|||||...
T Consensus         4 ~~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCCEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            367899999999999643

>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=93.28  E-value=0.017  Score=38.40  Aligned_cols=17  Identities=12%  Similarity=0.200  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      -+.+++.||+|+|||..
T Consensus         7 ~K~I~i~G~~GsGKTTl   23 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVL   23 (192)
T ss_dssp             CEEEEEECCTTSHHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            36899999999999964

>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=93.25  E-value=0.02  Score=37.26  Aligned_cols=14  Identities=36%  Similarity=0.435  Sum_probs=12.4

Q ss_pred             EEEEcCCCChHHHH
Q psy1539          54 ILCQAKSGMGKTAV   67 (175)
Q Consensus        54 ~ii~a~TGsGKT~~   67 (175)
                      ++++|++|||||..
T Consensus         5 Iii~G~pGsGKTTl   18 (152)
T d1ly1a_           5 ILTIGCPGSGKSTW   18 (152)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            67899999999974

>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=93.21  E-value=0.016  Score=38.46  Aligned_cols=19  Identities=26%  Similarity=0.372  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+-+++.+|+|||||...
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            5677899999999999743

>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=93.10  E-value=0.022  Score=40.25  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=17.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .++++.||+|+|||...- .+...+
T Consensus        36 ~~~Ll~GPpG~GKTtla~-~la~~~   59 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAH-VIAHEL   59 (239)
T ss_dssp             CCEEEECCTTSCHHHHHH-HHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHh
Confidence            689999999999996543 344433

>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=92.86  E-value=0.16  Score=38.78  Aligned_cols=53  Identities=21%  Similarity=0.171  Sum_probs=36.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCC------C---CeEEEEEecCHHHHHHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTD------S---NVYVLVMCHTRELAFQISKEYER  104 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~------~---~~~~lil~Pt~~L~~q~~~~~~~  104 (175)
                      -.++|.|+-|||||.+..-=++..+....      +   --+.|+|+=|+.=|.+..+.+..
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            45789999999999876655555543211      1   12588999998877776666544

>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=92.85  E-value=0.029  Score=39.93  Aligned_cols=17  Identities=29%  Similarity=0.417  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.||+|+|||...
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            45999999999999643

>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=92.81  E-value=0.025  Score=37.21  Aligned_cols=16  Identities=19%  Similarity=0.362  Sum_probs=13.5

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.||+|||||...
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999754

>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=92.71  E-value=0.056  Score=37.67  Aligned_cols=18  Identities=22%  Similarity=0.390  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      .++++.||+|+|||.+.-
T Consensus        37 ~~~ll~Gp~G~GKTt~a~   54 (224)
T d1sxjb2          37 PHMIISGMPGIGKTTSVH   54 (224)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCchhhHH
Confidence            469999999999997643

>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=92.61  E-value=0.018  Score=38.23  Aligned_cols=21  Identities=29%  Similarity=0.359  Sum_probs=17.4

Q ss_pred             HhcCCcEEEEcCCCChHHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      -.+|.-+++.|++|||||...
T Consensus         3 ~~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           3 ATQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TTCCEEEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            346778999999999999754

>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=92.55  E-value=0.039  Score=39.62  Aligned_cols=54  Identities=13%  Similarity=0.046  Sum_probs=30.6

Q ss_pred             cccccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHH--hcCCcEEEEcCCCChHHHHH
Q psy1539          12 TVKVLSSRNRREKEDRIGESQPFREQTSFQHECIPQA--VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        12 ~~~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~--~~g~~~ii~a~TGsGKT~~~   68 (175)
                      |-..|++++-..+..+.+.+.  -.+ -.+.+.+...  ..-+.+++.+|+|+|||...
T Consensus         4 p~~~~~di~G~~~~k~~l~~~--i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEI--VEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHH--HHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHH--HHH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            346788887677766666542  111 0011111111  11267999999999999653

>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=92.39  E-value=0.02  Score=41.43  Aligned_cols=56  Identities=16%  Similarity=0.163  Sum_probs=32.0

Q ss_pred             cccccccccCCCCHHHHHHHhhC--CCCCCcHHHHHhHHHHhcCCcEEEEcCCCChHHHHH
Q psy1539          10 GVTVKVLSSRNRREKEDRIGESQ--PFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        10 ~~~~~~~~~~~l~~~l~~~l~~~--g~~~~t~~Q~~~i~~~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+..+|++.+-.+...+.+.+.  -+..+..+|..   .....+.+++.+|+|+|||...
T Consensus         5 ~~~~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~---g~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           5 DQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CSSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCCCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHc---CCCCCCeEEeeCCCCCCccHHH
Confidence            34445678887777777666542  01122222221   1112378999999999999753

>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=92.25  E-value=0.087  Score=36.54  Aligned_cols=40  Identities=18%  Similarity=0.145  Sum_probs=25.4

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHHHHhHHHHhcC--CcEEEEcCCCChHHHHH
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQHECIPQAVLG--MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q~~~i~~~~~g--~~~ii~a~TGsGKT~~~   68 (175)
                      +.|+++--++++.+.|++.               +.++  .++++.||+|+|||...
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i~~~~~~~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------VDEGKLPHLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------HHTTCCCCEEEECSSSSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCChhHHH
Confidence            4555655566665555432               1223  36999999999999543

>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=92.14  E-value=0.15  Score=37.51  Aligned_cols=65  Identities=11%  Similarity=-0.056  Sum_probs=40.5

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHHhcCCCeEEE--eecCccCCCCceEE
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--LVNYETNLSGVVVN  153 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l~~~~~iiv~--l~~~~~~~~~~~~l  153 (175)
                      .+++++||+..-++++.+.+++.     +.+|..++|.....+..+......++||+  +....+.+ ++.+|
T Consensus        37 g~~~~F~~s~~~~~~~a~~L~~~-----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~~~~~~~~~-~~~~v  103 (299)
T d1yksa2          37 RPTAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANL-CVERV  103 (299)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSCC--------CCCSEEEESSSTTCCTTC-CCSEE
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhc-----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEechhhhceec-CceEE
Confidence            37999999999998887777653     66788899987755544433334567777  44445555 34444

>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=92.12  E-value=0.14  Score=35.61  Aligned_cols=44  Identities=18%  Similarity=0.211  Sum_probs=27.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS   99 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~   99 (175)
                      ..+++.||+|+|||- .+.++.+.....  +..++++ +..++..+..
T Consensus        37 n~l~l~G~~G~GKTH-Ll~A~~~~~~~~--~~~~~~~-~~~~~~~~~~   80 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTH-LLQAAGNEAKKR--GYRVIYS-SADDFAQAMV   80 (213)
T ss_dssp             SSEEEECSSSSSHHH-HHHHHHHHHHHT--TCCEEEE-EHHHHHHHHH
T ss_pred             CcEEEECCCCCcHHH-HHHHHHHHhccC--ccceEEe-chHHHHHHHH
Confidence            348999999999994 445666655542  3345444 5555554443

>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=91.87  E-value=0.037  Score=38.72  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.||+|+|||.+.
T Consensus        46 ~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            57999999999999654

>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=91.79  E-value=0.042  Score=36.45  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +|+++.+++|+|||...
T Consensus         1 k~I~liG~~GsGKsTi~   17 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLA   17 (161)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57999999999999754

>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=91.72  E-value=0.1  Score=37.32  Aligned_cols=41  Identities=27%  Similarity=0.157  Sum_probs=26.6

Q ss_pred             HhcCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          48 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      +..|.=+++.|+||+|||...+--+.+....  .+.++++++.
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~--~g~~v~~~s~   72 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAML   72 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHT--SCCCEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhh--cccceeEeee
Confidence            3456789999999999995444333332222  3446788874

>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=91.65  E-value=0.04  Score=38.96  Aligned_cols=59  Identities=10%  Similarity=-0.035  Sum_probs=33.2

Q ss_pred             cccccCCCCHHHHHHHhhCCCCCCcHHH-HHhHHH-----HhcCCcEEEEcCCCChHHHHHHHHHHHh
Q psy1539          14 KVLSSRNRREKEDRIGESQPFREQTSFQ-HECIPQ-----AVLGMDILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        14 ~~~~~~~l~~~l~~~l~~~g~~~~t~~Q-~~~i~~-----~~~g~~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      ++|+++-.++...+.|.+.  -.-.+.. ...++.     ....+.+++.||+|+|||.+. -.+++.
T Consensus        11 ~~~~dlig~~~~~~~L~~~--l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a-~~la~~   75 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNW--LANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA-HLVAQE   75 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHH--HHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH-HHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH--HHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH-HHHHHH
Confidence            4688888888888777652  1101100 111100     011257999999999999654 334443

>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=91.47  E-value=0.12  Score=39.23  Aligned_cols=43  Identities=19%  Similarity=0.118  Sum_probs=27.4

Q ss_pred             CCCCCcHHHHHhHHHHhcC----CcEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          33 PFREQTSFQHECIPQAVLG----MDILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        33 g~~~~t~~Q~~~i~~~~~g----~~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      ++......-.+++..++.|    +.+++.+|+|+|||.. ..+++..+
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~-~~~~~~~~  178 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTL-AAALLELC  178 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHH-HHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHH-HHHHHHHc
Confidence            4544444444555555554    6899999999999954 44555544

>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=91.18  E-value=0.09  Score=36.56  Aligned_cols=16  Identities=31%  Similarity=0.453  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      .++++.||+|+|||..
T Consensus        34 ~~lll~Gp~G~GKTtl   49 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTST   49 (237)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCChHHH
Confidence            4699999999999954

>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=91.07  E-value=0.041  Score=39.44  Aligned_cols=17  Identities=29%  Similarity=0.415  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.+|+|+|||...
T Consensus        41 ~~vLL~GppGtGKT~la   57 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46999999999999654

>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=91.06  E-value=0.14  Score=38.76  Aligned_cols=17  Identities=35%  Similarity=0.440  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .|++..+|||.|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            68999999999999654

>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=90.98  E-value=0.058  Score=35.44  Aligned_cols=19  Identities=21%  Similarity=0.268  Sum_probs=15.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+=+++.|++|||||...
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456889999999999654

>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=90.98  E-value=0.15  Score=35.42  Aligned_cols=37  Identities=16%  Similarity=0.158  Sum_probs=24.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      |.-+++.+++|+|||...+--+.+...   ++..+++++-
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~---~~~~~~~is~   62 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACA---NKERAILFAY   62 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHT---TTCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHH---hccccceeec
Confidence            478999999999999655443333322   3445667664

>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=90.55  E-value=0.06  Score=35.38  Aligned_cols=18  Identities=33%  Similarity=0.252  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVFV   69 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~~   69 (175)
                      +=+++.|++|||||...-
T Consensus         7 ~iivl~G~~GsGKsT~a~   24 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVAS   24 (171)
T ss_dssp             EEEEEECSTTSCHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            347889999999997543

>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=90.48  E-value=0.038  Score=37.21  Aligned_cols=18  Identities=39%  Similarity=0.493  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      |.-+++++++|||||...
T Consensus        19 g~vI~L~G~pGSGKTTiA   36 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVS   36 (195)
T ss_dssp             CEEEEEESSCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456779999999999754

>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=90.26  E-value=0.2  Score=32.87  Aligned_cols=16  Identities=19%  Similarity=0.351  Sum_probs=13.5

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      +-+++.|++|||||..
T Consensus         2 kiI~i~G~~GsGKsT~   17 (190)
T d1khta_           2 KVVVVTGVPGVGSTTS   17 (190)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4578999999999964

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.90  E-value=0.21  Score=32.79  Aligned_cols=23  Identities=13%  Similarity=0.010  Sum_probs=16.2

Q ss_pred             EEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          55 LCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        55 ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      -|.++.|||||. ++--++..+..
T Consensus         5 ~I~G~~gSGKTT-li~~l~~~L~~   27 (165)
T d1xjca_           5 QVVGYKHSGKTT-LMEKWVAAAVR   27 (165)
T ss_dssp             EEECCTTSSHHH-HHHHHHHHHHH
T ss_pred             EEEeCCCCCHHH-HHHHHHHHHHh
Confidence            489999999995 44455555554

>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=89.87  E-value=0.16  Score=34.75  Aligned_cols=39  Identities=18%  Similarity=0.178  Sum_probs=23.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEec
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH   90 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~P   90 (175)
                      .|.-+++.+++|+|||...+--+.+....  ++..++++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~--~~~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIE--FDEPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH--HCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCCcccccc
Confidence            35889999999999996543323322222  2224666654

>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=89.80  E-value=0.086  Score=35.57  Aligned_cols=19  Identities=21%  Similarity=0.272  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|..+++.+|+|||||...
T Consensus         2 ~~~riil~G~pGSGKsT~a   20 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQA   20 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CccEEEEECCCCCCHHHHH
Confidence            3667889999999999754

>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=89.69  E-value=1  Score=32.04  Aligned_cols=83  Identities=17%  Similarity=0.127  Sum_probs=53.6

Q ss_pred             HHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCch--------H---HhHHHHhc-CCCeEE
Q psy1539          71 ATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI--------Q---KDEEYLKT-HNPQIV  138 (175)
Q Consensus        71 ~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~--------~---~~~~~l~~-~~~iiv  138 (175)
                      -++..+.....+.++||.+.+++-+..+.+.+.+-     ++++..+.|....        +   ...+.+++ .+.++|
T Consensus       150 ~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv  224 (286)
T d1wp9a2         150 EIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLV  224 (286)
T ss_dssp             HHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEE
T ss_pred             HHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHc-----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEE
Confidence            34433333345568999999999998877766542     6777777765332        1   22334554 357888


Q ss_pred             E--eecCccCCCCceEEEEeCC
Q psy1539         139 G--LVNYETNLSGVVVNVMDVR  158 (175)
Q Consensus       139 ~--l~~~~~~~~~~~~lVlDEa  158 (175)
                      +  .....+++++++++|.=+.
T Consensus       225 ~T~~~~~Gld~~~~~~Vi~~d~  246 (286)
T d1wp9a2         225 ATSVGEEGLDVPEVDLVVFYEP  246 (286)
T ss_dssp             ECGGGGGGGGSTTCCEEEESSC
T ss_pred             EccceeccccCCCCCEEEEeCC
Confidence            7  5555889999999987444

>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=89.67  E-value=0.078  Score=35.07  Aligned_cols=23  Identities=30%  Similarity=0.588  Sum_probs=16.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHhh
Q psy1539          53 DILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      .+++.+|+|+|||.. +-.++..+
T Consensus         2 ki~I~G~~G~GKSTL-l~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTL-VKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHH-HHHHHHHH
T ss_pred             EEEEECCCCcHHHHH-HHHHHhcC
Confidence            478999999999963 33444444

>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=89.63  E-value=0.1  Score=35.06  Aligned_cols=22  Identities=18%  Similarity=0.037  Sum_probs=17.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLAT   72 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~   72 (175)
                      |+-+++.+|+|+|||...+--+
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la   44 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLA   44 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHH
Confidence            5789999999999996544333

>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=89.60  E-value=0.036  Score=38.80  Aligned_cols=80  Identities=15%  Similarity=0.175  Sum_probs=51.8

Q ss_pred             CCeEEEEEecCHHHHHH-----HHHHHHHHHh-hCCCeEEEEEECCCchHH---hHHHHhcC-CCeEEE--eecCccCCC
Q psy1539          81 SNVYVLVMCHTRELAFQ-----ISKEYERFSK-YMSNIKVGVFFGGLPIQK---DEEYLKTH-NPQIVG--LVNYETNLS  148 (175)
Q Consensus        81 ~~~~~lil~Pt~~L~~q-----~~~~~~~~~~-~~~~i~v~~~~g~~~~~~---~~~~l~~~-~~iiv~--l~~~~~~~~  148 (175)
                      .+.|+.++||..+-...     ..+....+.+ .+|+.++..++|..+.++   .+..++++ .+++|+  +....++.+
T Consensus        28 ~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip  107 (206)
T d1gm5a4          28 RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVP  107 (206)
T ss_dssp             TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCT
T ss_pred             cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhcccccc
Confidence            45588999998654332     2233444443 347889999999976443   34555555 688888  777799999


Q ss_pred             CceEEEEeCCCC
Q psy1539         149 GVVVNVMDVRSG  160 (175)
Q Consensus       149 ~~~~lVlDEad~  160 (175)
                      +..++|+..|+.
T Consensus       108 ~a~~iii~~a~~  119 (206)
T d1gm5a4         108 RANVMVIENPER  119 (206)
T ss_dssp             TCCEEEBCSCSS
T ss_pred             CCcEEEEEccCC
Confidence            999999999964

>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=89.39  E-value=0.085  Score=35.45  Aligned_cols=16  Identities=19%  Similarity=0.304  Sum_probs=13.3

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      .=++++|++|||||..
T Consensus        15 ~liil~G~pGsGKST~   30 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTF   30 (172)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             EEEEEECCCCCCHHHH
Confidence            3478899999999964

>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=89.36  E-value=0.093  Score=35.53  Aligned_cols=16  Identities=31%  Similarity=0.507  Sum_probs=13.9

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      +-++++||+|+|||..
T Consensus         2 rpIvl~GpsG~GK~tl   17 (186)
T d1gkya_           2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5689999999999963

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.36  E-value=0.49  Score=34.13  Aligned_cols=96  Identities=13%  Similarity=0.004  Sum_probs=51.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHHHHHHHHHHHHHHHhhCCCeEEEEEECCCchHHhHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  130 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~i~v~~~~g~~~~~~~~~~l  130 (175)
                      |+=+.+.+|+|+|||...+..+.+...   .+..++++-.-..+..+   .++++.-...+  + +++--.+..+..+.+
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~---~g~~~vyIDtE~~~~~e---~a~~~GvD~d~--i-l~~~~~~~E~~~~~~  130 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQA---AGGVAAFIDAEHALDPD---YAKKLGVDTDS--L-LVSQPDTGEQALEIA  130 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHH---TTCEEEEEESSCCCCHH---HHHHHTCCGGG--C-EEECCSSHHHHHHHH
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhc---CCCEEEEEECCccCCHH---HHHHhCCCHHH--e-EEecCCCHHHHHHHH
Confidence            467889999999999776555544332   34477777654444333   34444332212  2 222223333333322


Q ss_pred             hcCCCeEEEeecCccCCCCceEEEEeCCCCCC-HHHH
Q psy1539         131 KTHNPQIVGLVNYETNLSGVVVNVMDVRSGGW-WLDL  166 (175)
Q Consensus       131 ~~~~~iiv~l~~~~~~~~~~~~lVlDEad~~f-~~~v  166 (175)
                      ..           ...-..++++|+|-+...+ +.++
T Consensus       131 ~~-----------l~~~~~~~liIiDSi~al~~~~E~  156 (269)
T d1mo6a1         131 DM-----------LIRSGALDIVVIDSVAALVPRAEL  156 (269)
T ss_dssp             HH-----------HHHTTCEEEEEEECSTTCCCHHHH
T ss_pred             HH-----------HHhcCCCCEEEEecccccccHHHh
Confidence            21           1112467889999886555 4443

>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=89.24  E-value=0.098  Score=34.72  Aligned_cols=17  Identities=29%  Similarity=0.256  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++.+++|||||...
T Consensus         3 ~~Iil~G~~GsGKSTia   19 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVG   19 (170)
T ss_dssp             CCEEEESCTTSSHHHHH
T ss_pred             CCEEEECCCCCCHHHHH
Confidence            57899999999999754

>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=89.14  E-value=0.089  Score=37.73  Aligned_cols=16  Identities=38%  Similarity=0.495  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      +.+++.+|+|+|||..
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            6899999999999974

>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=89.05  E-value=0.17  Score=34.94  Aligned_cols=21  Identities=14%  Similarity=-0.018  Sum_probs=16.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVFVL   70 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~   70 (175)
                      .|+-+++.+++|+|||...+-
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq   53 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHT   53 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHH
Confidence            357899999999999965443

>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=89.03  E-value=0.23  Score=34.48  Aligned_cols=24  Identities=17%  Similarity=0.018  Sum_probs=17.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      |+-+++.+|+|+|||...+--+.+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~   59 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVM   59 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHH
Confidence            477999999999999655443333

>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=88.93  E-value=0.053  Score=38.52  Aligned_cols=15  Identities=27%  Similarity=0.375  Sum_probs=12.1

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      +++.||+|+|||.+.
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999654

>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=88.92  E-value=0.11  Score=36.08  Aligned_cols=19  Identities=32%  Similarity=0.489  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      +|+=++++||+|+|||...
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            4777899999999999643

>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=88.80  E-value=0.1  Score=34.66  Aligned_cols=16  Identities=19%  Similarity=0.304  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      ++++.||+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~a   17 (182)
T d1zina1           2 NLVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999754

>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=88.48  E-value=0.12  Score=35.20  Aligned_cols=16  Identities=25%  Similarity=0.478  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCChHHHH
Q psy1539          52 MDILCQAKSGMGKTAV   67 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~   67 (175)
                      +-+++.||+|+|||..
T Consensus         1 rpIvl~GPsGsGK~tl   16 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTL   16 (190)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            3589999999999974

>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=88.46  E-value=0.12  Score=34.67  Aligned_cols=17  Identities=29%  Similarity=0.493  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      |+=+++.+|+|+|||..
T Consensus         2 G~iivl~GpsG~GK~tl   18 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTV   18 (182)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            66789999999999974

>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=88.41  E-value=0.12  Score=34.91  Aligned_cols=17  Identities=12%  Similarity=0.294  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ..+++.||+|||||...
T Consensus         4 m~I~i~GppGsGKsT~a   20 (189)
T d1zaka1           4 LKVMISGAPASGKGTQC   20 (189)
T ss_dssp             CCEEEEESTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            35899999999998754

>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=88.36  E-value=0.19  Score=37.17  Aligned_cols=24  Identities=21%  Similarity=0.439  Sum_probs=18.6

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ++.+++|.|  ++..++||||||.+.
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            445567864  678899999999875

>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=88.32  E-value=0.12  Score=34.61  Aligned_cols=17  Identities=29%  Similarity=0.370  Sum_probs=14.3

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy1539          53 DILCQAKSGMGKTAVFV   69 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~~   69 (175)
                      ++++.||+|||||...-
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            68999999999997543

>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=88.03  E-value=0.076  Score=39.40  Aligned_cols=19  Identities=21%  Similarity=0.197  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .+.++++.+++|+|||...
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            4579999999999999753

>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=87.84  E-value=0.13  Score=34.35  Aligned_cols=16  Identities=19%  Similarity=0.115  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.+|+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~~   17 (179)
T d1e4va1           2 RIILLGAPVAGKGTQA   17 (179)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999754

>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=87.35  E-value=0.13  Score=34.67  Aligned_cols=16  Identities=19%  Similarity=0.264  Sum_probs=13.4

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.||+|||||...
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            4688999999999753

>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=87.29  E-value=0.15  Score=34.13  Aligned_cols=16  Identities=25%  Similarity=0.329  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      .+++.+|+|||||...
T Consensus         2 ~I~i~G~pGSGKsT~a   17 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999754

>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=87.16  E-value=0.24  Score=37.09  Aligned_cols=23  Identities=17%  Similarity=0.447  Sum_probs=17.8

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..|+||||||.+.
T Consensus        73 ~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          73 DDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHhhccCceeEEecccCCCCcceee
Confidence            44567866  677899999999764

>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=87.08  E-value=0.14  Score=34.20  Aligned_cols=17  Identities=35%  Similarity=0.407  Sum_probs=12.8

Q ss_pred             CCcEE-EEcCCCChHHHH
Q psy1539          51 GMDIL-CQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~i-i~a~TGsGKT~~   67 (175)
                      |+=++ |.|++|||||..
T Consensus        21 ~~~iIgI~G~~GSGKSTl   38 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTL   38 (198)
T ss_dssp             SSEEEEEEECTTSSHHHH
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            33344 899999999964

>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=87.03  E-value=0.2  Score=33.85  Aligned_cols=21  Identities=19%  Similarity=0.109  Sum_probs=17.0

Q ss_pred             HhcCCcEEEEcCCCChHHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~~   68 (175)
                      +.+++-+++.+|+|||||...
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            445677899999999999744

>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=86.98  E-value=0.13  Score=37.07  Aligned_cols=24  Identities=25%  Similarity=0.296  Sum_probs=17.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHh
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      .+.+++.||+|+|||... -.+...
T Consensus        41 ~~giLL~Gp~GtGKT~l~-~ala~~   64 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA-KAIANE   64 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH-HHHHHH
T ss_pred             CCeEEEECCCCCcchhHH-HHHHHH
Confidence            478999999999999643 334443

>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=86.98  E-value=0.15  Score=34.50  Aligned_cols=16  Identities=25%  Similarity=0.297  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      -+++.||+|||||...
T Consensus        10 iI~i~GppGSGKsT~a   25 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQC   25 (196)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999998654

>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=86.38  E-value=2.3  Score=28.09  Aligned_cols=15  Identities=27%  Similarity=0.255  Sum_probs=12.7

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      ++++|.+|||||..+
T Consensus         5 i~l~GlpgsGKSTla   19 (213)
T d1bifa1           5 IVMVGLPARGKTYIS   19 (213)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578899999999754

>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=86.13  E-value=0.29  Score=36.80  Aligned_cols=23  Identities=22%  Similarity=0.312  Sum_probs=17.3

Q ss_pred             HHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          46 PQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        46 ~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ..+++|.|  ++..+.||||||.+.
T Consensus       107 ~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         107 QTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHhccCceEEeeccCCCCCceee
Confidence            34567865  566689999999775

>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=85.80  E-value=0.21  Score=33.62  Aligned_cols=17  Identities=12%  Similarity=0.321  Sum_probs=14.4

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      +-++++||+|+||+...
T Consensus         4 k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            56899999999999643

>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=85.69  E-value=0.21  Score=32.75  Aligned_cols=17  Identities=18%  Similarity=0.196  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      .++++.++.|+|||...
T Consensus         2 p~IvliG~~G~GKSTig   18 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIG   18 (165)
T ss_dssp             CSEEEECSTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            46888899999999764

>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=85.57  E-value=0.19  Score=33.75  Aligned_cols=15  Identities=20%  Similarity=0.361  Sum_probs=13.0

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      +++.+|+|||||+..
T Consensus         4 I~i~GppGSGKsT~a   18 (194)
T d1teva_           4 VFVLGGPGAGKGTQC   18 (194)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999754

>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=85.53  E-value=0.31  Score=33.69  Aligned_cols=24  Identities=13%  Similarity=-0.112  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      |+-+++.+++|+|||...+.-+.+
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999765444433

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {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: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=85.51  E-value=0.52  Score=34.69  Aligned_cols=35  Identities=14%  Similarity=0.070  Sum_probs=19.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEe
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC   89 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~   89 (175)
                      +-|+|+.|||||...- .+...+.....++++.++.
T Consensus        83 IGIaG~sgSGKSTla~-~L~~lL~~~~~~~~v~~Is  117 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTAR-VLQALLSRWPEHRRVELIT  117 (308)
T ss_dssp             EEEEECTTSSHHHHHH-HHHHHHTTSTTCCCEEEEE
T ss_pred             EEEeCCCCCCCcHHHH-HHHHHHhhhcCCCceEEEe
Confidence            5589999999996432 2222222223445565554

>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=85.41  E-value=0.27  Score=37.05  Aligned_cols=24  Identities=33%  Similarity=0.528  Sum_probs=18.9

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      +..+++|.|  ++..++||||||.+.
T Consensus        67 v~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          67 VQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCceeeeccccCCCCccccc
Confidence            566678865  677889999999875

>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=85.25  E-value=0.29  Score=36.87  Aligned_cols=25  Identities=32%  Similarity=0.488  Sum_probs=19.3

Q ss_pred             hHHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          44 CIPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        44 ~i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      .++.+++|.|  ++..++||||||.+.
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            3456678865  677889999999774

>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=85.23  E-value=0.25  Score=34.04  Aligned_cols=28  Identities=21%  Similarity=0.076  Sum_probs=20.2

Q ss_pred             cCCCCceEEEEeCC----CCCCHHHHHHHHhh
Q psy1539         145 TNLSGVVVNVMDVR----SGGWWLDLEALILS  172 (175)
Q Consensus       145 ~~~~~~~~lVlDEa----d~~f~~~v~~il~~  172 (175)
                      ....+-+++++||-    |......+.+.|..
T Consensus       139 al~~~~~llllDEPt~gLD~~~~~~i~~~l~~  170 (200)
T d1sgwa_         139 TLLVNAEIYVLDDPVVAIDEDSKHKVLKSILE  170 (200)
T ss_dssp             HTTSCCSEEEEESTTTTSCTTTHHHHHHHHHH
T ss_pred             HHhcCCCEEEEcCcccccCHHHHHHHHHHHHH
Confidence            34578899999999    66666666655544

>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=85.15  E-value=0.36  Score=36.03  Aligned_cols=24  Identities=25%  Similarity=0.515  Sum_probs=18.3

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVF   68 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~   68 (175)
                      ++.+++|.|  ++..+.||||||.+.
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            344577855  677889999999875

>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=85.02  E-value=0.18  Score=35.85  Aligned_cols=18  Identities=33%  Similarity=0.333  Sum_probs=16.0

Q ss_pred             hcCCcEEEEcCCCChHHH
Q psy1539          49 VLGMDILCQAKSGMGKTA   66 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~   66 (175)
                      ..|.-+.+.+|+|||||.
T Consensus        27 ~~Ge~vaIvG~sGsGKST   44 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKST   44 (241)
T ss_dssp             ETTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            358899999999999996

>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=84.86  E-value=0.42  Score=33.84  Aligned_cols=20  Identities=30%  Similarity=0.424  Sum_probs=16.6

Q ss_pred             hcCCcEEEEcCCCChHHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~   68 (175)
                      ..+..+++.|++|+|||..+
T Consensus        21 ~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          21 CAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             TCCSCEEEECSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCcCHHHHH
Confidence            35689999999999999643

>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=84.85  E-value=0.25  Score=32.87  Aligned_cols=17  Identities=18%  Similarity=0.292  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy1539          52 MDILCQAKSGMGKTAVF   68 (175)
Q Consensus        52 ~~~ii~a~TGsGKT~~~   68 (175)
                      ..+++.+|+|||||...
T Consensus         3 mrIvl~G~pGSGKtT~a   19 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQA   19 (180)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45789999999999754

>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=84.73  E-value=0.22  Score=34.04  Aligned_cols=15  Identities=27%  Similarity=0.330  Sum_probs=11.7

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      +-|.|++|||||+..
T Consensus         5 IgI~G~~gSGKSTla   19 (213)
T d1uj2a_           5 IGVSGGTASGKSSVC   19 (213)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            347899999999643

>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=84.58  E-value=0.44  Score=32.16  Aligned_cols=34  Identities=18%  Similarity=0.142  Sum_probs=19.3

Q ss_pred             CcEEEEcC-CCChHHHHHHHHHHHhhhcCCCCeEEEEE
Q psy1539          52 MDILCQAK-SGMGKTAVFVLATLQQLETTDSNVYVLVM   88 (175)
Q Consensus        52 ~~~ii~a~-TGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (175)
                      |.++|++. ||.|||..-+ -+...+.+  .|.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~-~La~aLa~--~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASC-ALLQAAKA--AGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHH-HHHHHHHH--TTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHH-HHHHHHHH--CCCeEEEE
Confidence            45677776 7999997543 23333332  33455554

>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=84.57  E-value=0.22  Score=32.87  Aligned_cols=15  Identities=27%  Similarity=0.503  Sum_probs=12.3

Q ss_pred             EEEEcCCCChHHHHH
Q psy1539          54 ILCQAKSGMGKTAVF   68 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~   68 (175)
                      +++.|++|||||...
T Consensus         4 ivi~G~~GsGKTT~~   18 (194)
T d1nksa_           4 GIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567999999999643

>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=84.47  E-value=0.27  Score=33.26  Aligned_cols=18  Identities=22%  Similarity=0.180  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy1539          51 GMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~   68 (175)
                      ...+++.+|+|||||...
T Consensus         6 ~mrIiliG~PGSGKtT~a   23 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVS   23 (189)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceeEEEECCCCCCHHHHH
Confidence            357899999999999754

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

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: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=84.25  E-value=0.59  Score=32.07  Aligned_cols=22  Identities=23%  Similarity=0.262  Sum_probs=16.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHhh
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQQL   76 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~~l   76 (175)
                      +++.++.|||||. ++-.+++++
T Consensus         3 i~v~G~~GsGKTT-Ll~~ll~~~   24 (244)
T d1yrba1           3 VVFVGTAGSGKTT-LTGEFGRYL   24 (244)
T ss_dssp             EEEECSTTSSHHH-HHHHHHHHH
T ss_pred             EEEEcCCCCcHHH-HHHHHHHHH
Confidence            5789999999995 445555544

>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=84.12  E-value=0.4  Score=33.35  Aligned_cols=20  Identities=30%  Similarity=0.346  Sum_probs=14.1

Q ss_pred             EEEEcCCCChHHHHHHHHHHH
Q psy1539          54 ILCQAKSGMGKTAVFVLATLQ   74 (175)
Q Consensus        54 ~ii~a~TGsGKT~~~~~~~l~   74 (175)
                      .++.+.-|||||. ++--++.
T Consensus         6 ~iitGFLGaGKTT-ll~~lL~   25 (222)
T d1nija1           6 TLLTGFLGAGKTT-LLRHILN   25 (222)
T ss_dssp             EEEEESSSSSCHH-HHHHHHH
T ss_pred             EEEeeCCCCCHHH-HHHHHHh
Confidence            5788999999996 4433333

>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=83.75  E-value=0.27  Score=33.76  Aligned_cols=26  Identities=15%  Similarity=0.055  Sum_probs=19.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHh
Q psy1539          50 LGMDILCQAKSGMGKTAVFVLATLQQ   75 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~~~~~l~~   75 (175)
                      .|.-+++.+++|+|||...+--+.+.
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            35789999999999997655444443

>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=83.61  E-value=0.27  Score=35.11  Aligned_cols=27  Identities=33%  Similarity=0.279  Sum_probs=19.7

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhh
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLE   77 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~   77 (175)
                      ..|.-+.+.+|+|||||..  +-++..+.
T Consensus        38 ~~Ge~vaivG~sGsGKSTL--l~li~gl~   64 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTV--AALLQNLY   64 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHH--HHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHH--HHHHhccc
Confidence            3588999999999999963  33444443

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {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: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=83.57  E-value=0.84  Score=31.58  Aligned_cols=17  Identities=18%  Similarity=0.163  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCChHHHH
Q psy1539          51 GMDILCQAKSGMGKTAV   67 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~   67 (175)
                      ++.+++.||.|+|||..
T Consensus        29 ~~~i~i~G~~G~GKTsL   45 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSI   45 (283)
T ss_dssp             SSEEEEEESTTSSHHHH
T ss_pred             CCEEEEEcCCCCcHHHH
Confidence            46789999999999954

>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=83.42  E-value=0.24  Score=35.51  Aligned_cols=19  Identities=26%  Similarity=0.323  Sum_probs=16.4

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+++|||||..
T Consensus        42 ~~Ge~vaivG~sGsGKSTL   60 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTL   60 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            3588999999999999963

>d1l2ta_ c.37.1.12 (A:) MJ0796 {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: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=82.88  E-value=0.27  Score=34.75  Aligned_cols=28  Identities=25%  Similarity=0.294  Sum_probs=20.9

Q ss_pred             hcCCcEEEEcCCCChHHHHHHHHHHHhhhc
Q psy1539          49 VLGMDILCQAKSGMGKTAVFVLATLQQLET   78 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~   78 (175)
                      ..|.-+.+.+|+|||||..  +-++.-+..
T Consensus        29 ~~Ge~~~iiG~sGsGKSTL--l~~i~gl~~   56 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTM--LNIIGCLDK   56 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHH--HHHHTTSSC
T ss_pred             cCCCEEEEECCCCCCcchh--hHhccCCCC
Confidence            4688999999999999963  445555543

>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=82.84  E-value=0.44  Score=35.44  Aligned_cols=25  Identities=24%  Similarity=0.501  Sum_probs=18.6

Q ss_pred             HHHHhcCCc--EEEEcCCCChHHHHHH
Q psy1539          45 IPQAVLGMD--ILCQAKSGMGKTAVFV   69 (175)
Q Consensus        45 i~~~~~g~~--~ii~a~TGsGKT~~~~   69 (175)
                      ++.+++|.|  ++..+.||||||.+..
T Consensus        75 v~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          75 VQSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             HGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             hcchhcccccceeeeeccCCccccccc
Confidence            445567865  6778899999997763

>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=82.42  E-value=0.29  Score=36.03  Aligned_cols=16  Identities=38%  Similarity=0.576  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChHHHHH
Q psy1539          53 DILCQAKSGMGKTAVF   68 (175)
Q Consensus        53 ~~ii~a~TGsGKT~~~   68 (175)
                      +++..+|||+|||..+
T Consensus        54 ~~lf~Gp~GvGKT~la   69 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVT   69 (315)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCcchhHHHH
Confidence            6899999999999654

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

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: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=82.34  E-value=0.23  Score=35.34  Aligned_cols=17  Identities=29%  Similarity=0.233  Sum_probs=15.4

Q ss_pred             cCCcEEEEcCCCChHHH
Q psy1539          50 LGMDILCQAKSGMGKTA   66 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~   66 (175)
                      .|.-+.+.+|+|||||.
T Consensus        27 ~Ge~vaivG~sGsGKST   43 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKST   43 (242)
T ss_dssp             TTEEEEEECCTTSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57889999999999996

>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=82.07  E-value=0.61  Score=32.83  Aligned_cols=61  Identities=15%  Similarity=0.133  Sum_probs=34.8

Q ss_pred             HHHHhcCCcEEEEcCCCChHHHHHHHHHHHhhhcC--------CCCeEEEEEecCHHHHHHHHHHHHHHHh
Q psy1539          45 IPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETT--------DSNVYVLVMCHTRELAFQISKEYERFSK  107 (175)
Q Consensus        45 i~~~~~g~~~ii~a~TGsGKT~~~~~~~l~~l~~~--------~~~~~~lil~Pt~~L~~q~~~~~~~~~~  107 (175)
                      ++-+..|.-.++.|++|+|||...+. ++..+-..        ..+..++++.-- .-..++.+.+..+..
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~-la~~ia~g~~~~~~~~~~~~~vl~~~~E-~~~~~~~~Rl~~~~~   91 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQ-LAAQIAGGPDLLEVGELPTGPVIYLPAE-DPPTAIHHRLHALGA   91 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHH-HHHHHHTCCCTTCCCCCCCCCEEEEESS-SCHHHHHHHHHHHHT
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHH-HHHHHHcCCCcccccccCCCceEEEecc-chHHHHHHHHHHHhh
Confidence            45556688899999999999965443 33233211        123356776532 223444555555543

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {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: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=82.06  E-value=0.32  Score=34.74  Aligned_cols=19  Identities=26%  Similarity=0.469  Sum_probs=16.4

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|||||..
T Consensus        39 ~~Ge~iaivG~sGsGKSTL   57 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTI   57 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHH
T ss_pred             cCCCEEEEECCCCChHHHH
Confidence            3588999999999999963

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=81.79  E-value=3.1  Score=28.07  Aligned_cols=74  Identities=18%  Similarity=0.086  Sum_probs=45.5

Q ss_pred             eEEEEEecCHHHHHHHHHHHHHHHhhCCC-------------------------eEEEEEECCCchHHhH---HHHhcC-
Q psy1539          83 VYVLVMCHTRELAFQISKEYERFSKYMSN-------------------------IKVGVFFGGLPIQKDE---EYLKTH-  133 (175)
Q Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~-------------------------i~v~~~~g~~~~~~~~---~~l~~~-  133 (175)
                      .++||.||||.-|......+.........                         --++..+||.+..+..   +.++++ 
T Consensus        41 ~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g~  120 (201)
T d2p6ra4          41 GGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGN  120 (201)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCCC
Confidence            36899999998887777666654332100                         0156778888744332   233443 


Q ss_pred             CCeEEE--eecCccCCCCceEEEEe
Q psy1539         134 NPQIVG--LVNYETNLSGVVVNVMD  156 (175)
Q Consensus       134 ~~iiv~--l~~~~~~~~~~~~lVlD  156 (175)
                      ..++|+  .+...++++....+|.|
T Consensus       121 i~vlvaT~~l~~Gin~p~~~vvi~~  145 (201)
T d2p6ra4         121 IKVVVATPTLAAGVNLPARRVIVRS  145 (201)
T ss_dssp             CCEEEECSTTTSSSCCCBSEEEECC
T ss_pred             ceEEEechHHHhhcCCCCceEEEec
Confidence            466777  44457888877777754

>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=81.75  E-value=0.89  Score=29.32  Aligned_cols=40  Identities=10%  Similarity=0.101  Sum_probs=26.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHhhhcCCCCeEEEEEecCHH
Q psy1539          51 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE   93 (175)
Q Consensus        51 g~~~ii~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (175)
                      |.=-++.+|-.||||.- ++-.+++...  .+.+++++-|..+
T Consensus         7 G~l~lI~GpMfSGKTte-Li~~~~~~~~--~g~~vl~i~~~~D   46 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEE-LIRRIRRAKI--AKQKIQVFKPEID   46 (141)
T ss_dssp             CEEEEEECSTTSSHHHH-HHHHHHHHHH--TTCCEEEEEEC--
T ss_pred             eeEEEEEeccccHHHHH-HHHHHHHhhh--cCCcEEEEEeccc
Confidence            33457899999999954 4555555443  3447899999753

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {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: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=81.58  E-value=0.3  Score=34.68  Aligned_cols=20  Identities=25%  Similarity=0.232  Sum_probs=16.8

Q ss_pred             HhcCCcEEEEcCCCChHHHH
Q psy1539          48 AVLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        48 ~~~g~~~ii~a~TGsGKT~~   67 (175)
                      +.+|.-+.+.+|+|||||..
T Consensus        28 i~~Ge~~~iiG~sGsGKSTL   47 (240)
T d3dhwc1          28 VPAGQIYGVIGASGAGKSTL   47 (240)
T ss_dssp             ECSSCEEEEEESTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34688899999999999963

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=81.52  E-value=0.34  Score=32.79  Aligned_cols=19  Identities=32%  Similarity=0.691  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+.+++.+++|+|||...
T Consensus        14 ~g~gvli~G~sG~GKS~la   32 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECA   32 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHH
Confidence            5788999999999998654

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding 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: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.16  E-value=0.32  Score=35.37  Aligned_cols=17  Identities=29%  Similarity=0.407  Sum_probs=14.6

Q ss_pred             cCCcEEEEcCCCChHHH
Q psy1539          50 LGMDILCQAKSGMGKTA   66 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~   66 (175)
                      .|.-+.+.+|+|+|||.
T Consensus        61 ~Ge~vaivG~nGsGKST   77 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTS   77 (281)
T ss_dssp             TTCEEEEEESTTSSHHH
T ss_pred             CCCEEEEECCCCChHHH
Confidence            36678899999999996

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

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: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=81.07  E-value=0.33  Score=34.48  Aligned_cols=19  Identities=32%  Similarity=0.305  Sum_probs=16.3

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+-+.+|+|+|||..
T Consensus        27 ~~Ge~~~liG~sGaGKSTl   45 (240)
T d1g2912          27 KDGEFMILLGPSGCGKTTT   45 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCChHHHH
Confidence            3678899999999999964

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=81.01  E-value=0.37  Score=32.52  Aligned_cols=19  Identities=32%  Similarity=0.630  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy1539          50 LGMDILCQAKSGMGKTAVF   68 (175)
Q Consensus        50 ~g~~~ii~a~TGsGKT~~~   68 (175)
                      .|+.+++.++.|+|||...
T Consensus        13 ~g~gvl~~G~sG~GKStla   31 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETA   31 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHH
Confidence            5788999999999998654

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

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: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=80.15  E-value=0.34  Score=34.14  Aligned_cols=19  Identities=26%  Similarity=0.289  Sum_probs=16.2

Q ss_pred             hcCCcEEEEcCCCChHHHH
Q psy1539          49 VLGMDILCQAKSGMGKTAV   67 (175)
Q Consensus        49 ~~g~~~ii~a~TGsGKT~~   67 (175)
                      ..|.-+.+.+|+|+|||..
T Consensus        24 ~~Ge~~~liGpsGaGKSTl   42 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLF   42 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHH
Confidence            4578899999999999963